Chalfoun, Anna D.; Schmidt, Kenneth A.
The question of why animals choose particular habitats has important implications for understanding behavioral evolution and distribution of organisms in the wild and for delineating between habitats of different quality for conservation and management. Habitats chosen by animals can influence fitness outcomes via the costs (e.g., predation risk) and benefits (e.g., food availability) of habitat use. Habitat preferences should therefore be under selection to favor those that confer fitness advantages (Clark and Shutler 1999). Indeed, prevailing theory suggests that the habitat preferences of animals should be adaptive, such that fitness is higher in preferred habitats (Hildén 1965, Southwood 1977, Martin 1998). However, studies have often identified apparent mismatches between observed habitat preferences and fitness outcomes across a wide variety of taxa (Valladares and Lawton 1991, Mayhew 1997, Kolbe and Janzen 2002, Arlt and Pärt 2007, Mägi et al. 2009). Certainly, one limitation of studies may be that assessment of “fitness” is typically constrained to fitness surrogates such as nest success rather than lifetime reproductive success or classic Fisherian fitness (Endler 1986). Nevertheless, important habitat choices such as nest sites influence the probability that temporarily sedentary, dependent young are discovered by enemies such as predators and parasites. We therefore expect, on average, to see congruence between evolved habitat preferences and relevant components of fitness (e.g., nest success). Here, we (1) review the prevalence of apparent mismatches between avian breeding-habitat preferences and fitness outcomes using nest-site selection as a focus; (2) describe several potential mechanisms for such mismatches, including anthropogenic, methodological, and ecological–evolutionary; and (3) suggest a framework for understanding the contexts in which habitat preferences represent adaptive decisions, with a primary focus on ecological information
Moorman, C.E.; D.C. Guynn, Jr.
Research on the effects of creating group-selection openings of various sizes on breeding birds habitat use in a bottomland hardwood forest of the Upper Coastal Plain of South Carolina. Creation of 0.5-ha group selection openings in southern bottomland forests should provide breeding habitat for some field-edge species in gaps and habitat for forest-interior species and canopy-dwelling forest-edge species between gaps provided that enough mature forest is made available.
This study aimed to identify variables that affect habitat selection and nesting success of the African Crowned Eagle Stephanoaetus coronatus, the largest forest raptor, in north-eastern South Africa. A preference for nesting in the Northern Mistbelt Forest vegetation type was established and 82% of all nests were located in ...
Teresa J Lorenz
Full Text Available The marbled murrelet (Brachyramphus marmoratus is a declining seabird that is well-known for nesting in coastal old-growth forests in the Pacific Northwest. Most studies of habitat selection have focused on modeling terrestrial nesting habitat even though marine habitat is believed to be a major contributor to population declines in some regions. To address this information gap, we conducted a 5-year study of marine resource selection by murrelets in Washington, which contains a population experiencing the steepest documented declines and where marine habitat is believed to be compromised. Across five years we tracked 157 radio-tagged murrelets during the breeding season (May to August, and used discrete choice models to examine habitat selection. Using an information theoretic approach, our global model had the most support, suggesting that murrelet resource selection at-sea is affected by many factors, both terrestrial and marine. Locations with higher amounts of nesting habitat (β = 21.49, P < 0.001 that were closer to shore (β = -0.0007, P < 0.001 and in cool waters (β = -0.2026, P < 0.001 with low footprint (β = -0.0087, P < 0.001 had higher probabilities of use. While past conservation efforts have focused on protecting terrestrial nesting habitat, we echo many past studies calling for future efforts to protect marine habitat for murrelets, as the current emphasis on terrestrial habitat alone may be insufficient for conserving populations. In particular, marine areas in close proximity to old-growth nesting habitat appear important for murrelets during the breeding season and should be priorities for protection.
Prokešová, Jarmila; Kocian, Ľ.
Roč. 59, č. 5 (2004), s. 637-644 ISSN 0006-3088 Grant - others:VEGA(SK) 1/7197/20; VEGA(SK) 1/0017/03 Institutional research plan: CEZ:AV0Z6093917 Keywords : reed warblers * breeding * habitat selection Subject RIV: EH - Ecology, Behaviour Impact factor: 0.207, year: 2004 http://biologia.savba.sk/59_5_04/Prokesova_J.pdf
Danchin, E.; Boulinier, T.; Massot, M.
Habitat selection is a crucial process in the life cycle of animals because it can affect most components of fitness. It has been proposed that some animals cue on the reproductive success of conspecifics to select breeding habitats. We tested this hypothesis with demographic and behavioral data from a 17-yr study of the Black-legged Kittiwake (Rissa tridactyla), a cliff-nesting seabird. As the hypothesis assumes, the Black-legged Kittiwake nesting environment was patchy, and the relative quality of the different patches (i.e., breeding cliffs) varied in time. The average reproductive success of the breeders of a given cliff was predictable from one year to the next, but this predictability faded after several years. The dynamic nature of cliff quality in the long term is partly explained by the autocorrelation of the prevalence of an ectoparasite that influences reproductive success. As predicted by the performance-based conspecific attraction hypothesis, the reproductive success of current breeders on a given cliff was predictive of the reproductive success of new recruits on the cliff in the following year. Breeders tended to recruit to the previous year's most productive cliffs and to emigrate from the least productive ones. Consequently, the dynamics of breeder numbers on the cliffs were explained by local reproductive success on a year-to-year basis. Because, on average, young Black-legged Kittiwakes first breed when 4 yr old, such a relationship probably results from individual choices based on the assessment of previous-year local quality. When breeders changed breeding cliffs between years, they selected cliffs of per capita higher reproductive success. Furthermore, after accounting for the potential effects of age and sex as well as between-year variations, the effect of individual breeding performance on breeding dispersal was strongly influenced by the average reproductive success of other breeders on the same cliff. Individual breeding performance did
Bartelt, Paul E.; Peterson, Charles R.; Klaver, Robert W.
We used radio-telemetry to study the movements and habitat use of Western toads (Bufo boreas) in the Targhee National Forest in southeastern Idaho. Eighteen toads (10 male and 8 female) that bred in a seasonally flooded pond, were fitted with radio-transmitters, tracked, and their movements mapped and analyzed with global positioning and geographic information systems. We also analyzed their patterns of habitat selection at micro- and macro-scales by comparing sites used by toads with randomly selected sites. After breeding, two male and six female toads left the breeding pond and used terrestrial habitats extensively. Male and female toads showed different patterns of movement and habitat use, although all toads seemed to behave in ways that reduced loss of body water (e.g., such as traveling on nights of high humidity). Male toads traveled shorter distances from the pond than females (581 ± 98 m and 1105 ± 272 m, respectively). Female toads used terrestrial habitats extensively and were selective of cover types (e.g., shrub) that provided greater protection from dehydration. Female toads also preferred certain habitat edges and open forests over forests with closed canopies or clearcuts. Information from this study can assist land managers in establishing protective buffers and managing forests for the protection of toad populations.
Šálek, Martin; Lövy, M.
Roč. 22, č. 3 (2012), s. 328-338 ISSN 0959-2709 Institutional support: RVO:68081766 Keywords : Little Owl * home range size * habitat use * compositional analysis * grasslands * short-sward vegetation Subject RIV: EG - Zoology Impact factor: 1.074, year: 2012
Full Text Available The Au'au Channel between the islands of Maui and Lanai, Hawaii comprises critical breeding habitat for humpback whales (Megaptera novaeangliae of the Central North Pacific stock. However, like many regions where marine mega-fauna gather, these waters are also the focus of a flourishing local eco-tourism and whale watching industry. Our aim was to establish current trends in habitat preference in female-calf humpback whale pairs within this region, focusing specifically on the busy, eastern portions of the channel. We used an equally-spaced zigzag transect survey design, compiled our results in a GIS model to identify spatial trends and calculated Neu's Indices to quantify levels of habitat use. Our study revealed that while mysticete female-calf pairs on breeding grounds typically favor shallow, inshore waters, female-calf pairs in the Au'au Channel avoided shallow waters (<20 m and regions within 2 km of the shoreline. Preferred regions for female-calf pairs comprised water depths between 40-60 m, regions of rugged bottom topography and regions that lay between 4 and 6 km from a small boat harbor (Lahaina Harbor that fell within the study area. In contrast to other humpback whale breeding grounds, there was only minimal evidence of typical patterns of stratification or segregation according to group composition. A review of habitat use by maternal females across Hawaiian waters indicates that maternal habitat choice varies between localities within the Hawaiian Islands, suggesting that maternal females alter their use of habitat according to locally varying pressures. This ability to respond to varying environments may be the key that allows wildlife species to persist in regions where human activity and critical habitat overlap.
Cartwright, Rachel; Gillespie, Blake; Labonte, Kristen; Mangold, Terence; Venema, Amy; Eden, Kevin; Sullivan, Matthew
The Au'au Channel between the islands of Maui and Lanai, Hawaii comprises critical breeding habitat for humpback whales (Megaptera novaeangliae) of the Central North Pacific stock. However, like many regions where marine mega-fauna gather, these waters are also the focus of a flourishing local eco-tourism and whale watching industry. Our aim was to establish current trends in habitat preference in female-calf humpback whale pairs within this region, focusing specifically on the busy, eastern portions of the channel. We used an equally-spaced zigzag transect survey design, compiled our results in a GIS model to identify spatial trends and calculated Neu's Indices to quantify levels of habitat use. Our study revealed that while mysticete female-calf pairs on breeding grounds typically favor shallow, inshore waters, female-calf pairs in the Au'au Channel avoided shallow waters (<20 m) and regions within 2 km of the shoreline. Preferred regions for female-calf pairs comprised water depths between 40-60 m, regions of rugged bottom topography and regions that lay between 4 and 6 km from a small boat harbor (Lahaina Harbor) that fell within the study area. In contrast to other humpback whale breeding grounds, there was only minimal evidence of typical patterns of stratification or segregation according to group composition. A review of habitat use by maternal females across Hawaiian waters indicates that maternal habitat choice varies between localities within the Hawaiian Islands, suggesting that maternal females alter their use of habitat according to locally varying pressures. This ability to respond to varying environments may be the key that allows wildlife species to persist in regions where human activity and critical habitat overlap.
Kant, Rajni; Srivastava, H C
Water bodies infested with aquatic vegetations may pose problems in mosquito control through bio-environmental methods. Paucity of information pertaining to association of mosquito breeding with aquatic vegetation was the basis for present investigation. The mosquito breeding sites infested with solitary/dominating plant community viz., Eichhornia crassipes, Ipomoea aquatica, Hydrilla verticillata, Nymphea neuchali, Trapa bispinosa, Lemna paucicostata, Trachelomonas spp., Azolla pinnata, Algae spp. and Cynodon dactylon were selected for the study. The investigation revealed that breeding of eleven anopheline species was associated with Eichhornia in different habitats followed by Hydrilla, algae and Cynodon (8 each), Ipomoea and Trapa (6), Lemna. and Nymphea (5), Azolla and Trachelomonas (4). An. subpictus was associated with all types of vegetation. An. annularis, An. nigerrimus and An. barbirostris were associated with nine plant species. An. culicifacies, the principal malaria vector was found breeding in association with seven aquatic plants and showed strong association with Cynodon, Hydrilla and algae. The species diversity in habitats infested with Hydrilla, algae and Cynodon seems to be most favourable for the breeding of An. culicifacies. It is suggested that thinning or removal of such vegetations at regular interval may help to reduce vector population and enhance the efficacy of biological control agents particularly the larvivorous fishes in such habitats.
Newell, Mark A; Jannink, Jean-Luc
Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor and major marker effects. Thus, the GEBV may capture more of the genetic variation for the particular trait under selection.
Samplonius, Jelmer M; Both, Christiaan
Predicting habitat quality is a major challenge for animals selecting a breeding patch, because it affects reproductive success. Breeding site selection may be based on previous experience, or on social information from the density and success of competitors with an earlier phenology. Variation in animal breeding phenology is often correlated with variation in habitat quality. Generally, animals breed earlier in high-quality habitats that allow them to reach a nutritional threshold required for breeding earlier or avoid nest predation. In addition, habitat quality may affect phenological overlap between species and thereby interspecific competition. Therefore, we hypothesized that competitor breeding phenology can be used as social cue by settling migrants to locate high-quality breeding sites. To test this hypothesis, we experimentally advanced and delayed hatching phenology of two resident tit species on the level of study plots and studied male and female settlement patterns of migratory pied flycatchers Ficedula hypoleuca. The manipulations were assigned at random in two consecutive years, and treatments were swapped between years in sites that were used in both years. In both years, males settled in equal numbers across treatments, but later arriving females avoided pairing with males in delayed phenology plots. Moreover, male pairing probability declined strongly with arrival date on the breeding grounds. Our results demonstrate that competitor phenology may be used to assess habitat quality by settling migrants, but we cannot pinpoint the exact mechanism (e.g. resource quality, predation pressure or competition) that has given rise to this pattern. In addition, we show that opposing selection pressures for arrival timing may give rise to different social information availabilities between sexes. We discuss our findings in the context of climate warming, social information use and the evolution of protandry in migratory animals. © 2017 The Authors. Journal
Jedlikowski, Jan; Chibowski, Piotr; Karasek, Tomasz; Brambilla, Mattia
Habitat selection often involves choices made at different spatial scales, but the underlying mechanisms are still poorly understood, and studies that investigate the relative importance of individual scales are rare. We investigated the effect of three spatial scales (landscape, territory, nest-site) on the occurrence pattern of little crake Zapornia parva and water rail Rallus aquaticus at 74 ponds in the Masurian Lakeland, Poland. Habitat structure, food abundance and water chemical parameters were measured at nests and random points within landscape plots (from 300-m to 50-m radius), territory (14-m) and nest-site plots (3-m). Regression analyses suggested that the most relevant scale was territory level, followed by landscape, and finally by nest-site for both species. Variation partitioning confirmed this pattern for water rail, but also highlighted the importance of nest-site (the level explaining the highest share of unique variation) for little crake. The most important variables determining the occurrence of both species were water body fragmentation (landscape), vegetation density (territory) and water depth (at territory level for little crake, and at nest-site level for water rail). Finally, for both species multi-scale models including factors from different levels were more parsimonious than single-scale ones, i.e. habitat selection was likely a multi-scale process. The importance of particular spatial scales seemed more related to life-history traits than to the extent of the scales considered. In the case of our study species, the territory level was highly important likely because both rallids have to obtain all the resources they need (nest site, food and mates) in relatively small areas, the multi-purpose territories they defend.
Beerens, James M.; Frederick, Peter C; Noonburg, Erik G; Gawlik, Dale E.
Determining habitat quality for wildlife populations requires relating a species' habitat to its survival and reproduction. Within a season, species occurrence and density can be disconnected from measures of habitat quality when resources are highly seasonal, unpredictable over time, and patchy. Here we establish an explicit link among dynamic selection of changing resources, spatio-temporal species distributions, and fitness for predictive abundance and occurrence models that are used for short-term water management and long-term restoration planning. We used the wading bird distribution and evaluation models (WADEM) that estimate (1) daily changes in selection across resource gradients, (2) landscape abundance of flocks and individuals, (3) conspecific foraging aggregation, and (4) resource unit occurrence (at fixed 400 m cells) to quantify habitat quality and its consequences on reproduction for wetland indicator species. We linked maximum annual numbers of nests detected across the study area and nesting success of Great Egrets (Ardea alba), White Ibises (Eudocimus albus), and Wood Storks (Mycteria americana) over a 20-year period to estimated daily dynamics of food resources produced by WADEM over a 7490 km2 area. For all species, increases in predicted species abundance in March and high abundance in April were strongly linked to breeding responses. Great Egret nesting effort and success were higher when birds also showed greater conspecific foraging aggregation. Synthesis and applications: This study provides the first empirical evidence that dynamic habitat selection processes and distributions of wading birds over environmental gradients are linked with reproductive measures over periods of decades. Further, predictor variables at a variety of temporal (daily-multiannual) resolutions and spatial (400 m to regional) scales effectively explained variation in ecological processes that change habitat quality. The process used here allows managers to develop
Gauthreaux, Sidney, A.; Steven J. Wagner.
Gauthreaux, Sidney, A., and Steven J. Wagner. 2005. Breeding bird populations and habitat associations within the Savannah River Site (SRS). Final Report. USDA Forest Service, Savannah River, Aiken, SC. 48 pp. Abstract: During the 1970's and 1980's a dramatic decline occurred in the populations of Neotropical migratory birds, species that breed in North America and winter south of the border in Central and South America and in the Caribbean. In 1991 an international initiative was mounted by U. S. governmental land management agencies, nongovernmental conservation agencies, and the academic and lay ornithological communities to understand the decline of Neotropical migratory birds in the Americas. In cooperation with the USDA Forest Service - Savannah River (FS - SR) we began 1992 a project directed to monitoring population densities of breeding birds using the Breeding Bird Census (BBC) methodology in selected habitats within the Savannah River Site SRS. In addition we related point count data on the occurrence of breeding Neotropical migrants and other bird species to the habitat data gathered by the Forest Inventory and Analysis (FIA) program of the USDA Forest Service and data on habitat treatments within forest stands.
Jennifer C. Rock
Full Text Available Breeding seabirds are threatened by human activities that affect nesting and foraging habitat. In Canada, one of the seabirds most at risk of extirpation is the Roseate Tern, Sterna dougallii. Although critical nesting habitat has been identified for the Roseate Tern in Canada, its foraging locations and the diet of its chicks are unknown. Therefore, our goal was to determine the foraging locations and diet of chicks of Roseate Tern breeding on Country Island, Nova Scotia, which is one of Canada's two main breeding colonies. In 2003 and 2004, we radio-tracked the Roseate Tern by plane to locate foraging areas and conducted feeding watches to determine the diet of chicks. Roseate Tern foraged approximately 7 km from the breeding colony over shallow water < 5 m deep. In both years, sand lance, Ammodytes spp., was the most common prey item delivered to chicks, followed by hake, Urophycis spp. Our results are consistent with previous work at colonies in the northeastern United States, suggesting that throughout its range, this species may be restricted in both habitat use and prey selection. The reliance on a specific habitat type and narrow range of prey species makes the Roseate Tern generally susceptible to habitat perturbations and reductions in the availability of prey.
Wild, Teri C.; Kendall, Steven J.; Guldager, Nikki; Powell, Abby N.
Smith's Longspur (Calcarius pictus) is a species of conservation concern which breeds in Arctic habitats that are expected to be especially vulnerable to climate change. We used bird presence and habitat data from point-transect surveys conducted at 12 sites across the Brooks Range, Alaska, 2003–2009, to identify breeding areas, describe local habitat associations, and identify suitable habitat using a predictive model of Smith's Longspur distribution. Smith's Longspurs were observed at seven sites, where they were associated with a variety of sedge–shrub habitats composed primarily of mosses, sedges, tussocks, and dwarf shrubs; erect shrubs were common but sparse. Nonmetric multidimensional scaling ordination of ground cover revealed positive associations of Smith's Longspur presence with sedges and mosses and a negative association with high cover of shrubs. To model predicted distribution, we used boosted regression trees to relate landscape variables to occurrence. Our model predicted that Smith's Longspurs may occur in valleys and foothills of the northeastern and southeastern mountains and in upland plateaus of the western mountains, and farther west than currently documented, over a predicted area no larger than 15% of the Brooks Range. With climate change, shrubs are expected to grow larger and denser, while soil moisture and moss cover are predicted to decrease. These changes may reduce Smith's Longspur habitat quality and limit distribution in the Brooks Range to poorly drained lowlands and alpine plateaus where sedge–shrub tundra is likely to persist. Conversely, northward advance of shrubs into sedge tundra may create suitable habitat, thus supporting a northward longspur distribution shift.
Gizaw, S; Getachew, T; Tibbo, M; Haile, A; Dessie, T
Designing breeding schemes suitable for smallholder livestock production systems in developing regions has hitherto been a challenge. The suggested schemes either do not address farmers' breeding goals (centralized station-based nucleus schemes) or yield slow genetic progress (village-based schemes). A new breeding scheme that integrates the merits of previously suggested schemes has been designed for Menz sheep improvement in Ethiopia. It involves selection based on breeding values in nucleus flocks to produce elite rams, a one-time only provision of improved rams to villagers and a follow-up village-based selection to sustain genetic progress in village flocks. Here, we assessed whether conventional selection of breeding rams based on breeding values for production traits, which is the practice in station-based nucleus flocks, meets farmers' breeding objectives. We also elicited determinants of farmers' ram choice. Low but significant correlations were found between rankings of rams based on farmers' selection criteria, estimated breeding values (EBV) and body weight (BW). Appearance traits (such as color and horn) and meat production traits (BW and linear size traits) significantly determined farmers' breeding ram choice. The results imply that conventional selection criteria based solely on EBV for production traits do not address farmers' trait preferences fully, but only partially. Thus, a two-stage selection procedure involving selection on breeding values in nucleus centers followed by farmers' selection among top- ranking candidate rams is recommended. This approach accommodates farmers' preferences and speeds up genetic progress in village-based selection. The Menz sheep scheme could be applied elsewhere with similar situations to transform conventional station-based nucleus breeding activities into participatory breeding programs.
Full Text Available Farm ponds are important habitats for amphibians, birds, and other wildlife. In Taiwan, artificial ponds were originally created on farmlands for irrigation purposes and the needs of the domestic water supply. Although pond creation is a typical farming practice, it also provides habitats for pond-breeding amphibians. Thus, it is essential to understand the current status of habitats and their vulnerability regarding urgent conservation needs for target species. Günther’s frog (Hylarana guentheri, a pond-breeding amphibian, has a high sensitivity towards surrounding environmental changes, and can be used as an indicator species to assess habitat suitability. The purpose of this study is to establish a systematic framework to assess the habitat suitability of pond-breeding amphibians by using Günther’s frog as a pilot-study species. First, we collected frog survey data from Chiayi, Taiwan, from winter 2013 to spring 2015, and investigated the present status of the environmental conditions around the ponds. Next, expert questionnaires and the fuzzy Delphi method were applied to establish the hierarchical evaluation criteria regarding the habitat suitability assessment. Four indicators: the aquatic environments of farm ponds; the terrestrial environments around ponds; landscape connectivity; and the conservation perceptions of the residents, were determined as first-layer factors in the assessment criteria, while ten other indicators were defined as second-layer factors. Based on the established assessment criteria, we performed in situ habitat suitability evaluations on 69 selected sites and surveyed the perceptions of the residents using questionnaires. Results revealed that 19% of locations were rich in frog species with a high habitat suitability. However, 67% of locations showed signs of habitat degradation, which may imply a higher need in practicing habitat improvement or restoration. The Kappa value was 0.6061, which indicated a high
Michelot, Candice; Pinaud, David; Fortin, Matthieu; Maes, Philippe; Callard, Benjamin; Leicher, Marine; Barbraud, Christophe
Studies of habitat selection by higher trophic level species are necessary for using top predator species as indicators of ecosystem functioning. However, contrary to terrestrial ecosystems, few habitat selection studies have been conducted at a fine scale for coastal marine top predator species, and fewer have coupled diet data with habitat selection modeling to highlight a link between prey selection and habitat use. The aim of this study was to characterize spatially and oceanographically, at a fine scale, the habitats used by the European Shag Phalacrocorax aristotelis in the Special Protection Area (SPA) of Houat-Hœdic in the Mor Braz Bay during its foraging activity. Habitat selection models were built using in situ observation data of foraging shags (transect sampling) and spatially explicit environmental data to characterize marine benthic habitats. Observations were first adjusted for detectability biases and shag abundance was subsequently spatialized. The influence of habitat variables on shag abundance was tested using Generalized Linear Models (GLMs). Diet data were finally confronted to habitat selection models. Results showed that European shags breeding in the Mor Braz Bay changed foraging habitats according to the season and to the different environmental and energetic constraints. The proportion of the main preys also varied seasonally. Rocky and coarse sand habitats were clearly preferred compared to fine or muddy sand habitats. Shags appeared to be more selective in their foraging habitats during the breeding period and the rearing of chicks, using essentially rocky areas close to the colony and consuming preferentially fish from the Labridae family and three other fish families in lower proportions. During the post-breeding period shags used a broader range of habitats and mainly consumed Gadidae. Thus, European shags seem to adjust their feeding strategy to minimize energetic costs, to avoid intra-specific competition and to maximize access
Leclerc, Martin; Vander Wal, Eric; Zedrosser, Andreas; Swenson, Jon E; Kindberg, Jonas; Pelletier, Fanie
Habitat selection is a fundamental behaviour that links individuals to the resources required for survival and reproduction. Although natural selection acts on an individual's phenotype, research on habitat selection often pools inter-individual patterns to provide inferences on the population scale. Here, we expanded a traditional approach of quantifying habitat selection at the individual level to explore the potential for consistent individual differences of habitat selection. We used random coefficients in resource selection functions (RSFs) and repeatability estimates to test for variability in habitat selection. We applied our method to a detailed dataset of GPS relocations of brown bears (Ursus arctos) taken over a period of 6 years, and assessed whether they displayed repeatable individual differences in habitat selection toward two habitat types: bogs and recent timber-harvest cut blocks. In our analyses, we controlled for the availability of habitat, i.e. the functional response in habitat selection. Repeatability estimates of habitat selection toward bogs and cut blocks were 0.304 and 0.420, respectively. Therefore, 30.4 and 42.0 % of the population-scale habitat selection variability for bogs and cut blocks, respectively, was due to differences among individuals, suggesting that consistent individual variation in habitat selection exists in brown bears. Using simulations, we posit that repeatability values of habitat selection are not related to the value and significance of β estimates in RSFs. Although individual differences in habitat selection could be the results of non-exclusive factors, our results illustrate the evolutionary potential of habitat selection.
Zeigler, Sara; Thieler, E. Robert; Gutierrez, Ben; Plant, Nathaniel G.; Hines, Megan K.; Fraser, James D.; Catlin, Daniel H.; Karpanty, Sarah M.
Understanding patterns of habitat selection across a species’ geographic distribution can be critical for adequately managing populations and planning for habitat loss and related threats. However, studies of habitat selection can be time consuming and expensive over broad spatial scales, and a lack of standardized monitoring targets or methods can impede the generalization of site-based studies. Our objective was to collaborate with natural resource managers to define available nesting habitat for piping plovers (Charadrius melodus) throughout their U.S. Atlantic coast distribution from Maine to North Carolina, with a goal of providing science that could inform habitat management in response to sea-level rise. We characterized a data collection and analysis approach as being effective if it provided low-cost collection of standardized habitat-selection data across the species’ breeding range within 1–2 nesting seasons and accurate nesting location predictions. In the method developed, >30 managers and conservation practitioners from government agencies and private organizations used a smartphone application, “iPlover,” to collect data on landcover characteristics at piping plover nest locations and random points on 83 beaches and barrier islands in 2014 and 2015. We analyzed these data with a Bayesian network that predicted the probability a specific combination of landcover variables would be associated with a nesting site. Although we focused on a shorebird, our approach can be modified for other taxa. Results showed that the Bayesian network performed well in predicting habitat availability and confirmed predicted habitat preferences across the Atlantic coast breeding range of the piping plover. We used the Bayesian network to map areas with a high probability of containing nesting habitat on the Rockaway Peninsula in New York, USA, as an example application. Our approach facilitated the collation of evidence-based information on habitat selection
O'Neil, Shawn T.; Warren, Jeffrey M.; Takekawa, John Y.; De La Cruz, Susan E. W.; Cutting, Kyle A.; Parker, Michael W.; Yee, Julie L.
Prebreeding habitat selection in birds can often be explained in part by habitat characteristics. However, females may also select habitats on the basis of fidelity to areas of previous reproductive success or use by conspecifics. The relative influences of sociobehavioural attributes versus habitat characteristics in habitat selection has been primarily investigated in songbirds, while less is known about how these factors affect habitat selection processes in migratory waterfowl. Animal resource selection models often exhibit much unexplained variation; spatial patterns driven by social and behavioural characteristics may account for some of this. We radiomarked female lesser scaup, Aythya affinis, in the southwestern extent of their breeding range to explore hypotheses regarding relative roles of habitat quality, site fidelity and conspecific density in prebreeding habitat selection. We used linear mixed-effects models to relate intensity of use within female home ranges to habitat features, distance to areas of reproductive success during the previous breeding season and conspecific density. Home range habitats included shallow water (≤118 cm), moderate to high densities of flooded emergent vegetation/open water edge and open water areas with submerged aquatic vegetation. Compared with habitat features, conspecific female density and proximity to successful nesting habitats from the previous breeding season had greater influences on habitat use within home ranges. Fidelity and conspecific attraction are behavioural characteristics in some waterfowl species that may exert a greater influence than habitat features in influencing prebreeding space use and habitat selection within home ranges, particularly where quality habitat is abundant. These processes may be of critical importance to a better understanding of habitat selection in breeding birds.
Mikula, P.; Hromada, M.; Albrecht, Tomáš; Tryjanowski, P.
Roč. 49, č. 1 (2014), s. 83-92 ISSN 0001-6454 Institutional support: RVO:68081766 Keywords : breeding success * coexistence * nest-habitat partitioning * nest site selection * predation * synurbization * urban habitat * thrushes Subject RIV: EG - Zoology Impact factor: 0.745, year: 2014
Vafidis, James O; Vaughan, Ian P; Jones, T Hefin; Facey, Richard J; Parry, Rob; Thomas, Robert J
Migratory birds face significant challenges across their annual cycle, including occupying an appropriate non-breeding home range with sufficient foraging resources. This can affect demographic processes such as over-winter survival, migration mortality and subsequent breeding success. In the Sahel region of Africa, where millions of migratory songbirds attempt to survive the winter, some species of insectivorous warblers occupy both wetland and dry-scrubland habitats, whereas other species are wetland or dry-scrubland specialists. In this study we examine evidence for strategic regulation of body reserves and competition-driven habitat selection, by comparing invertebrate prey activity-density, warbler body size and extent of fat and pectoral muscle deposits, in each habitat type during the non-breeding season. Invertebrate activity-density was substantially higher in wetland habitats than in dry-scrubland. Eurasian reed warblers Acrocephalus scirpaceus occupying wetland habitats maintained lower body reserves than conspecifics occupying dry-scrub habitats, consistent with buffering of reserves against starvation in food-poor habitat. A similar, but smaller, difference in body reserves between wet and dry habitat was found among subalpine warblers Sylvia cantillans but not in chiffchaffs Phylloscopus collybita inhabiting dry-scrub and scrub fringing wetlands. Body reserves were relatively low among habitat specialist species; resident African reed warbler A. baeticatus and migratory sedge warbler A. schoenobaenus exclusively occupying wetland habitats, and Western olivaceous warblers Iduna opaca exclusively occupying dry habitats. These results suggest that specialists in preferred habitats and generalists occupying prey-rich habitats can reduce body reserves, whereas generalists occupying prey-poor habitats carry an increased level of body reserves as a strategic buffer against starvation.
Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa in order to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on p...
The ultimate goal of plant breeding is the development of new varieties. An important phase in the development process is testing and selecting potential new varieties. The varieties are tested by means of experiments at various sites, (sometimes) in several years. The observations from the
.... This manual contains chapters on general principles, basic genetics, selection for qualitative phenotypes, selection for quantitative phenotypes, and how to conduct simple selective breeding programmes...
Boyce, Mark S; Johnson, Chris J; Merrill, Evelyn H; Nielsen, Scott E; Solberg, Erling J; van Moorter, Bram
Habitats have substantial influence on the distribution and abundance of animals. Animals' selective movement yields their habitat use. Animals generally are more abundant in habitats that are selected most strongly. Models of habitat selection can be used to distribute animals on the landscape or their distribution can be modelled based on data of habitat use, occupancy, intensity of use or counts of animals. When the population is at carrying capacity or in an ideal-free distribution, habitat selection and related metrics of habitat use can be used to estimate abundance. If the population is not at equilibrium, models have the flexibility to incorporate density into models of habitat selection; but abundance might be influenced by factors influencing fitness that are not directly related to habitat thereby compromising the use of habitat-based models for predicting population size. Scale and domain of the sampling frame, both in time and space, are crucial considerations limiting application of these models. Ultimately, identifying reliable models for predicting abundance from habitat data requires an understanding of the mechanisms underlying population regulation and limitation. © 2015 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.
Clark, Steven M.; Dunham, Jason B.; McEnroe, Jeffery R.; Lightcap, Scott W.
The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four fitness components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. We evaluated the relative influences of habitat features linked to these fitness components with respect to selection of breeding sites by coho salmon (Oncorhynchus kisutch). We also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. We used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. Results of this work suggest that female coho salmon likely select breeding sites based on a wide range of habitat features linked to all four hypothesized fitness components. More specifically, model parameter estimates indicated that breeding site selection was most strongly influenced by proximity to pool-tail crests and deeper water (mean and maximum depths). Linkages between large wood and breeding site selection were less clear. Overall, our findings suggest that breeding site selection by coho salmon is influenced by a suite of fitness components in addition to the egg incubation environment, which has been the emphasis of much work in the past.
Stephen A. Laymon
The California Wildlife-Habitat Relationship (WHR) system was tested for birds breeding in the Valley-Foothill Riparian habitat along California's Sacramento and South Fork Kern rivers. The model performed poorly with 33 pct and 21 pct correct predictions respectively at the two locations. Changes to the model for 60 species on the Sacramento River and 66 species...
Unglaub, Bianca; Steinfartz, Sebastian; Drechsler, Axel; Schmidt, Benedikt R
Elucidating the relationship between habitat characteristics and population parameters is critical for effective conservation. Habitat suitability index (HSI) models are often used in wildlife management and conservation practice assuming that they predict species occurrence, abundance and demography. However, the relationship between vital rates such as survival and reproduction and habitat suitability has rarely been evaluated. In this study, we used pond occupancy and mark-recapture data to test whether HSI predicts occupancy, reproduction and survival probabilities. Our model species is the great crested newt (Triturus cristatus), a pond-breeding amphibian protected under the European Habitats Directive. Our results show a positive relationship between the HSI and reproduction probability, whereas pond occupancy and survival probabilities were not related to HSI. Mortality was found to be higher during breeding seasons when newts are in ponds than during terrestrial phases of adult newts. Habitat suitability models are increasingly applied to wildlife management and conservation practice. We found that the HSI model predicted reproduction probability, rather than occurrence or survival. If HSI models indicate breeding populations rather than mere species occurrences, they may be used to identify habitats of higher priority for conservation. Future HSI models might be improved through modelling breeding populations vs. non-breeding populations rather than presence/absence data. However, according to our results the most suitable habitat is not necessarily the habitat where demographic performance is best. We recommend that conservation practitioners should use HSI models cautiously because there may be no direct link between habitat suitability, demography and consequently, population viability.
Björklund, Heidi; Valkama, Jari; Tomppo, Erkki; Laaksonen, Toni
Habitat loss causes population declines, but the mechanisms are rarely known. In the European Boreal Zone, loss of old forest due to intensive forestry is suspected to cause declines in forest-dwelling raptors by reducing their breeding performance. We studied the boreal breeding habitat and habitat-associated breeding performance of the northern goshawk (Accipiter gentilis), common buzzard (Buteo buteo) and European honey buzzard (Pernis apivorus). We combined long-term Finnish bird-of-prey data with multi-source national forest inventory data at various distances (100-4000 m) around the hawk nests. We found that breeding success of the goshawk was best explained by the habitat within a 2000-m radius around the nests; breeding was more successful with increasing proportions of old spruce forest and water, and decreasing proportions of young thinning forest. None of the habitat variables affected significantly the breeding success of the common buzzard or the honey buzzard, or the brood size of any of the species. The amount of old spruce forest decreased both around goshawk and common buzzard nests and throughout southern Finland in 1992-2010. In contrast, the area of young forest increased in southern Finland but not around hawk nests. We emphasize the importance of studying habitats at several spatial and temporal scales to determine the relevant species-specific scale and to detect environmental changes. Further effort is needed to reconcile the socioeconomic and ecological functions of forests and habitat requirements of old forest specialists.
Full Text Available Habitat loss causes population declines, but the mechanisms are rarely known. In the European Boreal Zone, loss of old forest due to intensive forestry is suspected to cause declines in forest-dwelling raptors by reducing their breeding performance. We studied the boreal breeding habitat and habitat-associated breeding performance of the northern goshawk (Accipiter gentilis, common buzzard (Buteo buteo and European honey buzzard (Pernis apivorus. We combined long-term Finnish bird-of-prey data with multi-source national forest inventory data at various distances (100-4000 m around the hawk nests. We found that breeding success of the goshawk was best explained by the habitat within a 2000-m radius around the nests; breeding was more successful with increasing proportions of old spruce forest and water, and decreasing proportions of young thinning forest. None of the habitat variables affected significantly the breeding success of the common buzzard or the honey buzzard, or the brood size of any of the species. The amount of old spruce forest decreased both around goshawk and common buzzard nests and throughout southern Finland in 1992-2010. In contrast, the area of young forest increased in southern Finland but not around hawk nests. We emphasize the importance of studying habitats at several spatial and temporal scales to determine the relevant species-specific scale and to detect environmental changes. Further effort is needed to reconcile the socioeconomic and ecological functions of forests and habitat requirements of old forest specialists.
Full Text Available Animals make choices about where to spend their time in complex and dynamic landscapes, choices that reveal information about their biology that in turn can be used to guide their conservation. Using GPS collars, we conducted a novel individual-based analysis of habitat use and selection by the elusive and endangered giant pandas (Ailuropoda melanoleuca. We constructed spatial autoregressive resource utilization functions (RUF to model the relationship between the pandas' utilization distributions and various habitat characteristics over a continuous space across seasons. Results reveal several new insights, including use of a broader range of habitat characteristics than previously understood for the species, particularly steep slopes and non-forest areas. We also used compositional analysis to analyze habitat selection (use with respect to availability of habitat types at two selection levels. Pandas selected against low terrain position and against the highest clumped forest at the at-home range level, but no significant factors were identified at the within-home range level. Our results have implications for modeling and managing the habitat of this endangered species by illustrating how individual pandas relate to habitat and make choices that differ from assumptions made in broad scale models. Our study also highlights the value of using a spatial autoregressive RUF approach on animal species for which a complete picture of individual-level habitat use and selection across space is otherwise lacking.
Hull, Vanessa; Zhang, Jindong; Huang, Jinyan; Zhou, Shiqiang; Viña, Andrés; Shortridge, Ashton; Li, Rengui; Liu, Dian; Xu, Weihua; Ouyang, Zhiyun; Zhang, Hemin; Liu, Jianguo
Animals make choices about where to spend their time in complex and dynamic landscapes, choices that reveal information about their biology that in turn can be used to guide their conservation. Using GPS collars, we conducted a novel individual-based analysis of habitat use and selection by the elusive and endangered giant pandas (Ailuropoda melanoleuca). We constructed spatial autoregressive resource utilization functions (RUF) to model the relationship between the pandas' utilization distributions and various habitat characteristics over a continuous space across seasons. Results reveal several new insights, including use of a broader range of habitat characteristics than previously understood for the species, particularly steep slopes and non-forest areas. We also used compositional analysis to analyze habitat selection (use with respect to availability of habitat types) at two selection levels. Pandas selected against low terrain position and against the highest clumped forest at the at-home range level, but no significant factors were identified at the within-home range level. Our results have implications for modeling and managing the habitat of this endangered species by illustrating how individual pandas relate to habitat and make choices that differ from assumptions made in broad scale models. Our study also highlights the value of using a spatial autoregressive RUF approach on animal species for which a complete picture of individual-level habitat use and selection across space is otherwise lacking.
Leopold, Christina R.; Hess, Steven C.
After a severe population reduction during the mid-20th century, the endangered Hawaiian Goose (Branta sandvicensis), or Nēnē, has only recently re-established its seasonal movement patterns on Hawai‘i Island. Little is currently understood about its movements and habitat use during the nonbreeding season. The objectives of this research were to identify habitats preferred by two subpopulations of the Nēnē and how preferences shift seasonally at both meso-and fine scales. From 2009 to 2011, ten Nēnē ganders were outfitted with 40-to 45-g satellite transmitters with GPS capability. We used binary logistic regression to compare habitat use versus availability and an information-theoretic approach for model selection. Meso-scale habitat modeling revealed that Nēnē preferred exotic grass and human-modified landscapes during the breeding and molting seasons and native subalpine shrubland during the nonbreeding season. Fine-scale habitat modeling further indicated preference for exotic grass, bunch grass, and absence of trees. Proximity to water was important during molt, suggesting that the presence of water may provide escape from introduced mammalian predators while Nēnē are flightless. Finescale species-composition data added relatively little to understanding of Nēnē habitat preferences modeled at the meso scale, suggesting that the meso-scale is appropriate for management planning. Habitat selection during our study was consistent with historical records, although dissimilar from more recent studies of other subpopulations. Nēnē make pronounced seasonal movements between existing reserves and use distinct habitat types; understanding annual patterns has implications for the protection and restoration of important seasonal habitats.
Dale M. Becker; Carolyn Hull Sieg
Home range size and habitat utilization of three breeding male Richardsonâs Merlins (Falco columbarius richardsonii) in southeastern Montana were studied using radio telemetry. Home ranges of these birds encompassed 13,23, and 28 km2. Each bird traveled up to 9 km from its nest. Each home range encompassed five habitats;...
Organic dairy farming started to take off in the early 1990s, when the European Union laid down organic standards for animal production. Until now, however, only incidental steps have been taken towards organic breeding and organic farmers mainly use breeding stock from conventional breeding
Bluso-Demers, Jill; Ackerman, Joshua T.; Takekawa, John Y.; Peterson, Sarah
The highly urbanized San Francisco Bay Estuary, California, USA, is currently undergoing large-scale habitat restoration, and several thousand hectares of former salt evaporation ponds are being converted to tidal marsh. To identify potential effects of this habitat restoration on breeding waterbirds, habitat selection of radiotagged Forster's Terns (Sterna forsteri) was examined at multiple spatial scales during the pre-breeding and breeding seasons of 2005 and 2006. At each spatial scale, habitat selection ratios were calculated by season, year, and sex. Forster's Terns selected salt pond habitats at most spatial scales and demonstrated the importance of salt ponds for foraging and roosting. Salinity influenced the types of salt pond habitats that were selected. Specifically, Forster's Terns strongly selected lower salinity salt ponds (0.5–30 g/L) and generally avoided higher salinity salt ponds (≥31 g/L). Forster's Terns typically used tidal marsh and managed marsh habitats in proportion to their availability, avoided upland and tidal flat habitats, and strongly avoided open bay habitats. Salt ponds provide important habitat for breeding waterbirds, and restoration efforts to convert former salt ponds to tidal marsh may reduce the availability of preferred breeding and foraging areas.
Janssen, K.; Chavanne, H.; Berentsen, P.; Komen, H.
Objectives of this study were to determine the combined market share of breeding companies in aquaculture production in Europe, to describe the main characteristics of breeding companies and their programs, and to provide per species estimates on cumulative genetic gain in growth performance.
Julianna M A Jenkins
Full Text Available Habitat selection is a fundamental component of community ecology, population ecology, and evolutionary biology and can be especially important to species with complex annual habitat requirements, such as migratory birds. Resource preferences on the breeding grounds may change during the postfledging period for migrant songbirds, however, the degree to which selection changes, timing of change, and whether all or only a few species alter their resource use is unclear. We compared resource selection for nest sites and resource selection by postfledging juvenile ovenbirds (Seiurus aurocapilla and Acadian flycatchers (Empidonax virescens followed with radio telemetry in Missouri mature forest fragments from 2012-2015. We used Bayesian discrete choice modeling to evaluate support for local vegetation characteristics on the probability of selection for nest sites and locations utilized by different ages of postfledging juveniles. Patterns of resource selection variation were species-specific. Resource selection models indicated that Acadian flycatcher habitat selection criteria were similar for nesting and dependent postfledging juveniles and selection criteria diverged when juveniles became independent from adults. After independence, flycatcher resource selection was more associated with understory foliage density. Ovenbirds differed in selection criteria between the nesting and postfledging periods. Fledgling ovenbirds selected areas with higher densities of understory structure compared to nest sites, and the effect of foliage density on selection increased as juveniles aged and gained independence. The differences observed between two sympatric forest nesting species, in both the timing and degree of change in resource selection criteria over the course of the breeding season, illustrates the importance of considering species-specific traits and postfledging requirements when developing conservation efforts, especially when foraging guilds or
The aim of this thesis was to optimise the selective breeding program for Nile tilapia in the Mekong Delta region of Vietnam. Two breeding schemes, the “classic” BLUP scheme following the GIFT method (with pair mating) and a rotational mating scheme with own performance selection and
Todd, Brian D; Halstead, Brian J.; Chiquoine, Lindsay P.; Peaden, J. Mark; Buhlmann, Kurt A.; Tuberville, Tracey D.; Nafus, Melia G.
Growing pressure to develop public lands for renewable energy production places several protected species at increased risk of habitat loss. One example is the Mojave desert tortoise (Gopherus agassizii), a species often at the center of conflicts over public land development. For this species and others on public lands, a better understanding of their habitat needs can help minimize negative impacts and facilitate protection or restoration of habitat. We used radio-telemetry to track 46 neonate and juvenile tortoises in the Eastern Mojave Desert, California, USA, to quantify habitat at tortoise locations and paired random points to assess habitat selection. Tortoise locations near burrows were more likely to be under canopy cover and had greater coverage of perennial plants (especially creosote [Larrea tridentata]), more coverage by washes, a greater number of small-mammal burrows, and fewer white bursage (Ambrosia dumosa) than random points. Active tortoise locations away from burrows were closer to washes and perennial plants than were random points. Our results can help planners locate juvenile tortoises and avoid impacts to habitat critical for this life stage. Additionally, our results provide targets for habitat protection and restoration and suggest that diverse and abundant small-mammal populations and the availability of creosote bush are vital for juvenile desert tortoises in the Eastern Mojave Desert.
Nakaya, Akihiro; Isobe, Sachiko N.
Background Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information avail...
Nakaya, Akihiro; Isobe, Sachiko N
Genomic selection or genome-wide selection (GS) has been highlighted as a new approach for marker-assisted selection (MAS) in recent years. GS is a form of MAS that selects favourable individuals based on genomic estimated breeding values. Previous studies have suggested the utility of GS, especially for capturing small-effect quantitative trait loci, but GS has not become a popular methodology in the field of plant breeding, possibly because there is insufficient information available on GS for practical use. In this review, GS is discussed from a practical breeding viewpoint. Statistical approaches employed in GS are briefly described, before the recent progress in GS studies is surveyed. GS practices in plant breeding are then reviewed before future prospects are discussed. Statistical concepts used in GS are discussed with genetic models and variance decomposition, heritability, breeding value and linear model. Recent progress in GS studies is reviewed with a focus on empirical studies. For the practice of GS in plant breeding, several specific points are discussed including linkage disequilibrium, feature of populations and genotyped markers and breeding scheme. Currently, GS is not perfect, but it is a potent, attractive and valuable approach for plant breeding. This method will be integrated into many practical breeding programmes in the near future with further advances and the maturing of its theory.
Full Text Available Objective Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully achieved the farm tracing of 6,018 multi-breed pigs, using single nucleotide polymorphism (SNP markers strictly selected through least absolute shrinkage and selection operator (LASSO feature selection. Methods We performed farm tracing of domesticated pig (Sus scrofa from SNP markers and selected the most relevant features for accurate prediction. Considering multi-breed composition of our data, we performed feature selection using LASSO penalization on 4,002 SNPs that are shared between breeds, which also includes 179 SNPs with small between-breed difference. The 100 highest-scored features were extracted from iterative simulations and then evaluated using machine-leaning based classifiers. Results We selected 1,341 SNPs from over 45,000 SNPs through iterative LASSO feature selection, to minimize between-breed differences. We subsequently selected 100 highest-scored SNPs from iterative scoring, and observed high statistical measures in classification of breeding farms by cross-validation only using these SNPs. Conclusion The study represents a successful application of LASSO feature selection on multi-breed pig SNP data to trace the farm information, which provides a valuable method and possibility for further researches on genetic traceability.
Janos C Hennicke
Full Text Available In seabirds, equal bi-parental care is the rule, as it is considered crucial for raising chicks successfully because seabirds forage in an environment with unpredictable and highly variable food supply. Frigatebirds forage in poor tropical waters, yet males reduce and even stop parental care soon after chick brooding, leaving the female to provision the chick alone for an extended fledging period. Using bird-borne tracking devices, male and female Christmas Island Frigatebirds (Fregata andrewsi were investigated during the brooding, late chick rearing and post-fledging period to examine whether sexes exhibit foraging strategies that may be linked to differential breeding investments. During brooding, males and females showed similar foraging behaviour under average marine productivity of oceanic waters close to the colony, but males shifted to more distant and more productive habitats when conditions deteriorated to continue with reduced chick provisioning. During the late chick rearing period, females progressively increased their foraging range to the more distant but productive marine areas that only males had visited during brooding. Birds spent the non-breeding period roosting in highly productive waters of the Sunda Shelf. The sex-specific utilisation of three different foraging habitats with different primary productivity (oceanic, coastal, and shelf areas allowed for temporal and spatial segregation in the exploitation of favourable habitats which seems to enable each sex to optimise its foraging profitability. In addition, post-fledging foraging movements of females suggest a biennial breeding cycle, while limited information on males suggests the possibility of an annual breeding cycle.
Cristina Santos Sotomaior
Full Text Available It is well known that the susceptibility of sheep to scrapie is determined by the host’s prion protein gene (PRNP. PRNP polymorphisms at codons 136 (alanine, A/valine, V, 154 (histidine, H/arginine, R and 171 (glutamine, Q/histidine, H/arginine, R are the main determinants of sheep susceptibility/resistance to classical scrapie. There are four major variants of the wild-type ARQ allele: VRQ, AHQ, ARH and ARR. Breeding programs have been developed in the European Union and the USA to increase the frequency of the resistant ARR allele while decreasing the frequency of the susceptible VRQ allele in sheep populations. In Brazil, little PRNP genotyping data are available for sheep, and thus far, no controlled breeding scheme for scrapie has been implemented. This review will focus on important epidemiological aspects of scrapie and the use of genetic resistance as a tool in breeding programs to control the disease.
Peanut breeding has played a significant role in yield increases and disease control. Conventional breeding focuses on field selection and phenotypic analysis and it typically takes 12-15 years before a new cultivar can be released. Molecular markers developed from sequencing data can be of great ...
Groff, Luke A.; Calhoun, Aram J.K.; Loftin, Cynthia S.
Identification of essential habitat is a fundamental component of amphibian conservation; however, species with complex life histories frequently move among habitats. To better understand dynamic habitat use, we evaluated Wood Frog (Lithobates sylvaticus (LeConte, 1825)) habitat selection and movement patterns during the spring migration and foraging periods and described the spatiotemporal variability of habitats used during all annual life-history periods. We radio-tracked 71 frogs in Maine during 2011–2013 and evaluated spring migration, foraging activity center (FAC), and within-FAC habitat selection. Telemetered frogs spent the greatest percentage of each field season in hibernacula (≥54.4%), followed by FACs (≥25.5%), migration habitat (≥16.9%), and breeding sites (≥4.5%). FACs ranged 49 – 1 335 m2 (568.0 ± 493.4 m2) and annual home ranges spanned 1 413 – 32 165 m2 (11 780.6 ± 12 506.1 m2). During spring migration, Wood Frogs exhibited different movement patterns (e.g., turn angles), selected different habitat features, and selected habitat features less consistently than while occupying FACs, indicating that the migration and foraging periods are ecologically distinct. Habitat-use studies that do not discriminate among annual life-history periods may obscure true ecological relationships and fail to identify essential habitat necessary for sustaining amphibian populations.
Full Text Available The study was undertaken in bale zone to assess farmer’s selective breeding objectives, trait preferences, selection criteria and breeding system October 2012 to November 2013. A purposive and multistage sampling technique was applied for selection of 3 district and 9 kebeles. Then 360 households were selected by using simple random sampling techniques after the list of pastoralist having goats was identified. Statistical analysis system version 9.1 was used for analysis of data. Indices, effective population size and rate of inbreeding were calculated on average each respondent holds about 14 goats. Milk production is the main reason of goat keeping in the study area. Appearance is the first rank as selection criteria for male and female in all studies area. About 47.8% of the respondents have their own buck. The main use of breeding buck in the study area was for mating purpose (76.2%. Mean estimate of effective population size and mean rate of inbreeding was 2.43 and 0.21, respectively when a household flock is herded alone and under random mating. Therefore, any breed improvement strategies that are intended to be implemented in the study area and else- where should consider the traditional breeding practices and breeding objectives of the community.
Forsman, J.T.; Martin, T.E.
Choice of breeding habitat can have a major impact on fitness. Sensitivity of habitat choice to environmental cues predicting reproductive success, such as density of harmful enemy species, should be favored by natural selection. Yet, experimental tests of this idea are in short supply. Brown-headed cowbirds Molothrus ater commonly reduce reproductive success of a wide diversity of birds by parasitizing their nests. We used song playbacks to simulate high cowbird density and tested whether cowbird hosts avoid such areas in habitat selection. Host species that made settlement decisions during manipulations were significantly less abundant in the cowbird treatment as a group. In contrast, hosts that settled before manipulations started and non-host species did not respond to treatments. These results suggest that hosts of cowbirds can use vocal cues to assess parasitism risk among potential habitat patches and avoid high risk habitats. This can affect community structure by affecting habitat choices of species with differential vulnerability.
Jeremiah R. Alexander
Full Text Available Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic life stages. One approach to management of pond-breeding species is protection of core upland habitat surrounding the breeding pond. We used genetic variation as an indicator of population status in a common amphibian species, spotted salamanders (Ambystoma maculatum, to determine how amount of suitable upland habitat relates to population status in the greater Charlotte, North Carolina, USA metropolitan area. We developed candidate models to evaluate the relative influence of historical and contemporary forested habitat availability on population genetic variation at two spatial scales of upland area (164 m and 2000 m at four time intervals over the past seven decades (1938, 1978, 1993, 2005. We found that historical land cover best predicted contemporary allelic richness. Inbreeding coefficient and observed heterozygosity were not effectively predicted by forest cover at either spatial or temporal scales. Allelic richness was best predicted at the smaller spatial scale in the 1993 time interval. Predicting and understanding how future landscape configuration affects genetic variation of common and rare species is imperative for the conservation of amphibian and other wildlife populations.
Zhao, Yusheng; Gowda, Manje; Liu, Wenxin; Würschum, Tobias; Maurer, Hans P; Longin, Friedrich H; Ranc, Nicolas; Reif, Jochen C
Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3-4 locations. As for maize up to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds great promise for maize breeding programs.
Jonas, Elisabeth; de Koning, Dirk-Jan
Plant breeding largely depends on phenotypic selection in plots and only for some, often disease-resistance-related traits, uses genetic markers. The more recently developed concept of genomic selection, using a black box approach with no need of prior knowledge about the effect or function of individual markers, has also been proposed as a great opportunity for plant breeding. Several empirical and theoretical studies have focused on the possibility to implement this as a novel molecular method across various species. Although we do not question the potential of genomic selection in general, in this Opinion, we emphasize that genomic selection approaches from dairy cattle breeding cannot be easily applied to complex plant breeding. Copyright © 2013 Elsevier Ltd. All rights reserved.
-introduction of selected primate species in the wild using Centre for Education, Research and Conservation of Primates and Nature (CERCOPAN) and Drill Rehabilitation and Breeding Center (PANDRILLUS) of Cross Rivers State as case ...
Full Text Available In breeders’ general opinion small breed females produce less numerous litters. The aim of the study was to analyse the litter size and the frequency of the gender ratio in selected small dog breeds in view of their popularity in Poland. The data set comprised information on 639 litters (in total 2578 puppies of eight breeds, which were born between January 2003 and end December 2014. The results were statistically analysed using statistical program SPSS 20.0. Medium-size litters were observed in the analysed small dog breeds (4.034±0.1. Comparison of the selected breeds of the Fédération Cynologique Internationale (FCI Groups showed that the mean litter size in Group IX was higher (4.36±0.08 than that in Group III (3.87±0.14 and the differences were statistically significant. The study has confirmed the hypothesis that larger females produce more numerous litters, but there are large intra-individual variations in the number of pups born in individual breeds. Additionally, the gender ratio in the puppies born in the analysed breeds was equal, despite the fluctuations in the individual breeds.
Full Text Available Distinct preference of species for habitats is most often driven by long term differences in demographic rates between habitats. Estimating variation in those rates is key for developing successful conservation strategies. Stochastic events can interact with underlying variation in habitat quality in regulating demography but the opportunities to explore such interactions are rare. Whimbrels in Iceland show a strong preference for sparsely vegetated riverplains. Such habitats in Iceland face various threats, e.g., climate change, river regulation and spread of alien plant species. In this study we compared demographic parameters of breeding Whimbrels between riverplains and other habitats before, during and after volcanic eruption events to estimate the importance of the habitats for the species and the effect of ash deposit on breeding success. We found that an estimated minimum of 23% of the Icelandic population of Whimbrels and c. 10% of the world population of the species breed in riverplain habitats in Iceland. Whimbrels bred consistently at much higher densities in riverplain habitats than in other habitats and riverplains also had higher densities of pairs with fledglings although the proportion of successful breeders was similar between habitats. Predation by livestock may have had a considerable negative effect on breeding success on our study sites. Breeding was negatively affected by the volcanic activity, probably through the effects of ash on the invertebrate food supply, with breeding success being gradually worse closer to the eruption. Breeding success was equally affected by volcanism across habitats which differed in underlying habitat quality. This study gives an example of how populations can be regulated by factors which operate at different spatial scales, such as local variation in habitat quality and stochastic events which impact larger areas.
Steen, Valerie A.; Powell, Abby N.
We examined wetland selection by the Black Tern (Chlidonias niger), a species that breeds primarily in the prairie pothole region, has experienced population declines, and is difficult to manage because of low site fidelity. To characterize its selection of wetlands in this region, we surveyed 589 wetlands throughout North and South Dakota. We documented breeding at 5% and foraging at 17% of wetlands. We created predictive habitat models with a machine-learning algorithm, Random Forests, to explore the relative role of local wetland characteristics and those of the surrounding landscape and to evaluate which characteristics were important to predicting breeding versus foraging. We also examined area-dependent wetland selection while addressing the passive sampling bias by replacing occurrence of terns in the models with an index of density. Local wetland variables were more important than landscape variables in predictions of occurrence of breeding and foraging. Wetland size was more important to prediction of foraging than of breeding locations, while floating matted vegetation was more important to prediction of breeding than of foraging locations. The amount of seasonal wetland in the landscape was the only landscape variable important to prediction of both foraging and breeding. Models based on a density index indicated that wetland selection by foraging terns may be more area dependent than that by breeding terns. Our study provides some of the first evidence for differential breeding and foraging wetland selection by Black Terns and for a more limited role of landscape effects and area sensitivity than has been previously shown.
Full Text Available Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed.We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality and EDAR (associated with hair thickness were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9 were associated with pre-weaning gain in our previous genome-wide association study.Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.
Wang, Huihua; Zhang, Li; Cao, Jiaxve; Wu, Mingming; Ma, Xiaomeng; Liu, Zhen; Liu, Ruizao; Zhao, Fuping; Wei, Caihong; Du, Lixin
Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study. Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.
However, the two species appeared to differ in nest site selection; Rudd's Lark nests were most frequently built in unburned grass and Botha's Lark nests on recently burned land. First egg dates of 93 Rudd's Lark nests ranged from late October to late March, with peak laying in January and February. Most clutches were of ...
Boelman, Natalie T; Gough, Laura; Wingfield, John; Goetz, Scott; Asmus, Ashley; Chmura, Helen E; Krause, Jesse S; Perez, Jonathan H; Sweet, Shannan K; Guay, Kevin C
Climate warming is affecting the Arctic in multiple ways, including via increased dominance of deciduous shrubs. Although many studies have focused on how this vegetation shift is altering nutrient cycling and energy balance, few have explicitly considered effects on tundra fauna, such as the millions of migratory songbirds that breed in northern regions every year. To understand how increasing deciduous shrub dominance may alter breeding songbird habitat, we quantified vegetation and arthropod community characteristics in both graminoid and shrub dominated tundra. We combined measurements of preferred nest site characteristics for Lapland longspurs (Calcarius lapponicus) and Gambel's White-crowned sparrows (Zonotrichia leucophrys gambelii) with modeled predictions for the distribution of plant community types in the Alaskan arctic foothills region for the year 2050. Lapland longspur nests were found in sedge-dominated tussock tundra where shrub height does not exceed 20 cm, whereas White-crowned sparrows nested only under shrubs between 20 cm and 1 m in height, with no preference for shrub species. Shrub canopies had higher canopy-dwelling arthropod availability (i.e. small flies and spiders) but lower ground-dwelling arthropod availability (i.e. large spiders and beetles). Since flies are the birds' preferred prey, increasing shrubs may result in a net enhancement in preferred prey availability. Acknowledging the coarse resolution of existing tundra vegetation models, we predict that by 2050 there will be a northward shift in current White-crowned sparrow habitat range and a 20-60% increase in their preferred habitat extent, while Lapland longspur habitat extent will be equivalently reduced. Our findings can be used to make first approximations of future habitat change for species with similar nesting requirements. However, we contend that as exemplified by this study's findings, existing tundra modeling tools cannot yet simulate the fine-scale habitat
The American kestrel, Falco sparveriushas sex-related differences in habitat use during the non-breeding season, with females occupying more open habitats than males. Two competing hypotheses have been proposed to explain this phenomenon: (1) males and females prefer different habitats, and (2) males and females prefer similar habitats, but larger females exclude smaller males from preferred areas. This study experimentally investigated habitat selection in wintering kestrels by temporarily removing kestrels from areas, and then observing the numbers and sex of the kestrels that occupied vacated areas. The home ranges of 20 birds (10 males and 10 females) were mapped and their occupants removed. Areas vacated in early winter (November 1994) were filled more quickly than those vacated in late winter (February 1995). Areas previously held by females were reoccupied more frequently than were those previously occupied by males. Female kestrels reoccupied vacated female areas more than vacated male areas. Male kestrels reoccupied vacated female and male areas equally. The results demonstrate that (1) high-quality kestrel habitat may be limited in the non-breeding season, (2) vacated areas are more likely to be reoccupied in the early winter than in late winter, (3) female kestrels appear at an advantage relative to males in occupying scarce and competed-for areas, and (4) male kestrels will use female areas when female occupants have been removed. It is hypothesized that open habitats are preferred over less open habitats because the former offer reduced risk of predation from bird-eating hawks.
Boal, C.W.; Estabrook, T.S.; Duerr, A.E.
Declines in loggerhead shrike (Lanius ludovicianus) populations have been associated in part with habitat loss and degradation, including that resulting from urbanization. We monitored the productivity and examined nesting habitat of loggerhead shrikes nesting in an urban environment in Tucson, Arizona. We located 22 breeding pairs in 1997 and 26 breeding pairs in 1998, with a 72% breeding area reoccupancy between years. Mean fledgling numbers were 2.28/ nesting attempt and 3.11/successful nest. Although some pairs initially failed and renested, 91% and 73% of shrike pairs successfully fledged young in 1997 and 1998, respectively. Mayfield estimates of nesting success were 78% in 1997 and 65% in 1998. Nest sites were characterized by more trees >3 m in height, taller nest trees than those randomly available, and a greater proportion of bare ground surface than at random sites. Shrike breeding territories had lower proportions of residential and commercial development and greater proportions of open areas with low-growing vegetation than randomly available. Some shrikes nested in school playgrounds, residential front yards, and parking lots, if adjacent open space was available.
Moncaz, Aviad; Kirstein, Oscar; Gebresellassie, Araya; Lemma, Wossenseged; Gebre-Michael, Teshome; Balkew, Meshesha; Belay, Shewaye; Hailu, Asrat; Warburg, Alon
Sand flies belonging to the genus Sergentomyia Franca & Parrot, 1920, are hematophagous insects feeding mostly on reptiles and birds, but some species feed also on mammals including humans. Sergentomyia spp. frequently comprise the vast majority of sand flies trapped along with Phlebotomus spp., the vectors of mammalian leishmaniasis. Within the framework of a project on the ecology and transmission of visceral leishmaniasis in Ethiopia, putative breeding sites of phlebotomine sand flies were studied. Large horizontal sticky traps (LHSTs) covered with sand fly-proof mesh were deployed over cracked vertisol and related habitats for up to 3 nights, and emerging sand flies were collected daily. Emergence traps (ETs) were also adapted to sample other putative breeding sites including tree trunks, termite mounds, rock piles and vertical river banks. Productive breeding sites were identified in the trunks and roots systems of trees, vertisol fields, cracks and burrows in vertisol dry river banks and termite mounds. Emerging flies were also collected form a stone wall and a rock pile situated inside a village. Significantly more Sergentomyia spp. were trapped in vertisols by ETs deployed over root system than in open fields. Similarly, more sand flies emerged from cracks in the vertisol in fallow Sorghum than in fallow sesame fields. Productive breeding sites were characterized by stable micro-climatic conditions. Species composition of emerging sand flies varied with habitat, season and geographical location. Copyright © 2014 Elsevier B.V. All rights reserved.
FAO estimates that there are around 200 species in aquaculture. However, only a few species have ongoing selective breeding programmes. Marker-assisted selection (MAS) is not used in any aquaculture breeding scheme today. The aim of this chapter, therefore, is to review briefly the current status of aquaculture breeding schemes and to evaluate the possibilities for MAS of aquaculture species. Genetic marker maps have been published for some species in culture. The marker density of these maps is, in general, rather low and the maps are composed of many amplified fragment length polymorphism (AFLP) markers anchored to few microsatellites. Some quantitative trait loci (QTL) have been identified for economically important traits, but they are not yet mapped at a high density. Computer simulations of within-family MAS schemes show a very high increase in genetic gain compared with conventional family-based breeding schemes, mainly due to the large family sizes that are typical for aquaculture breeding schemes. The use of genetic markers to identify individuals and their implications for breeding schemes with control of inbreeding are discussed. (author)
Ney Sussumu Sakiyama
Full Text Available Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the Brazilian public institutions few breeding programs use it efficiently. The possible reasons are: lack of know-how, lack of appropriate laboratories, few validated markers, high cost, and lack of urgency in obtaining cultivars. In this article we analyze the use and the constraints of marker-assisted selection in plant breeding programs of Brazilian public institutes
Anteau, Michael J; Sherfy, Mark H; Wiltermuth, Mark T
Animals use proximate cues to select resources that maximize individual fitness. When animals have a diverse array of available habitats, those selected could give insights into true habitat preferences. Since the construction of the Garrison Dam on the Missouri River in North Dakota, Lake Sakakawea (SAK) has become an important breeding area for federally threatened piping plovers (Charadrius melodus; hereafter plovers). We used conditional logistic regression to examine nest-site selection at fine scales (1, 3, and 10 m) during summers 2006-2009 by comparing characteristics at 351 nests to those of 668 random sites within nesting territories. Plovers selected sites (1 m(2)) that were lower than unused random sites, increasing the risk of nest inundation. Plovers selected nest sites that were flat, had little silt, and at least 1 cobble; they also selected for 3-m radius nest areas that were relatively flat and devoid of vegetation and litter. Ninety percent of nests had <38% coverage of silt and <10% slope at the site, and <15% coverage of vegetation or litter and <31% slope within the 3-m radius. Gravel was selected for at nest sites (11% median), but against in the area 10-m from the nest, suggesting plovers select for patches or strips of gravel. Although elevation is rarely evaluated in studies of ground-nesting birds, our results underscore its importance in habitat-selection studies. Relative to where plovers historically nested, habitat at SAK has more diverse topography, substrate composition, vegetation communities, and greater water-level fluctuations. Accordingly, our results provide an example of how habitat-selection results can be interpreted as habitat preferences because they are not influenced by desired habitats being scarce or absent. Further, our results will be useful for directing habitat conservation for plovers and interpreting other habitat-selection studies.
Michael J Anteau
Full Text Available Animals use proximate cues to select resources that maximize individual fitness. When animals have a diverse array of available habitats, those selected could give insights into true habitat preferences. Since the construction of the Garrison Dam on the Missouri River in North Dakota, Lake Sakakawea (SAK has become an important breeding area for federally threatened piping plovers (Charadrius melodus; hereafter plovers. We used conditional logistic regression to examine nest-site selection at fine scales (1, 3, and 10 m during summers 2006-2009 by comparing characteristics at 351 nests to those of 668 random sites within nesting territories. Plovers selected sites (1 m(2 that were lower than unused random sites, increasing the risk of nest inundation. Plovers selected nest sites that were flat, had little silt, and at least 1 cobble; they also selected for 3-m radius nest areas that were relatively flat and devoid of vegetation and litter. Ninety percent of nests had <38% coverage of silt and <10% slope at the site, and <15% coverage of vegetation or litter and <31% slope within the 3-m radius. Gravel was selected for at nest sites (11% median, but against in the area 10-m from the nest, suggesting plovers select for patches or strips of gravel. Although elevation is rarely evaluated in studies of ground-nesting birds, our results underscore its importance in habitat-selection studies. Relative to where plovers historically nested, habitat at SAK has more diverse topography, substrate composition, vegetation communities, and greater water-level fluctuations. Accordingly, our results provide an example of how habitat-selection results can be interpreted as habitat preferences because they are not influenced by desired habitats being scarce or absent. Further, our results will be useful for directing habitat conservation for plovers and interpreting other habitat-selection studies.
Sunde, Peter; Thorup, Kasper; Jacobsen, Lars Bo
Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability) of foraging, radio-tagged little owls (Athene noctua), a nocturnal, year-rou...
Full Text Available Abstract Background The prediction of the outcomes from multistage breeding schemes is especially important for the introduction of genomic selection in dairy cattle. Decorrelated selection indices can be used for the optimisation of such breeding schemes. However, they decrease the accuracy of estimated breeding values and, therefore, the genetic gain to an unforeseeable extent and have not been applied to breeding schemes with different generation intervals and selection intensities in each selection path. Methods A grid search was applied in order to identify optimum breeding plans to maximise the genetic gain per year in a multistage, multipath dairy cattle breeding program. In this program, different values of the accuracy of estimated genomic breeding values and of their costs per individual were applied, whereby the total breeding costs were restricted. Both decorrelated indices and optimum selection indices were used together with fast multidimensional integration algorithms to produce results. Results In comparison to optimum indices, the genetic gain with decorrelated indices was up to 40% less and the proportion of individuals undergoing genomic selection was different. Additionally, the interaction between selection paths was counter-intuitive and difficult to interpret. Independent of using decorrelated or optimum selection indices, genomic selection replaced traditional progeny testing when maximising the genetic gain per year, as long as the accuracy of estimated genomic breeding values was ≥ 0.45. Overall breeding costs were mainly generated in the path "dam-sire". Selecting males was still the main source of genetic gain per year. Conclusion Decorrelated selection indices should not be used because of misleading results and the availability of accurate and fast algorithms for exact multidimensional integration. Genomic selection is the method of choice when maximising the genetic gain per year but genotyping females may not
The main goals of breeding programmes for fish and shellfish are to increase the profitability and sustainability of aquaculture. Traditionally, these have been carried out successfully using pedigree information by selecting individuals based on breeding values predicted for traits measured on candidates using an 'animal model'. This methodology assumes that phenotypes are explained by a large number of genes with small effects and random environmental deviations. However, information on individual genes with medium or large effects cannot be used in this manner. In selective breeding programmes using pedigree information, molecular markers have been used primarily for parentage assignment when tagging individual fish is difficult and to avoid causing common environmental effects from rearing families in separate tanks. The use of these techniques in such conventional breeding programmes is discussed in detail. Exploiting the great biological diversity of many fish and shellfish species, different experimental designs may use either chromosomal manipulations or large family sizes to increase the likelihood of finding the loci affecting quantitative traits, the so-called QTL, by screening the segregation of molecular markers. Using information on identified loci in breeding schemes in aquaculture is expected to be cost-effective compared with traditional breeding methods only when the accuracy of predicting breeding values is rather low, e.g. for traits with low heritability such as disease resistance or carcass quality. One of the problems facing aquaculture is that some of the resources required to locate QTL accurately, such as dense linkage maps, are not yet available for the many species. Recently, however, information from expressed sequence tag (EST) databases has been used for developing molecular markers such as microsatellites and single nucleotide polymorphisms (SNPs). Marker-assisted selection (MAS) or genome-wide marker-assisted selection (G-MAS) using
Brooke, Jarred M.; Peters, David C.; Unger, Ashley M.; Tanner, Evan P.; Harper, Craig A.; Keyser, Patrick D.; Clark, Joseph D.; Morgan, John J.
More than 600,000 ha of mine land have been reclaimed in the eastern United States, providing large contiguous tracts of early successional vegetation that can be managed for northern bobwhite (Colinus virginianus). However, habitat quality on reclaimed mine land can be limited by extensive coverage of non-native invasive species, which are commonly planted during reclamation. We used discrete-choice analysis to investigate bobwhite resource selection throughout the year on Peabody Wildlife Management Area, a 3,330-ha reclaimed surface mine in western Kentucky. We used a treatment-control design to study resource selection at 2 spatial scales to identify important aspects of mine land vegetation and whether resource selection differed between areas with habitat management (i.e., burning, disking, herbicide; treatment) and unmanaged units (control). Our objectives were to estimate bobwhite resource selection on reclaimed mine land and to estimate the influence of habitat management practices on resource selection. We used locations from 283 individuals during the breeding season (1 Apr–30 Sep) and 136 coveys during the non-breeding season (1 Oct–Mar 31) from August 2009 to March 2014. Individuals were located closer to shrub cover than would be expected at random throughout the year. During the breeding season, individuals on treatment units used areas with smaller contagion index values (i.e., greater interspersion) compared with individuals on control units. During the non-breeding season, birds selected areas with greater shrub-open edge density compared with random. At the microhabitat scale, individuals selected areas with increased visual obstruction >1 m aboveground. During the breeding season, birds were closer to disked areas (linear and non-linear) than would be expected at random. Individuals selected non-linear disked areas during winter but did not select linear disked areas (firebreaks) because they were planted to winter wheat each fall and
Longin, C Friedrich H; Mi, Xuefei; Würschum, Tobias
The implementation of genomic selection in breeding programs can be recommended for hybrid and line breeding in wheat. High prediction accuracies from genomic selection (GS) were reported for grain yield in wheat asking for the elaboration of efficient breeding strategies applying GS. Our objectives were therefore, (1) to optimize the number of lines, locations and testers in different multi-stage breeding strategies with and without GS, (2) to elaborate the most efficient breeding strategy based on the selection gain and its standard deviation, and (3) to investigate the potential of GS to improve the relative efficiency of hybrid versus line breeding in wheat. We used the open source software package "selectiongain" to optimize the allocation of resources in different breeding strategies by predicting the expected selection gain for a fixed budget. Classical two-stage phenotypic selection was compared with three GS breeding strategies for line and hybrid breeding in wheat. The ranking of the alternative breeding strategies varied largely in dependence of the GS prediction accuracy. Fast-track breeding strategies based solely on GS were only advantageous for high GS prediction accuracies that is >0.50 and >0.65 for hybrid and line breeding, respectively. However, a GS prediction accuracy across breeding cycles of 0.3 or even less must be assumed as realistic for grain yield in wheat. For this low GS prediction accuracy, the use of GS is advantageous for line but especially for hybrid breeding in wheat. Furthermore, the use of GS in hybrid wheat breeding increased the relative efficiency of hybrid versus line breeding and, thus, might be an important pillar for the establishment of hybrid wheat.
Crossa, José; Pérez-Rodríguez, Paulino; Cuevas, Jaime; Montesinos-López, Osval; Jarquín, Diego; de Los Campos, Gustavo; Burgueño, Juan; González-Camacho, Juan M; Pérez-Elizalde, Sergio; Beyene, Yoseph; Dreisigacker, Susanne; Singh, Ravi; Zhang, Xuecai; Gowda, Manje; Roorkiwal, Manish; Rutkoski, Jessica; Varshney, Rajeev K
Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding. Copyright © 2017 Elsevier Ltd. All rights reserved.
also, slightly different broeding objectives. Very little is known about the actual advantases of selection on BLUP of breeding values to the Merino stud breeder who must neces- sarily conform to other prerequisites, notably, visual accep- tance, dictated by the market-place. Material and Methods. Animals. From 1966 to 1912, ...
Radović, Andreja; Jelaska, Sven D
Changes in habitat suitable for breeding of two sympatric raptor species (Haliaeetus albicilla and Aquila pomarina) were analysed along one of the most important breeding sites in Croatia for both species. The habitat suitability modelling was used to assess the influence of forestry practice during 2000-2006 using the known data on nesting places along research area. The four most important variables for lesser spotted eagle were elevation, distance from the nearest pasture, vertical distance to the nearest channel network and broadleaved forest placement (second axis from the principal component analysis of the enhanced vegetation index (EVI) index of MODIS images; November-March). The variables where white-tailed eagles showed greatest shift from overall habitat characteristics in the research area were broadleaved forest (second axis from the principal component analysis of the EVI index), height above the sea level, distance from the small settlements, vertical distance to channel network - all with negative loadings. The results clearly reveal the disproportion of suitable forests for raptors that were cut down in comparison to maturation of suitable forests.
Sae-Lim, P; Kause, A; Mulder, H A; Olesen, I
Aquaculture is the fastest growing food production sector and it contributes significantly to global food security. Based on Food and Agriculture Organization (FAO) of the United Nations, aquaculture production must increase significantly to meet the future global demand for aquatic foods in 2050. According to Intergovernmental Panel on Climate Change (IPCC) and FAO, climate change may result in global warming, sea level rise, changes of ocean productivity, freshwater shortage, and more frequent extreme climate events. Consequently, climate change may affect aquaculture to various extents depending on climatic zones, geographical areas, rearing systems, and species farmed. There are 2 major challenges for aquaculture caused by climate change. First, the current fish, adapted to the prevailing environmental conditions, may be suboptimal under future conditions. Fish species are often poikilothermic and, therefore, may be particularly vulnerable to temperature changes. This will make low sensitivity to temperature more important for fish than for livestock and other terrestrial species. Second, climate change may facilitate outbreaks of existing and new pathogens or parasites. To cope with the challenges above, 3 major adaptive strategies are identified. First, general 'robustness' will become a key trait in aquaculture, whereby fish will be less vulnerable to current and new diseases while at the same time thriving in a wider range of temperatures. Second, aquaculture activities, such as input power, transport, and feed production contribute to greenhouse gas emissions. Selection for feed efficiency as well as defining a breeding goal that minimizes greenhouse gas emissions will reduce impacts of aquaculture on climate change. Finally, the limited adoption of breeding programs in aquaculture is a major concern. This implies inefficient use of resources for feed, water, and land. Consequently, the carbon footprint per kg fish produced is greater than when fish from
Laskowski, Jessica; Gillespie, Caitlyn R.; Corral, Lucia; Oden, Amy; Fricke, Kent A.; Fontaine, Joseph J.
We present a hands-on outdoor activity coupled with classroom discussion to teach students about wildlife habitat selection, the process by which animals choose where to live. By selecting locations or habitats with many benefits (e.g., food, shelter, mates) and few costs (e.g., predators), animals improve their ability to survive and reproduce. Biologists track animal movement using radio telemetry technology to study habitat selection so they can better provide species with habitats that promote population growth. We present a curriculum in which students locate “animals” (transmitters) using radio telemetry equipment and apply math skills (use of fractions and percentages) to assess their “animal's” habitat selection by comparing the availability of habitat types with the proportion of “animals” they find in each habitat type.
Full Text Available There is a lack of data on the population densities of birds breeding in a mosaic of typical urbanized habitats. This study was undertaken to partly fulfil this gap in our knowledge. Counts were conducted in 2008 by means of simplified territory mapping method in a fragment (1197 ha of a large Central European city (Wrocław, SW Poland. In total, 50 bird species were breeding in the study area in 2008. The House Sparrow Passer domesticus, Common Swift Apus apus and Rock Dove comprised about 3/5 of all breeding pairs. The other group of species, each one with a density between 6 and 13 pairs per 100 ha, included seven species, namely the Starling, Sturnus vulgaris, Greenfinch, Carduelis chloris, House Martin, Delichon urbica, Tree Sparrow, Passer montanus, Great Tit, Parus major, Blue Tit, Parus caeruleus, and Jackdaw, Corvus monedula. They comprised together about 1/5. The remaining 40 species nested in a density between 0.1 and 3.5 pairs per 100 ha. The most numerous feeding guild were granivores (53.8% and insectivores (37.9 %. Birds nesting on buildings comprised together 74 % of all breeding pairs. For a few species (Luscinia megarhynchos, Saxicola torquata, Corvus cornix and Turdus pilaris an increase in their numbers in the last three decades has been evidenced.
Geomorphic / floristic variables are useful as general habitat indicators on coastal foredunes. Variables used in this study were vegetation cover, plant community structure and sand movement. Three distinct zones, four habitats and six subhabitats were identified. Zonation and habitat selection appeared to be related to ...
Nov 8, 1988 ... Geomorphic / floristic variables are useful as general habitat indicators on coastal foredunes. Variables used in this study were vegetation cover, plant community structure and sand movement. Three distinct zones, four habitats and six subhabitats were identified. Zonation and habitat selection appeared to ...
Marulanda, Jose J; Mi, Xuefei; Melchinger, Albrecht E; Xu, Jian-Long; Würschum, T; Longin, C Friedrich H
A breeding strategy with moderate nursery selection followed by genomic selection and one-stage phenotypic selection maximizes annual selection gain for grain yield across a wide range of hybrid breeding scenarios. Genomic selection (GS) is a promising method for the selection of quantitatively inherited traits but its most effective implementation in routine hybrid breeding schemes requires further research. We compared five breeding strategies and varied their available budget, the costs for doubled haploid (DH) line and hybrid seed production as well as variance components for grain yield in a wide range. In contrast to previous studies, we included a nursery selection for disease resistance just before GS on grain yield. The breeding strategy GSrapid with moderate nursery selection followed by one stage GS and one final stage with phenotypic selection on grain yield had the highest annual selection gain across all strategies, budgets, costs and variance components considered and we, therefore, highly recommend its use in hybrid breeding of cereals. Although selecting on traits not correlated with grain yield in the observation nursery, this selection reduced the selection gain of grain yield, especially in the breeding schemes with GS and for selected fractions smaller than 0.3. Owing to the very high number of test candidates entering breeding strategies with GS, the costs for DH line production had a larger impact on the annual selection gain than the hybrid seed production costs. The optimum allocation of test resources maximizing annual selection gain in classical two-stage phenotypic selection on grain yield and for the recommended breeding strategy GSrapid is finally explored for maize, wheat, rye, barley, rice and triticale.
Johnson, Matthew J.; Hatten, James R.; Holmes, Jennifer A.; Shafroth, Patrick B.
The western population of the yellow-billed cuckoo (Coccyzus americanus) was recently listed as threatened under the federal Endangered Species Act. Yellow-billed cuckoo conservation efforts require the identification of features and area requirements associated with high quality, riparian forest habitat at spatial scales that range from nest microhabitat to landscape, as well as lower-suitability areas that can be enhanced or restored. Spatially explicit models inform conservation efforts by increasing ecological understanding of a target species, especially at landscape scales. Previous yellow-billed cuckoo modelling efforts derived plant-community maps from aerial photography, an expensive and oftentimes inconsistent approach. Satellite models can remotely map vegetation features (e.g., vegetation density, heterogeneity in vegetation density or structure) across large areas with near perfect repeatability, but they usually cannot identify plant communities. We used aerial photos and satellite imagery, and a hierarchical spatial scale approach, to identify yellow-billed cuckoo breeding habitat along the Lower Colorado River and its tributaries. Aerial-photo and satellite models identified several key features associated with yellow-billed cuckoo breeding locations: (1) a 4.5 ha core area of dense cottonwood-willow vegetation, (2) a large native, heterogeneously dense forest (72 ha) around the core area, and (3) moderately rough topography. The odds of yellow-billed cuckoo occurrence decreased rapidly as the amount of tamarisk cover increased or when cottonwood-willow vegetation was limited. We achieved model accuracies of 75–80% in the project area the following year after updating the imagery and location data. The two model types had very similar probability maps, largely predicting the same areas as high quality habitat. While each model provided unique information, a dual-modelling approach provided a more complete picture of yellow-billed cuckoo habitat
Franck A Hollander
Full Text Available In human-altered environments, organisms may preferentially settle in poor-quality habitats where fitness returns are lower relative to available higher-quality habitats. Such ecological trapping is due to a mismatch between the cues used during habitat selection and the habitat quality. Maladaptive settlement decisions may occur when organisms are time-constrained and have to rapidly evaluate habitat quality based on incomplete knowledge of the resources and conditions that will be available later in the season. During a three-year study, we examined settlement decision-making in the long-distance migratory, open-habitat bird, the Red-backed shrike (Lanius collurio, as a response to recent land-use changes. In Northwest Europe, the shrikes typically breed in open areas under a management regime of extensive farming. In recent decades, Spruce forests have been increasingly managed with large-size cutblocks in even-aged plantations, thereby producing early-successional vegetation areas that are also colonised by the species. Farmland and open areas in forests create mosaics of two different types of habitats that are now occupied by the shrikes. We examined redundant measures of habitat preference (order of settlement after migration and distribution of dominant individuals and several reproductive performance parameters in both habitat types to investigate whether habitat preference is in line with habitat quality. Territorial males exhibited a clear preference for the recently created open areas in forests with higher-quality males settling in this habitat type earlier. Reproductive performance was, however, higher in farmland, with higher nest success, offspring quantity, and quality compared to open areas in forests. The results showed strong among-year consistency and we can therefore exclude a transient situation. This study demonstrates a case of maladaptive habitat selection in a farmland bird expanding its breeding range to human
Full Text Available The diet of non-breeding White Storks was studied by pellet analysis and included mainly insects (99.9%, n=28947 with a predominance of grasshoppers (Orthoptera, 76.1%, and beetles (Coleoptera, 26.1%. The bush crickets Decticus albifrons/verrucivorus were the most numerous prey (29.9% by items, occurring in almost all pellets (98% occurrence in pellets, n=147 and predominating in half of them (49.7%. The grasshopper associations in the pellets specify foraging mainly in mesophytic grasslands that usually replace abandoned fields and overgrown pastures with a low level of grazing. The xerophytic grass-shrubby habitats, not rare on stony terrains, were of less importance, providing around 20% by prey. The typical aquatic inhabitants and the use of carrion around villages were exceptions in the study diet. The number of innutritious materials in the pellets rose when the White Storks hunted on nippy and agile grasshoppers and decreased when the main pray was slower beetles taken from the ground. The roosting of non-breeding White Storks disappeared when their preferred feeding habitats were ploughed up in the following years.
Liu, X.; Toxopeus, A.G.; Skidmore, A.K.; Shao, X.; Dang, D.; Wang, T.; Prins, H.H.T.
Little is known about habitat selection of the giant panda (Ailuropoda melanoleuca), especially about the relationship between giant panda presence and bamboo and tree structures. We presented data on giant panda habitat use and selection in Foping Nature Reserve (NR), China. We used 1,066
Laskowski, Jessica; Gillespie, Caitlyn; Corral, Lucia; Oden, Amy; Fricke, Kent; Fontaine, Joseph J.
We present a hands-on outdoor activity coupled with classroom discussion to teach students about wildlife habitat selection, the process by which animals choose where to live. By selecting locations or habitats with many benefits (e.g., food, shelter, mates) and few costs (e.g., predators), animals improve their ability to survive and reproduce.…
Steven F. Railsback; Bret C. Harvey; John W. Hayse; Kirk E. Lagory
For many animals, selecting whether to forage during day or night is a critical fitness problem: at night, predation risks are lower but feeding is less efficient. Habitat selection is a closely related problem: the best location for nocturnal foraging could be too risky during daytime, and habitat that is safe and profitable in daytime may be unprofitable at night. We...
Bartelt, Paul E.; Gallant, Alisa L.; Klaver, Robert W.; Wright, C.K.; Patla, Debra A.; Peterson, Charles R.
The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000-2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probability, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from (1) field survey site data only, (2) field data combined with data from geospatial models, and (3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from 0.70 to 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from 0.30 to 0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from 0.60 to 0.80. Combining results from the geospatial multiyear models yielded maps of "core" breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative areas that could be protected for each species
Rodrigo B Ferreira
Full Text Available Understanding the response of species with differing life-history traits to habitat edges and habitat conversion helps predict their likelihood of persistence across changing landscape. In Brazil's Atlantic Forest, we evaluated frog richness and abundance by breeding guild at four distances from the edge of a reserve: i 200 m inside the forest, ii 50 m inside the forest, iii at the forest edge, and iv 50 m inside three different converted habitats (coffee plantation, non-native Eucalyptus plantation, and abandoned pastures, hereafter matrix types. By sampling a dry and a wet season, we recorded 622 individual frogs representing 29 species, of which three were undescribed. Breeding guild (i.e. bromeliad, leaf-litter, and water-body breeders was the most important variable explaining frog distributions in relation to edge effects and matrix types. Leaf-litter and bromeliad breeders decreased in richness and abundance from the forest interior toward the matrix habitats. Water-body breeders increased in richness toward the matrix and remained relatively stable in abundance across distances. Number of large trees (i.e. DBH > 15 cm and bromeliads best explained frog richness and abundance across distances. Twenty species found in the interior of the forest were not found in any matrix habitat. Richness and abundance across breeding guilds were higher in the rainy season but frog distributions were similar across the four distances in the two seasons. Across matrix types, leaf-litter species primarily used Eucalyptus plantations, whereas water-body species primarily used coffee plantations. Bromeliad breeders were not found inside any matrix habitat. Our study highlights the importance of primary forest for bromeliad and leaf-litter breeders. We propose that water-body breeders use edge and matrix habitats to reach breeding habitats along the valleys. Including life-history characteristics, such as breeding guild, can improve predictions of frog
Ferreira, Rodrigo B; Beard, Karen H; Crump, Martha L
Understanding the response of species with differing life-history traits to habitat edges and habitat conversion helps predict their likelihood of persistence across changing landscape. In Brazil's Atlantic Forest, we evaluated frog richness and abundance by breeding guild at four distances from the edge of a reserve: i) 200 m inside the forest, ii) 50 m inside the forest, iii) at the forest edge, and iv) 50 m inside three different converted habitats (coffee plantation, non-native Eucalyptus plantation, and abandoned pastures, hereafter matrix types). By sampling a dry and a wet season, we recorded 622 individual frogs representing 29 species, of which three were undescribed. Breeding guild (i.e. bromeliad, leaf-litter, and water-body breeders) was the most important variable explaining frog distributions in relation to edge effects and matrix types. Leaf-litter and bromeliad breeders decreased in richness and abundance from the forest interior toward the matrix habitats. Water-body breeders increased in richness toward the matrix and remained relatively stable in abundance across distances. Number of large trees (i.e. DBH > 15 cm) and bromeliads best explained frog richness and abundance across distances. Twenty species found in the interior of the forest were not found in any matrix habitat. Richness and abundance across breeding guilds were higher in the rainy season but frog distributions were similar across the four distances in the two seasons. Across matrix types, leaf-litter species primarily used Eucalyptus plantations, whereas water-body species primarily used coffee plantations. Bromeliad breeders were not found inside any matrix habitat. Our study highlights the importance of primary forest for bromeliad and leaf-litter breeders. We propose that water-body breeders use edge and matrix habitats to reach breeding habitats along the valleys. Including life-history characteristics, such as breeding guild, can improve predictions of frog distributions in
Full Text Available Risk of predation is an evolutionary force that affects behaviors of virtually all animals. In this study, we examined how habitat selection by roe deer was affected by risk of predation by Eurasian lynx - the main predator of roe deer in Scandinavia. Specifically, we compared how habitat selection by roe deer varied (1 before and after lynx re-established in the study area and (2 in relation to habitat-specific risk of predation by lynx. All analyses were conducted at the spatial and temporal scales of home ranges and seasons. We did not find any evidence that roe deer avoided habitats in which the risk of predation by lynx was greatest and information-theoretic model selection showed that re-colonization by lynx had limited impact on habitat selection by roe deer despite lynx predation causing 65% of known mortalities after lynx re-colonized the area. Instead we found that habitat selection decreased when habitat availability increased for 2 of 5 habitat types (a pattern referred to as functional response in habitat selection. Limited impact of re-colonization by lynx on habitat selection by roe deer in this study differs from elk in North America altering both daily and seasonal patterns in habitat selection at the spatial scales of habitat patches and home ranges when wolves were reintroduced to Yellowstone National Park. Our study thus provides further evidence of the complexity by which animals respond to risk of predation and suggest that it may vary between ecosystems and predator-prey constellations.
Samelius, Gustaf; Andrén, Henrik; Kjellander, Petter; Liberg, Olof
Risk of predation is an evolutionary force that affects behaviors of virtually all animals. In this study, we examined how habitat selection by roe deer was affected by risk of predation by Eurasian lynx - the main predator of roe deer in Scandinavia. Specifically, we compared how habitat selection by roe deer varied (1) before and after lynx re-established in the study area and (2) in relation to habitat-specific risk of predation by lynx. All analyses were conducted at the spatial and temporal scales of home ranges and seasons. We did not find any evidence that roe deer avoided habitats in which the risk of predation by lynx was greatest and information-theoretic model selection showed that re-colonization by lynx had limited impact on habitat selection by roe deer despite lynx predation causing 65% of known mortalities after lynx re-colonized the area. Instead we found that habitat selection decreased when habitat availability increased for 2 of 5 habitat types (a pattern referred to as functional response in habitat selection). Limited impact of re-colonization by lynx on habitat selection by roe deer in this study differs from elk in North America altering both daily and seasonal patterns in habitat selection at the spatial scales of habitat patches and home ranges when wolves were reintroduced to Yellowstone National Park. Our study thus provides further evidence of the complexity by which animals respond to risk of predation and suggest that it may vary between ecosystems and predator-prey constellations.
Jacobsen, Lars Bo; Chrenkova, Monika; Sunde, Peter
The population of Little Owls in Denmark is close to extinction. The main cause is food limitation during the breeding season. Efforts to improve breeding success include providing breeding pairs with supplementary food and attempts to improve foraging habitats by creating short grass areas near...... the nests. In addition to increasing the reproductive output, feeding and habitat management may cause parents to work less hard improving their future reproductive value. We studied working efforts of five radio-tagged Little Owl pairs in years of absence and presence of food provisioning, and/or access...... sward vegetation, males but not females reduced their MFD and DN significantly. If MFD was adjusted for DN (the two measures correlated positively), both sexes reduced their DN-adjusted MFD as response to food provisioning but not to habitat provisioning. Good provisioning therefore had similar...
Hinton, Joseph W; Proctor, Christine; Kelly, Marcella J; van Manen, Frank T; Vaughan, Michael R; Chamberlain, Michael J
Recovery of large carnivores remains a challenge because complex spatial dynamics that facilitate population persistence are poorly understood. In particular, recovery of the critically endangered red wolf (Canis rufus) has been challenging because of its vulnerability to extinction via human-caused mortality and hybridization with coyotes (Canis latrans). Therefore, understanding red wolf space use and habitat selection is important to assist recovery because key aspects of wolf ecology such as interspecific competition, foraging, and habitat selection are well-known to influence population dynamics and persistence. During 2009-2011, we used global positioning system (GPS) radio-telemetry to quantify space use and 3rd-order habitat selection for resident and transient red wolves on the Albemarle Peninsula of eastern North Carolina. The Albemarle Peninsula was a predominantly agricultural landscape in which red wolves maintained spatially stable home ranges that varied between 25 km2 and 190 km2. Conversely, transient red wolves did not maintain home ranges and traversed areas between 122 km2 and 681 km2. Space use by transient red wolves was not spatially stable and exhibited shifting patterns until residency was achieved by individual wolves. Habitat selection was similar between resident and transient red wolves in which agricultural habitats were selected over forested habitats. However, transients showed stronger selection for edges and roads than resident red wolves. Behaviors of transient wolves are rarely reported in studies of space use and habitat selection because of technological limitations to observed extensive space use and because they do not contribute reproductively to populations. Transients in our study comprised displaced red wolves and younger dispersers that competed for limited space and mating opportunities. Therefore, our results suggest that transiency is likely an important life-history strategy for red wolves that facilitates
Han, Xuesong; Guo, Yumin; Mi, Chunrong; Huettmann, Falk; Wen, Lijia
The black-necked crane (Grus nigricollis) is the only alpine crane species and is endemic to the Tibetan Plateau. The breeding habitats of this species are poorly understood, which greatly hampers practical research and conservation work. Using machine learning methods and the best-available data from our 7,000-kilometer mega-transect survey and open access data, we built the first species distribution model (SDM) to analyze the black-necked crane's breeding habitats. Our model showed that current conservation gaps account for 26.7% of its predicted breeding habitats. Specifically, the northern parts of the Hengduan Mountains and the southeastern Tibet Valley, the northern side of the middle Kunlun Mountains, parts of the Pamir Plateau, the northern Pakistan Highlands and the western Hindu Kush should be considered as its main potential breeding areas. Additionally, our model suggested that the crane prefers to breed in alpine meadows at an elevation over 2,800 m, a maximum temperature of the warmest month below 20.5 °C, and a temperature seasonality above 7,800 units. The identified conservation gaps and potential breeding areas can aid in clearly prioritizing future conservation and research, but more attention and study should be directed to the unassessed Western Development of China to secure this endangered crane lineage and other wildlife on the Tibetan Plateau.
Vepsaelaeinen, Ville [Finnish Museum of Natural History, P.O. Box 17, University of Helsinki, FI-00014 Helsinki (Finland)
Here, I present the first comparison of the abundance of farmland birds in energy grass fields and in cereal-dominated conventionally cultivated fields (CCFs). I demonstrate that in boreal farmland, skylark (Alauda arvensis) densities were significantly lower in reed canary grass (RCG) (Phalaris arundinacea) fields than in CCFs. I found that during the early breeding season RCG fields and CCFs are equally good habitats, but over the ensuing couple of weeks RCG rapidly grows too tall and dense for field-nesting species. Consequently, RCG is an inferior habitat for skylark for laying replacement clutches (after failure of first nesting) or for a second clutch after one successful nesting. The results imply that if RCG cultivation is to be expanded, the establishment of large monocultures should be avoided in farmland landscapes; otherwise the novel habitat may affect detrimentally the seriously depleted skylark population, and probably also other field-nesting bird species with similar breeding habitats. (author)
Carpenter, Jennifer L.; Aldridge, Cameron L.; Boyce, Mark S.
Greater sage-grouse (Centrocercus urophasianus) are dependent on sagebrush (Artemisia spp.) for food and shelter during winter, yet few studies have assessed winter habitat selection, particularly at scales applicable to conservation planning. Small changes to availability of winter habitats have caused drastic reductions in some sage-grouse populations. We modeled winter habitat selection by sage-grouse in Alberta, Canada, by using a resource selection function. Our purpose was to 1) generate a robust winter habitat-selection model for Alberta sage-grouse; 2) spatially depict habitat suitability in a Geographic Information System to identify areas with a high probability of selection and thus, conservation importance; and 3) assess the relative influence of human development, including oil and gas wells, in landscape models of winter habitat selection. Terrain and vegetation characteristics, sagebrush cover, anthropogenic landscape features, and energy development were important in top Akaike's Information Criterionselected models. During winter, sage-grouse selected dense sagebrush cover and homogenous less rugged areas, and avoided energy development and 2-track truck trails. Sage-grouse avoidance of energy development highlights the need for comprehensive management strategies that maintain suitable habitats across all seasons. ?? 2010 The Wildlife Society.
Gopal, Murali; Gupta, Alka
" No plant is an island too …" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer
Sadeh, Asaf; Mangel, Marc; Blaustein, Leon
Structural complexity generally reduces predation and cannibalism rates. Although the benefits from this effect vary among environmental contexts and through time, it has been the common explanation for high species abundance in complex habitats. We hypothesized that oviposition habitat selection for structural complexity depends on the expected trophic function of the progeny. In Salamandra infraimmaculata larvae, expected trophic function is dictated by their sequence of deposition. First cohorts cannibalize later-arriving cohorts, while all compete for shared prey resources. In a mesocosm experiment, we show that gravid salamanders facing conspecific-free pools preferred structurally simple habitats (no rocks), while females facing only pools with older conspecific larvae preferred complex habitats (with rocks). Context-dependent preference of habitat complexity for managing food/safety trade-offs may be extended from classic foraging patch decisions to breeding habitat selection. These trade-offs vary with dynamic larval processes such as priority effects and ontogenetic diet shifts, potentially leading to complex maternal parturition behaviours.
McFarland, Heather R.; Kendall, Steve J.; Powell, Abby
Despite changes in shrub cover and weather patterns associated with climate change in the Arctic, little is known about the breeding requirements of most passerines tied to northern regions. We investigated the nesting biology and nest habitat characteristics of Smith's Longspurs (Calcarius pictus) in 2 study areas in the Brooks Range of Alaska, USA. First, we examined variation in nesting phenology in relation to local temperatures. We then characterized nesting habitat and analyzed nest-site selection for a subset of nests (n = 86) in comparison with paired random points. Finally, we estimated the daily survival rate of 257 nests found in 2007–2013 with respect to both habitat characteristics and weather variables. Nest initiation was delayed in years with snow events, heavy rain, and freezing temperatures early in the breeding season. Nests were typically found in open, low-shrub tundra, and never among tall shrubs (mean shrub height at nests = 26.8 ± 6.7 cm). We observed weak nest-site selection patterns. Considering the similarity between nest sites and paired random points, coupled with the unique social mating system of Smith's Longspurs, we suggest that habitat selection may occur at the neighborhood scale and not at the nest-site scale. The best approximating model explaining nest survival suggested a positive relationship with the numbers of days above 21°C that an individual nest experienced; there was little support for models containing habitat variables. The daily nest survival rate was high (0.972–0.982) compared with that of most passerines in forested or grassland habitats, but similar to that of passerines nesting on tundra. Considering their high nesting success and ability to delay nest initiation during inclement weather, Smith's Longspurs may be resilient to predicted changes in weather regimes on the breeding grounds. Thus, the greatest threat to breeding Smith's Longspurs associated with climate change may be the loss of low
Langevelde, van F.
Landscape fragmentation constrains movement of animals between habitat patches. Fragmentation may, therefore, limit the possibilities to explore and select the best habitat patches, and some animals may have to cope with low-quality patches due to these movement constraints. If so, these individuals
Study conducted in the forested bitumen belt of Ode-Irele, Ondo state, Nigeria evaluated habitat use by birds using 20- minutes birds point count to a radius of 30 meters, carried out in six selected habitats. The vegetation cover was sampled using 5x5-meters and 1m2quadrants. Data collected were subjected to t-test of ...
Full Text Available Animals almost always use habitats non-randomly, but the costs and benefits of using specific habitat types remain unknown for many types of organisms. In a large lake in northwestern Australia (Lake Argyle, most hatchling (<12-month-old freshwater crocodiles (Crocodylus johnstoni are found in floating vegetation mats or grassy banks rather than the more widely available open banks. Mean body sizes of young crocodiles did not differ among the three habitat types. We tested four potential explanations for non-random habitat selection: proximity to nesting sites, thermal conditions, food availability, and exposure to predation. The three alternative habitat types did not differ in proximity to nesting sites, or in thermal conditions. Habitats with higher food availability harboured more hatchlings, and feeding rates (obtained by stomach-flushing of recently-captured crocodiles were highest in such areas. Predation risk may also differ among habitats: we were twice as likely to capture a crocodile after seeing it in open-bank sites than in the other two habitat types. Thus, habitat selection of hatchling crocodiles in this system may be driven both by prey availability and by predation risk.
Piatt, John F.; Naslund, Nancy L.; van Pelt, Thomas I.
On 13 June 1993, a new Kittlitz's murrelet (Brachyramphus brevirostris) nest was discovered near Red Mountain on the Kenai Peninsula, Alaska. The nest was on a 22° slope at about 900 m elevation with a northeast aspect, and contained a 60.2 × 40.6 mm egg that weighed 49.0 g. Downy feathers and weathered fecal material found at the nest indicated re-use from a previous year, suggesting possible nest site fidelity. The nest was located in an area scoured by winds and free of snow during early spring, suggesting that this may be an important mesoscale factor influencing selection of nesting habitat. Proximity to suitable foraging habitat, particularly sheltered bays and glacial river outflows, may affect breeding habitat choice over larger spatial scales.
Adam Duarte,; Hatfield, Jeffrey; Todd M. Swannack,; Michael R. J. Forstner,; M. Clay Green,; Floyd W. Weckerly,
Population viability analyses provide a quantitative approach that seeks to predict the possible future status of a species of interest under different scenarios and, therefore, can be important components of large-scale species’ conservation programs. We created a model and simulated range-wide population and breeding habitat dynamics for an endangered woodland warbler, the golden-cheeked warbler (Setophaga chrysoparia). Habitat-transition probabilities were estimated across the warbler's breeding range by combining National Land Cover Database imagery with multistate modeling. Using these estimates, along with recently published demographic estimates, we examined if the species can remain viable into the future given the current conditions. Lastly, we evaluated if protecting a greater amount of habitat would increase the number of warblers that can be supported in the future by systematically increasing the amount of protected habitat and comparing the estimated terminal carrying capacity at the end of 50 years of simulated habitat change. The estimated habitat-transition probabilities supported the hypothesis that habitat transitions are unidirectional, whereby habitat is more likely to diminish than regenerate. The model results indicated population viability could be achieved under current conditions, depending on dispersal. However, there is considerable uncertainty associated with the population projections due to parametric uncertainty. Model results suggested that increasing the amount of protected lands would have a substantial impact on terminal carrying capacities at the end of a 50-year simulation. Notably, this study identifies the need for collecting the data required to estimate demographic parameters in relation to changes in habitat metrics and population density in multiple regions, and highlights the importance of establishing a common definition of what constitutes protected habitat, what management goals are suitable within those protected
Michael J Whitehouse
Full Text Available Previous studies of the consequences for breeding birds of climate change have explored how their populations may respond to increasing temperatures. However, few have considered the likely outcome of predicted extreme conditions and the relative vulnerability of populations in different habitats. Here, we compare phenology and breeding success in great tits and blue tits over a 10 year period, including the extremely harsh conditions during spring 2012, at three sites in eastern England--mixed deciduous woodland, riparian and urban habitat. Production, measured as brood biomass, was significantly lower in 2012 compared with the previous 9 years, with the decrease in productivity relatively greatest in woodland habitat. Production was related to hatch delay, i.e. birds not initiating incubation immediately after clutch completion, which was more common in 2012 than in previous years. The best predictor of hatch delay was daytime temperature (not nighttime minimum temperature and rainfall, which convincingly reflected low growth and activity of caterpillar prey. We found that birds breeding in riparian and urban habitats were less vulnerable to the extremes of weather than those breeding in mixed deciduous woodland.
Groff, Luke A.; Calhoun, Aram J.K.; Loftin, Cynthia S.
Poikilothermic species, such as amphibians, endure harsh winter conditions via freeze-tolerance or freeze-avoidance strategies. Freeze-tolerance requires a suite of complex, physiological mechanisms (e.g., cryoprotectant synthesis); however, behavioral strategies (e.g., hibernal habitat selection) may be used to regulate hibernaculum temperatures and promote overwintering survival. We investigated the hibernal ecology of the freeze-tolerant Wood Frog (Lithobates sylvaticus) in north-central Maine. Our objectives were to characterize the species hibernaculum microclimate (temperature, relative humidity), evaluate hibernal habitat selection, and describe the spatial arrangement of breeding, post-breeding, and hibernal habitats. We monitored 15 frogs during two winters (2011/12: N = 10; 2012/13: N = 5), measured hibernal habitat features at micro (2 m) and macro (10 m) spatial scales, and recorded microclimate hourly in three strata (hibernaculum, leaf litter, ambient air). We compared these data to that of 57 random locations with logistic regression models, Akaike Information Criterion, and Kolmogorov–Smirnov tests. Hibernaculum microclimate was significantly different and less variable than leaf litter, ambient air, and random location microclimate. Model averaging indicated that canopy cover (−), leaf litter depth (+), and number of logs and stumps (+; microhabitat only) were important predictors of Wood Frog hibernal habitat. These habitat features likely act to insulate hibernating frogs from extreme and variable air temperatures. For example, decreased canopy cover facilitates increased snowpack depth and earlier snowpack accumulation and melt. Altered winter temperature and precipitation patterns attributable to climate change may reduce snowpack insulation, facilitate greater temperature variation in the underlying hibernacula, and potentially compromise Wood Frog winter survival.
Full Text Available Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbours in different plant tissues i.e the ‘plant microbiome’, form the holobiome which is now considered as unit of selection: ‘the holobiont’. The ‘plant microbiome’ not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding.
Guo Yahua; Xie Libo; Wang Xue; Deng Liping
New pepper variety Yujiao No.1 and new pepper lines with different horticultural characters are obtained by new breeding technique: combination of space inducement and regular breeding, field selection and inherited marker
Trudelle, Laurène; Cerchio, Salvatore; Zerbini, Alexandre N; Geyer, Ygor; Mayer, François-Xavier; Jung, Jean-Luc; Hervé, Maxime R; Pous, Stephane; Sallée, Jean-Baptiste; Rosenbaum, Howard C; Adam, Olivier; Charrassin, Jean-Benoit
Assessing the movement patterns and key habitat features of breeding humpback whales is a prerequisite for the conservation management of this philopatric species. To investigate the interactions between humpback whale movements and environmental conditions off Madagascar, we deployed 25 satellite tags in the northeast and southwest coast of Madagascar. For each recorded position, we collated estimates of environmental variables and computed two behavioural metrics: behavioural state of 'transiting' (consistent/directional) versus 'localized' (variable/non-directional), and active swimming speed (i.e. speed relative to the current). On coastal habitats (i.e. bathymetry humpback whales probably exploit prevailing ocean currents to maximize displacement. This study provides evidence that coastal areas, generally subject to strong human pressure, remain the core habitat of humpback whales off Madagascar. Our results expand the knowledge of humpback whale habitat use in oceanic habitat and response to variability of environmental factors such as oceanic current and chlorophyll level.
Elferink, Martin G.; Megens, Hendrik-Jan; Vereijken, Addie; Hu, Xiaoxiang; Crooijmans, Richard P. M. A.; Groenen, Martien A. M.
Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations. PMID:22384281
Meuwissen Theo HE
Full Text Available Abstract Background Genomic selection is a selection method where effects of dense genetic markers are first estimated in a test population and later used to predict breeding values of selection candidates. The aim of this paper was to investigate genetic gains, inbreeding and the accuracy of selection in a general genomic selection scheme for aquaculture, where the test population consists of sibs of the candidates. Methods The selection scheme started after simulating 4000 generations in a Fisher-Wright population with a size of 1000 to create a founder population. The basic scheme had 3000 selection candidates, 3000 tested sibs of the candidates, 100 full-sib families, a trait heritability of 0.4 and a marker density of 0.5Ne/M. Variants of this scheme were also analysed. Results The accuracy of selection in generation 5 was 0.823 for the basic scheme when the sib-testing was performed every generation. The accuracy was hardly reduced by selection, probably because the increased frequency of favourable alleles compensated for the Bulmer effect. When sib-testing was performed only in the first generation, in order to reduce costs, accuracy of selection in generation 5 dropped to 0.304, the main reduction occurring in the first generation. The genetic level in generation 5 was 6.35σa when sib-testing was performed every generation, which was 72%, 12% and 9% higher than when sib-testing was performed only in the first generation, only in the first three generations or every second generation, respectively. A marker density above 0.5Ne/M hardly increased accuracy of selection further. For the basic scheme, rates of inbreeding were reduced by 81% in these schemes compared to traditional selection schemes, due to within-family selection. Increasing the number of sibs to 6000 hardly affected the accuracy of selection, and increasing the number of candidates to 6000 increased genetic gain by 10%, mainly because of increased selection intensity
Chatterjee, Soumendranath; Chakraborty, Arunima; Sinha, Shuvra Kanti
Dengue infection is endemic in several areas and the dengue virus is transmitted by Aedes mosquitoes. Thus, it becomes important to understand the breeding ecology of dengue vector and characterize the physicochemical parameters of its breeding habitat. The objective of this study was to analyze the physicochemical parameters of the breeding habitat of the dengue vector and to find out the nutrient composition of the habitat in and around Kolkata, West Bengal. In addition, a geographic information system (GIS) was used to map the disease prone areas for its effective management and prevention. Water samples were collected from various breeding habitats of Aedes mosquitoes of Kolkata and adjoining areas and were analysed for various physicochemical properties like acidity, alkalinity, hardness, electrical conductivity, total dissolved solids, concentration of chloride (Cl - ), sodium (Na + ), potassium (K + ), fluoride (F - ) in relation to larval prevalence. Parameters like water pH, total dissolved solids, total hardness, electrical conductivity, concentration of chloride, sodium and potassium were seen to vary throughout the year. Certain parameters were found to be dependent on container type, like concentration of fluoride. Significant positive correlations were seen between per dip larval density and total dissolved solids (TDS) and electrical conductivity. Water pH, electrical conductivity, total dissolved solids were seen to play a major role in the ovipositional preferences. Container type did not seem to affect TDS. Tyres had the highest TDS in most of the cases. Nutrient composition like sodium concentration was mostly found in the coconut shells, potassium concentration also showed the same. Thus, container type and various parameters and nutrients play a major role in determining where a gravid female mosquito will lay its eggs. It was observed that by altering various chemical and physical properties of breeding habitats it was possible to control the
Full Text Available In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare
Dimitrijevic, Aleksandra; Horn, Renate
In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi , or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches
Dimitrijevic, Aleksandra; Horn, Renate
In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches
Nocera, Joseph J; Forbes, Graham J; Giraldeau, Luc-Alain
Several species use the number of young produced as public information (PI) to assess breeding site quality. PI is inaccessible for synchronously breeding birds because nests are empty by the time the young can collect this information. We investigate if location cues are the next best source of inadvertent social information (ISI) used by young prospectors during breeding site choice. We experimentally deployed ISI as decoys and song playbacks of breeding males in suitable and sub-optimal habitats during pre- and post-breeding periods, and monitored territory establishment during the subsequent breeding season for a social, bobolink (Dolichonyx oryzivorus), and a more solitary species, Nelson's sharp-tailed sparrow (Ammodramus nelsoni). The sparrows did not respond to treatments, but bobolinks responded strongly to post-breeding location cues, irrespective of habitat quality. The following year, 17/20 sub-optimal plots to which bobolink males were recruited were defended for at least two weeks, indicating that song heard the previous year could exert a ‘carry-over attraction’ effect on conspecifics the following year. Sixteen recruited males were natal dispersers, as expected when animals have little opportunity to directly sample their natal habitat quality. We suggest that differences in breeding synchronicity may induce an equivalent clinal distribution of ISI use. PMID:16543178
Northrup, Joseph M; Anderson, Charles R; Wittemyer, George
Extraction of oil and natural gas (hydrocarbons) from shale is increasing rapidly in North America, with documented impacts to native species and ecosystems. With shale oil and gas resources on nearly every continent, this development is set to become a major driver of global land-use change. It is increasingly critical to quantify spatial habitat loss driven by this development to implement effective mitigation strategies and develop habitat offsets. Habitat selection is a fundamental ecological process, influencing both individual fitness and population-level distribution on the landscape. Examinations of habitat selection provide a natural means for understanding spatial impacts. We examined the impact of natural gas development on habitat selection patterns of mule deer on their winter range in Colorado. We fit resource selection functions in a Bayesian hierarchical framework, with habitat availability defined using a movement-based modeling approach. Energy development drove considerable alterations to deer habitat selection patterns, with the most substantial impacts manifested as avoidance of well pads with active drilling to a distance of at least 800 m. Deer displayed more nuanced responses to other infrastructure, avoiding pads with active production and roads to a greater degree during the day than night. In aggregate, these responses equate to alteration of behavior by human development in over 50% of the critical winter range in our study area during the day and over 25% at night. Compared to other regions, the topographic and vegetative diversity in the study area appear to provide refugia that allow deer to behaviorally mediate some of the impacts of development. This study, and the methods we employed, provides a template for quantifying spatial take by industrial activities in natural areas and the results offer guidance for policy makers, mangers, and industry when attempting to mitigate habitat loss due to energy development. © 2015 The Authors
Full Text Available At our work we have analysed the organisation of calving in Charolais breed during the years from 1998 to 2001 at selected farm. Our monitoring of calving during winter season (from January to February shows the percentage of calving was in particular years ranged from 43.2 to 71.1. The most calves were born in February. We found out (total all years diffi cult calving (value 3 in 2 cases in April (1998 and 1999 and 1 case in February (1998 and 1 in March (1999. Calving marked with value 2 (total of all years we found out in January (2 cases, February (3 cases, March (4 cases and from September to December past one case. From 18 cases of diffi cult calving what we found out, 11 calves (61.11 % come from CHV 529 bull. In calves born by normal calving was found out average weight 34.75 kg, in ones born by calving with level 2 of diffi culty 36.36 kg, and in calves born by calving with diffi culty 3 was recorded average weight 41.5 kg. Recorded weight at 210 days of age in mostly cases was similar like in published breed standard.
Sakata, Masayuki K.; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi
Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.
Jannink, Jean-Luc; Lorenz, Aaron J; Iwata, Hiroyoshi
We intuitively believe that the dramatic drop in the cost of DNA marker information we have experienced should have immediate benefits in accelerating the delivery of crop varieties with improved yield, quality and biotic and abiotic stress tolerance. But these traits are complex and affected by many genes, each with small effect. Traditional marker-assisted selection has been ineffective for such traits. The introduction of genomic selection (GS), however, has shifted that paradigm. Rather than seeking to identify individual loci significantly associated with a trait, GS uses all marker data as predictors of performance and consequently delivers more accurate predictions. Selection can be based on GS predictions, potentially leading to more rapid and lower cost gains from breeding. The objectives of this article are to review essential aspects of GS and summarize the important take-home messages from recent theoretical, simulation and empirical studies. We then look forward and consider research needs surrounding methodological questions and the implications of GS for long-term selection.
Sawyer, H.; Nielson, R.M.; Lindzey, F.G.; Keith, L.; Powell, J.H.; Abraham, A.A.
Recent expansions by Rocky Mountain elk (Cervus elaphus) into nonforested habitats across the Intermountain West have required managers to reconsider the traditional paradigms of forage and cover as they relate to managing elk and their habitats. We examined seasonal habitat selection patterns of a hunted elk population in a nonforested high-desert region of southwestern Wyoming, USA. We used 35,246 global positioning system locations collected from 33 adult female elk to model probability of use as a function of 6 habitat variables: slope, aspect, elevation, habitat diversity, distance to shrub cover, and distance to road. We developed resource selection probability functions for individual elk, and then we averaged the coefficients to estimate population-level models for summer and winter periods. We used the population-level models to generate predictive maps by assigning pixels across the study area to 1 of 4 use categories (i.e., high, medium-high, medium-low, or low), based on quartiles of the predictions. Model coefficients and predictive maps indicated that elk selected for summer habitats characterized by higher elevations in areas of high vegetative diversity, close to shrub cover, northerly aspects, moderate slopes, and away from roads. Winter habitat selection patterns were similar, except elk shifted to areas with lower elevations and southerly aspects. We validated predictive maps by using 528 locations collected from an independent sample of radiomarked elk (n = 55) and calculating the proportion of locations that occurred in each of the 4 use categories. Together, the high- and medium-high use categories of the summer and winter predictive maps contained 92% and 74% of summer and winter elk locations, respectively. Our population-level models and associated predictive maps were successful in predicting winter and summer habitat use by elk in a nonforested environment. In the absence of forest cover, elk seemed to rely on a combination of shrubs
González, Luis M.; Bustamante, Javier; Hiraldo, F.
Nesting habitat selection by the Spanish imperial eagle Aquila adalberti was quantitatively assessed. Nest sites chosen did not differ from the available habitat with regard to physiography and vegetation, but the eagles tended to avoid areas affected by human disturbance. Nest sites used by subadults and those of adults that were recently established tended to be in more disturbed areas than those used by adults or in traditional nesting localities. Management recommendations for more e...
Full Text Available Despite the dynamic nature of habitat selection, temporal variation as arising from factors such as weather are rarely quantified in species-habitat relationships. We analysed habitat use and selection (use/availability of foraging, radio-tagged little owls (Athene noctua, a nocturnal, year-round resident generalist predator, to see how this varied as a function of weather, season and availability. Use of the two most frequently used land cover types, gardens/buildings and cultivated fields varied more than 3-fold as a simple function of season and weather through linear effects of wind and quadratic effects of temperature. Even when controlling for the temporal context, both land cover types were used more evenly than predicted from variation in availability (functional response in habitat selection. Use of two other land cover categories (pastures and moist areas increased linearly with temperature and was proportional to their availability. The study shows that habitat selection by generalist foragers may be highly dependent on temporal variables such as weather, probably because such foragers switch between weather dependent feeding opportunities offered by different land cover types. An opportunistic foraging strategy in a landscape with erratically appearing feeding opportunities in different land cover types, may possibly also explain decreasing selection of the two most frequently used land cover types with increasing availability.
Boligon, A A; Long, N; Albuquerque, L G; Weigel, K A; Gianola, D; Rosa, G J M
Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0,) and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection
Greenberg, Cathryn H. [USDA Forest Service, New Ellenton, SC (United States); Tanner, George W. [USDA Forest Service, New Ellenton, SC (United States)
Cathryn H. Greenberg and George W. Tanner. 2004. Breeding pond selection and movement patterns by eastern spadefoot toads (Scaphiopus holbrookii) in relation to weather and edaphic conditions. J. Herp. 38(4):569-577. Abstract: Eastern Spadefoot Toads (Scaphiopus holbrookii) require fish-free, isolated, ephemeral ponds for breeding but otherwise inhabit the surrounding uplands, commonly xeric longleaf pine (Pinus palustris) wiregrass (Aristida beyrichiana). Hence both pond and upland conditions can potentially affect their breeding biology, and population persistence. Hardwood invasion due to fire suppression in sandhills could alter upland and pond suitability by higher hardwood density and increased transpiration. In this paper we explore breeding and neonatal emigration movements in relation to weather, hydrological conditions of ponds, and surrounding upland matrices. We use 9 years of data from continuous monitoring with drift fences and pitfall traps at 8 ephemeral ponds in 2 upland matrices: regularly-burned, savanna-like sandhills (n = 4), and hardwood-invaded sandhills (n = 4). Neither adult nor neonate captures differed between ponds within the 2 upland matrices, suggesting that they are tolerant of upland heterogeneity created by fire frequency. Explosive breeding occurred during 9 periods and in all seasons; adults were captured rarely otherwise. At a landscape-level rainfall, maximum change in barometric pressure, and an interaction between those 2 variables were significant predictors of explosive breeding. At a pond-level, rainfall, change in pond depth during the month prior to breeding, and days since a pond was last dry were significant predictors of adult captures. Transformation date, rather than weather, was associated with neonatal emigrations, which usually were complete within a week. Movement by first-captured adults and neonates was directional, but adult emigrations were apparently not always toward their origin. Our results suggest that
Donovan, Therese M.; Cornell, Kerri L.
Habitat selection theory predicts that individuals choose breeding habitats that maximize fitness returns on the basis of indirect environmental cues at multiple spatial scales. We performed a 3-year field experiment to evaluate five alternative hypotheses regarding whether individuals choose breeding territories in heterogeneous landscapes on the basis of (1) shrub cover within a site, (2) forest land-cover pattern surrounding a site, (3) conspecific song cues during prebreeding settlement periods, (4) a combination of these factors, and (5) interactions among these factors. We tested hypotheses with playbacks of conspecific song across a gradient of landscape pattern and shrub density and evaluated changes in territory occupancy patterns in a forest-nesting passerine, the Black-throated Blue Warbler (Dendroica caerulescens). Our results support the hypothesis that vegetation structure plays a primary role during presettlement periods in determining occupancy patterns in this species. Further, both occupancy rates and territory turnover were affected by an interaction between local shrub density and amount of forest in the surrounding landscape, but not by interactions between habitat cues and social cues. Although previous studies of this species in unfragmented landscapes found that social postbreeding song cues played a key role in determining territory settlement, our prebreeding playbacks were not associated with territory occupancy or turnover. Our results suggest that in heterogeneous landscapes during spring settlement, vegetation structure may be a more reliable signal of reproductive performance than the physical location of other individuals.
Van Moorter, Bram; Rolandsen, Christer M; Basille, Mathieu; Gaillard, Jean-Michel
Animal space use has been studied by focusing either on geographic (e.g. home ranges, species' distribution) or on environmental (e.g. habitat use and selection) space. However, all patterns of space use emerge from individual movements, which are the primary means by which animals change their environment. Individuals increase their use of a given area by adjusting two key movement components: the duration of their visit and/or the frequency of revisits. Thus, in spatially heterogeneous environments, animals exploit known, high-quality resource areas by increasing their residence time (RT) in and/or decreasing their time to return (TtoR) to these areas. We expected that spatial variation in these two movement properties should lead to observed patterns of space use in both geographic and environmental spaces. We derived a set of nine predictions linking spatial distribution of movement properties to emerging space-use patterns. We predicted that, at a given scale, high variation in RT and TtoR among habitats leads to strong habitat selection and that long RT and short TtoR result in a small home range size. We tested these predictions using moose (Alces alces) GPS tracking data. We first modelled the relationship between landscape characteristics and movement properties. Then, we investigated how the spatial distribution of predicted movement properties (i.e. spatial autocorrelation, mean, and variance of RT and TtoR) influences home range size and hierarchical habitat selection. In landscapes with high spatial autocorrelation of RT and TtoR, a high variation in both RT and TtoR occurred in home ranges. As expected, home range location was highly selective in such landscapes (i.e. second-order habitat selection); RT was higher and TtoR lower within the selected home range than outside, and moose home ranges were small. Within home ranges, a higher variation in both RT and TtoR was associated with higher selectivity among habitat types (i.e. third-order habitat
Nmor, Jephtha C; Sunahara, Toshihiko; Goto, Kensuke; Futami, Kyoko; Sonye, George; Akweywa, Peter; Dida, Gabriel; Minakawa, Noboru
Background Identification of malaria vector breeding sites can enhance control activities. Although associations between malaria vector breeding sites and topography are well recognized, practical models that predict breeding sites from topographic information are lacking. We used topographic variables derived from remotely sensed Digital Elevation Models (DEMs) to model the breeding sites of malaria vectors. We further compared the predictive strength of two different DEMs and evaluated the ...
Reginia H Y Yan
Full Text Available The ratio of the length of the second digit (index finger divided by the fourth digit (ring finger tends to be lower in men than in women. This 2D:4D digit ratio is often used as a proxy for prenatal androgen exposure in studies of human health and behavior. For example, 2D:4D ratio is lower (i.e. more "masculinized" in both men and women of greater physical fitness and/or sporting ability. Lab mice have also shown variation in 2D:4D as a function of uterine environment, and mouse digit ratios seem also to correlate with behavioral traits, including daily activity levels. Selective breeding for increased rates of voluntary exercise (wheel running in four lines of mice has caused correlated increases in aerobic exercise capacity, circulating corticosterone level, and predatory aggression. Here, we show that this selection regime has also increased 2D:4D. This apparent "feminization" in mice is opposite to the relationship seen between 2D:4D and physical fitness in human beings. The present results are difficult to reconcile with the notion that 2D:4D is an effective proxy for prenatal androgen exposure; instead, it may more accurately reflect effects of glucocorticoids, or other factors that regulate any of many genes.
Wang, Yu; Bennewitz, Jörn; Wellmann, Robin
Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle. In most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS. For local
Jonas, Elisabeth; de Koning, Dirk Jan
Genomic Selection is an important topic in quantitative genetics and breeding. Not only does it allow the full use of current molecular genetic technologies, it stimulates also the development of new methods and models. Genomic selection, if fully implemented in commercial farming, should have a major impact on the productivity of various agricultural systems. But suggested approaches need to be applicable in commercial breeding populations. Many of the published research studies focus on methodologies. We conclude from the reviewed publications, that a stronger focus on strategies for the implementation of genomic selection in advanced breeding lines, introduction of new varieties, hybrids or multi-line crosses is needed. Efforts to find solutions for a better prediction and integration of environmental influences need to continue within applied breeding schemes. Goals of the implementation of genomic selection into crop breeding should be carefully defined and crop breeders in the private sector will play a substantial part in the decision-making process. However, the lack of published results from studies within, or in collaboration with, private companies diminishes the knowledge on the status of genomic selection within applied breeding programmes. Studies on the implementation of genomic selection in plant breeding need to evaluate models and methods with an enhanced emphasis on population-specific requirements and production environments. Adaptation of methods to breeding schemes or changes to breeding programmes for a better integration of genomic selection strategies are needed across species. More openness with a continuous exchange will contribute to successes.
Wallace, Cynthia S.A.; Villarreal, Miguel; van Riper, Charles
Aim: The western yellow-billed cuckoo (Coccyzus americanus occidentalis), a Neotropical migrant bird, is facing steep population declines in its western breeding grounds owing primarily to loss of native habitat. The favoured esting habitat for the cuckoo in the south-western United States is low-elevation riparian forests and woodlands. Our aim was to explore relationships between vegetation phenology patterns captured by satellite phenometrics and the distribution of the yellow-billed cuckoo, and to use this information to map cuckoo habitat. Location: Arizona, USA. Methods: Land surface phenometrics were derived from satellite Advanced Very High-Resolution Radiometer (AVHRR), bi-weekly time-composite, ormalized difference vegetation index (NDVI) data for 1998 and 1999 at a resolution of 1 km. Fourier harmonics were used to analyse the waveform of the annual NDVI profile in each pixel. To create the models, we coupled 1998 satellite phenometrics with 1998 field survey data of cuckoo presence or absence and with point data that sampled riparian and cottonwood–willow vegetation types. Our models were verified and refined using field and satellite data collected in 1999. Results: The models reveal that cuckoos prefer areas that experience peak greenness 29 days later, are 36% more dynamic and slightly (< 1%) more productive than their average cottonwood–willow habitat. The results support a scenario in which cuckoos migrate northwards, following the greening of riparian corridors and surrounding landscapes in response to monsoon precipitation, but then select a nesting site based on optimizing the near-term foraging potential of the neighbourhood. Main conclusions: The identification of preferred phenotypes within recognized habitat can be used to refine future habitat models, inform habitat response to climate change, and suggest adaptation strategies. For example, models of phenotype preferences can guide management actions by identifying and prioritizing for
Full Text Available Success of migration in birds in part depends on habitat selection. Overall, it is still poorly known whether there is habitat selection amongst landbird migrants moving across landscapes. Europe is chiefly covered by agro-forestry mosaic landscapes, so migratory species associated to either agricultural landscapes or woodland habitats should theoretically find suitable stopover sites along migration. During migration from wintering to breeding quarters, woodcocks (Scolopax rusticola tagged with PTT satellite-tracking transmitters were used to test for the hypothesis that migrants associated to agro-forest habitats have no habitat selection during migration, at a meso-scale level. Using a GIS platform we extracted at a meso-scale range habitat cover at stopover localities. Results obtained from comparisons of soil covers between points randomly selected and true stopover localities sites revealed, as expected, the species may not select for particular habitats at a meso-scale range, because the habitat (or habitats required by the species can be found virtually everywhere on their migration route. However, those birds stopping over in places richer in cropland or mosaic habitats including both cropland and forest and with proportionally less closed forest stayed for longer than in areas with lower surfaces of cropland and mosaic and more closed forest. This suggests that areas rich in cropland or mosaic habitat were optimal.
Taylor, Caz M; Stutchbury, Bridget J M
Many migratory species are in decline and understanding these declines is challenging because individuals occupy widely divergent and geographically distant habitats during a single year and therefore populations across the range are interconnected in complex ways. Network modeling has been used to show, theoretically, that shifts in migratory connectivity patterns can occur in response to habitat or climate changes and that habitat loss in one region can affect sub-populations in regions that are not directly connected. Here, we use a network model, parameterized by integrating long-term monitoring data with direct tracking of -100 individuals, to explain population trends in the rapidly declining Wood Thrush (Hylocichla mustelina) and to predict future trends. Our model suggests that species-level declines in Wood Thrush are driven primarily by tropical deforestation in Central America but that protection of breeding habitat in some regions is necessary to prevent shifts in migratory connectivity and to sustain populations in all breeding regions. The model illustrates how shifts in migratory connectivity may lead to unexpected population declines in key regions. We highlight current knowledge gaps that make modeling full life-cycle population demographics in migratory species challenging but also demonstrate that modeling can inform conservation while these gaps are being filled.
Rybinski, Jakub; Sirkiä, Päivi M; McFarlane, S Eryn; Vallin, Niclas; Wheatcroft, David; Ålund, Murielle; Qvarnström, Anna
Competition-driven evolution of habitat isolation is an important mechanism of ecological speciation but empirical support for this process is often indirect. We examined how an on-going displacement of pied flycatchers from their preferred breeding habitat by collared flycatchers in a young secondary contact zone is associated with (a) access to an important food resource (caterpillar larvae), (b) immigration of pied flycatchers in relation to habitat quality, and (c) the risk of hybridization in relation to habitat quality. Over the past 12 years, the estimated access to caterpillar larvae biomass in the habitat surrounding the nests of pied flycatchers has decreased by a fifth due to shifted establishment possibilities, especially for immigrants. However, breeding in the high quality habitat has become associated with such a high risk of hybridization for pied flycatchers that overall selection currently favors pied flycatchers that were forced to immigrate into the poorer habitats (despite lower access to preferred food items). Our results show that competition-driven habitat segregation can lead to fast habitat isolation, which per se caused an opportunity for selection to act in favor of future "voluntarily" altered immigration patterns and possibly strengthened habitat isolation through reinforcement. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.
Full Text Available Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies. It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating genomic selection into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken and fish. It outlines tasks to help understanding possible consequences when applying genomic information in
Genomic selection (GS) uses genome-wide molecular marker data to predict the genetic value of selection candidates in breeding programs. In plant breeding, the ability to produce large numbers of progeny per cross allows GS to be conducted within each family. However, this approach requires phenotyp...
Pedersen, L D; Sørensen, A C; Henryon, M
ADAM is a computer program that models selective breeding schemes for animals using stochastic simulation. The program simulates a population of animals and traces the genetic changes in the population under different selective breeding scenarios. It caters to different population structures...
Full Text Available Although translocation has been used in mitigating human-carnivore conflict for decades, few studies have been conducted on the behavioral ecology of released animals. Such information is necessary in the context of sustainable forest management. In this study we determine the type of land cover used as main habitat and examine the activity pattern of translocated tigers. Between 2008 and 2010 we captured six conflict tigers and translocated them 74-1,350 km from their capture sites in Sumatera. All tigers were fitted with global positioning system (GPS collars. The collars were set to fix 24-48 location coordinates per day. All translocated tigers showed a preference for a certain habitat type within their new home range, and tended to select the majority of natural land cover type within the landscape as their main habitat, but the availability of natural forest habitat within the landscape remains essensial for their survival. The activity of male translocated tigers differed significantly between the six time intervals of 24 hours, and their most active periods were in the afternoon (14:00-18:00 hours and in the evening (18:00-22:00 hours. Despite being preliminary, the findings of this study-which was the first such study conducted in Sumatera-highlight the conservation value of tiger translocation and provide valuable information for improving future management of conflict tigers.Keywords: activity pattern, GPS collars, habitat selection, sumateran tiger, translocation
LaGory, K.E.; Chang, Young-Soo; Chun, K.C.; Reeves, T.; Liebich, R.; Smith, K.
This report, conducted from May through July 2000, addressed the potential effect of compressor noise on breeding birds in gas-production areas administered by the FFO, specifically in the Rattlesnake Canyon Habitat Management Area northeast of Farmington, New Mexico. The study was designed to quantify and characterize noise output from these compressors and to determine if compressor noise affected bird populations in adjacent habitat during the breeding season.
Ram Sharan Lamichhane
Full Text Available While the development of land for residential housing along the Swan and Canning Rivers in Perth, WA, Australia has reduced natural mosquito breeding sites, the role of backyard container breeding remains a relatively unknown factor. Local Governments responsible for these areas focus management and control efforts on low lying, tidally driven mosquito habitats to control Aedes vigilax (Skuse and Aedes camptorhynchus (Thomson mosquitoes in an effort to reduce both the nuisance and disease risk to residents. In spite of their efforts, Local Governments continue to receive complaints regarding mosquito nuisance, even when environmental conditions do not favor hatching and development of the two species in the Swan River tidal flats. In this study, 150 backyard inspections were conducted in the residential suburb of Bassendean, Perth, WA, Australia, situated in close proximity to the Swan River tidal plain. The occurrence and species composition of the mosquito fauna found in residential backyards was documented. Of the backyards inspected, 94% were found to possess containers capable of breeding mosquitoes, although only 3% contained mosquito larvae. Nine species of mosquito were collected from containers ranging in capacity from 0.05 to 50 L across the study area. Additionally, encephalitis virus surveillance trapping was conducted within residential properties and compared to the tidally driven natural habitat at Ashfield Flats and a tidally influenced brackish creekline at Bindaring Park. The species composition of the fauna at the three habitat types differed significantly, with Aedes notoscriptus (Skuse dominating residential lots and A. vigilax more prevalent at the saltmarsh site. Bindaring Park had an adult composition at the mid-point of these two habitats, reflecting its proximity to both the Swan River and residential lots.
William, Gaudry; Jean-Michel, Gaillard; Sonia, Saïd; Christophe, Bonenfant; Atle, Mysterud; Nicolas, Morellet; Maryline, Pellerin; Clément, Calenge
With the surge of GPS-technology, many studies uncovered space use of mobile animals and shed light on the underlying behavioral mechanisms of habitat selection. Habitat selection and variation in either occurrence or strength of functional responses (i.e. how selection changes with availability) have given new insight into such mechanisms within populations in different ecosystems. However, linking variation in habitat selection to site-specific conditions in different populations facing contrasting environmental conditions but the same habitat type has not yet been investigated. We aimed to fill this knowledge gap by comparing within-home range habitat selection across 61 female roe deer (Capreolus capreolus) during the most critical life history stage in three study areas showing the same habitat types but with different environmental conditions. Female roe deer markedly differed in habitat selection within their home range, both within and among populations. Females facing poor environmental conditions clearly displayed a functional response, whereas females facing rich environmental conditions did not show any functional response. These results demonstrate how the use of a given habitat relative to its availability strongly varies in response to environmental conditions. Our findings highlight that the same habitat composition can lead to very different habitat selection processes across contrasted environments.
Full Text Available Every year, thousands of purebred domestic dogs are bred by registered dog breeders. Yet, little is known about the rearing environment of these dogs, or the attitudes and priorities surrounding breeding practices of these dog breeders. The objective of this study was to explore some of the factors that dog breeders consider important for stock selection, with a particular emphasis on issues relating to the dam. Two-hundred and seventy-four Australian purebred dog breeders, covering 91 breeds across all Australian National Kennel Club breed groups, completed an online survey relating to breeding practices. Most breeders surveyed (76% reported specialising in one breed of dog, the median number of dogs and bitches per breeder was two and three respectively, and most breeders bred two litters or less a year. We identified four components, relating to the dam, that were considered important to breeders. These were defined as Maternal Care, Offspring Potential, Dam Temperament, and Dam Genetics and Health. Overall, differences were observed in attitudes and beliefs across these components, showing that there is variation according to breed/breed groups. In particular, the importance of Maternal Care varied according to dog breed group. Breeders of brachycephalic breeds tended to differ the most in relation to Offspring Potential and Dam Genetics and Health. The number of breeding dogs/bitches influenced breeding priority, especially in relation to Dam Temperament, however no effect was found relating to the number of puppies bred each year. Only 24% of breeders used their own sire for breeding. The finding that some breeders did not test for diseases relevant to their breed, such as hip dysplasia in Labrador Retrievers and German Shepherds, provides important information on the need to educate some breeders, and also buyers of purebred puppies, that screening for significant diseases should occur. Further research into the selection of breeding dams
Full Text Available In birds, the environmental variables and intrinsic characteristics of the nest have important fitness consequences through its influence on the selection of nesting sites. However, the extent to which these variables interact with variables that operate at the landscape scale, and whether there is a hierarchy among the different scales that influences nest-site selection, is unknown. This interaction could be crucial in burrowing birds, which depend heavily on the availability of suitable nesting locations. One representative of this group is the burrowing parrot, Cyanoliseus patagonus that breeds on specific ravines and forms large breeding colonies. At a particular site, breeding aggregations require the concentration of adequate environmental elements for cavity nesting, which are provided by within ravine characteristics. Therefore, intrinsic ravine characteristics should be more important in determining nest site selection compared to landscape level characteristics. Here, we assess this hypothesis by comparing the importance of ravine characteristics operating at different scales on nest-site selection and their interrelation with reproductive success. We quantified 12 characteristics of 105 ravines in their reproductive habitat. For each ravine we quantified morphological variables, distance to resources and disturbance as well as nest number and egg production in order to compare selected and non-selected ravines and determine the interrelationship among variables in explaining ravine differences. In addition, the number of nests and egg production for each reproductive ravine was related to ravine characteristics to assess their relation to reproductive success. We found significant differences between non-reproductive and reproductive ravines in both intrinsic and extrinsic characteristics. The multidimensional environmental gradient of variation between ravines, however, shows that differences are mainly related to intrinsic
Sonntag, Nicole; Garthe, Stefan; Adler, Sven
After the breeding season, Slavonian grebes ( Podiceps auritus) leave their freshwater breeding habitats and migrate to wintering grounds in marine or brackish waters. The most important wintering area in northwestern Europe is located in the southern Baltic Sea, with the largest concentrations in the offshore area of the Pommeranian Bight. Analysis of ship-based surveys revealed that the habitat selection of Slavonian grebes in this brackish area is significantly influenced by water depth and bottom sediment type. The grebes prefer shallow waters of 4-14 m depth and occur only over sandy sediments. While the diving depths of endothermic animals is limited due to energetic constraints and thermoregulation, sediment type is regarded to be a proxy for food choice. The diet of Slavonian grebes in the Pomeranian Bight consists mainly of demersal gobies (Gobiidae) that frequently occur over sandy bottom substrates.
Stanley, Thomas R.; Newmark, William D.
Most tropical insectivorous birds, unlike their temperate counterparts, hold and defend a feeding and breeding territory year-around. However, our understanding of ecological factors influencing territory selection and size in tropical insectivores is limited. Here we examine three prominent hypotheses relating food abundance, food dispersion (spatial arrangement of food items), and habitat structure to territoriality in the Usambara Thrush Turdus roehli. We first compared leaf-litter macro-invertebrate abundance and dispersion, and habitat structure between territories and random sites. We then examined the relation between these same ecological factors and territory size. Invertebrate abundance and dispersion were sparsely and evenly distributed across our study system and did not vary between territories and random sites. In contrast, habitat structure did vary between territories and random sites indicating the Usambara Thrush selects territories with open understorey and closed overstorey habitat. Invertebrate abundance and dispersion within territories of the Usambara Thrush were not associated with habitat structure. We believe the most likely explanation for the Usambara Thrush’s preference for open understorey and closed overstorey habitat relates to foraging behavior. Using information-theoretic model selection we found that invertebrate abundance was the highest-ranked predictor of territory size and was inversely related, consistent with food value theory of territoriality.
Full Text Available Genomic selection (GS is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD and minor allele frequency (MAF thresholds for selecting markers, the relative size of the training population (TP and of the validation population (VP, the selected trait and the genomic prediction models (frequentist and Bayesian on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%, and differentiation between the four synthetic populations was low (FST ≤0.06. The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.
Grenier, Cécile; Cao, Tuong-Vi; Ospina, Yolima; Quintero, Constanza; Châtel, Marc Henri; Tohme, Joe; Courtois, Brigitte; Ahmadi, Nourollah
Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.
Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice
Mariafe N. Calingacion
Most rice breeding programs have focused on improving agronomic traits such as yield, while enhancing grain quality traits
Gunia, M.; Phocas, F.; Gourdine, J.L.; Bijma, P.; Mandonnet, N.
The Creole goat is a local breed used for meat production in Guadeloupe (French West Indies). As in other tropical countries, improvement of parasite resistance is needed. In this study, we compared predicted selection responses for alternative breeding programs with or without parasites resistance
Empowering breeding programs with new approaches to overcome constraints for selecting superior quality traits of rice Mariafe N. Calingacion Most rice breeding programs have focused on improving agronomic traits such as yield, while enhancing grain quality traits such as flavour
Full Text Available Lewis's Woodpecker (Melanerpes lewis has experienced population declines in both Canada and the United States and in 2010 was assigned a national listing of threatened in Canada. We conducted a two-year study (2004-2005 of this species at its northern range limit, the South Okanagan Valley in British Columbia, Canada. Our main objective was to determine whether the habitat features that influenced nest-site selection also predicted nest success, or whether other factors (e.g. cavity dimensions, clutch initiation date or time of season were more important. Nest tree decay class, density of suitable cavities and total basal area of large trees were the best predictors of nest-site selection, but these factors were unrelated to nesting success. Estimates of demographic parameters (mean ± SE included daily nest survival rate (0.988±0.003, years combined, nest success (0.52±0.08, clutch size (5.00±0.14 eggs, female fledglings per successful nest (1.31±0.11, and annual productivity (0.68±0.12 female fledglings per nest per year. Although higher nest survival was associated with both early and late initiated clutches, early-initiated clutches allowed birds to gain the highest annual productivity as early clutches were larger. Nests in deep cavities with small entrances experienced lower predation risk especially during the peak period of nest predation. We concluded that nest-site selection can be predicted by a number of easily measured habitat variables, whereas nest success depended on complicated ecological interactions among nest predators, breeding behaviors, and cavity features. Thus, habitat-based conservation strategies should also consider ecological factors that may not be well predicted by habitat.
Altman, Bob; Hagar, Joan
This document (hereafter Guide) has been prepared to assist land managers interested in conducting conservation and management activities to benefit breeding birds associated with young conifer forests in the Pacific Northwest. Audiences targeted for use of the Guide include land trusts, watershed councils, non-commercial private land owners, forest products companies, land-managing conservation organizations, government agencies, tribes, and First Nations. We hope the Guide will be a useful and valuable tool to support any of the variety of reasons to manage for bird habitat in young conifer forests (for example, regulatory, biodiversity, bird conservation, and forest certification standards).
Deirdre C Purfield
Full Text Available Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH. Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat
Vaysse, Amaury; Ratnakumar, Abhirami; Derrien, Thomas
across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.......The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse...... breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary...
Full Text Available The aim of this study was to evaluate the conformation of stallions of the breeds American Quarter Horse (AQH, American Paint Horse (APH, Appaloosa (Appa, the Lipizzaner horse (LH and the Old Kladruby horse (OKH. Representatives of these breeds are characterized as the descendants of horses on the base of the Arab-Berber blood. Western breeds (AQH, APH, Appa due to different environmental conditions, nutrition and the other structure under the influence of a different type of use, type of riding demands differed considerably from the original Spanish-type horses. It was measured a total of 24 body dimensions. Representatives of The American western breeds are statistically highly conclusively (P ≤ 0.01 in 23 of the 24 observed effects. To be precise, they are: smaller wither height as measured by stick, lower at the tail-set, longer neck, narrower chest, longer oblique body length, wider front pelvis length, longer pelvis bones, longer femur bones, shorter hind cannons.A statistically significant difference (P ≤ 0.05 was found in the length of the humerus, where the Old Kladruby Horse has a humerus that is longer by 2.34 cm than that of the APH. The Lipizzaner horse differs statistically highly conclusively (P ≤ 0.01 from the Appaloosa and Old Kladruby horse in the tape length of its head.
McDermot, Joy Marie
American Kestrel populations have declined since the 1960s, and the cause has yet to be identified. To further comprehend the decline of the American Kestrel, my study examined kestrel breeding productivity including occupancy, hatching success, and fledging success in nest boxes in conjunction with the identification of dietary resources. In this thesis, I monitored and documented the breeding success of the American Kestrel from nest boxes on the UC Merced’s Vernal Pools and Grassland Res...
Sundman, A-S; Johnsson, M; Wright, D; Jensen, P
Selection during the last decades has split some established dog breeds into morphologically and behaviourally divergent types. These breed splits are interesting models for behaviour genetics since selection has often been for few and well-defined behavioural traits. The aim of this study was to explore behavioural differences between selection lines in golden and Labrador retriever, in both of which a split between a common type (pet and conformation) and a field type (hunting) has occurred. We hypothesized that the behavioural profiles of the types would be similar in both breeds. Pedigree data and results from a standardized behavioural test from 902 goldens (698 common and 204 field) and 1672 Labradors (1023 and 649) were analysed. Principal component analysis revealed six behavioural components: curiosity, play interest, chase proneness, social curiosity, social greeting and threat display. Breed and type affected all components, but interestingly there was an interaction between breed and type for most components. For example, in Labradors the common type had higher curiosity than the field type (F 1,1668 = 18.359; P selection pressures. In conclusion, in spite of similar genetic origin and similar recent selection criteria, types behave differently in the breeds. This suggests that the genetic architecture related to behaviour differs between the breeds. © 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.
Flockhart, D T Tyler; Pichancourt, Jean-Baptiste; Norris, D Ryan; Martin, Tara G
Threats to migratory animals can occur at multiple periods of the annual cycle that are separated by thousands of kilometres and span international borders. Populations of the iconic monarch butterfly (Danaus plexippus) of eastern North America have declined over the last 21 years. Three hypotheses have been posed to explain the decline: habitat loss on the overwintering grounds in Mexico, habitat loss on the breeding grounds in the United States and Canada, and extreme weather events. Our objectives were to assess population viability, determine which life stage, season and geographical region are contributing the most to population dynamics and test the three hypotheses that explain the observed population decline. We developed a spatially structured, stochastic and density-dependent periodic projection matrix model that integrates patterns of migratory connectivity and demographic vital rates across the annual cycle. We used perturbation analysis to determine the sensitivity of population abundance to changes in vital rate among life stages, seasons and geographical regions. Next, we compared the singular effects of each threat to the full model where all factors operate concurrently. Finally, we generated predictions to assess the risk of host plant loss as a result of genetically modified crops on current and future monarch butterfly population size and extinction probability. Our year-round population model predicted population declines of 14% and a quasi-extinction probability (5% within a century. Monarch abundance was more than four times more sensitive to perturbations of vital rates on the breeding grounds than on the wintering grounds. Simulations that considered only forest loss or climate change in Mexico predicted higher population sizes compared to milkweed declines on the breeding grounds. Our model predictions also suggest that mitigating the negative effects of genetically modified crops results in higher population size and lower extinction
Michael A. Bozek; Clayton J. Edwards; Martin J. Jennings; Steven P. Newman
Anthropogenic disturbances in nearshore littoral zones of lakes may affect spawning habitat and recruitment of smallmouth bass Micropterus dolomieu, yet habitat models that quantify habitat selection by smallmouth bass in lakes are not well developed nor are their limitations understood. In this study we quantified smallmouth bass spawning habitat in...
Hargitai, Rita; Nagy, Gergely; Nyiri, Zoltán; Bervoets, Lieven; Eke, Zsuzsanna; Eens, Marcel; Török, János
In an urban environment, birds are exposed to metals, which may accumulate in their tissues and cause oxidative stress. Female birds may eliminate these pollutants through depositing them into eggs, thus eggs become suitable bioindicators of pollution. In this study, we aimed to analyse whether eggshell spotting pattern, egg volume, eggshell thickness and egg yolk antioxidant (lutein, tocopherol, retinol and selenium) levels were related to the breeding area (woodland versus urban) and the metal levels in the eggshell of a small passerine species, the great tit (Parus major). In the urban habitat, soil and eggshells contained higher concentrations of metals, and soil calcium level was also higher than that in the woodland. Eggshell spotting intensity and egg volume did not differ between eggs laid in the woodland and the urban park, and these traits were not related to the metal levels of the eggshell, suggesting that these egg characteristics are not sensitive indicators of metal pollution. A more aggregated eggshell spotting distribution indicated a higher Cu concentration of the eggshell. We found that eggshells were thinner in the less polluted woodland habitat, which is likely due to the limited Ca availability of the woodland area. Great tit eggs laid in the urban environment had lower yolk lutein, retinol and selenium concentrations, however, as a possible compensation for these lower antioxidant levels, urban females deposited more tocopherol into the egg yolk. It appears that females from different breeding habitats may provide similar antioxidant protection for their offspring against oxidative damage by depositing different specific dietary antioxidants. Egg yolk lutein and retinol levels showed a negative relationship with lead concentration of the eggshell, which may suggest that lead had a negative impact on the amount of antioxidants available for embryos during development in great tits. Copyright © 2015 Elsevier B.V. All rights reserved.
Johnson, J. Matthew; Haig, Susan M.; Schwarz, Carl J.; Glendening, John W.; Burnett, L. Joseph; George, Daniel; Grantham, Jesse
Condors and vultures are distinct from most other terrestrial birds because they use extensive soaring flight for their daily movements. Therefore, assessing resource selection by these avian scavengers requires quantifying the availability of terrestrial-based habitats, as well as meteorological variables that influence atmospheric conditions necessary for soaring. In this study, we undertook the first quantitative assessment of habitat- and meteorological-based resource selection in the endangered California condor (Gymnogyps californianus) within its California range and across the annual cycle. We found that condor use of terrestrial areas did not change markedly within the annual cycle, and that condor use was greatest for habitats where food resources and potential predators could be detected and where terrain was amenable for taking off from the ground in flight (e.g., sparse habitats, coastal areas). Condors originating from different release sites differed in their use of habitat, but this was likely due in part to variation in habitats surrounding release sites. Meteorological conditions were linked to condor use of ecological subregions, with thermal height, thermal velocity, and wind speed having both positive (selection) and negative (avoidance) effects on condor use in different areas. We found little evidence of systematic effects between individual characteristics (i.e., sex, age, breeding status) or components of the species management program (i.e., release site, rearing method) relative to meteorological conditions. Our findings indicate that habitat type and meteorological conditions can interact in complex ways to influence condor resource selection across landscapes, which is noteworthy given the extent of anthropogenic stressors that may impact condor populations (e.g., lead poisoning, wind energy development). Additional studies will be valuable to assess small-scale condor movements in light of these stressors to help minimize their risk to
James W Rivers
Full Text Available Condors and vultures are distinct from most other terrestrial birds because they use extensive soaring flight for their daily movements. Therefore, assessing resource selection by these avian scavengers requires quantifying the availability of terrestrial-based habitats, as well as meteorological variables that influence atmospheric conditions necessary for soaring. In this study, we undertook the first quantitative assessment of habitat- and meteorological-based resource selection in the endangered California condor (Gymnogyps californianus within its California range and across the annual cycle. We found that condor use of terrestrial areas did not change markedly within the annual cycle, and that condor use was greatest for habitats where food resources and potential predators could be detected and where terrain was amenable for taking off from the ground in flight (e.g., sparse habitats, coastal areas. Condors originating from different release sites differed in their use of habitat, but this was likely due in part to variation in habitats surrounding release sites. Meteorological conditions were linked to condor use of ecological subregions, with thermal height, thermal velocity, and wind speed having both positive (selection and negative (avoidance effects on condor use in different areas. We found little evidence of systematic effects between individual characteristics (i.e., sex, age, breeding status or components of the species management program (i.e., release site, rearing method relative to meteorological conditions. Our findings indicate that habitat type and meteorological conditions can interact in complex ways to influence condor resource selection across landscapes, which is noteworthy given the extent of anthropogenic stressors that may impact condor populations (e.g., lead poisoning, wind energy development. Additional studies will be valuable to assess small-scale condor movements in light of these stressors to help minimize
Full Text Available Abstract Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites. The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent and low frequency alleles (30 percent in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.
Ngugi, Harun N; Mutuku, Francis M; Ndenga, Bryson A; Musunzaji, Peter S; Mbakaya, Joel O; Aswani, Peter; Irungu, Lucy W; Mukoko, Dunstan; Vulule, John; Kitron, Uriel; LaBeaud, Angelle D
Aedes aegypti, the principal vector for dengue and other emerging arboviruses, breeds preferentially in various man-made and natural container habitats. In the absence of vaccine, epidemiological surveillance and vector control remain the best practices for preventing dengue outbreaks. Effective vector control depends on a good understanding of larval and adult vector ecology of which little is known in Kenya. In the current study, we sought to characterize breeding habitats and establish container productivity profiles of Ae. aegypti in rural and urban sites in western and coastal Kenya. Twenty sentinel houses in each of four study sites (in western and coastal Kenya) were assessed for immature mosquito infestation once a month for a period of 24 months (June 2014 to May 2016). All water-holding containers in and around the households were inspected for Ae. aegypti larvae and pupae. Collections were made from a total of 22,144 container visits: Chulaimbo (7575) and Kisumu (8003) in the west, and from Msambweni (3199) and Ukunda (3367) on the coast. Of these, only 4-5.6% were positive for Ae. aegypti immatures. In all four sites, significantly more positive containers were located outdoors than indoors. A total of 17,537 Ae. aegypti immatures were sampled from 10 container types. The most important habitat types were buckets, drums, tires, and pots, which produced over 75% of all the pupae. Key outdoor containers in the coast were buckets, drums and tires, which accounted for 82% of the pupae, while pots and tires were the only key containers in the western region producing 70% of the pupae. Drums, buckets and pots were the key indoor containers, producing nearly all of the pupae in the coastal sites. No pupae were collected indoors in the western region. The coastal region produced significantly more Ae. aegypti immatures than the western region both inside and outside the sentinel houses. These results indicate that productive Ae. aegypti larval habitats are
Frye, Graham G; Connelly, John W; Musil, David D; Forbey, Jennifer S
Animal habitat selection is a process that functions at multiple, hierarchically. structured spatial scales. Thus multi-scale analyses should be the basis for inferences about factors driving the habitat selection process. Vertebrate herbivores forage selectively on the basis of phytochemistry, but few studies have investigated the influence of selective foraging (i.e., fine-scale habitat selection) on habitat selection at larger scales. We tested the hypothesis that phytochemistry is integral to the habitat selection process for vertebrate herbivores. We predicted that habitats selected at three spatial scales would be characterized by higher nutrient concentrations and lower concentrations of plant secondary metabolites (PSMs) than unused habitats. We used the Greater Sage-Grouse (Centrocercus urophasianus), an avian herbivore with a seasonally specialized diet of sagebrush, to test our hypothesis. Sage-Grouse selected a habitat type (black sagebrush, Artemisia nova) with lower PSM concentrations than the alternative (Wyoming big sagebrush, A. tridentata wyomingensis). Within black sagebrush habitat, Sage-Grouse selected patches and individual plants within those patches that were higher in nutrient concentrations and lower in PSM concentrations than those not used. Our results provide the first evidence for multi-scale habitat selection by an avian herbivore on the basis of phytochemistry, and they suggest that phytochemistry may be a fundamental driver of habitat selection for vertebrate herbivores.
Muranty, Hélène; Troggio, Michela; Sadok, Ben Inès; Rifaï, Al Mehdi; Auwerkerken, Annemarie; Banchi, E.; Velasco, Riccardo; Stevanato, P.; Weg, van de W.E.; Guardo, Di M.; Kumar, S.; Laurens, François; Bink, M.C.A.M.
The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in
Full Text Available Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea and the sympatric small tree finch (Camarhynchus parvulus, on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundanceis lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss.
Beerens, James M.; Gawlik, Dale E.; Herring, Garth; Cook, Mark I.
Seasonal and annual variation in food availability during the breeding season plays an influential role in the population dynamics of many avian species. In highly dynamic ecosystems like wetlands, finding and exploiting food resources requires a flexible behavioral response that may produce different population trends that vary with a species' foraging strategy. We quantified dynamic foraging-habitat selection by breeding and radiotagged White Ibises (Eudocimus albus) and Great Egrets (Ardea alba) in the Florida Everglades, where fluctuation in food resources is pronounced because of seasonal drying and flooding. The White Ibis is a tactile “searcher” species in population decline that specializes on highly concentrated prey, whereas the Great Egret, in a growing population, is a visual “exploiter” species that requires lower prey concentrations. In a year with high food availability, resource-selection functions for both species included variables that changed over multiannual time scales and were associated with increased prey production. In a year with low food availability, resource-selection functions included short-term variables that concentrated prey (e.g., water recession rates and reversals in drying pattern), which suggests an adaptive response to poor foraging conditions. In both years, the White Ibis was more restricted in its use of habitats than the Great Egret. Real-time species—habitat suitability models were developed to monitor and assess the daily availability and quality of spatially explicit habitat resources for both species. The models, evaluated through hindcasting using independent observations, demonstrated that habitat use of the more specialized White Ibis was more accurately predicted than that of the more generalist Great Egret.
Derrien, Thomas; Axelsson, Erik; Rosengren Pielberg, Gerli; Sigurdsson, Snaevar; Fall, Tove; Seppälä, Eija H.; Hansen, Mark S. T.; Lawley, Cindy T.; Karlsson, Elinor K.; Bannasch, Danika; Vilà, Carles; Lohi, Hannes; Galibert, Francis; Fredholm, Merete; Häggström, Jens; Hedhammar, Åke; André, Catherine; Lindblad-Toh, Kerstin; Hitte, Christophe; Webster, Matthew T.
The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease. PMID:22022279
Hart, Kristen M.; Zawada, David G.; Sartain-Iverson, Autumn R.; Fujisaki, Ikuko
We used satellite telemetry to identify in-water habitat used by individuals in the smallest North-west Atlantic subpopulation of adult nesting loggerhead turtles Caretta caretta during the breeding season. During 2010, 2011 and 2012 breeding periods, a total of 20 adult females used habitats proximal to nesting beaches with various levels of protection within Dry Tortugas National Park. We then used a rapid, high-resolution, digital imaging system to map habitat adjacent to nesting beaches, revealing the diversity and distribution of available benthic cover. Turtle behaviour showing measurable site-fidelity to these diverse habitats has implications for managing protected areas and human activities within them. Protecting diverse benthic areas adjacent to loggerhead turtle nesting beaches here and elsewhere could provide benefits for overall biodiversity conservation.
Lammerts van Bueren, E.T.; Backes, G.; de Vriend, H.
Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular...... markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture...... was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder’s perspectives and perspectives seen from the organic sector’s standpoint. Clear strengths were...
Clark, Samuel A; Kinghorn, Brian P; Hickey, John M; van der Werf, Julius H J
Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity. The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences. Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data. The use of genomic estimated breeding values increased genetic gain in
Full Text Available Due to their extreme popularity as fresh cut flowers and garden plants, and being used extensively for landscaping, tulips undergone a continuous process of selective breeding. For almost nine decades, classical cytogenetic studies, mainly the chromosome counts, have been an important part in the breeding programme for polyploid tulips. The efficiency of breeding is greatly aided by a thorough knowledge of the occurrence of polyploidy in the plant material. While the traditional cytogenetic approaches are still highly useful in selecting polyploids and aneuploids arising from crosses involving (most often parents of different ploidy or from the material subjected to ploidy manipulation, the new strategies for inducing polyploidy in tulips, either in vivo or in vitro, and advances in molecular cytogenetics are expected to allow a significant increase in breeding efficiency. Together with the shortening of breeding cycle, major genetic improvements could be made for specific traits. In this we review the development of cytogenetic studies in tulips, and the most relevant achievements so far, providing an overview of what we consider to be valuable tools for the processes of selective breeding .
Bassi, Filippo M; Bentley, Alison R; Charmet, Gilles; Ortiz, Rodomiro; Crossa, Jose
In the last decade the breeding technology referred to as 'genomic selection' (GS) has been implemented in a variety of species, with particular success in animal breeding. Recent research shows the potential of GS to reshape wheat breeding. Many authors have concluded that the estimated genetic gain per year applying GS is several times that of conventional breeding. GS is, however, a new technology for wheat breeding and many programs worldwide are still struggling to identify the best strategy for its implementation. This article provides practical guidelines on the key considerations when implementing GS. A review of the existing GS literature for a range of species is provided and used to prime breeder-oriented considerations on the practical applications of GS. Furthermore, this article discusses potential breeding schemes for GS, genotyping considerations, and methods for effective training population design. The components of selection intensity, progress toward inbreeding in half- or full-sibs recurrent schemes, and the generation of selection are also presented. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
Banerjee, Soumyajit; Aditya, Gautam; Saha, Goutam K
Highlights: ► An assessment of different household wastes as larval habitats of dengue vectors Aedes aegypti and Aedes albopictus was made using Kolkata, India as a model geographical area. ► Household wastes of four major categories namely earthen, porcelain, plastic and coconut shells varied significantly for Aedes immature depending on species, month and location. ► Based on the relative density of Aedes immature, cluster analyses allowed segregation and classification of the waste containers and relative importance as mosquito larval habitats. ► Conversion of disposed wastes into larval habitats cautions for continuance of Aedes population in Kolkata and similar cities of tropics lacking suitable waste management practices. - Abstract: An assessment of the household wastes as larval habitats of the dengue vectors was made considering Kolkata, India, as geographical area. Wastes of four major categories, namely, earthen, porcelain, plastic and coconut shells were monitored for positive with immature of either Aedes aegypti or Aedes albopictus. Twenty six types of wastes with varying size and shape, resembling containers, were identified that hosted mosquito immature. The number of waste containers positive for Aedes immature varied significantly (P < 0.05) with respect to location, type and month. The relative density of Aedes immature in the waste containers varied significantly (P < 0.05) with the types and months. The significant interaction between the month, waste container types and density of Aedes immature suggest that the household wastes are important contributors to the maintenance of the population of Aedes mosquito in the city. Based on the relative density of mosquito immature in the wastes, cluster analysis allowed segregation and classification of the wastes and their importance as mosquito larval habitats. Apparently, the containers that are most frequently disposed off contributed largely to the sustenance of Aedes mosquito population
Banerjee, Soumyajit, E-mail: email@example.com [Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019 (India); Aditya, Gautam, E-mail: firstname.lastname@example.org [Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019 (India); Department of Zoology, The University of Burdwan, Golapbag, Burdwan 713 104 (India); Saha, Goutam K, E-mail: email@example.com [Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700 019 (India)
Highlights: Black-Right-Pointing-Pointer An assessment of different household wastes as larval habitats of dengue vectors Aedes aegypti and Aedes albopictus was made using Kolkata, India as a model geographical area. Black-Right-Pointing-Pointer Household wastes of four major categories namely earthen, porcelain, plastic and coconut shells varied significantly for Aedes immature depending on species, month and location. Black-Right-Pointing-Pointer Based on the relative density of Aedes immature, cluster analyses allowed segregation and classification of the waste containers and relative importance as mosquito larval habitats. Black-Right-Pointing-Pointer Conversion of disposed wastes into larval habitats cautions for continuance of Aedes population in Kolkata and similar cities of tropics lacking suitable waste management practices. - Abstract: An assessment of the household wastes as larval habitats of the dengue vectors was made considering Kolkata, India, as geographical area. Wastes of four major categories, namely, earthen, porcelain, plastic and coconut shells were monitored for positive with immature of either Aedes aegypti or Aedes albopictus. Twenty six types of wastes with varying size and shape, resembling containers, were identified that hosted mosquito immature. The number of waste containers positive for Aedes immature varied significantly (P < 0.05) with respect to location, type and month. The relative density of Aedes immature in the waste containers varied significantly (P < 0.05) with the types and months. The significant interaction between the month, waste container types and density of Aedes immature suggest that the household wastes are important contributors to the maintenance of the population of Aedes mosquito in the city. Based on the relative density of mosquito immature in the wastes, cluster analysis allowed segregation and classification of the wastes and their importance as mosquito larval habitats. Apparently, the containers that
[Chen X., Sun H., Tian S., Xiang H., Zhou L., Dun W. and Zhao X. 2015 Increasing litter size in a sheep breed by marker-assisted selection of BMPR1B A746G ... selection pressure on traits and leads to the promotion of genetic gain, which can be used for ... from frozen blood samples (Sambrook and Russell 2001). Figure 1.
Elliot L. Heffner
Full Text Available Genomic selection (GS uses genome-wide molecular marker data to predict the genetic value of selection candidates in breeding programs. In plant breeding, the ability to produce large numbers of progeny per cross allows GS to be conducted within each family. However, this approach requires phenotypes of lines from each cross before conducting GS. This will prolong the selection cycle and may result in lower gains per year than approaches that estimate marker-effects with multiple families from previous selection cycles. In this study, phenotypic selection (PS, conventional marker-assisted selection (MAS, and GS prediction accuracy were compared for 13 agronomic traits in a population of 374 winter wheat ( L. advanced-cycle breeding lines. A cross-validation approach that trained and validated prediction accuracy across years was used to evaluate effects of model selection, training population size, and marker density in the presence of genotype × environment interactions (G×E. The average prediction accuracies using GS were 28% greater than with MAS and were 95% as accurate as PS. For net merit, the average accuracy across six selection indices for GS was 14% greater than for PS. These results provide empirical evidence that multifamily GS could increase genetic gain per unit time and cost in plant breeding.
Full Text Available Studies were carried out in 2010 by mean of simplified version of the mapping method. The study area (395 ha was located close to the city centre. It comprised a mosaic of urbanized habitats, with a clear dominance of green areas, such as parks (41.1 ha, gardens, cemeteries and tree clumps. A total of 48 breeding bird species were recorded in the whole study area. The most common (<25 pairs/100 ha were Passer domesticus, Passer montanus, Sturnus vulgaris, Parus caeruleus, Parus major, Apus apus and Columba livia. Numerous (7-15 pairs/100 ha were also the following species: Columba palumbus, Turdus pilaris, Sylvia atricapilla, Serinus serinus, Turdus merula and Pica pica. Insectivorous birds were the most common birds constituting 63.3%, and granivorous -32.6% of all pairs recorded. Most birds nested in tree holes (39.3%, in/on buildings (30.2% and in trees/shrubs (25.6%. Distribution of breeding pairs of 23 bird species was presented on maps. Population trends for 17 species were documented. Rapid increase in numbers of Turdus pilaris, Corvus cornix and Phoenicurus phoenicurus and decrease of Pica pica were recorded.
The influence of competition is discussed and quantified for unselected bulk propagation, single-plant selection and yield testing of progenies in row plots. A mathematical model is introduced that defines the influence of intergenotypic competition and density of stand on the response to selection.
Chavanne, Hervé; Janssen, Kasper; Hofherr, Johann
reared fish species were targeted. A total of 31 respondents contributed to the survey, representing 75 % of European breeding organizations. Family-based breeding schemes were predominant, but individual selection was more frequently applied in marine species. Artificial fertilization is the preferred...... of molecular tools is now common in all programs, mainly for pedigree traceability. An increasing number of programs use either genomic or marker-assisted selection. Results related to the seed production market confirmed that for Atlantic salmon there are a few dominant players at the European level, with 30......–50 % market share. Only part of the European fish aquaculture industry today fully exploits selective breeding to the best advantage. A larger impact assessment still needs to be made by the remainder, particularly on the market share of fish seed (eggs, larvae or juveniles) and its consequences for hatchery...
Lawson, Christopher E; Strachan, Cameron R; Williams, Dominique D; Koziel, Susan; Hallam, Steven J; Budwill, Karen
Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
Borges, Friederike; Glemnitz, Michael; Schultz, Alfred; Stachow, Ulrich
Many of the processes behind the decline of farmland birds can be related to modifications in landscape structure (composition and configuration), which can partly be expressed quantitatively with measurable or computable indices, i.e. landscape metrics. This paper aims to identify statistical relationships between the occurrence of birds and the landscape structure. We present a method that combines two comprehensive procedures: the "landscape-centred approach" and "guild classification". Our study is based on more than 20,000 individual bird observations based on a 4-year bird monitoring approach in a typical agricultural area in the north-eastern German lowlands. Five characteristic bird guilds, each with three characteristic species, are defined for the typical habitat types of that area: farmland, grassland, hedgerow, forest and settlement. The suitability of each sample plot for each guild is indicated by the level of persistence (LOP) of occurrence of three respective species. Thus, the sample plots can be classified as "preferred" or "less preferred" depending on the lower and upper quartiles of the LOP values. The landscape structure is characterized by 16 different landscape metrics expressing various aspects of landscape composition and configuration. For each guild, the three landscape metrics with the strongest rank correlation with the LOP values and that are not mutually dependent were identified. For four of the bird guilds, the classification success was better than 80%, compared with only 66% for the grassland bird guild. A subset of six landscape metrics proved to be the most meaningful and sufficiently classified the sample areas with respect to bird guild suitability. In addition, derived logistic functions allowed the production of guild-specific habitat suitability maps for the whole landscape. The analytical results show that the proposed approach is appropriate to assess the habitat suitability of agricultural landscapes for characteristic
Full Text Available Migrating humpback whales from northern and southern feeding grounds come to the tropical waters near Osa Peninsula, Pacific of Costa Rica, to reproduce and raise their calves. Planning effective marine protected areas that encompass humpback critical habitats require data about which oceanographic features influence distribution during the breeding period. This study examines the relationship between water depth and ocean floor slope with humpback whale distribution, based on sightings during two breeding seasons (2005 and 2006. Data are from the Southern and Northern subpopulations in the Eastern Tropical Pacific (ETP. Analysis followed the basic principles of the Ecological Niche Factors Analysis (ENFA, where indices of Marginality and Tolerance provide insights on the restrictiveness of habitat use. At a fine scale, physical factors such as water depth and slope define the critical breeding and nursing habitat for M. novaeangliae. Divergence in the subsamples means of depths and slope distribution, with the global mean of the study area in both eco-geographical variables, determine habitat requirements restricted by topographic features such as depths (Las ballenas jorobadas viajan a aguas tropicales para reproducirse y criar a sus ballenatos. Es importante entender las características oceanográficas que influencian su distribución para lograr una planificación efectiva de áreas marinas protegidas con hábitats críticos para estos cetáceos. Este estudio examina la relación entre la profundidad, la pendiente del suelo oceánico y la distribución de estas ballenas, usando avistamientos del 2005 y 2006 en la costa Pacífica de la Península de Osa, Costa Rica (temporada de reproducción del sur y norte en el Pacífico Tropical Oriental. Usamos Análisis de Factores de Nicho Ecológico (ENFA por sus siglas en inglés, donde los índices de Marginalidad y Tolerancia ilustran las restricciones en uso de hábitat. En una escala local
Muposhi, Victor K; Gandiwa, Edson; Chemura, Abel; Bartels, Paul; Makuza, Stanley M; Madiri, Tinaapi H
An understanding of the habitat selection patterns by wild herbivores is critical for adaptive management, particularly towards ecosystem management and wildlife conservation in semi arid savanna ecosystems. We tested the following predictions: (i) surface water availability, habitat quality and human presence have a strong influence on the spatial distribution of wild herbivores in the dry season, (ii) habitat suitability for large herbivores would be higher compared to medium-sized herbivores in the dry season, and (iii) spatial extent of suitable habitats for wild herbivores will be different between years, i.e., 2006 and 2010, in Matetsi Safari Area, Zimbabwe. MaxEnt modeling was done to determine the habitat suitability of large herbivores and medium-sized herbivores. MaxEnt modeling of habitat suitability for large herbivores using the environmental variables was successful for the selected species in 2006 and 2010, except for elephant (Loxodonta africana) for the year 2010. Overall, large herbivores probability of occurrence was mostly influenced by distance from rivers. Distance from roads influenced much of the variability in the probability of occurrence of medium-sized herbivores. The overall predicted area for large and medium-sized herbivores was not different. Large herbivores may not necessarily utilize larger habitat patches over medium-sized herbivores due to the habitat homogenizing effect of water provisioning. Effect of surface water availability, proximity to riverine ecosystems and roads on habitat suitability of large and medium-sized herbivores in the dry season was highly variable thus could change from one year to another. We recommend adaptive management initiatives aimed at ensuring dynamic water supply in protected areas through temporal closure and or opening of water points to promote heterogeneity of wildlife habitats.
Victor K Muposhi
Full Text Available An understanding of the habitat selection patterns by wild herbivores is critical for adaptive management, particularly towards ecosystem management and wildlife conservation in semi arid savanna ecosystems. We tested the following predictions: (i surface water availability, habitat quality and human presence have a strong influence on the spatial distribution of wild herbivores in the dry season, (ii habitat suitability for large herbivores would be higher compared to medium-sized herbivores in the dry season, and (iii spatial extent of suitable habitats for wild herbivores will be different between years, i.e., 2006 and 2010, in Matetsi Safari Area, Zimbabwe. MaxEnt modeling was done to determine the habitat suitability of large herbivores and medium-sized herbivores. MaxEnt modeling of habitat suitability for large herbivores using the environmental variables was successful for the selected species in 2006 and 2010, except for elephant (Loxodonta africana for the year 2010. Overall, large herbivores probability of occurrence was mostly influenced by distance from rivers. Distance from roads influenced much of the variability in the probability of occurrence of medium-sized herbivores. The overall predicted area for large and medium-sized herbivores was not different. Large herbivores may not necessarily utilize larger habitat patches over medium-sized herbivores due to the habitat homogenizing effect of water provisioning. Effect of surface water availability, proximity to riverine ecosystems and roads on habitat suitability of large and medium-sized herbivores in the dry season was highly variable thus could change from one year to another. We recommend adaptive management initiatives aimed at ensuring dynamic water supply in protected areas through temporal closure and or opening of water points to promote heterogeneity of wildlife habitats.
Heinrichs, Julie; Aldridge, Cameron L.; O'Donnell, Michael; Schumaker, Nathan
Prioritizing habitats for conservation is a challenging task, particularly for species with fluctuating populations and seasonally dynamic habitat needs. Although the use of resource selection models to identify and prioritize habitat for conservation is increasingly common, their ability to characterize important long-term habitats for dynamic populations are variable. To examine how habitats might be prioritized differently if resource selection was directly and dynamically linked with population fluctuations and movement limitations among seasonal habitats, we constructed a spatially explicit individual-based model for a dramatically fluctuating population requiring temporally varying resources. Using greater sage-grouse (Centrocercus urophasianus) in Wyoming as a case study, we used resource selection function maps to guide seasonal movement and habitat selection, but emergent population dynamics and simulated movement limitations modified long-term habitat occupancy. We compared priority habitats in RSF maps to long-term simulated habitat use. We examined the circumstances under which the explicit consideration of movement limitations, in combination with population fluctuations and trends, are likely to alter predictions of important habitats. In doing so, we assessed the future occupancy of protected areas under alternative population and habitat conditions. Habitat prioritizations based on resource selection models alone predicted high use in isolated parcels of habitat and in areas with low connectivity among seasonal habitats. In contrast, results based on more biologically-informed simulations emphasized central and connected areas near high-density populations, sometimes predicted to be low selection value. Dynamic models of habitat use can provide additional biological realism that can extend, and in some cases, contradict habitat use predictions generated from short-term or static resource selection analyses. The explicit inclusion of population
Sherfy, Mark H.; Stucker, Jennifer H.; Buhl, Deborah A.
Federally endangered interior least terns (Sternula antillarum) nest on bare or sparsely vegetated sandbars on midcontinent river systems. Loss of nesting habitat has been implicated as a cause of population declines, and managing these habitats is a major initiative in population recovery. One such initiative involves construction of mid-channel sandbars on the Missouri River, where natural sandbar habitat has declined in quantity and quality since the late 1990s. We evaluated nest-site habitat selection by least terns on constructed and natural sandbars by comparing vegetation, substrate, and debris variables at nest sites (n = 798) and random points (n = 1,113) in bare or sparsely vegetated habitats. Our logistic regression models revealed that a broader suite of habitat features was important in nest-site selection on constructed than on natural sandbars. Odds ratios for habitat variables indicated that avoidance of habitat features was the dominant nest-site selection process on both sandbar types, with nesting terns being attracted to nest-site habitat features (gravel and debris) and avoiding vegetation only on constructed sandbars, and avoiding silt and leaf litter on both sandbar types. Despite the seemingly uniform nature of these habitats, our results suggest that a complex suite of habitat features influences nest-site choice by least terns. However, nest-site selection in this social, colonially nesting species may be influenced by other factors, including spatial arrangement of bare sand habitat, proximity to other least terns, and prior habitat occupancy by piping plovers (Charadrius melodus). We found that nest-site selection was sensitive to subtle variation in habitat features, suggesting that rigor in maintaining habitat condition will be necessary in managing sandbars for the benefit of least terns. Further, management strategies that reduce habitat features that are avoided by least terns may be the most beneficial to nesting least terns.
Conallin, J.; Boegh, E.; Olsen, M.
Physical habitat is important in determining the carrying capacity of juvenile brown trout, and within freshwater management. Summer daytime physical habitat selection for the parr lifestage (7-20 cm) juvenile brown trout (Salmo trutta) was assessed in 6 small lowland streams. Habitat preference ...
Conallin, J.; Boegh, E.; Olsen, M.
Physical habitat is important in determining the carrying capacity of juvenile brown trout, and within freshwater management. Summer daytime physical habitat selection for the parr lifestage (7-20 cm) juvenile brown trout (Salmo trutta) was assessed in 6 small lowland streams. Habitat preference...
Dayane Cristina Lima
Full Text Available A common bean (Phaseolus vulgarisL. cultivar must combine desirable genotypes for several traits in order to be accepted by producers and consumers. This study aimed to evaluate selection efficiency when segregating bean populations for traits, by means of a selection index, in order to obtain superior progenies for traits considered. A total of 16 populations from the F4 and F5generations were evaluated in 2011 and 2012, respectively. The traits evaluated were plant architecture, plant disease, grain type and yield. Using standard scores (Z, the sum of the four traits (∑Z was obtained and, based on this information, the best populations were identified. The evaluation of selection effectiveness was performed on 31 progenies from each population. The 496 progenies plus eight controls were evaluated in the F5:6and F5:7 generations for the same traits in July and November 2012, respectively. The selection, using the index based on the sum of standardized variables (∑Z, was efficient for identifying populations with superior progenies for all the traits considered.
Stolen, Eric D.; Collazo, J.A.; Percival, H.F.
Foraging habitat selection of nesting Great Egrets (Ardea alba) and Snowy Egrets (Egretta thula) was investigated within an estuary with extensive impounded salt marsh habitat. Using a geographic information system, available habitat was partitioned into concentric bands at five, ten, and 15 km radius from nesting colonies to assess the relative effects of habitat composition and distance on habitat selection. Snowy Egrets were more likely than Great Egrets to depart colonies and travel to foraging sites in groups, but both species usually arrived at sites that were occupied by other wading birds. Mean flight distances were 6.2 km (SE = 0.4, N = 28, range 1.8-10.7 km) for Great Egrets and 4.7 km (SE = 0.48, N = 31, range 0.7-12.5 km) for Snowy Egrets. At the broadest spatial scale both species used impounded (mostly salt marsh) and estuarine edge habitat more than expected based on availability while avoiding unimpounded (mostly fresh water wetland) habitat. At more local scales habitat use matched availability. Interpretation of habitat preference differed with the types of habitat that were included and the maximum distance that habitat was considered available. These results illustrate that caution is needed when interpreting the results of habitat preference studies when individuals are constrained in their choice of habitats, such as for central place foragers.
Anteau, Michael J.; Shaffer, Terry L.; Wiltermuth, Mark T.; Sherfy, Mark H.
How breeding birds distribute in relation to landscape-scale habitat features has important implications for conservation because those features may constrain habitat suitability. Furthermore, knowledge of these associations can help build models to improve area-wide demographic estimates or to develop a sampling stratification for research and monitoring. This is particularly important for rare species that have uneven distributions across vast areas, such as the federally listed piping plover (Charadrius melodus; hereafter plover). We examined how remotely-sensed landscape features influenced the distribution of breeding plover pairs among 2-km shoreline segments during 2006–2009 at Lake Sakakawea in North Dakota, USA. We found strong associations between remotely-sensed landscape features and plover abundance and distribution (R2 = 0.65). Plovers were nearly absent from segments with bluffs (>25 m elevation increase within 250 m of shoreline). Relative plover density (pairs/ha) was markedly greater on islands (4.84 ± 1.22 SE) than on mainlands (0.85 ± 0.17 SE). Pair numbers increased with abundance of nesting habitat (unvegetated-flat areas β^=0.28±0.08SE ). On islands, pair numbers also increased with the relative proportion of the total area that was habitat ( β^=3.27±0.46SE ). Our model could be adapted to estimate the breeding population of plovers or to make predictions that provide a basis for stratification and design of future surveys. Knowledge of landscape features, such as bluffs, that exclude use by birds refines habitat suitability and facilitates more accurate estimates of habitat and population abundance, by decreasing the size of the sampling universe. Furthermore, techniques demonstrated here are applicable to other vast areas where birds breed in sparse or uneven densities.
Sprague, Tiffany A; Bateman, Heather L
Species conservation requires a thorough understanding of habitat requirements. The northern Mexican gartersnake (Thamnophis eques megalops) was listed as threatened under the U.S. Endangered Species Act in 2014. Natural resource managers are interested in understanding the ecology of this subspecies to guide management decisions and to determine what features are necessary for habitat creation and restoration. Our objective was to identify habitat selection of northern Mexican gartersnakes in a highly managed, constructed wetland hatchery. We deployed transmitters on 42 individual gartersnakes and documented use of habitat types and selection of specific habitat features. Habitat selection was similar between males and females and varied seasonally. During the active season (March-October), gartersnakes primarily selected wetland edge habitat with abundant cover. Gestating females selected similar locations but with less dense cover. During the inactive season (November-February), gartersnakes selected upland habitats, including rocky slopes with abundant vegetation. These results of this study can help inform management of the subspecies, particularly in human-influenced habitats. Conservation of this subspecies should incorporate a landscape-level approach that includes abundant wetland edge habitat with a mosaic of dense cover for protection and sparsely vegetated areas for basking connected to terrestrial uplands for overwintering.
Tiffany A Sprague
Full Text Available Species conservation requires a thorough understanding of habitat requirements. The northern Mexican gartersnake (Thamnophis eques megalops was listed as threatened under the U.S. Endangered Species Act in 2014. Natural resource managers are interested in understanding the ecology of this subspecies to guide management decisions and to determine what features are necessary for habitat creation and restoration. Our objective was to identify habitat selection of northern Mexican gartersnakes in a highly managed, constructed wetland hatchery. We deployed transmitters on 42 individual gartersnakes and documented use of habitat types and selection of specific habitat features. Habitat selection was similar between males and females and varied seasonally. During the active season (March-October, gartersnakes primarily selected wetland edge habitat with abundant cover. Gestating females selected similar locations but with less dense cover. During the inactive season (November-February, gartersnakes selected upland habitats, including rocky slopes with abundant vegetation. These results of this study can help inform management of the subspecies, particularly in human-influenced habitats. Conservation of this subspecies should incorporate a landscape-level approach that includes abundant wetland edge habitat with a mosaic of dense cover for protection and sparsely vegetated areas for basking connected to terrestrial uplands for overwintering.
Rudolf von May
Full Text Available The loss of hearing structures and loss of advertisement calls in many terrestrial breeding frogs (Strabomantidae living at high elevations in South America are common and intriguing phenomena. The Andean frog genus Phrynopus Peters, 1873 has undergone an evolutionary radiation in which most species lack the tympanic membrane and tympanic annulus, yet the phylogenetic relationships among species in this group remain largely unknown. Here, we present an expanded molecular phylogeny of Phrynopus that includes 24 nominal species. Our phylogeny includes Phrynopus peruanus, the type species of the genus, and 10 other species for which genetic data were previously unavailable. We found strong support for monophyly of Phrynopus, and that two nominal species—Phrynopus curator and Phrynopus nicoleae—are junior synonyms of Phrynopus tribulosus. Using X-ray computed tomography (CT imaging, we demonstrate that the absence of external hearing structures is associated with complete loss of the auditory skeletal elements (columella in at least one member of the genus. We mapped the tympanum condition on to a species tree to infer whether the loss of hearing structures took place once or multiple times. We also assessed whether tympanum condition, body size, and body shape are associated with the elevational distribution and habitat use. We identified a single evolutionary transition that involved the loss of both the tympanic membrane and tympanic annulus, which in turn is correlated with the absence of advertisement calls. We also identified several species pairs where one species inhabits the Andean grassland and the other montane forest. When accounting for phylogenetic relatedness among species, we detected a significant pattern of increasing body size with increasing elevation. Additionally, species at higher elevations tend to develop shorter limbs, shorter head, and shorter snout than species living at lower elevations. Our findings strongly suggest
Home; Journals; Journal of Genetics; Volume 94; Issue 1. Increasing litter size in a sheep breed by marker-assisted selection of BMPR1B A746G mutation. Xiaoyong Chen Hongxin Sun Shujun Tian Hai Xiang Liansheng Zhou Weitao Dun Xingbo Zhao. Research Note Volume 94 Issue 1 March 2015 pp 139-142 ...
Burger, J.; Howe, M.A.; Hahn, D.C.; Chase, J.
We studied assemblages of feeding shorebirds in three intertidal habitats on the coast of New Jersey during August to document how species segregate spatially both among and within habitats and to determine the effects of tidal cycles on these patterns. The habitats were a sandy beach facing the ocean proper (outer beach), a sandy beach on the mainland side of a barrier island (inner beach), and a small mudflat adjacent to a Spartina alterniflora salt marsh. We were able to identify several microhabitats on the outer beach and mudflat. Most species fed in more than one habitat, but only two, Charadrius semipalmatus and Calidris canutus, used all three habitats regularly. Within habitats, most species exhibited strong preferences for the wettest areas, but we found differences among species in degrees of preference. The least amount of partitioning occurred on the inner beach, where birds crowded into a small zone near the water's edge and had frequent agonistic encounters suggesting intense competition. Shorebird feeding activity was partly a function of tide time: each habitat had a characteristic temporal pattern of use by shorebirds related to tide time rather than diel time; within habitats, we found species-characteristic feeding activity rhythms that were also a function of tide time. Feeding by most species peaked during the first 2 hours after low tide on the outer beach and mudflat. The results are discussed in terms of feeding strategies and interspecific competition.
Full Text Available Genomic selection (GS provides an attractive option for accelerating genetic gain in perennial ryegrass ( improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditional breeding strategies for key traits (persistency, yield, and flowering time. Base population genomes were simulated through random mating for 60,000 generations at an effective population size of 10,000. The degree of linkage disequilibrium (LD in the resulting population was compared with that obtained from empirical studies. Initial parental varieties were simulated to match diversity of current commercial cultivars. Genomic selection was designed to fit into a company breeding program at two selection points in the breeding cycle (spaced plants and miniplot. Genomic estimated breeding values (GEBVs for productivity traits were trained with phenotypes and genotypes from plots. Accuracy of GEBVs was 0.24 for persistency and 0.36 for yield for single plants, while for plots it was lower (0.17 and 0.19, respectively. Higher accuracy of GEBVs was obtained for flowering time (up to 0.7, partially as a result of the larger reference population size that was available from the clonal row stage. The availability of GEBVs permit a 4-yr reduction in cycle time, which led to at least a doubling and trebling genetic gain for persistency and yield, respectively, than the traditional program. However, a higher rate of inbreeding per cycle among varieties was also observed for the GS strategy.
Lopes, Marcos S; Bovenhuis, Henk; Hidalgo, André M; van Arendonk, Johan A M; Knol, Egbert F; Bastiaansen, John W M
Breed-specific effects are observed when the same allele of a given genetic marker has a different effect depending on its breed origin, which results in different allele substitution effects across breeds. In such a case, single-breed breeding values may not be the most accurate predictors of crossbred performance. Our aim was to estimate the contribution of alleles from each parental breed to the genetic variance of traits that are measured in crossbred offspring, and to compare the prediction accuracies of estimated direct genomic values (DGV) from a traditional genomic selection model (GS) that are trained on purebred or crossbred data, with accuracies of DGV from a model that accounts for breed-specific effects (BS), trained on purebred or crossbred data. The final dataset was composed of 924 Large White, 924 Landrace and 924 two-way cross (F1) genotyped and phenotyped animals. The traits evaluated were litter size (LS) and gestation length (GL) in pigs. The genetic correlation between purebred and crossbred performance was higher than 0.88 for both LS and GL. For both traits, the additive genetic variance was larger for alleles inherited from the Large White breed compared to alleles inherited from the Landrace breed (0.74 and 0.56 for LS, and 0.42 and 0.40 for GL, respectively). The highest prediction accuracies of crossbred performance were obtained when training was done on crossbred data. For LS, prediction accuracies were the same for GS and BS DGV (0.23), while for GL, prediction accuracy for BS DGV was similar to the accuracy of GS DGV (0.53 and 0.52, respectively). In this study, training on crossbred data resulted in higher prediction accuracy than training on purebred data and evidence of breed-specific effects for LS and GL was demonstrated. However, when training was done on crossbred data, both GS and BS models resulted in similar prediction accuracies. In future studies, traits with a lower genetic correlation between purebred and crossbred
Wei, Caihong; Wang, Huihua; Liu, Gang; Wu, Mingming; Cao, Jiaxve; Liu, Zhen; Liu, Ruizao; Zhao, Fuping; Zhang, Li; Lu, Jian; Liu, Chousheng; Du, Lixin
Traditionally, Chinese indigenous sheep were classified geographically and morphologically into three groups: Mongolian, Kazakh and Tibetan. Herein, we aimed to evaluate the population structure and genome selection among 140 individuals from ten representative Chinese indigenous sheep breeds: Ujimqin, Hu, Tong, Large-Tailed Han and Lop breed (Mongolian group); Duolang and Kazakh (Kazakh group); and Diqing, Plateau-type Tibetan, and Valley-type Tibetan breed (Tibetan group). We analyzed the population using principal component analysis (PCA), STRUCTURE and a Neighbor-Joining (NJ)-tree. In PCA plot, the Tibetan and Mongolian groups were clustered as expected; however, Duolang and Kazakh (Kazakh group) were segregated. STRUCTURE analyses suggested two subpopulations: one from North China (Kazakh and Mongolian groups) and the other from the Southwest (Tibetan group). In the NJ-tree, the Tibetan group formed an independent branch and the Kazakh and Mongolian groups were mixed. We then used the d i statistic approach to reveal selection in Chinese indigenous sheep breeds. Among the 599 genome sequence windows analyzed, sixteen (2.7%) exhibited signatures of selection in four or more breeds. We detected three strong selection windows involving three functional genes: RXFP2, PPP1CC and PDGFD. PDGFD, one of the four subfamilies of PDGF, which promotes proliferation and inhibits differentiation of preadipocytes, was significantly selected in fat type breeds by the Rsb (across pairs of populations) approach. Two consecutive selection regions in Duolang sheep were obviously different to other breeds. One region was in OAR2 including three genes (NPR2, SPAG8 and HINT2) the influence growth traits. The other region was in OAR 6 including four genes (PKD2, SPP1, MEPE, and IBSP) associated with a milk production quantitative trait locus. We also identified known candidate genes such as BMPR1B, MSRB3, and three genes (KIT, MC1R, and FRY) that influence lambing percentage, ear size
Niemuth, Neil D.; Ryba, Adam J.; Pearse, Aaron T.; Kvas, Susan M.; Brandt, David; Wangler, Brian; Austin, Jane; Carlisle, Martha J.
The Whooping Crane (Grus americana) is a federally endangered species in the United States and Canada that relies on wetland, grassland, and cropland habitat during its long migration between wintering grounds in coastal Texas, USA, and breeding sites in Alberta and Northwest Territories, Canada. We combined opportunistic Whooping Crane sightings with landscape data to identify correlates of Whooping Crane occurrence along the migration corridor in North Dakota and South Dakota, USA. Whooping Cranes selected landscapes characterized by diverse wetland communities and upland foraging opportunities. Model performance substantially improved when variables related to detection were included, emphasizing the importance of accounting for biases associated with detection and reporting of birds in opportunistic datasets. We created a predictive map showing relative probability of occurrence across the study region by applying our model to GIS data layers; validation using independent, unbiased locations from birds equipped with platform transmitting terminals indicated that our final model adequately predicted habitat use by migrant Whooping Cranes. The probability map demonstrated that existing conservation efforts have protected much top-tier Whooping Crane habitat, especially in the portions of North Dakota and South Dakota that lie east of the Missouri River. Our results can support species recovery by informing prioritization for acquisition and restoration of landscapes that provide safe roosting and foraging habitats. Our results can also guide the siting of structures such as wind towers and electrical transmission and distribution lines, which pose a strike and mortality risk to migrating Whooping Cranes.
Elizabeth Hillard; Laura E. DeWald
Great Smoky Mountains National Park (GSMNP) in North Carolina and Tennessee now has an established elk (Cervus elaphus) population 10 years after reintroduction. Although elk typically elect more open habitat, elk in GSMNP are showing they are capable of doing well in predominantly forested habitats. Evaluating how the established herd of elk is...
Strickland, Bradley A; Vilella, Francisco J; Belant, Jerrold L
Habitat selection is an active behavioral process that may vary across spatial and temporal scales. Animals choose an area of primary utilization (i.e., home range) then make decisions focused on resource needs within patches. Dominance may affect the spatial distribution of conspecifics and concomitant habitat selection. Size-dependent social dominance hierarchies have been documented in captive alligators, but evidence is lacking from wild populations. We studied habitat selection for adult male American alligators (Alligator mississippiensis; n = 17) on the Pearl River in central Mississippi, USA, to test whether habitat selection was scale-dependent and individual resource selectivity was a function of conspecific body size. We used K-select analysis to quantify selection at the home range scale and patches within the home range to determine selection congruency and important habitat variables. In addition, we used linear models to determine if body size was related to selection patterns and strengths. Our results indicated habitat selection of adult male alligators was a scale-dependent process. Alligators demonstrated greater overall selection for habitat variables at the patch level and less at the home range level, suggesting resources may not be limited when selecting a home range for animals in our study area. Further, diurnal habitat selection patterns may depend on thermoregulatory needs. There was no relationship between resource selection or home range size and body size, suggesting size-dependent dominance hierarchies may not have influenced alligator resource selection or space use in our sample. Though apparent habitat suitability and low alligator density did not manifest in an observed dominance hierarchy, we hypothesize that a change in either could increase intraspecific interactions, facilitating a dominance hierarchy. Due to the broad and diverse ecological roles of alligators, understanding the factors that influence their social dominance
Bradley A Strickland
Full Text Available Habitat selection is an active behavioral process that may vary across spatial and temporal scales. Animals choose an area of primary utilization (i.e., home range then make decisions focused on resource needs within patches. Dominance may affect the spatial distribution of conspecifics and concomitant habitat selection. Size-dependent social dominance hierarchies have been documented in captive alligators, but evidence is lacking from wild populations. We studied habitat selection for adult male American alligators (Alligator mississippiensis; n = 17 on the Pearl River in central Mississippi, USA, to test whether habitat selection was scale-dependent and individual resource selectivity was a function of conspecific body size. We used K-select analysis to quantify selection at the home range scale and patches within the home range to determine selection congruency and important habitat variables. In addition, we used linear models to determine if body size was related to selection patterns and strengths. Our results indicated habitat selection of adult male alligators was a scale-dependent process. Alligators demonstrated greater overall selection for habitat variables at the patch level and less at the home range level, suggesting resources may not be limited when selecting a home range for animals in our study area. Further, diurnal habitat selection patterns may depend on thermoregulatory needs. There was no relationship between resource selection or home range size and body size, suggesting size-dependent dominance hierarchies may not have influenced alligator resource selection or space use in our sample. Though apparent habitat suitability and low alligator density did not manifest in an observed dominance hierarchy, we hypothesize that a change in either could increase intraspecific interactions, facilitating a dominance hierarchy. Due to the broad and diverse ecological roles of alligators, understanding the factors that influence their
Strickland, Bradley A.; Vilella, Francisco; Belant, Jerrold L.
Habitat selection is an active behavioral process that may vary across spatial and temporal scales. Animals choose an area of primary utilization (i.e., home range) then make decisions focused on resource needs within patches. Dominance may affect the spatial distribution of conspecifics and concomitant habitat selection. Size-dependent social dominance hierarchies have been documented in captive alligators, but evidence is lacking from wild populations. We studied habitat selection for adult male American alligators (Alligator mississippiensis; n = 17) on the Pearl River in central Mississippi, USA, to test whether habitat selection was scale-dependent and individual resource selectivity was a function of conspecific body size. We used K-select analysis to quantify selection at the home range scale and patches within the home range to determine selection congruency and important habitat variables. In addition, we used linear models to determine if body size was related to selection patterns and strengths. Our results indicated habitat selection of adult male alligators was a scale-dependent process. Alligators demonstrated greater overall selection for habitat variables at the patch level and less at the home range level, suggesting resources may not be limited when selecting a home range for animals in our study area. Further, diurnal habitat selection patterns may depend on thermoregulatory needs. There was no relationship between resource selection or home range size and body size, suggesting size-dependent dominance hierarchies may not have influenced alligator resource selection or space use in our sample. Though apparent habitat suitability and low alligator density did not manifest in an observed dominance hierarchy, we hypothesize that a change in either could increase intraspecific interactions, facilitating a dominance hierarchy. Due to the broad and diverse ecological roles of alligators, understanding the factors that influence their social dominance
McConnel, M B; Galligan, D T
Optimization programs are currently used to aid in the selection of bulls to be used in herd breeding programs. While these programs offer a systematic approach to the problem of semen selection, they ignore the impact of volume discounts. Volume discounts are discounts that vary depending on the number of straws purchased. The dynamic nature of volume discounts means that, in order to be adequately accounted for, they must be considered in the optimization routine. Failing to do this creates a missed economic opportunity because the potential benefits of optimally selecting and combining breeding company discount opportunities are not captured. To address these issues, an integer program was created which used binary decision variables to incorporate the effects of quantity discounts into the optimization program. A consistent set of trait criteria was used to select a group of bulls from 3 sample breeding companies. Three different selection programs were used to select the bulls, 2 traditional methods and the integer method. After the discounts were applied using each method, the integer program resulted in the lowest cost portfolio of bulls. A sensitivity analysis showed that the integer program also resulted in a low cost portfolio when the genetic trait goals were changed to be more or less stringent. In the sample application, a net benefit of the new approach over the traditional approaches was a 12.3 to 20.0% savings in semen cost.
Mahanty, Madan M; Latha, G; Thirunavukkarasu, A
The primary objective of this work was to present the acoustical identification of humpback whales, detected by using an autonomous ambient noise measurement system, deployed in the shallow waters of the Southeastern Arabian Sea (SEAS) during the period January to May 2011. Seven types of sounds were detected. These were characteristically upsweeps and downsweeps along with harmonics. Sounds produced repeatedly in a specific pattern were referred to as phrases (PQRS and ABC). Repeated phrases in a particular pattern were referred to as themes, and from the spectrographic analysis, two themes (I and II) were identified. The variation in the acoustic characteristics such as fundamental frequency, range, duration of the sound unit, and the structure of the phrases and themes are discussed. Sound units were recorded from mid-January to mid-March, with a peak in February, when the mean SST is approx. 28 degree C, and no presence was recorded after mid-March. The temporal and thematic structures strongly determine the functions of the humpback whale song form. Given the use of song in the SEAS, this area is possibly used as an active breeding habitat by humpback whales during the winter season.
Tara Szkorupa; Fiona Schmiegelow
This research suggests that mountain caribou select a suite of winter habitats, at multiple spatial scales, and under a range of snow conditions. Our findings lead to several management recommendations. In general, habitat selection by caribou necessitates management over large spatial and temporal scales.
Kevin McGarigal; Ho Yi Wan; Kathy A. Zeller; Brad C. Timm; Samuel A. Cushman
Scale is the lens that focuses ecological relationships. Organisms select habitat at multiple hierarchical levels and at different spatial and/or temporal scales within each level. Failure to properly address scale dependence can result in incorrect inferences in multi-scale habitat selection modeling studies.
Muranty, Hélène; Troggio, Michela; Sadok, Inès Ben; Rifaï, Mehdi Al; Auwerkerken, Annemarie; Banchi, Elisa; Velasco, Riccardo; Stevanato, Piergiorgio; van de Weg, W Eric; Di Guardo, Mario; Kumar, Satish; Laurens, François; Bink, Marco C A M
The application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.
Full Text Available Alfalfa ( L. is a widely planted perennial forage legume grown throughout temperate and dry subtropical regions in the world. Long breeding cycles limit genetic improvement of alfalfa, particularly for complex traits such as biomass yield. Genomic selection (GS, based on predicted breeding values obtained using genome-wide molecular markers, could enhance breeding efficiency in terms of gain per unit time and cost. In this study, we genotyped tetraploid alfalfa plants that had previously been evaluated for yield during two cycles of phenotypic selection using genotyping-by-sequencing (GBS. We then developed prediction equations using yield data from three locations. Approximately 10,000 single nucleotide polymorphism (SNP markers were used for GS modeling. The genomic prediction accuracy of total biomass yield ranged from 0.34 to 0.51 for the Cycle 0 population and from 0.21 to 0.66 for the Cycle 1 population, depending on the location. The GS model developed using Cycle 0 as the training population in predicting total biomass yield in Cycle 1 resulted in accuracies up to 0.40. Both genotype × environment interaction and the number of harvests and years used to generate yield phenotypes had effects on prediction accuracy across generations and locations, Based on our results, the selection efficiency per unit time for GS is higher than phenotypic selection, although accuracies will likely decline across multiple selection cycles. This study provided evidence that GS can accelerate genetic gain in alfalfa for biomass yield.
D. T. Tyler Flockhart
Full Text Available Successful conservation of migratory birds demands we understand how habitat factors on the breeding grounds influences breeding success. Multiple factors are known to directly influence breeding success in territorial songbirds. For example, greater food availability and fewer predators can have direct effects on breeding success. However, many of these same habitat factors can also result in higher conspecific density that may ultimately reduce breeding success through density dependence. In this case, there is a negative indirect effect of habitat on breeding success through its effects on conspecific density and territory size. Therefore, a key uncertainty facing land managers is whether important habitat attributes directly influence breeding success or indirectly influence breeding success through territory size. We used radio-telemetry, point-counts, vegetation sampling, predator observations, and insect sampling over two years to provide data on habitat selection of a steeply declining songbird species, the Canada Warbler (Cardellina canadensis. These data were then applied in a hierarchical path modeling framework and an AIC model selection approach to determine the habitat attributes that best predict breeding success. Canada Warblers had smaller territories in areas with high shrub cover, in the presence of red squirrels (Tamiasciurus hudsonicus, at shoreline sites relative to forest-interior sites and as conspecific density increased. Breeding success was lower for birds with smaller territories, which suggests competition for limited food resources, but there was no direct evidence that food availability influenced territory size or breeding success. The negative relationship between shrub cover and territory size in our study may arise because these specific habitat conditions are spatially heterogeneous, whereby individuals pack into patches of preferred breeding habitat scattered throughout the landscape, resulting in reduced
Mayor, Stephen J.; Schaefer, James A.; Schneider, David C.; Mahoney, Shane P.
Greater understanding of habitat selection requires investigation at the scales at which organisms perceive and respond to their environment. Such knowledge could reveal the relative importance of factors limiting populations and the extent of response to habitat changes, and so guide conservation initiatives. We conducted a novel, spatially explicit analysis of winter habitat selection by caribou ( Rangifer tarandus) in Newfoundland, Canada, to elucidate the spatial scales of habitat selection. We combined conventional hierarchical habitat analysis with a newly developed geospatial approach that quantifies selection across scales as the difference in variance between available and used sites. We used both ordination and univariate analyses of lichen and plant cover, snow hardness and depth. This represents the first use of ordination with geostatistics for the assessment of habitat selection. Caribou habitat selection was driven by shallow, soft snow and high cover of Cladina lichens and was strongest at feeding microsites (craters) and broader feeding areas. Habitat selection was most evident at distance lags of up to 15 km, perhaps an indication of the perceptual abilities of caribou.
Maria C. Mateo Sanchez; Samuel A. Cushman; Santiago Saura
Animals select habitat resources at multiple spatial scales. Thus, explicit attention to scale dependency in species-habitat relationships is critical to understand the habitat suitability patterns as perceived by organisms in complex landscapes. Identification of the scales at which particular environmental variables influence habitat selection may be as important as...
Donna D W Hauser
Full Text Available There has been extensive sea ice loss in the Chukchi and Beaufort seas where two beluga whale (Delphinapterus leucas populations occur between July-November. Our goal was to develop population-specific beluga habitat selection models that quantify relative use of sea ice and bathymetric features related to oceanographic processes, which can provide context to the importance of changing sea ice conditions. We established habitat selection models that incorporated daily sea ice measures (sea ice concentration, proximity to ice edge and dense ice and bathymetric features (slope, depth, proximity to the continental slope, Barrow Canyon, and shore to establish quantitative estimates of habitat use for the Eastern Chukchi Sea ('Chukchi' and Eastern Beaufort Sea ('Beaufort' populations. We applied 'used v. available' resource selection functions to locations of 65 whales tagged from 1993-2012, revealing large variations in seasonal habitat selection that were distinct between sex and population groups. Chukchi whales of both sexes were predicted to use areas in close proximity to Barrow Canyon (typically <200 km as well as the continental slope in summer, although deeper water and denser ice were stronger predictors for males than females. Habitat selection differed more between sexes for Beaufort belugas. Beaufort males selected higher ice concentrations (≥40% than females (0-40% in July-August. Proximity to shore (<200 km strongly predicted summer habitat of Beaufort females, while distance to the ice edge was important for male habitat selection, especially during westward migration in September. Overall, our results indicate that sea ice variables were rarely the primary drivers of beluga summer-fall habitat selection. While diminished sea ice may indirectly affect belugas through changes in the ecosystem, associations with bathymetric features that affect prey availability seemed key to habitat selection during summer and fall. These results
Sarita Zhe Ying Guy
Full Text Available The benefits of improved health and welfare in pigs have driven refinements in management and selection practices, one of which is the production of pig phenotypes that can maintain health and productivity by improving response against pathogens. Selection has traditionally been made for host resistance; but the alternative host defence mechanism – host tolerance – is now being considered, as breeding for disease tolerance allows maintenance of high performance across environments of increasing pathogenic load. A distinction must be made between these two mechanisms as they vary in their influence on host-pathogen interactions and pathogen evolution, and consequently on the results of breeding programmes. Many pig production studies have failed to distinguish between resistance and tolerance; although a distinction may not always be possible. This article reviews current perspectives in selective breeding for disease resistance and tolerance in growing pigs, and the attendant industry implications. To assess the viability of breeding for resistance and/or tolerance for improved response to disease and other environmental challenges, we propose the use of routine farm records, instead of data measurements taken from laboratory experiments. Consequently, a number of factors need to be taken into account simultaneously for a multidimensional modelling approach. This includes not only genotype and disease variables, but also descriptors of the environment, as well as any possible interactions. It may not be feasible to record individual pathogen loads, and therefore true tolerance, on farm using routinely collected data. However, it may be estimated with group (farm means, or other proxy measures. Although this results in a bias, this may still be useful for modelling and quantifying resistance and tolerance. We can then quantify success of selection, and this may enable us to decide whether to select for disease resistance versus disease
Lipka, Alexander E.; Lu, Fei; Cherney, Jerome H.; Buckler, Edward S.; Casler, Michael D.; Costich, Denise E.
Switchgrass (Panicum virgatum L.) is a perennial grass undergoing development as a biofuel feedstock. One of the most important factors hindering breeding efforts in this species is the need for accurate measurement of biomass yield on a per-hectare basis. Genomic selection on simple-to-measure traits that approximate biomass yield has the potential to significantly speed up the breeding cycle. Recent advances in switchgrass genomic and phenotypic resources are now making it possible to evaluate the potential of genomic selection of such traits. We leveraged these resources to study the ability of three widely-used genomic selection models to predict phenotypic values of morphological and biomass quality traits in an association panel consisting of predominantly northern adapted upland germplasm. High prediction accuracies were obtained for most of the traits, with standability having the highest ten-fold cross validation prediction accuracy (0.52). Moreover, the morphological traits generally had higher prediction accuracies than the biomass quality traits. Nevertheless, our results suggest that the quality of current genomic and phenotypic resources available for switchgrass is sufficiently high for genomic selection to significantly impact breeding efforts for biomass yield. PMID:25390940
Khan, Khurshaid; Wahid, Sobia; Khan, Nazma Habib; Ali, Naheed
Despite their medical importance, natural breeding sites of sand flies have been poorly explored. Detecting such sites is imperative in vector control strategies. This study aimed to identify potential breeding and resting microhabitats of sand flies and household risk factors associated with cutaneous leishmaniasis transmission in Dir districts, Khyber Pakhtunkhwa, Pakistan. Survey of indoor and outdoor habitats in four tehsils (subdistricts) of upper and lower Dir districts was carried out using sticky traps, flit method, and aspirator. To assess risk factors associated with cutaneous leishmaniasis (CL), questionnaires were administered to household heads. Mud houses and plants belonging to Cucurbitaceae family sheltered highest number of sand flies. Excessive number of flies were collected from indoor sites (common rooms used for both people and animals) compared to outdoor habitats (cattle dungs). Phlebotomus salangensis Artemiev, 1978 and Phlebotomus sergenti were the most widely distributed species, while Sergentomyia bailyi peaked in caves with high organic content in soil. Roof material and ownership of fans were associated with significant risk of CL. Findings of this study present a list of potential breeding sites for sand flies and CL risk factors that can be targeted and implemented in control programs for CL. Further studies are required to elucidate the breeding behavior and preferences of these medically important vectors. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: firstname.lastname@example.org.
Muhammad Shahzad Sarfraz
Full Text Available The spread of dengue fever depends mainly on the availability of favourable breeding sites for its mosquito vectors around human dwellings. To investigate if the various factors influencing breeding habitats can be mapped from space, dengue indices, such as the container index, the house index and the Breteau index, were calculated from Ministry of Public health data collected three times annually in Phitsanulok, Thailand between 2009 and 2011. The most influential factors were found to be temperature, humidity, rainfall, population density, elevation and land cover. Models were worked out using parameters mostly derived from freely available satellite images and fuzzy logic software with parameter synchronisation and a predication algorithm based on data mining and the Decision Tree method. The models developed were found to be sufficiently flexible to accommodate additional parameters and sampling data that might improve prediction of favourable breeding hotspots. The algorithm applied can not only be used for the prediction of near real-time scenarios with respect to dengue, but can also be applied for monitoring other diseases influenced by environmental and climatic factors. The multi-criteria model presented is a cost-effective way of identifying outbreak hotspots and early warning systems lend themselves for development based on this strategy. The proposed approach demonstrates the successful utilisation of remotely sensed images to map mosquito breeding habitats.
Full Text Available In metapopulations in which habitat patches vary in quality and occupancy it can be complicated to calculate the net time-averaged contribution to reproduction of particular populations. Surprisingly, few indices have been proposed for this purpose. We combined occupancy, abundance, frequency of occurrence, and reproductive success to determine the net value of different sites through time and applied this method to a bird of conservation concern. The Tricolored Blackbird (Agelaius tricolor has experienced large population declines, is the most colonial songbird in North America, is largely confined to California, and breeds itinerantly in multiple habitat types. It has had chronically low reproductive success in recent years. Although young produced per nest have previously been compared across habitats, no study has simultaneously considered site occupancy and reproductive success. Combining occupancy, abundance, frequency of occurrence, reproductive success and nest failure rate we found that that large colonies in grain fields fail frequently because of nest destruction due to harvest prior to fledging. Consequently, net time-averaged reproductive output is low compared to colonies in non-native Himalayan blackberry or thistles, and native stinging nettles. Cattail marshes have intermediate reproductive output, but their reproductive output might be improved by active management. Harvest of grain-field colonies necessitates either promoting delay of harvest or creating alternative, more secure nesting habitats. Stinging nettle and marsh colonies offer the main potential sources for restoration or native habitat creation. From 2005-2011 breeding site occupancy declined 3x faster than new breeding colonies were formed, indicating a rapid decline in occupancy. Total abundance showed a similar decline. Causes of variation in the value for reproduction of nesting substrates and factors behind continuing population declines merit urgent
Battagin, Mara; Gorjanc, Gregor; Faux, Anne-Michelle; Johnston, Susan E; Hickey, John M
In this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs. We carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %. Increasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination. Higher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in
Full Text Available Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010. The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015. A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017. Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007 was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity. Acknowledgement The research was funded by INNOVAGEN project.
McCoy, J.R.; Wright, J.E.
The male boll weevil, Anthonomus grandis grandis Boheman, uses an aggregating pheromone to attract females, after which mating often occurs. Sterile boll weevil release programs depend upon this phenomenon to produce sterile matings with feral females. In an effort to increase the effectiveness of the individual sterile male and thereby reduce the number of sterile males required per hectare, a selective-breeding system was used to increase the total pheromone produced by individual male boll weevils. This breeding program increased the total pheromone production by individual male boll weevils to 4.5 times that of the parent population. After irradiation-induced sterilization, there remained 2.2 times more pheromone produced by the selected strain. Therefore, these sterile weevils should be about 2.2 times more attractive to feral females than the parent weevils now in use, and they have the potential to reduce the number of sterile males required in a sterile release program
М. П. Чебаков
Full Text Available Giving regard to the main elements of Winter Wheat varieties assessment when selecting frost resistant plants and taking into account genetic potential of the parents, date of hybrids sowing and their assessment by the speed of spring vegetation, it is possible in the sense of successful breeding to derive the most steady genotypes by the specified characteristics starting from F1. hybrids.
Full Text Available Here we present the first in a series of articles about the ecology of immature stages of anophelines in the Brazilian Yanomami area. We propose a new larval habitat classification and a new larval sampling methodology. We also report some preliminary results illustrating the applicability of the methodology based on data collected in the Brazilian Amazon rainforest in a longitudinal study of two remote Yanomami communities, Parafuri and Toototobi. In these areas, we mapped and classified 112 natural breeding habitats located in low-order river systems based on their association with river flood pulses, seasonality and exposure to sun. Our classification rendered seven types of larval habitats: lakes associated with the river, which are subdivided into oxbow lakes and nonoxbow lakes, flooded areas associated with the river, flooded areas not associated with the river, rainfall pools, small forest streams, medium forest streams and rivers. The methodology for larval sampling was based on the accurate quantification of the effective breeding area, taking into account the area of the perimeter and subtypes of microenvironments present per larval habitat type using a laser range finder and a small portable inflatable boat. The new classification and new sampling methodology proposed herein may be useful in vector control programs.
Sánchez-Ribas, Jordi; Oliveira-Ferreira, Joseli; Rosa-Freitas, Maria Goreti; Trilla, Lluís; Silva-do-Nascimento, Teresa Fernandes
Here we present the first in a series of articles about the ecology of immature stages of anophelines in the Brazilian Yanomami area. We propose a new larval habitat classification and a new larval sampling methodology. We also report some preliminary results illustrating the applicability of the methodology based on data collected in the Brazilian Amazon rainforest in a longitudinal study of two remote Yanomami communities, Parafuri and Toototobi. In these areas, we mapped and classified 112 natural breeding habitats located in low-order river systems based on their association with river flood pulses, seasonality and exposure to sun. Our classification rendered seven types of larval habitats: lakes associated with the river, which are subdivided into oxbow lakes and nonoxbow lakes, flooded areas associated with the river, flooded areas not associated with the river, rainfall pools, small forest streams, medium forest streams and rivers. The methodology for larval sampling was based on the accurate quantification of the effective breeding area, taking into account the area of the perimeter and subtypes of microenvironments present per larval habitat type using a laser range finder and a small portable inflatable boat. The new classification and new sampling methodology proposed herein may be useful in vector control programs.
Viana, Duarte S; Granados, José Enrique; Fandos, Paulino; Pérez, Jesús M; Cano-Manuel, Francisco Javier; Burón, Daniel; Fandos, Guillermo; Aguado, María Ángeles Párraga; Figuerola, Jordi; Soriguer, Ramón C
Space use by animals is determined by the interplay between movement and the environment, and is thus mediated by habitat selection, biotic interactions and intrinsic factors of moving individuals. These processes ultimately determine home range size, but their relative contributions and dynamic nature remain less explored. We investigated the role of habitat selection, movement unrelated to habitat selection and intrinsic factors related to sex in driving space use and home range size in Iberian ibex, Capra pyrenaica . We used GPS collars to track ibex across the year in two different geographical areas of Sierra Nevada, Spain, and measured habitat variables related to forage and roost availability. By using integrated step selection analysis (iSSA), we show that habitat selection was important to explain space use by ibex. As a consequence, movement was constrained by habitat selection, as observed displacement rate was shorter than expected under null selection. Selection-independent movement, selection strength and resource availability were important drivers of seasonal home range size. Both displacement rate and directional persistence had a positive relationship with home range size while accounting for habitat selection, suggesting that individual characteristics and state may also affect home range size. Ibex living at higher altitudes, where resource availability shows stronger altitudinal gradients across the year, had larger home ranges. Home range size was larger in spring and autumn, when ibex ascend and descend back, and smaller in summer and winter, when resources are more stable. Therefore, home range size decreased with resource availability. Finally, males had larger home ranges than females, which might be explained by differences in body size and reproductive behaviour. Movement, selection strength, resource availability and intrinsic factors related to sex determined home range size of Iberian ibex. Our results highlight the need to integrate
Full Text Available Marker-assisted selection (MAS refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP, have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping by sequencing (GBS has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS, genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection (GS under a large scale of plant breeding programs.
Wiener, Pamela; Sánchez-Molano, Enrique; Clements, Dylan N; Woolliams, John A; Haskell, Marie J; Blott, Sarah C
Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.
Lacko, J.; Topercer, J.
The middle stream of the Vah river (Piestany - Nove Mesto nad Vahom) can be considered mainly from the natural aspect as a very interesting and precious area. It creates vast alluvium with authentic, little aggrieved floodplain forest, which is surrounded with orographic units of Povazsky Inovec from the east side and Little Carpathian Mountains from the west side. This contribution focuses on the analysis of structure and population dynamics of bird communities in two transects on the Vah river alluvium currently between cities Piestany and Nove Mesto nad Vahom. We derived the basic ecological metrics and quantitative characteristics of bird communities such as the abundance, dominance, diversity for the breeding season 2014. We find the significance differences between these two transect in all defined metrics. As a potential reasons for these differences values we supposed the diverse habitat character of these transects (Piestany are closer to the suburban area than Nove Mesto nad Vahom, which represented intact landscape mosaic area). (authors)
Parlin, Adam F; do Amaral, José Pedro S; Dougherty, John Kelly; Stevens, M Henry H
Abstract Environmental conditions may affect individual physiological processes that influence short-term performance and ultimately growth, survival and reproduction. As such, habitats selected by animals must provide suitable and adequate resources. Ectothermic species are highly dependent on climatic conditions and ambient temperatures that dictate body temperature regulation and in turn physiological processes. We investigated the thermoregulatory performance, habitat selection, and movements of an ectothermic vertebrate, the Eastern box turtle (Terrapene carolina carolina) to assess the importance of thermoregulatory physiology in habitat selection. We evaluated the relationship between habitat selection and thermoregulatory performance in Southwest Ohio over two active seasons from May until October. We found that T. carolina selected shaded habitats, including evergreen and deciduous forests, as well as herbaceous grasslands, conformed to the ambient temperatures throughout the active season, although these habitats had temperatures below those expected based on thermal optima of box turtles. Further, we found that movement was not correlated with internal body temperature. Our study shows that thermal conditions are not paramount in habitat selection of box turtles, but that cooler temperatures do not have an effect on the extent of their locomotion. PMID:29255608
Claire A. Zugmeyer; John L. Koprowski
Severe disturbance may alter or eliminate important habitat structure that helps preserve food caches of foodhoarding species. Recent recolonization of an insect-damaged forest by the endangered Mt. Graham red squirrel (Tamiasciurus hudsonicus grahamensis) provided an opportunity to examine habitat selection for midden (cache) sites following...
Full Text Available Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle and in China (Yanbian. These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN. We identified 37 significant SNPs (FDR corrected in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes, reproduction including mammary gland development (3 genes, coat color (2 genes, and genes affecting behavioral traits in a broader sense (2 genes. We subsequently sequenced (Illumina HiSeq 2000 platform 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.
Lim, Dajeong; Strucken, Eva M; Choi, Bong Hwan; Chai, Han Ha; Cho, Yong Min; Jang, Gul Won; Kim, Tae-Hun; Gondro, Cedric; Lee, Seung Hwan
Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.
Tonnis, Brandon; Grant, Peter R; Grant, B Rosemary; Petren, Kenneth
We investigated phylogeographic divergence among populations of Galápagos warble finches. Their broad distribution, lack of phenotypic differentiation and low levels of genetic divergence make warbler finches an appropriate model to study speciation in allopatry. A positive relationship between genetic and geographical distance is expected for island taxa. Warbler finches actually showed a negative isolation by distance relationship, causing us to reject the hypothesis of distance-limited dispersal. An alternative hypothesis, that dispersal is limited by habitat similarity, was supported. We found a positive correlation between genetic distances and differences in maximum elevation among islands, which is an indicator of ecological similarity. MtDNA sequence variation revealed monophyletic support for two distinct species. Certhidea olivacea have recently dispersed among larger central islands, while some Certhidea fusca have recently dispersed to small islands at opposite ends of the archipelago. We conclude that females have chosen to breed on islands with habitats similar to their natal environment. Habitat selection is implicated as an important component of speciation of warbler finches, which is the earliest known divergence of the adaptive radiation of Darwin's finches. These results suggest that small populations can harbour cryptic but biologically meaningful variation that may affect longer term evolutionary processes.
Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.
We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418
Lidianne L. Rocha
Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.
Haas, de E.M.; Wagner, C.; Koelmans, A.A.; Kraak, M.H.S.; Admiraal, W.
1. Sediments have been considered as a habitat, a cover from predators and a source of food, but also as a source of potential toxic compounds. Therefore, the choice of a suitable substrate is essential for the development of chironomids. 2. For the midge Chironomus riparius (Meigen 1804) the growth
de Haas, E.M.; Wagner, C.; Koelmans, A.A.; Kraak, M.H.S.; Admiraal, W.
1. Sediments have been considered as a habitat, a cover from predators and a source of food, but also as a source of potential toxic compounds. Therefore, the choice of a suitable substrate is essential for the development of chironomids. 2. For the midge Chironomus riparius (Meigen 1804) the growth
Lado, Bettina; Battenfield, Sarah; Guzmán, Carlos; Quincke, Martín; Singh, Ravi P; Dreisigacker, Susanne; Peña, R Javier; Fritz, Allan; Silva, Paula; Poland, Jesse; Gutiérrez, Lucía
The single most important decision in plant breeding programs is the selection of appropriate crosses. The ideal cross would provide superior predicted progeny performance and enough diversity to maintain genetic gain. The aim of this study was to compare the best crosses predicted using combinations of mid-parent value and variance prediction accounting for linkage disequilibrium (V) or assuming linkage equilibrium (V). After predicting the mean and the variance of each cross, we selected crosses based on mid-parent value, the top 10% of the progeny, and weighted mean and variance within progenies for grain yield, grain protein content, mixing time, and loaf volume in two applied wheat ( L.) breeding programs: Instituto Nacional de Investigación Agropecuaria (INIA) Uruguay and CIMMYT Mexico. Although the variance of the progeny is important to increase the chances of finding superior individuals from transgressive segregation, we observed that the mid-parent values of the crosses drove the genetic gain but the variance of the progeny had a small impact on genetic gain for grain yield. However, the relative importance of the variance of the progeny was larger for quality traits. Overall, the genomic resources and the statistical models are now available to plant breeders to predict both the performance of breeding lines per se as well as the value of progeny from any potential crosses. Copyright © 2017 Crop Science Society of America.
Donald P. Knowles
Full Text Available Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus and goats (caprine arthritis encephalitis virus [CAEV]. Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.
White, Stephen N.; Knowles, Donald P.
Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions. PMID:23771240
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Taher, Taherah Mohd; Lihan, Tukimat; Mustapha, Muzzneena Ahmad; Nor, Shukor Mohd
Large areas are converted into commercial land use such as agriculture and urban as a result from the increasing economic and population demand. This situation is largely affecting wildlife and its habitat. Malaysia as one of the largest oil palm-producing countries, should take precaution into conserving its forest and wildlife diversity. Although big mammal such as elephant and tiger are significant for wildlife diversity, medium and small mammals also contribute to the biological richness in Malaysia. This study aims to predict suitable habitat of medium mammal, Tragulus napu and Tragulus javanicus in the study area and identify its habitat characteristics. The method applied in this study uses maximum entropy (MaxEnt) modeling which utilized species distribution data and selected environmental variables to alienate potential habitat in the study area. The characteristic of the habitat was identified from the result of MaxEnt analysis. This method of habitat modeling shows different extent of predicted suitable habitat in the study area of both species in which Tragulus napu has a limited distribution compared to Tragulus javanicus. However, some characteristics are similar in both habitats. The knowledge on species habitat characteristics is important to predict wildlife habitat in order to make best decision on land use management and conservation.
MacLachlan, Ian R; Yeaman, Sam; Aitken, Sally N
Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca × Picea engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow (AGF) polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits, and climate to understand the implications of selective breeding for climate adaptations and AGF strategies. The effects of selection on associations among hybrid index estimated from ~6,500 SNPs, adaptive traits, and provenance climates were assessed for ~2,400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average -7%, range -24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12%-86%). Clines in growth with temperature-related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration-related climate variables were stronger in selected than in natural seedlings, indicating possible preadaptation to drier future climates. Associations among cold hardiness, hybrid ancestry, and cold-related climate variables dominated signals of local adaptation and were preserved in breeding populations. Strong hybrid ancestry-phenotype-climate associations suggest that AGF will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in
Hallander, Jon; Waldmann, Patrik
The combination of optimized contribution dynamic selection and various mating schemes was investigated over seven generations for a typical tree breeding scenario. The allocation of mates was optimized using a simulated annealing algorithm for various object functions including random mating (RM), positive assortative mating (PAM) and minimization of pair-wise coancestry between mates (MCM) all combined with minimization of variance in family size and coancestry. The present study considered two levels of heritability (0.05 and 0.25), two restrictions on relatedness (group coancestry; 1 and 2%) and two maximum permissible numbers of crosses in each generation (100 and 400). The infinitesimal genetic model was used to simulate the genetic architecture of the trait that was the subject of selection. A framework of the long term genetic contribution of ancestors was used to examine the impacts of the mating schemes on population parameters. MCM schemes produced on average, an increased rate of genetic gain in the breeding population, although the difference between schemes was small but significant after seven generations (up to 7.1% more than obtained with RM). In addition, MCM reduced the level of inbreeding by as much as 37% compared with RM, although the rate of inbreeding was similar after three generations of selection. PAM schemes yielded levels of genetic gain similar to those produced by RM, but the increase in the level of inbreeding was substantial (up to 43%). The main reason why MCM schemes yielded higher genetic gains was the improvement in managing the long term genetic contribution of founders in the population; this was achieved by connecting unrelated families. In addition, the accumulation of inbreeding was reduced by MCM schemes since the variance in long term genetic contributions of founders was smaller than in the other schemes. Consequently, by combining an MCM scheme with an algorithm that optimizes contributions of the selected individuals
Sim, S-C; Robbins, M D; Van Deynze, A; Michel, A P; Francis, D M
Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise F(st) (θ) and Nei's standard genetic distance. We also identified a total of 19 loci under positive selection between processing, fresh-market and vintage germplasm by using an F(st)-outlier method based on the deviation from the expected distribution of F(st) and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato.
He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin
Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broad...
Full Text Available In diverse taxa, photoperiodic responses that cause seasonal physiological and behavioural shifts are controlled by genes, including the vertebrate Clock orthologues, that encode for circadian oscillator mechanisms. While the genetic network behind circadian rhythms is well described, relatively few reports exist of the phenological consequences of and selection on Clock genes in the wild. Here, we investigated variation in breeding phenology in relation to Clock genetic diversity in a long-distance migratory bird, the barn swallow (Hirundo rustica.In a sample of 922 adult barn swallows from a single population breeding in Italy we found one very common (Q(7 and three rare (Q(5, Q(6, Q(8 length variants of a functionally significant polyglutamine repeat. Rare (2.9% Q(7/Q(8 heterozygous females, but not males, bred significantly later than common (91.5% Q(7/Q(7 females, consistent with the expectation that 'long' alleles cause late breeding, as observed in a resident population of another bird species. Because breeding date depends on arrival date from migration, present results suggest that the association between breeding date and Clock might be mediated by migration phenology. In addition, fecundity selection appears to be operating against Q(7/Q(8 because late migrating/breeding swallows have fewer clutches per season, and late breeding has additional negative selection effects via reduced offspring longevity. Genotype frequencies varied marginally non-significantly with age, as Q(7/Q(8 frequency showed a 4-fold reduction in old individuals. This result suggests negative viability selection against Q(7/Q(8, possibly mediated by costs of late breeding.This is the first study of migratory birds showing an association between breeding phenology and Clock genotype and suggesting that negative selection occurs on a phenologically deviant genotype. Low polymorphism at Clock may constrain microevolutionary phenological response to changing climate
Júnior, V A P; Melo, P G S; Pereira, H S; Bassinello, P Z; Melo, L C
Gastrointestinal health is of great importance due to the increasing consumption of functional foods, especially those concern-ing diets rich in fiber content. The common bean has been valorized as a nutritious food due to its appreciable fiber content and the fact that it is consumed in many countries. The current study aimed to evaluate and compare the genetic potential of common bean progenies of the carioca group, developed through different breeding methods, for crude fiber content. The progenies originated through hybridization of two advanced strains, CNFC 7812 and CNFC 7829, up to the F7 generation using three breeding methods: bulk-population, bulk within F2 families, and single seed descent. Fifteen F8 progenies were evaluated in each method, as well as two check cultivars and both parents, us-ing a 7 x 7 simple lattice design, with experimental plots comprised of two 4-m long rows. Field trials were conducted in eleven environments encompassing four Brazilian states and three different sowing times during 2009 and 2010. Estimates of genetic parameters indicate differences among the breeding methods, which seem to be related to the different processes for sampling the advanced progenies inherent to each method, given that the trait in question is not subject to natural selection. Variability amongst progenies occurred within the three breeding methods and there was also a significant effect of environment on the progeny for all methods. Progenies developed by bulk-population attained the highest estimates of genetic parameters, had less interaction with the environment, and greater variability.
Bhat, Javaid A; Ali, Sajad; Salgotra, Romesh K; Mir, Zahoor A; Dutta, Sutapa; Jadon, Vasudha; Tyagi, Anshika; Mushtaq, Muntazir; Jain, Neelu; Singh, Pradeep K; Singh, Gyanendra P; Prabhu, K V
Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.
A. H. Sallam
Full Text Available Prediction accuracy of genomic selection (GS has been previously evaluated through simulation and cross-validation; however, validation based on progeny performance in a plant breeding program has not been investigated thoroughly. We evaluated several prediction models in a dynamic barley breeding population comprised of 647 six-row lines using four traits differing in genetic architecture and 1536 single nucleotide polymorphism (SNP markers. The breeding lines were divided into six sets designated as one parent set and five consecutive progeny sets comprised of representative samples of breeding lines over a 5-yr period. We used these data sets to investigate the effect of model and training population composition on prediction accuracy over time. We found little difference in prediction accuracy among the models confirming prior studies that found the simplest model, random regression best linear unbiased prediction (RR-BLUP, to be accurate across a range of situations. In general, we found that using the parent set was sufficient to predict progeny sets with little to no gain in accuracy from generating larger training populations by combining the parent set with subsequent progeny sets. The prediction accuracy ranged from 0.03 to 0.99 across the four traits and five progeny sets. We explored characteristics of the training and validation populations (marker allele frequency, population structure, and linkage disequilibrium, LD as well as characteristics of the trait (genetic architecture and heritability, . Fixation of markers associated with a trait over time was most clearly associated with reduced prediction accuracy for the mycotoxin trait DON. Higher trait in the training population and simpler trait architecture were associated with greater prediction accuracy.
Wilson, Ryan R.; Regehr, Eric V.; Rode, Karyn D.; St Martin, Michelle
Climate change is expected to alter many species' habitat. A species' ability to adjust to these changes is partially determined by their ability to adjust habitat selection preferences to new environmental conditions. Sea ice loss has forced polar bears (Ursus maritimus) to spend longer periods annually over less productive waters, which may be a primary driver of population declines. A negative population response to greater time spent over less productive water implies, however, that prey are not also shifting their space use in response to sea ice loss. We show that polar bear habitat selection in the Chukchi Sea has not changed between periods before and after significant sea ice loss, leading to a 75% reduction of highly selected habitat in summer. Summer was the only period with loss of highly selected habitat, supporting the contention that summer will be a critical period for polar bears as sea ice loss continues. Our results indicate that bears are either unable to shift selection patterns to reflect new prey use patterns or that there has not been a shift towards polar basin waters becoming more productive for prey. Continued sea ice loss is likely to further reduce habitat with population-level consequences for polar bears.
Cabrera-Bosquet, Llorenç; Crossa, José; von Zitzewitz, Jarislav; Serret, María Dolors; Araus, José Luis
Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the crop breeding community from both the public and private sectors world-wide. Both approaches promise to revolutionize the prediction of complex traits, including growth, yield and adaptation to stress. Whereas high-throughput phenotyping may help to improve understanding of crop physiology, most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and comparable to genomic selection. Despite the fact that the two methodological approaches represent the extremes of what is understood as the breeding process (phenotype versus genome), they both consider the targeted traits (e.g. grain yield, growth, phenology, plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e. physiological) putatively related to the target trait. Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology. This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as crop growth and yield. © 2012 Institute of Botany, Chinese Academy of Sciences.
Leonardo de Azevedo Peixoto
Full Text Available Genomic wide selection is a promising approach for improving the selection accuracy in plant breeding, particularly in species with long life cycles, such as Jatropha. Therefore, the objectives of this study were to estimate the genetic parameters for grain yield (GY and the weight of 100 seeds (W100S using restricted maximum likelihood (REML; to compare the performance of GWS methods to predict GY and W100S; and to estimate how many markers are needed to train the GWS model to obtain the maximum accuracy. Eight GWS models were compared in terms of predictive ability. The impact that the marker density had on the predictive ability was investigated using a varying number of markers, from 2 to 1,248. Because the genetic variance between evaluated genotypes was significant, it was possible to obtain selection gain. All of the GWS methods tested in this study can be used to predict GY and W100S in Jatropha. A training model fitted using 1,000 and 800 markers is sufficient to capture the maximum genetic variance and, consequently, maximum prediction ability of GY and W100S, respectively. This study demonstrated the applicability of genome-wide prediction to identify useful genetic sources of GY and W100S for Jatropha breeding. Further research is needed to confirm the applicability of the proposed approach to other complex traits.
Azevedo Peixoto, Leonardo de; Laviola, Bruno Galvêas; Alves, Alexandre Alonso; Rosado, Tatiana Barbosa; Bhering, Leonardo Lopes
Genomic wide selection is a promising approach for improving the selection accuracy in plant breeding, particularly in species with long life cycles, such as Jatropha. Therefore, the objectives of this study were to estimate the genetic parameters for grain yield (GY) and the weight of 100 seeds (W100S) using restricted maximum likelihood (REML); to compare the performance of GWS methods to predict GY and W100S; and to estimate how many markers are needed to train the GWS model to obtain the maximum accuracy. Eight GWS models were compared in terms of predictive ability. The impact that the marker density had on the predictive ability was investigated using a varying number of markers, from 2 to 1,248. Because the genetic variance between evaluated genotypes was significant, it was possible to obtain selection gain. All of the GWS methods tested in this study can be used to predict GY and W100S in Jatropha. A training model fitted using 1,000 and 800 markers is sufficient to capture the maximum genetic variance and, consequently, maximum prediction ability of GY and W100S, respectively. This study demonstrated the applicability of genome-wide prediction to identify useful genetic sources of GY and W100S for Jatropha breeding. Further research is needed to confirm the applicability of the proposed approach to other complex traits.
Sujkowski, Alyson; Bazzell, Brian; Carpenter, Kylie; Arking, Robert; Wessells, Robert J
Endurance exercise has emerged as a powerful intervention that promotes healthy aging by maintaining the functional capacity of critical organ systems. In addition, long-term exercise reduces the incidence of age-related diseases in humans and in model organisms. Despite these evident benefits, the genetic pathways required for exercise interventions to achieve these effects are still relatively poorly understood. Here, we compare gene expression changes during endurance training in Drosophila melanogaster to gene expression changes during selective breeding for longevity. Microarrays indicate that 65% of gene expression changes found in flies selectively bred for longevity are also found in flies subjected to three weeks of exercise training. We find that both selective breeding and endurance training increase endurance, cardiac performance, running speed, flying height, and levels of autophagy in adipose tissue. Both interventions generally upregulate stress defense, folate metabolism, and lipase activity, while downregulating carbohydrate metabolism and odorant receptor expression. Several members of the methuselah-like (mthl) gene family are downregulated by both interventions. Knockdown of mthl-3 was sufficient to provide extension of negative geotaxis behavior, endurance and cardiac stress resistance. These results provide support for endurance exercise as a broadly acting anti-aging intervention and confirm that exercise training acts in part by targeting longevity assurance pathways.
Arandas, Janaina Kelli Gomes; Alves, Ângelo Giuseppe Chaves; Facó, Olivardo; Belchior, Ernandes Barboza; Shiotsuki, Luciana; de Arruda Leite, Paulo Márcio Barbosa; Ribeiro, Maria Norma
The implementation of sustainable breeding programs requires genetic breeding strategies that are appropriate for the reality production systems. It is also essential that the choice of animal selection criteria be based on breeders' knowledge and objectives. This work is an ethno-zootechnical study of the Morada Nova sheep breed and its crossbreeds. The goals of this study were to register and analyze indigenous breeders' knowledge and practices regarding animal selection criteria and to generate technical information to support a participatory breeding program of the breed. This study was conducted in the Morada Nova municipality in the state of Ceará, Brazil. Semi-structured interviews were evaluated using two groups of individuals, purebred Morada Nova sheep breeders (RMN, n = 13) and breeders of Morada Nova crossbreeds (MMN, n = 48). Interview questions were used to identify local selection criteria adopted by each group in the choice of animals for breeding. Data from the interviews were submitted to frequency distribution analysis and the Shapiro-Wilk test to verify their distribution. Later, the Kruskal-Wallis test was used to compare the two groups of farmers based on that information, in addition to multivariate statistical analysis and evaluation of Smith salience index. Breeders in the RMN group used selection criteria related to breed standards, such as pelage color. In contrast, breeders of the MMN group used criteria related to productivity, such as body conformation and milk production. Breeders should be engaged in the development of breeding programs, and it is important to consider their preferences and objectives when evaluating breeding animals.
Ulonska, E.; Gaul, H.; Baumer, M.; Gesellschaft fuer Strahlen- und Umweltforschung m.b.H., Gruenbach
This mutation breeding programme is investigating the qualification of micro-mutations for the selection of improved protein quality and quantity. Normally, improvement of protein content in micro-mutations is rather small. Therefore, it is important to develop methods and conditions of selection being (a) capable of measuring these small deviations in protein content and quality, and (b) simple to use. In two experiments carried out in 1971 and 1972 nitrogen fertilization was found to be the most important factor in the improvement of selection conditions. There is a highly significant negative correlation between crude protein content and the standard deviation; i.e. the higher the content of crude protein, the lower the variation coefficient. This in turn leads to an increase of genetic variation necessary for better selection progress. Nitrogen fertilization, especially during ear emergence, covers environmental influences - e.g., planting space, sowing rate, growing in different plots (6, 3, 2, 1 rows or in half-ear hills) - to a great extent. Thus, by applying high doses of nitrogen dressings comparable results can be achieved. In an overall selection experiment (testing the entire crossing and mutation material available at Weihenstephan in a stepwise selection from 1971 to 1973) and two selection experiments conducted in 1971 to 1973 with micro-mutants - variety Nota, 4 times X-rayed and the naked barley strain 1606 treated once with EMS - significant selection results were found. (author)
Full Text Available Grasslands host a high diversity of plant and animal species. In Serbia, most alkali grasslands are located in the province of Vojvodina. The majority are not subject to conservation. The aim of the study was to investigate the relationship between the proportion of croplands and (1 the number of breeding species and (2 the number of breeding pairs in the alkali grasslands of the upper Mostonga River catchment basin (NW Serbia. The size of the study area was 400 ha. Birds were surveyed along seven parallel transects eight times per breeding season. Lengths of the cross sections of both grasslands and croplands were measured. The proportion of croplands per transect was calculated by dividing the total length of cross sections of croplands by the total length of transect. The relationship between the proportion of croplands and the number of breeding pairs and the number of breeding species, respectively, was studied using simple linear regression. We recorded a total of 171 nesting pairs belonging to 23 species in the alkali grassland investigated, with breeding densities between 2.2 and 10.3 pairs per 10 ha. The number of species per transect ranged between 6 and 11. The most abundant species were Skylark Alauda arvensis, Yellow Wagtail Motacilla flava and Corn Bunting Emberiza calandra. The numbers of breeding pairs (F6 = 21.761, P < 0.0001 and of breeding species (F6 = 13.758, P = 0.001 were both influenced negatively by the proportion of croplands. These findings highlight the need for coordinated conservation measures on the alkali grasslands of Vojvodina.
Full Text Available Habitat selection studies generally assume that animals select habitat and food resources at multiple scales to maximise their fitness. However, animals sometimes prefer habitats of apparently low quality, especially when considering the costs associated with spatially heterogeneous human disturbance. We used spatial variation in human disturbance, and its consequences on lynx survival, a direct fitness component, to test the Hierarchical Habitat Selection hypothesis from a population of Eurasian lynx Lynx lynx in southern Norway. Data from 46 lynx monitored with telemetry indicated that a high proportion of forest strongly reduced the risk of mortality from legal hunting at the home range scale, while increasing road density strongly increased such risk at the finer scale within the home range. We found hierarchical effects of the impact of human disturbance, with a higher road density at a large scale reinforcing its negative impact at a fine scale. Conversely, we demonstrated that lynx shifted their habitat selection to avoid areas with the highest road densities within their home ranges, thus supporting a compensatory mechanism at fine scale enabling lynx to mitigate the impact of large-scale disturbance. Human impact, positively associated with high road accessibility, was thus a stronger driver of lynx space use at a finer scale, with home range characteristics nevertheless constraining habitat selection. Our study demonstrates the truly hierarchical nature of habitat selection, which aims at maximising fitness by selecting against limiting factors at multiple spatial scales, and indicates that scale-specific heterogeneity of the environment is driving individual spatial behaviour, by means of trade-offs across spatial scales.
Beaulieu, Jean; Doerksen, Trevor K; MacKay, John; Rainville, André; Bousquet, Jean
Genomic selection (GS) may improve selection response over conventional pedigree-based selection if markers capture more detailed information than pedigrees in recently domesticated tree species and/or make it more cost effective. Genomic prediction accuracies using 1748 trees and 6932 SNPs representative of as many distinct gene loci were determined for growth and wood traits in white spruce, within and between environments and breeding groups (BG), each with an effective size of Ne ≈ 20. Marker subsets were also tested. Model fits and/or cross-validation (CV) prediction accuracies for ridge regression (RR) and the least absolute shrinkage and selection operator models approached those of pedigree-based models. With strong relatedness between CV sets, prediction accuracies for RR within environment and BG were high for wood (r = 0.71-0.79) and moderately high for growth (r = 0.52-0.69) traits, in line with trends in heritabilities. For both classes of traits, these accuracies achieved between 83% and 92% of those obtained with phenotypes and pedigree information. Prediction into untested environments remained moderately high for wood (r ≥ 0.61) but dropped significantly for growth (r ≥ 0.24) traits, emphasizing the need to phenotype in all test environments and model genotype-by-environment interactions for growth traits. Removing relatedness between CV sets sharply decreased prediction accuracies for all traits and subpopulations, falling near zero between BGs with no known shared ancestry. For marker subsets, similar patterns were observed but with lower prediction accuracies. Given the need for high relatedness between CV sets to obtain good prediction accuracies, we recommend to build GS models for prediction within the same breeding population only. Breeding groups could be merged to build genomic prediction models as long as the total effective population size does not exceed 50 individuals in order to obtain high prediction accuracy such as that
Tardy, Olivia; Massé, Ariane; Pelletier, Fanie; Fortin, Daniel
Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in heterogeneous landscapes without having to predefine habitat types. The method consists in randomly placing blocks over the survey area and dividing those blocks in two adjacent sub-blocks of the same size. Animal abundance is then estimated within the two sub-blocks. This process is done 100 times. Different functional forms of isodars can be investigated by relating animal abundance and differences in habitat features between sub-blocks. We applied this method to abundance data of raccoons and striped skunks, two of the main hosts of rabies virus in North America. Habitat selection by raccoons and striped skunks depended on both conspecific abundance and the difference in landscape composition and structure between sub-blocks. When conspecific abundance was low, raccoons and striped skunks favored areas with relatively high proportions of forests and anthropogenic features, respectively. Under high conspecific abundance, however, both species preferred areas with rather large corn-forest edge densities and corn field proportions. Based on random sampling techniques, we provide a robust method that is applicable to a broad range of species, including medium- to large-sized mammals with high mobility. The method is sufficiently flexible to incorporate multiple environmental covariates that can reflect key requirements of the focal species. We thus illustrate how isodar theory can be used with wildlife surveys to assess density-dependent habitat selection over large
José Marcelo Soriano Viana
Full Text Available ABSTRACT To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL. This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs depends on linkage disequilibrium (LD between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.
Downs, J. L; Tiller, B. L [Pacific Northwest Lab., Richland, WA (United States); Witter, M. [Shannon and Wilson, Inc., Seattle, WA (United States). Geotechnical and Environmental Consultants, Seattle, Washington (United States); Mazaika, R. [Corps of Engineers, Portland, OR (United States)
Studies in this document were initiated to establish baseline information on riparian and wetland habitat conditions at the areas studied under the current reservoir operations on the lower Snake River. Two approaches were used to assess habitat at 28 study sites selected on the four pools on the lower Snake River. These areas all contribute significant riparian habitat along the river, and several of these areas are designated habitat management units. At 14 of the 28 sites, we monitored riparian habitat on three dates during the growing season to quantify vegetation abundance and composition along three transects: soil nutrients, moisture, and pH and water level and pH. A second approach involved identifying any differences in the extent and amount of riparian/wetland habitat currently found at the study areas from that previously documented. We used both ground and boat surveys to map and classify the changes in vegetative cover along the shoreline at the 14 monitoring sites and at 14 additional sites along the lower Snake selected to represent various riparian/wetland habitat conditions. Results of these mapping efforts are compared with maps of cover types previously generated using aerial photography taken in 1987.
Tomiyama, Takeshi; Omori, Michio
Juveniles of both stone flounder Platichthys bicoloratus and starry flounder Platichthys stellatus utilize estuaries as nursery grounds. To understand their habitat selection and the functions of habitats such as food supply, we defined the seasonal distribution of recently settled fish of these species in shallow nursery areas and investigated their feeding habits in the Natori River estuary, Japan. Distribution of stone flounder was limited to the lower estuary (olivacea and the mysid Neomysis awatschensis, respectively; however, 1- and 2-yr-old fish of both stone and starry flounders fed mainly on the bivalve siphons. These results indicate that habitat selections of juvenile stone and starry flounders enable utilization of preferred prey and predator avoidance, respectively, and that non-overlap of these species' habitats results in avoidance of inter-specific competition for food between these two species.
Ochsner, K P; MacNeil, M D; Lewis, R M; Spangler, M L
An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits 1 at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values for the objective traits calving difficultly direct (CDd), calving difficulty maternal (CDm), weaning weight direct (WWd), weaning weight maternal (WWm), mature cow weight (MW), and heifer pregnancy (HP) were -2.11, -1.53, 18.49, 11.28, -33.46, and 1.19, respectively. Consequently, under the scenario assumed herein, the greatest improvements in profitability could be made by decreasing maintenance energy costs associated with MW followed by improvements in weaning weight. The accuracy of the index lies between 0.218 (phenotypic-based index selection) and 0.428 (breeding values known without error). Implementation of this index would facilitate genetic improvement and increase profitability of Beefmaster cattle operations with a general-purpose breeding objective when replacement females are retained and with weaned calves as the sale end point.
Riedelsheimer, Christian; Melchinger, Albrecht E
We developed a universally applicable planning tool for optimizing the allocation of resources for one cycle of genomic selection in a biparental population. The framework combines selection theory with constraint numerical optimization and considers genotype × environment interactions. Genomic selection (GS) is increasingly implemented in plant breeding programs to increase selection gain but little is known how to optimally allocate the resources under a given budget. We investigated this problem with model calculations by combining quantitative genetic selection theory with constraint numerical optimization. We assumed one selection cycle where both the training and prediction sets comprised double haploid (DH) lines from the same biparental population. Grain yield for testcrosses of maize DH lines was used as a model trait but all parameters can be adjusted in a freely available software implementation. An extension of the expected selection accuracy given by Daetwyler et al. (2008) was developed to correctly balance between the number of environments for phenotyping the training set and its population size in the presence of genotype × environment interactions. Under small budget, genotyping costs mainly determine whether GS is superior over phenotypic selection. With increasing budget, flexibility in resource allocation increases greatly but selection gain leveled off quickly requiring balancing the number of populations with the budget spent for each population. The use of an index combining phenotypic and GS predicted values in the training set was especially beneficial under limited resources and large genotype × environment interactions. Once a sufficiently high selection accuracy is achieved in the prediction set, further selection gain can be achieved most efficiently by massively expanding its size. Thus, with increasing budget, reducing the costs for producing a DH line becomes increasingly crucial for successfully exploiting the
Full Text Available Javan rhino (Rhinoceros sondaicus Desmarest 1822 is one of world's rarest endangered species (IUCN 2008. Currently, their distribution is limited to Ujung Kulon National Park (UKNP of Indonesia. Natural disasters, disease, poaching, encroachment, and competition are threats facing Javan rhino's population, hence creating pockets of habitats outside the UKNP was necessary and should be based on scientific studies of javan rhino utilization distribution and habitat selection in UKNP as the natural habitat. The objectives of the study were to determine the utilization distribution of Javan rhino and its habitat characteristics and determine javan rhino habitat selection within UKNP. The research indicated that Javan rhinos highest use of areas comprised of swampy shrub (w = 2.197 and shrub (w = 2.012, relatively open habitat (w = 4.233, flat area (w = 1.313 and slightly sloping areas (w = 1.007, lowland (w = 1.346, close to river (w = 1.087, close to road network (w = 1.395, close to coasts/beaches (w = 1.862, close to wallowing areas (w = 3.709, and close to rumpang (w = 3.783. The results suggested that javan rhino showed selection and preferences for its habitat.Keywords: javan rhino, utilization distribution, habitat selection, preferences
All previous behavioural studies of Temminck's ground pangolins (Smutsia temminckii) have focused on populations in mesic regions. We examined home range size, activity periods, habitat selectivity and refuge site selection of 13 individuals over three years in the Kalahari Desert of South Africa, near the western edge of ...
Gretchen H. Roffler; Michael K. Schwartz; Kristine Pilgrim; Sandra L. Talbot; George K. Sage; Layne G. Adams; Gordon Luikart
Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is...
Northrup, Joseph; Anderson, Charles R.; Hooten, Mevin B.; Wittemyer, George
Ecological processes operate across temporal and spatial scales. Anthropogenic disturbances impact these processes, but examinations of scale dependence in impacts are infrequent. Such examinations can provide important insight to wildlife–human interactions and guide management efforts to reduce impacts. We assessed spatiotemporal scale dependence in habitat selection of mule deer (Odocoileus hemionus) in the Piceance Basin of Colorado, USA, an area of ongoing natural gas development. We employed a newly developed animal movement method to assess habitat selection across scales defined using animal-centric spatiotemporal definitions ranging from the local (defined from five hour movements) to the broad (defined from weekly movements). We extended our analysis to examine variation in scale dependence between night and day and assess functional responses in habitat selection patterns relative to the density of anthropogenic features. Mule deer displayed scale invariance in the direction of their response to energy development features, avoiding well pads and the areas closest to roads at all scales, though with increasing strength of avoidance at coarser scales. Deer displayed scale-dependent responses to most other habitat features, including land cover type and habitat edges. Selection differed between night and day at the finest scales, but homogenized as scale increased. Deer displayed functional responses to development, with deer inhabiting the least developed ranges more strongly avoiding development relative to those with more development in their ranges. Energy development was a primary driver of habitat selection patterns in mule deer, structuring their behaviors across all scales examined. Stronger avoidance at coarser scales suggests that deer behaviorally mediated their interaction with development, but only to a degree. At higher development densities than seen in this area, such mediation may not be possible and thus maintenance of sufficient
Marcio P. Arruda
Full Text Available Genomic selection (GS is a breeding method that uses marker–trait models to predict unobserved phenotypes. This study developed GS models for predicting traits associated with resistance to head blight (FHB in wheat ( L.. We used genotyping-by-sequencing (GBS to identify 5054 single-nucleotide polymorphisms (SNPs, which were then treated as predictor variables in GS analysis. We compared how the prediction accuracy of the genomic-estimated breeding values (GEBVs was affected by (i five genotypic imputation methods (random forest imputation [RFI], expectation maximization imputation [EMI], -nearest neighbor imputation [kNNI], singular value decomposition imputation [SVDI], and the mean imputation [MNI]; (ii three statistical models (ridge-regression best linear unbiased predictor [RR-BLUP], least absolute shrinkage and operator selector [LASSO], and elastic net; (iii marker density ( = 500, 1500, 3000, and 4500 SNPs; (iv training population (TP size ( = 96, 144, 192, and 218; (v marker-based and pedigree-based relationship matrices; and (vi control for relatedness in TPs and validation populations (VPs. No discernable differences in prediction accuracy were observed among imputation methods. The RR-BLUP outperformed other models in nearly all scenarios. Accuracies decreased substantially when marker number decreased to 3000 or 1500 SNPs, depending on the trait; when sample size of the training set was less than 192; when using pedigree-based instead of marker-based matrix; or when no control for relatedness was implemented. Overall, moderate to high prediction accuracies were observed in this study, suggesting that GS is a very promising breeding strategy for FHB resistance in wheat.
Kawaguchi, Toshinori; Desrochers, André
Ideal free distribution theory predicts that increased conspecific density redistributes individuals to low-density, suboptimal habitat. However, possible lags in response to population density remain poorly documented. Snowshoe hares (Lepus americanus) may exhibit density-dependent habitat selection due to its marked variation in population density. Based on 11 years (2004-2014) of snow tracking in Quebec (Canada), we investigated snowshoe hares' short-term and delayed habitat selection responses to population density. We predicted that at high densities, hare distribution expands into low-density habitat, thus weakening the association between hares and high-density habitat. We surveyed hare tracks along 95 km of transects on average each year and georeferenced 14,240 tracks. We used Generalized Estimating Equations for track count per 100 m transect segment as a function of the proportion of different forest age classes (0-20 y, 20-40 y and 40-80 y) within 50 m of the segments. We used model coefficients for each age class as a measure of habitat preference, and modeled those coefficients as a function of a population density index in current and previous winters. Coefficients for 20- to 40-y-old forests were positive each year, indicating that this habitat was preferred. The association between track counts and 20- to 40-y-old forest significantly declined with density during the previous winter, suggesting that hare spread from preferred forest with a lagged response to density. To our knowledge, no previous empirical studies have documented a lagged habitat selection response to population density. Time lags offer possible explanation for documented deviations from ideal free distribution models.
This report summarizes the results of a study to identify the habitat use and behavior of the upland sandpiper, : a state-endangered bird species, at Portsmouth International Airport (PSM), which is near the Great Bay National : Wildlife Refuge (GBNW...
Gourdine, Jean-Luc; Sørensen, Anders Christian; Rydhmer, Lotta
at random. With optimum contribution selection, genetic progress can be achieved that is almost as great as that with truncation selection based on BLUP breeding values (0.2 to 0.5 vs. 0.3 to 0.5 genetic SD, P
Lammerts Van Bueren, E.; Ostergard, H.; Vriend, H.; Backes, G.
Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular
Klaassen, Marcel; Ens, Bruno J.
We tried to unravel the possible links between the skewed predation risk in Uca tangeri (where large individuals are more at risk from avian predators) and size-dependent changes in the physiology and habitat choice of this fiddler crab species. Over a transect running from low to high in the tidal zone of a beach in Mauritania, the temperature profile at various depths in the substrate, the water-table level of seep water, salt concentration of seep water, depth of the aerobic level, operative temperatures on the surface, and size distribution of crabs were assessed. In addition, resting metabolic rates, Q 10 and thermal and starvation tolerances were estimated. Going from low to high in the tidal zone, crab size and burrow depth increased. At the preferred burrowing depth, microclimatological conditions appeared to be equally favourable at all sites. At the surface, conditions were more favourable low in the tidal zone, where also food availability is sufficient to enable small crabs to forage in the vicinity of their burrows. Large crabs have higher energy requirements and are thereby forced to forage in flocks low in the tidal zone where food is probably more abundant. Low in the tidal zone, digging deeply is impossible as the aerobic layer is rather thin. Large crabs prefer living high in the tidal zone as (1) deep burrows ensure better protection against predators, (2) more time is available for digging holes and (3) the substrate is better suited for reproduction. Energy reserves in late summer ensured an average of 34 days of survival. It is argued that the allotment of energy to growth must be considerable even in reproducing animals; the rewards of growth being the disproportional increase in reproductive output with size.
Kraus, J.M.; Vonesh, J.R.
1. Non-consumptive effects of predators are increasingly recognized as important drivers of community assembly and structure. Specifically, habitat selection responses to top predators during colonization and oviposition can lead to large differences in aquatic community structure, composition and diversity. 2. These differences among communities due to predators may develop as communities assemble, potentially altering the relative quality of predator vs. predator-free habitats through time. If so, community assembly would be expected to modify the subsequent behavioural responses of colonists to habitats containing top predators. Here, we test this hypothesis by manipulating community assembly and the presence of fish in experimental ponds and measuring their independent and combined effects on patterns of colonization by insects and amphibians. 3. Assembly modified habitat selection of dytscid beetles and hylid frogs by decreasing or even reversing avoidance of pools containing blue-spotted sunfish (Enneacanthus gloriosus). However, not all habitat selection responses to fish depended on assembly history. Hydrophilid beetles and mosquitoes avoided fish while chironomids were attracted to fish pools, regardless of assembly history. 4. Our results show that community assembly causes taxa-dependent feedbacks that can modify avoidance of habitats containing a top predator. Thus, non-consumptive effects of a top predator on community structure change as communities assemble and effects of competitors and other predators combine with the direct effects of top predators to shape colonization. 5. This work reinforces the importance of habitat selection for community assembly in aquatic systems, while illustrating the range of factors that may influence colonization rates and resulting community structure. Directly manipulating communities both during colonization and post-colonization is critical for elucidating how sequential processes interact to shape communities.
Demers, Scott A.; Takekawa, John Y.; Ackerman, Joshua T.; Warnock, N.; Athearn, N.D.
San Francisco Bay is a wintering area for shorebirds, including American Avocets (Recurvirostra americana). Recently, a new resident population of avocets has emerged, presumably because of the development of tidal marshes into salt-evaporation ponds. In habitat restoration now underway, as many as 90% of salt ponds will be restored to tidal marsh. However, it is unknown if wintering and resident avocets coexist and if their requirements for space and habitat differ, necessitating different management for their populations to be maintained during restoration. We captured and radio-marked wintering avocets at a salt pond and a tidal flat to determine their population status (migrant or resident) and examine their space use and habitat selection. Of the radio-marked avocets, 79% were migrants and 21% were residents. At the salt pond, residents' fidelity to their location of capture was higher, and residents moved less than did migrants from the same site. Conversely, on the tidal flat, fidelity of residents to their site of capture was lower, and residents' home ranges were larger than those of migrants from the same site. Habitat selection of migrants and residents differed little; however, capture site influenced habitat selection far more than the birds' status as migrants or residents. Our study suggests that individual avocets have high site fidelity while wintering in San Francisco Bay, although the avocet as a species is plastic in its space use and habitat selection. This plasticity may allow wintering migrant and resident avocets to adapt to habitat change in San Francisco Bay. ?? The Cooper Ornithological Society 2010.
Pickens, Bradley A.; King, Sammy L.; Vasseur, Phillip L.; Zimorski, Sara E.; Selman, Will
Eleven of 15 species of cranes (family: Gruidae) are considered vulnerable or endangered, and the increase of agriculture and aquaculture at the expense of natural wetlands and grasslands is a threat to Gruidae worldwide. A reintroduced population of Whooping Crane (Grus americana) was studied in coastal and agricultural wetlands of Louisiana and Texas, USA. The objectives were to compare Whooping Crane movements across seasons, quantify multiscale habitat selection, and identify seasonal shifts in selection. Whooping Cranes (n = 53) were tracked with satellite transmitters to estimate seasonal core-use areas (50% home range contours) via Brownian bridge movement models and assess habitat selection. Whooping Crane core-use areas (n = 283) ranged from 4.7 to 438.0 km2, and habitat selection changed seasonally as shallow water availability varied. Whooping Crane core-use areas were composed of more fresh marsh in spring/summer, but shifted towards rice and crawfish (Procambarus spp.) aquaculture in the fall/winter. Within core-use areas, aquaculture was most strongly selected, particularly in fall when fresh marsh became unsuitable. Overall, the shifting of Whooping Crane habitat selection over seasons is likely to require large, heterogeneous areas. Whooping Crane use of agricultural and natural wetlands may depend on spatio-temporal dynamics of water depth.
Wegenast, Thilo; Longin, C Friedrich H; Utz, H Friedrich; Melchinger, Albrecht E; Maurer, Hans Peter; Reif, Jochen C
Parental selection influences the gain from selection and the optimum allocation of test resources in breeding programs. We compared two hybrid maize (Zea mays L.) breeding schemes with evaluation of testcross progenies: (a) doubled haploid (DH) lines in both stages (DHTC) and (b) S(1) families in the first stage and DH lines within S(1) families in the second stage (S(1)TC-DHTC). Our objectives were to (1) determine the optimum allocation regarding the number of crosses, S(1) families, DH lines, and test locations, (2) investigate the impact of parental selection on the optimum allocation and selection gain (DeltaG), and (3) compare the maximum DeltaG achievable with each breeding scheme. Selection gain was calculated by numerical integration. Different assumptions were made regarding the budget, variance components, correlation between the mean phenotypic performance of the parents and the mean genotypic value of the testcross performance of their progenies (rho( P )), and the composition of the finally selected test candidates. In comparison with randomly chosen crosses, maximum DeltaG was largely increased with parental selection in both breeding schemes. With an increasing correlation rho( P ), this superiority increased strongly, while the optimum number of crosses decreased in favor of an increased number of test candidates within crosses. Thus, concentration on few crosses among the best parental lines might be a promising approach for short-term success in advanced cycle breeding. Breeding scheme S(1)TC-DHTC led to a larger DeltaG but had a longer cycle length than DHTC. However, with further improvements in the DH technique and the realization of more than two generations per year, early testing of S(1) families prior to production of DH lines would become very attractive in hybrid maize breeding.
Stevick, P. T.; Berrow, Simon D.; Berube, Martine; Bouveret, Laurent; Broms, Fredrik; Jann, Beatrice; Kennedy, Amy; Suarez, Pedro Lopez; Meunier, Marine; Ryan, Conor; Wenzel, Frederick
In species that aggregate for reproduction, the social and fitness costs of movement between groups frequently lead to restricted exchange between breeding areas. We report on four individual humpback whales identified in both the Cape Verde Islands and Guadeloupe; locations separated by an ocean
Kijas, James W.; Lenstra, Johannes A.; Hayes, Ben; Boitard, Simon; Porto Neto, Laercio R.; San Cristobal, Magali; Servin, Bertrand; McCulloch, Russell; Whan, Vicki; Gietzen, Kimberly; Paiva, Samuel; Barendse, William; Ciani, Elena; Raadsma, Herman; McEwan, John; Dalrymple, Brian
Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species. PMID:22346734
James W Kijas
Full Text Available Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species.
van Beest, Floris M; Uzal, Antonio; Vander Wal, Eric; Laforge, Michel P; Contasti, Adrienne L; Colville, David; McLoughlin, Philip D
Density is a fundamental driver of many ecological processes including habitat selection. Theory on density-dependent habitat selection predicts that animals should be distributed relative to profitability of habitat, resulting in reduced specialization in selection (i.e. generalization) as density increases and competition intensifies. Despite mounting empirical support for density-dependent habitat selection using isodars to describe coarse-grained (interhabitat) animal movements, we know little of how density affects fine-grained resource selection of animals within habitats [e.g. using resource selection functions (RSFs)]. Using isodars and RSFs, we tested whether density simultaneously modified habitat selection and within-habitat resource selection in a rapidly growing population of feral horses (Equus ferus caballus Linnaeus; Sable Island, Nova Scotia, Canada; 42% increase in population size from 2008 to 2012). Among three heterogeneous habitat zones on Sable Island describing population clusters distributed along a west-east resource gradient (west-central-east), isodars revealed that horses used available habitat in a density-dependent manner. Intercepts and slopes of isodars demonstrated a pattern of habitat selection that first favoured the west, which generalized to include central and east habitats with increasing population size consistent with our understanding of habitat quality on Sable Island. Resource selection functions revealed that horses selected for vegetation associations similarly at two scales of extent (total island and within-habitat zone). When densities were locally low, horses were able to select for sites of the most productive forage (grasslands) relative to those of poorer quality. However, as local carrying capacity was approached, selection for the best of available forage types weakened while selection for lower-quality vegetation increased (and eventually exceeded that of grasslands). Isodars can effectively describe coarse
Full Text Available Maize is the principal crop and major staple food in the most countries of Sub-Saharan Africa. However, due to the influence of abiotic and biotic stress factors, maize production faces serious constraints. Among the agro-ecological conditions, the main constraints are: lack and poor distribution of rainfall; low soil fertility; diseases (maize streak virus, downy mildew, leaf blights, rusts, gray leaf spot, stem/cob rots and pests (borers and storage pests. Among the socio-economic production constraints are: poor economy, serious shortage of trained manpower; insufficient management expertise, lack of use of improved varieties and poor cultivation practices. To develop desirable varieties, and thus consequently alleviate some of these constraints, appropriate breeding approaches and field-based methodologies in selection for multiple stress tolerance, were implemented. These approaches are mainly based on: a Crossing selected genotypes with more desirable stress tolerant and other agronomic traits; b Using the disease/pest spreader row method, combined with testing and selection of created progenies under strong to intermediate pressure of drought and low soil fertility in nurseries; and c Evaluation of the varieties developed in multi-location trials under low and "normal" inputs. These approaches provide testing and selection of large number of progenies, which is required for simultaneous selection for multiple stress tolerance. Data obtained revealed that remarkable improvement of the traits under selection was achieved. Biggest progress was obtained in selection for maize streak virus and downy mildew resistance, flintiness and earliness. In the case of drought stress, statistical analyses revealed significant negative correlation between yield and anthesis-silking interval, and between yield and days to silk, but positive correlation between yield and grain weight per ear.
Wallis de Vries, M.F.
Livestock grazing in low-intensity farming systems is a key aspect in the conservation of Europe's biodiversity, which reaches high levels of species richness in semi-natural grasslands. With the demise of traditional grazing systems, the design of viable low-intensity grazing systems for the future requires a good understanding of grazing impacts on biodiversity. Here, I review various scale-dependent aspects of selective grazing and how they may affect biodiversity. Insects such as butterfl...
Zhou, Muchu; Fuller, Rebecca C
Elaborate, sexually dimorphic traits are widely thought to evolve under sexual selection through female preference, male-male competition, or both. The orangethroat darter ( Etheostoma spectabile ) is a sexually dichromatic fish in which females exhibit no preferences for male size or coloration. We tested whether these traits affect individual reproductive success in E. spectabile when multiple males are allowed to freely compete for a female. The quality and quantity of male coloration were associated with greater success in maintaining access to the female and in spawning as the primary male (first male to participate). On the other hand, sneaking behavior showed little correlation with coloration. Male breeding coloration in E. spectabile may therefore demonstrate how intrasexual competition can be a predominant factor underlying the evolution of male ornaments.
Richard Le Boucher
Full Text Available Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively. Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.
Roberto A. Moreno-García
Full Text Available Aim of study: Our objective was to find habitat associations at a microhabitat level for two endemic birds in a Chilean temperate forest (biodiversity “hotspots”, in order to integrate biodiversity into forest planning.Area of study: Nahuelbuta Range, Chile.Material and methods: The two birds studied were Scelorchilus rubecula (Chucao Tapaculo and Scytalopus magellanicus (Magellanic Tapaculo, both belonging to the Rhinocryptidae family. Presence or absence of the two species was sampled in 57 census spots. Habitat was categorized according to presence/absence results. We assessed the influence of abiotic variables (altitude, exposure, slope and vegetation structure (percentage of understory cover, number of strata using a statistical cluster analysis.Main results: The two bird species selected the habitat. Most frequent presence was detected at a range of 600-1100 masl, but Magellanic Tapaculo was associated to more protected sites in terms of vegetation structure (50-75% for understory cover and 2-3 strata. Slope was the most relevant abiotic variable in habitat selection due to its linkage to vegetation traits in this area.Research highlights: Our results can help managers to integrate biodiversity (endemic fauna species into forest planning by preserving certain traits of the vegetation as part of a habitat (at a microhabitat level selected by the fauna species. That planning should be implemented with both an adequate wood harvesting cuts system and specific silvicultural treatments.Key words: Chile; Nahuelbuta; rhinocryptidae; cluster analysis; rorest planning; vegetation structure.
Coker, Darren James
Hawkfishes (family: Cirrhitidae) are small conspicuous reef predators that commonly perch on, or shelter within, the branches of coral colonies. This study examined habitat associations of hawkfishes, and explicitly tested whether hawkfishes associate with specific types of live coral. Live coral use and habitat selectivity of hawkfishes was explored at six locations from Chagos in the central Indian Ocean extending east to Fiji in the Pacific Ocean. A total of 529 hawkfishes from seven species were recorded across all locations with 63% of individuals observed perching on, or sheltering within, live coral colonies. Five species (all except Cirrhitus pinnulatus and Cirrhitichthys oxycephalus) associated with live coral habitats. Cirrhitichthys falco selected for species of Pocillopora while Paracirrhites arcatus and P. forsteri selected for both Pocillopora and Acropora, revealing that these habitats are used disproportionately more than expected based on the local cover of these coral genera. Habitat selection was consistent across geographic locations, and species of Pocillopora were the most frequently used and most consistently selected even though this coral genus never comprised more than 6% of the total coral cover at any of the locations. Across locations, Paracirrhites arcatus and P. forsteri were the most abundant species and variation in their abundance corresponded with local patterns of live coral cover and abundance of Pocilloporid corals, respectively. These findings demonstrate the link between small predatory fishes and live coral habitats adding to the growing body of literature highlighting that live corals (especially erect branching corals) are critically important for sustaining high abundance and diversity of fishes on coral reefs.
R. L. Lin
Full Text Available In China and South East Asia, the duck (common duck is important in egg production for human consumption. Plumage color is a breed characteristic and of economic importance, together with egg production. Our aim in this study was to investigate the inheritance of plumage color in three Chinese indigenous egg-type duck breeds, Shan Ma (S, Putian White (F and Putian black (P, and some of their crossbreds. These three breeds have different plumage color and are used in crossbreeding. The crossbred laying ducks F×(P×S and F×(S×P showed highly improved laying ability but heterogeneous plumage color. Genotypes at four relevant loci were investigated by studying down color and pattern in ducklings after crossbreeding. F1 ducklings from the matings F×S and S×F, P×S, and S×P were classified into four classes of plumage color (the Shan Ma plumage color, black, white, or multicolored over three generations. Parents were selected for the Shan Ma plumage color of their progeny. In the fourth generation, P male and P female ducks were selected according to the frequency of the desired class of plumage color (Shan Ma of their F1 progeny to obtain the so-called “Brown Putian Ma duck”. The Shan Ma duck genotype was identified as having the restricted mallard color pattern (MRMR, full expression of any of the patterns or colors (CC, no extended black (ee and no brown dilution D (D. The Putian White genotype was recessive white (cc, no extended black (ee and no brown dilution D (D. The Putian Black genotype exhibited full expression of extended black (E gene and no brown dilution (CCEE D [D]. It was shown that F×S and S×F tests should be implemented to eliminate the recessive white c allele in the S line and the dominant extended black E allele in the F line. It was also shown that the Brown Putian Ma obtained from Putian Black, with no extended black genotype (ee, could be used to get rid of the black plumage (E gene in the crossbred ducks. This
Full Text Available Coral-reef fishes experience a major challenge when facing settlement in a multi-threat environment, within which, using settlement cues, they need to select a suitable site. Studies in laboratories and artificial setups have shown that the presence of conspecific adults often serves as a positive settlement cue, whose value is explained by the increased survival of juveniles in an already proven fit environment. However, settlement in already inhabited corals may expose the recruits to adult aggression. Daily observations and manipulation experiments were used in the present study, which was conducted in the natural reef. We revealed differential strategies of settlers, which do not necessarily join conspecific adults. Dascyllus aruanus prefer to settle near (not with their aggressive adults, and to join them only after gaining in size; whereas Dascyllus marginatus settlers in densely populated reefs settle independently of their adult distribution. Our results present different solutions to the challenges faced by fish recruits while selecting their microhabitat, and emphasize the complexity of habitat selection by the naïve settlers. Although laboratory experiments are important to the understanding of fish habitat selection, further studies in natural habitats are essential in order to elucidate the actual patterns of settlement and habitat selection, which are crucial for the survival of coral-reef fish populations.
Lewis, Jeffrey C.; Jenkins, Kurt J.; Happe, Patricia J.; Manson, David J.; McCalmon, Marc
The fisher was extirpated from much of the Pacific Northwestern United States during the mid- to late-1900s and is now proposed for federal listing as a threatened species in all or part of its west coast range. Following the translocation of 90 fishers from central British Columbia, Canada, to the Olympic Peninsula of Washington State from 2008 to 2010, we investigated the landscape-scale habitat selection of reintroduced fishers across a broad range of forest ages and disturbance histories, providing the first information on habitat relationships of newly reintroduced fishers in coastal coniferous forests in the Pacific Northwest. We developed 17 a priori models to evaluate several habitat-selection hypotheses based on premises of habitat models used to forecast habitat suitability for the reintroduced population. Further, we hypothesized that female fishers, because of their smaller body size than males, greater vulnerability to predation, and specific reproductive requirements, would be more selective than males for mid- to late-seral forest communities, where complex forest structural elements provide secure foraging, resting, and denning sites. We assessed 11 forest structure and landscape characteristics within the home range core-areas used by 19 females and 12 males and within randomly placed pseudo core areas that represented available habitats. We used case-controlled logistic regression to compare the characteristics of used and pseudo core areas and to assess selection by male and female fishers. Females were more selective of core area placement than males. Fifteen of 19 females (79%) and 5 of 12 males (42%) selected core areas within federal lands that encompassed primarily forests with an overstory of mid-sized or large trees. Male fishers exhibited only weak selection for core areas dominated by forests with an overstory of small trees, primarily on land managed for timber production or at high elevations. The amount of natural open area best
Xia, Qin; Yang, Zhao-wu; Li, Min; Xia, Dong-mei
To breed a new good cultivar of Curcuma phaeocaulis. Three rounds of selection were systematically made for screening the new cultivar using biological technology. Firstly, individual plant selection. Promising individual plant selection was made based on the thousands of Curcuma phaeocaulis resources collected from all over the country. Secondly, strain selection. The promising strain was selected continually from the superior individuals on basis of specificities such as biological characteristics, yield, content of volatile oil and resistance. Thirdly, strain comparison test. The superior strain was selected through strain trial and regional trial. For the new cultivar "ChuanPeng 1" , its main rhizome was in ovoid or spindle shape, and it was fleshy and corpulent. Average amount of rhizome was 4, with 6. 27 cm in length and 3. 37 cm in diameter, while the secondary roots were cylindrical-like, with a yellow green cross section as the main rhizome. Slender root ends were inflated into the fleshy spindle shape, average amount of whose was 25, 3. 20 cm in length and 1. 33 cm in diameter with a yellow green or near white cross section. Average yield of rhizome is 5 314. 5 kg/hm2, while the root is 1 942. 5 kg/hm2, which was 32. 9% and 22. 7% higher than the local main cultivar respectively. The average extract content of rhizome was 15. 41% and content of volatile oil was 2. 82%, which was 15. 60% and 9. 30% higher than the local cultivar respectively. " ChuanPeng 1" has good stability and strong adaptability with high yield and superior internal quality. It can be cultivated and promoted in Jinma River Valley,Sichuan.
Full Text Available This survey, conducted with 461 racehorse owners-breeders in Algeria between 2009 and 2011, investigates their perceptions, objectives and practices regarding selective breeding. Racehorse breeding is a full-time professional activity for a third of interviewees. The holdings are small-sized with 77% owning one or two mares. The regular practice of mating is here used to categorize breeders according to their degree of professionalization (38.4% professional vs. 61.6% occasional breeders. Experience in the sector was also used to classify breeders, considering as "junior" the breeders under 10 years experience (38.8% and as "senior" those above 10 years (61.2%. More than professionalization, experience shows a significant impact on practices and objectives. Thus, experience influences breed choice (junior breeders tend to specialize while senior own both Arabian and Thoroughbreds, age at first foaling (sooner among senior breeders, information sources considered for selecting stallions (senior use more diversified sources, the importance granted to the price of mating (greater for junior breeders, the importance granted to the ranking compared to earnings (the ranking being more important to junior breeders, and the priority given to breeding (junior breeders give higher priority to a buy-race-resell activity. Finally, racehorse breeding is poorly professionalized, the only financial goal being cost coverage. Despite inappropriate practices, an interest for selection is noticed.
Melo, C A F; Souza, M M; Sousa, A G R; Viana, A P; Santos, E A
The Ward-MLM procedure was used to evaluate genetic variation in four backcross progenies and in their parents, hybrid F1 HD13 and donor parent Passiflora sublanceolata. Sixteen quantitative descriptors and five qualitative characteristics of relevance to ornamental flower production were assessed. Using the pseudo-F and pseudo-T² criteria, we identified four groups among these plants in two evaluation periods. In both evaluations, the BC1 plants showed greater dissimilarity to their recurrent parent, but showed high genetic similarity with the P. sublanceolata parent. The first two canonical variables produced by the Ward-MLM procedure accounted for over 90% of the variation in both evaluation periods, enabling the representation of diversity through two-dimensional graphics. Groups II and IV were formed in the first assessment period. Groups I and IV formed in the second period and showed plants with selection potential. We found that it was essential to use both qualitative and quantitative variables for this analysis. Assessments of quantitative descriptors indicate that the selection of BC1 plants can be performed in any of the four progenies. Because of the similarities observed for some floral descriptors between BC1 and the P. sublanceolata parent, a second generation backcross was not recommended. However, the selection of BC1 plants for evaluation and direct use as an ornamental cultivar, or as a resource in other breeding programs, can be recommended.
Zebrowska, Jadwiga Irena
Genetic resistance to pathogenetic soil-borne fungus Verticillium dahliae Kleb. was examined in two strawberry somaclones. Strawberry somaclones were obtained in sterile culture from runner tips of cultivars 'Merton Dawn' and 'Selva'. In vitro selection was performed with the use of homogenate of liquid cultures of Verticillium dahliae. Microplants of both somaclones were inoculated at stage of 4. Leaves. Disease symptoms were observed at 15., 30., 45., 60. and 75. days post inoculation. Extent of leaf chlorosis was rated on a scale of 0-4. Under the controlled in vitro culture conditions a different response to infection by this pathogenic fungus was observed. After 75. days post inoculation the contribution of necrotic plants in somaclone of 'Merton Dawn' reached the value of 76%, whereas in somaclone of 'Selva' this value reached 86%. In control somaclones of 'Merton Dawn' and 'Selva' the contribution of necrotic plants after 75. days post mock-inoculation with sterile distilled water reached the considerably lower value of 13%. These results revealed that somaclone of 'Merton Dawn' was more genetically resistant to infection by V. dahliae than somaclone of 'Selva'. The observed response to in vitro infection caused by Verticillium dahliae in examined somaclones was similar in comparison with original cultivars. Furthermore, somaclonal variation induced in tissue cultured strawberry was sufficient to select variants that showed enhanced genetic resistance to Verticillium wilt caused by V. dahliae. In vitro selection can be efficiently used as an alternative program to conventional resistance breeding in strawberry.
Cram, Jeremy M.; Torgersen, Christian E.; Klett, Ryan S.; Pess, George R.; May, Darran; Pearsons, Todd N.; Dittman, Andrew H.
Spawning site selection by female salmon is based on complex and poorly understood tradeoffs between the homing instinct and the availability of appropriate habitat for successful reproduction. Previous studies have shown that hatchery-origin Chinook salmon (Oncorhynchus tshawytscha) released from different acclimation sites return with varying degrees of fidelity to these areas. To investigate the possibility that homing fidelity is associated with aquatic habitat conditions, we quantified physical habitat throughout 165 km in the upper Yakima River basin (Washington, USA) and mapped redd and carcass locations from 2004 to 2008. Principal components analysis identified differences in substrate, cover, stream width, and gradient among reaches surrounding acclimation sites, and canonical correspondence analysis revealed that these differences in habitat characteristics were associated with spatial patterns of spawning (p < 0.01). These analyses indicated that female salmon may forego spawning near their acclimation area if the surrounding habitat is unsuitable. Evaluating the spatial context of acclimation areas in relation to surrounding habitat may provide essential information for effectively managing supplementation programs and prioritizing restoration actions.
Belaire, J Amy; Kreakie, Betty J; Keitt, Timothy; Minor, Emily
Migratory stopover habitats are often not part of planning for conservation or new development projects. We identified potential stopover habitats within an avian migratory flyway and demonstrated how this information can guide the site-selection process for new development. We used the random forests modeling approach to map the distribution of predicted stopover habitat for the Whooping Crane (Grus americana), an endangered species whose migratory flyway overlaps with an area where wind energy development is expected to become increasingly important. We then used this information to identify areas for potential wind power development in a U.S. state within the flyway (Nebraska) that minimize conflicts between Whooping Crane stopover habitat and the development of clean, renewable energy sources. Up to 54% of our study area was predicted to be unsuitable as Whooping Crane stopover habitat and could be considered relatively low risk for conflicts between Whooping Cranes and wind energy development. We suggest that this type of analysis be incorporated into the habitat conservation planning process in areas where incidental take permits are being considered for Whooping Cranes or other species of concern. Field surveys should always be conducted prior to construction to verify model predictions and understand baseline conditions. © 2013 Society for Conservation Biology.
Pitman, James W.; Cain, James W.; Liley, Stewart; Gould, William R.; Quintana, Nichole T.; Ballard, Warren
Neonatal survival and juvenile recruitment are crucial to maintaining viable elk (Cervus elaphus) populations. Neonate survival is known to be influenced by many factors, including bed-site selection. Although neonates select the actual bed-site location, they must do so within the larger calf-rearing area selected by the mother. As calves age, habitat selection should change to meet the changing needs of the growing calf. Our main objectives were to characterize habitat selection at 2 spatial scales and in areas with different predator assemblages in New Mexico. We evaluated bed-site selection by calves and calf-rearing area selection by adult females. We captured 108 elk calves by hand and fitted them with ear tag transmitters in two areas in New Mexico: the Valle Vidal and Blue Range Wolf Recovery Area. In both study areas, we found that concealing cover structure and distance to that cover influenced bed-site selection of young calves (i.e., g., rocks, shrubs, and logs) and other variables important to the hiding calves were still in the most supported models, but selection was also influenced by forage availability and indices of forage quality. Studies that seek to obtain insight into microhabitat selection of ungulate neonates should consider selection by the neonate and selection by the adult female, changes in selection as neonates age, and potential selection differences in areas of differing predation risk. By considering these influences together and at multiple scales, studies can achieve a broader understanding of neonatal ungulate habitat requirements.
Jennifer L. Reidy; Frank R. Thompson; Sarah W. Kendrick
Savanna and woodland were once common in the Midwest, but land use changes have led to increasing scarcity of these communities. These transitional habitats are being restored across the Midwest, but few studies have evaluated the response of wildlife to restoration or the vegetative gradient created by management. We conducted point counts for 25 songbirds at sites...
Buch, Line Hjortø; Sørensen, Morten Kargo; Berg, Peer
) a positive interaction exists between the use of genotypic information and a short generation interval on ΔGAG and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔGAG if genotypic information about the breeding goal trait is known. We examined......We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔGAG), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii...... four breeding schemes with or without genomic selection and with or without intensive use of young bulls using pseudo-genomic stochastic simulations. The breeding goal consisted of a milk production trait and a functional trait. The two breeding schemes with genomic selection resulted in higher ΔGAG...
Milakovic, B.; Parker, K.L.; Gustine, D.D.; Lay, R.J.; Walker, A.B.D.; Gillingham, M.P.
We defined patterns of habitat use and selection by female grizzly bears (Ursus arctos) in the Besa-Prophet watershed of northern British Columbia. We fitted 13 adult females with Geographic Positioning System (GPS) radio-collars and monitored them between 2001 and 2004. We examined patterns of habitat selection by grizzly bears relative to topographical attributes and 3 potential surrogates of food availability: land-cover class, vegetation biomass or quality (as measured by the Normalized Difference Vegetation Index), and selection value for prey species themselves (moose [Alces alces], elk [Cervus elaphus], woodland caribou [Rangifer tarandus], Stone's sheep [Ovis dalli stonei]). Although vegetation biomass and quality, and selection values for prey were important in seasonal selection by some individual bears, land-cover class, elevation, aspect, and vegetation diversity most influenced patterns of habitat selection across grizzly bears, which rely on availability of plant foods and encounters with ungulate prey. Grizzly bears as a group avoided conifer stands and areas of low vegetation diversity, and selected for burned land-cover classes and high vegetation diversity across seasons. They also selected mid elevations from what was available within seasonal ranges. Quantifying relative use of different attributes helped place selection patterns within the context of the landscape. Grizzly bears used higher elevations (1,595??31 m SE) in spring and lower elevations (1,436??27 m) in fall; the range of average elevations used among individuals was highest (500 m) during the summer. During all seasons, grizzly bears most frequented aspects with high solar gain. Use was distributed across 10 land-cover classes and depended on season. Management and conservation actions must maintain a diverse habitat matrix distributed across a large elevational gradient to ensure persistence of grizzly bears as levels of human access increase in the northern Rocky Mountains
Rohan Benjankar; Daniele Tonina; Alessandra Marzadri; Jim McKean; Daniel J. Isaak
Understanding the role of stream hydrologic and morphologic variables on the selection of spawning sites by salmonid fishes at high resolution across broad scales is needed for effective habitat restoration and protection. Here we used remotely sensed meter-scale channel bathymetry for a 13.5 km reach of Chinook salmon spawning stream in central Idaho to...
Jonathan G. Dudley; Victoria A. Saab; Jeffrey P. Hollenbeck
We examined foraging-habitat selection of Black-backed Woodpeckers (Picoides arcticus) in burned forests of southwestern Idaho during 2000 and 2002 (6 and 8 years following wildfire). This woodpecker responds positively to large-scale fire disturbances and may be at risk from logging and post-fire management. With 100 radio-locations of four adult males, we used...
McCue, M E; Anderson, S M; Valberg, S J; Piercy, R J; Barakzai, S Z; Binns, M M; Distl, O; Penedo, M C T; Wagner, M L; Mickelson, J R
The GYS1 gene mutation that is causative of Type 1 Polysaccharide Storage Myopathy (PSSM) has been identified in more than 20 breeds of horses. However, the GYS1 mutation frequency or Type 1 PSSM prevalence within any given breed is unknown. The purpose of this study was to determine the frequency of the GYS1 mutation and prevalence of genetic susceptibility to Type 1 PSSM in selected breeds from Europe and North America. The GYS1 mutation was detected in 11 breeds, including, in order of increasing allele frequency, Shires, Morgans, Appaloosas, Quarter Horses, Paints, Exmoor Ponies, Saxon-Thuringian Coldbloods, South German Coldbloods, Belgians, Rhenish German Coldbloods and Percherons. The prevalence of genetic susceptibility to Type 1 PSSM in these breeds varied from 0.5% to 62.4%. The GYS1 mutation was not found in the sampled Thoroughbreds, Akhal-Tekes, Connemaras, Clydesdales, Norwegian Fjords, Welsh Ponies, Icelandics, Schleswig Coldbloods or Hanoverians, but failure to detect the mutation does not guarantee its absence. This knowledge will help breed associations determine whether they should screen for the GYS1 mutation and will alert veterinarians to a possible differential diagnosis for muscle pain, rhabdomyolysis or gait abnormalities. © 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.
Brito, Luiz F; Kijas, James W; Ventura, Ricardo V; Sargolzaei, Mehdi; Porto-Neto, Laercio R; Cánovas, Angela; Feng, Zeny; Jafarikia, Mohsen; Schenkel, Flávio S
The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean H O and H E was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures F EH , F VR , F LEUT , F ROH and F PED was 0.129, -0.012, -0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds' development history. The information reported here will be useful for
Steyaert, Sam M J G; Zedrosser, Andreas; Rosell, Frank
Habitat selection is a context-dependent mechanism, in which both the internal state as well as external factors affect the behavior and decisions of an individual. This is well known for polygamous mammals, which are typically sexually dimorphic, and often express great variability in behavior and habitat selection between individuals as well between the sexes. Among monogamous mammals, however, variability in habitat selection should be explained by group characteristics and the presence of offspring rather than by sex. We evaluated this hypothesis in a socially monogamous rodent, the Eurasian beaver (Castor fiber), in a saturated Norwegian population. For the first time in this species we applied GPS tracking devices (N = 22 adult beavers, in 15 territories, 2009-2013), and used resource selection functions (i) to document population-wide habitat selection and the importance of 'territory' therein, and (ii) to evaluate which socio-ecological factors explained potential individual differences in habitat selection. We found that variation in habitat selection was stronger between territories than between years or individuals nested by territory. We identified that family size and the presence of kits, but not sex, explained individual variation in habitat selection. Adults with kits and/or larger families tended to exhibit low risk-taking behavior (avoiding human-related variables such as roads, buildings, and agricultural land), and stayed close to their main lodge (parental care). Our results show that habitat selection is a context-dependent mechanism even in a species which expresses very little behavioral and morphological dimorphism.
Laury Cullen Junior
Full Text Available We used data from VHF and GPS radio-tagged jaguars, Panthera onca (Linnaeus, 1758 to quantify jaguar habitat selection and how adult individuals in the Upper Paraná River region selected among the available habitat types. We followed the framework in which animals make decisions about resource use at hierarchical stages, namely selection of home range within a study area (second-order selection and selection of patches within a home range (third-order selection. We quantified habitat preferences at two orders of selection with respect to habitat types and to test the null hypothesis that habitat utilization by jaguars was random at both study sites. Using compositional analysis, we assessed habitat selection by jaguars at second- and third-orders of selection. Jaguars consistently preferred dense marshes and primary forests, and avoided human-dominated areas such as intensively managed open pastures. Although the avoidance of disturbed and developed habitat types by jaguars is not surprising, this is the first study to document it. If small protected areas, such as the ones already existing in the Upper Paraná region, are to sustain jaguar populations they, must include and protect as many primary forests and marshlands as possible, so that jaguars can disperse, hunt wild prey and take care of their cubs without being disturbed. What is urgently needed in these jaguar-protected areas is the creation of larger protected areas that can sustain jaguars in their favored habitat.
Takouridis, Simon J; Tribe, David E; Gras, Sally L; Martin, Gregory J O
The potential for Chlamydomonas reinhardtii to be utilized for biofuel production was strengthened by developing it for growth in elevated salinity via the selective breeding method of genome shuffling. A population was constructed via random mutagenesis and subjected to multiple rounds of sex and growth in increasing salinity. This sexual line was capable of growth in up to 700 mM NaCl, unlike its progenitor, which could only grow in 300 mM NaCl. An asexual control line was capable of growth in 500 mM NaCl. Palmelloid aggregations increased in size and the concentration of final biomass decreased as a function of NaCl concentration, which poses considerations for future strain development. The sexual line maintained sexual efficiencies of up to 50% over the course of selection. This investigation achieved significant strain improvement of C. reinhardtii and demonstrated the clear advantage of its ability to participate in laboratory controlled and reproducible high efficiency sex. Copyright © 2014 Elsevier Ltd. All rights reserved.
Dou, Jinzhuang; Li, Xue; Fu, Qiang; Jiao, Wenqian; Li, Yangping; Li, Tianqi; Wang, Yangfan; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin
The recently developed 2b-restriction site-associated DNA (2b-RAD) sequencing method provides a cost-effective and flexible genotyping platform for aquaculture species lacking sufficient genomic resources. Here, we evaluated the performance of this method in the genomic selection (GS) of Yesso scallop (Patinopecten yessoensis) through simulation and real data analyses using six statistical models. Our simulation analysis revealed that the prediction accuracies obtained using the 2b-RAD markers were slightly lower than those obtained using all polymorphic loci in the genome. Furthermore, a small subset of markers obtained from a reduced tag representation (RTR) library presented comparable performance to that obtained using all markers, making RTR be an attractive approach for GS purpose. Six GS models exhibited variable performance in prediction accuracy depending on the scenarios (e.g., heritability, sample size, population structure), but Bayes-alphabet and BLUP-based models generally outperformed other models. Finally, we performed the evaluation using an empirical dataset composed of 349 Yesso scallops that were derived from five families. The prediction accuracy for this empirical dataset could reach 0.4 based on optimal GS models. In summary, the genotyping flexibility and cost-effectiveness make 2b-RAD be an ideal genotyping platform for genomic selection in aquaculture breeding programs.
Switchgrass breeding and genetics research was conducted from 1992-2002 at the Oklahoma State University as part of the national DOE-Bioenergy Feedstock Development Program (BFDP) effort to develop the species as a bioenergy feedstock crop. The fundamental objective of the program was to implement and conduct a breeding program to increase biomass yield capability in switchgrass and develop cultivars for the central and southern United States. Supporting research objectives included: (1) switchgrass germplasm collection, characterization, and enhancement; (2) elucidation of cytogenetic and breeding behavior; and (3) identification of best breeding procedures.
Sarah D. Battenfield
Full Text Available Wheat ( L. cultivars must possess suitable end-use quality for release and consumer acceptability. However, breeding for quality traits is often considered a secondary target relative to yield largely because of amount of seed needed and expense. Without testing and selection, many undesirable materials are advanced, expending additional resources. Here, we develop and validate whole-genome prediction models for end-use quality phenotypes in the CIMMYT bread wheat breeding program. Model accuracy was tested using forward prediction on breeding lines ( = 5520 tested in unbalanced yield trials from 2009 to 2015 at Ciudad Obregon, Sonora, Mexico. Quality parameters included test weight, 1000-kernel weight, hardness, grain and flour protein, flour yield, sodium dodecyl sulfate sedimentation, Mixograph and Alveograph performance, and loaf volume. In general, prediction accuracy substantially increased over time as more data was available to train the model. Reflecting practical implementation of genomic selection (GS in the breeding program, forward prediction accuracies ( for quality parameters were assessed in 2015 and ranged from 0.32 (grain hardness to 0.62 (mixing time. Increased selection intensity was possible with GS since more entries can be genotyped than phenotyped and expected genetic gain was 1.4 to 2.7 times higher across all traits than phenotypic selection. Given the limitations in measuring many lines for quality, we conclude that GS is a powerful tool to facilitate early generation selection for end-use quality in wheat, leaving larger populations for selection on yield during advanced testing and leading to better gain for both quality and yield in bread wheat breeding programs.
Clennon, Julie A; Kamanga, Aniset; Musapa, Mulenga; Shiff, Clive; Glass, Gregory E
Abstract Background Malaria, caused by the parasite Plasmodium falciparum, is a significant source of morbidity and mortality in southern Zambia. In the Mapanza Chiefdom, where transmission is seasonal, Anopheles arabiensis is the dominant malaria vector. The ability to predict larval habitats can help focus control measures. Methods A survey was conducted in March-April 2007, at the end of the rainy season, to identify and map locations of water pooling and the occurrence anopheline larval h...
The ability to predict individual breeding values in natural populations with known pedigrees has provided a powerful tool to separate phenotypic values into their genetic and environmental components in a nonexperimental setting. This has allowed sophisticated analyses of selection, as well as
Jeremy J Vaudo
Full Text Available Habitat selection decisions by consumers has the potential to shape ecosystems. Understanding the factors that influence habitat selection is therefore critical to understanding ecosystem function. This is especially true of mesoconsumers because they provide the link between upper and lower tropic levels. We examined the factors influencing microhabitat selection of marine mesoconsumers - juvenile giant shovelnose rays (Glaucostegus typus, reticulate whiprays (Himantura uarnak, and pink whiprays (H. fai - in a coastal ecosystem with intact predator and prey populations and marked spatial and temporal thermal heterogeneity. Using a combination of belt transects and data on water temperature, tidal height, prey abundance, predator abundance and ray behavior, we found that giant shovelnose rays and reticulate whiprays were most often found resting in nearshore microhabitats, especially at low tidal heights during the warm season. Microhabitat selection did not match predictions derived from distributions of prey. Although at a course scale, ray distributions appeared to match predictions of behavioral thermoregulation theory, fine-scale examination revealed a mismatch. The selection of the shallow nearshore microhabitat at low tidal heights during periods of high predator abundance (warm season suggests that this microhabitat may serve as a refuge, although it may come with metabolic costs due to higher temperatures. The results of this study highlight the importance of predators in the habitat selection decisions of mesoconsumers and that within thermal gradients, factors, such as predation risk, must be considered in addition to behavioral thermoregulation to explain habitat selection decisions. Furthermore, increasing water temperatures predicted by climate change may result in complex trade-offs that might have important implications for ecosystem dynamics.
Full Text Available When large carnivores occupy peripheral human lands conflict with humans becomes inevitable, and the reduction of human-carnivore interactions must be the first consideration for those concerned with conflict mitigation. Studies designed to identify areas of high human-bear interaction are crucial for prioritizing management actions. Due to a surge in conflicts, against a background of social intolerance to wildlife and the prevalent use of lethal control throughout Japan, Asiatic black bears (Ursus thibetanus are now threatened by high rates of mortality. There is an urgent need to reduce the frequency of human-bear encounters if bear populations are to be conserved. To this end, we estimated the habitats that relate to human-bear interactions by sex and season using resource selection functions (RSF. Significant seasonal differences in selection for and avoidance of areas by bears were estimated by distance-effect models with interaction terms of land cover and sex. Human-bear boundaries were delineated on the basis of defined bear-habitat edges in order to identify areas that are in most need of proactive management strategies. Asiatic black bears selected habitats in close proximity to forest edges, forest roads, rivers, and red pine and riparian forests during the peak conflict season and this was correctly predicted in our human-bear boundary maps. Our findings demonstrated that bears selected abandoned forests and agricultural lands, indicating that it should be possible to reduce animal use near human lands by restoring season-specific habitat in relatively remote areas. Habitat-based conflict mitigation may therefore provide a practical means of creating adequate separation between humans and these large carnivores.
Takahata, Chihiro; Nielsen, Scott Eric; Takii, Akiko; Izumiyama, Shigeyuki
When large carnivores occupy peripheral human lands conflict with humans becomes inevitable, and the reduction of human-carnivore interactions must be the first consideration for those concerned with conflict mitigation. Studies designed to identify areas of high human-bear interaction are crucial for prioritizing management actions. Due to a surge in conflicts, against a background of social intolerance to wildlife and the prevalent use of lethal control throughout Japan, Asiatic black bears (Ursus thibetanus) are now threatened by high rates of mortality. There is an urgent need to reduce the frequency of human-bear encounters if bear populations are to be conserved. To this end, we estimated the habitats that relate to human-bear interactions by sex and season using resource selection functions (RSF). Significant seasonal differences in selection for and avoidance of areas by bears were estimated by distance-effect models with interaction terms of land cover and sex. Human-bear boundaries were delineated on the basis of defined bear-habitat edges in order to identify areas that are in most need of proactive management strategies. Asiatic black bears selected habitats in close proximity to forest edges, forest roads, rivers, and red pine and riparian forests during the peak conflict season and this was correctly predicted in our human-bear boundary maps. Our findings demonstrated that bears selected abandoned forests and agricultural lands, indicating that it should be possible to reduce animal use near human lands by restoring season-specific habitat in relatively remote areas. Habitat-based conflict mitigation may therefore provide a practical means of creating adequate separation between humans and these large carnivores.
James M Beerens
Full Text Available Species distribution models (SDM link species occurrence with a suite of environmental predictors and provide an estimate of habitat quality when the variable set captures the biological requirements of the species. SDMs are inherently more complex when they include components of a species' ecology such as conspecific attraction and behavioral flexibility to exploit resources that vary across time and space. Wading birds are highly mobile, demonstrate flexible habitat selection, and respond quickly to changes in habitat quality; thus serving as important indicator species for wetland systems. We developed a spatio-temporal, multi-SDM framework using Great Egret (Ardea alba, White Ibis (Eudocimus albus, and Wood Stork (Mycteria Americana distributions over a decadal gradient of environmental conditions to predict species-specific abundance across space and locations used on the landscape over time. In models of temporal dynamics, species demonstrated conditional preferences for resources based on resource levels linked to differing temporal scales. Wading bird abundance was highest when prey production from optimal periods of inundation was concentrated in shallow depths. Similar responses were observed in models predicting locations used over time, accounting for spatial autocorrelation. Species clustered in response to differing habitat conditions, indicating that social attraction can co-vary with foraging strategy, water-level changes, and habitat quality. This modeling framework can be applied to evaluate the multi-annual resource pulses occurring in real-time, climate change scenarios, or restorative hydrological regimes by tracking changing seasonal and annual distribution and abundance of high quality foraging patches.
Beerens, James M.; Noonberg, Erik G.; Gawlik, Dale E.
Species distribution models (SDM) link species occurrence with a suite of environmental predictors and provide an estimate of habitat quality when the variable set captures the biological requirements of the species. SDMs are inherently more complex when they include components of a species' ecology such as conspecific attraction and behavioral flexibility to exploit resources that vary across time and space. Wading birds are highly mobile, demonstrate flexible habitat selection, and respond quickly to changes in habitat quality; thus serving as important indicator species for wetland systems. We developed a spatio-temporal, multi-SDM framework using Great Egret (Ardea alba), White Ibis (Eudocimus albus), and Wood Stork (Mycteria Americana) distributions over a decadal gradient of environmental conditions to predict species-specific abundance across space and locations used on the landscape over time. In models of temporal dynamics, species demonstrated conditional preferences for resources based on resource levels linked to differing temporal scales. Wading bird abundance was highest when prey production from optimal periods of inundation was concentrated in shallow depths. Similar responses were observed in models predicting locations used over time, accounting for spatial autocorrelation. Species clustered in response to differing habitat conditions, indicating that social attraction can co-vary with foraging strategy, water-level changes, and habitat quality. This modeling framework can be applied to evaluate the multi-annual resource pulses occurring in real-time, climate change scenarios, or restorative hydrological regimes by tracking changing seasonal and annual distribution and abundance of high quality foraging patches.
van Klink, Roel; Mandema, Freek S.; Bakker, Jan P.; Tinbergen, Joost M.
Capsule Breeding Meadow Pipits foraged for caterpillars and large spiders in vegetation that was less heterogeneous than vegetation at random locations.Aims To gain a better understanding of the foraging ecology of breeding Meadow Pipits on grazed coastal salt marshes, we tested three hypotheses:
Predation by feral cats (Felis silvestris catus), presumed to be the main cause of chick mortality, may be adversely impacting breeding success and could lead to the virtual extirpation of the yellow-legged gull and other breeding birds from the island. Key words: Laridae, seabirds, yellow-legged gull, reproductive ecology, ...
Herridge, D.F.; Holland, J.F.; Rose, I.A.; Redden, R.J.
During the period 1980-87, the areas sown to grain legumes in Australia increased dramatically, from 0.25 Mha to 1.65 Mha. These increases occurred in the western and southern cereal belts, but not in the north which N continued to be supplied by the mineralization of soil organic matter. Therefore, there was a need to promote the use of N 2 -fixing legumes in the cereal-dominated northern cropping belt. Certain problems had to be addressed before farmers would accept legumes and change established patterns of cropping. Here we describe our efforts to improve N 2 fixation by soybean, common bean and pigeon pea. Selection and breeding for enhanced N 2 fixation of soybean commenced at Tamworth in 1980 after surveys of commercial crops indicated that nodulation was sometimes inadequate, particularly on new land, and that the levels of fixed-N inputs were variable and often low. Similar programmes were established in 1985 (common bean) and 1988 (pigeon bean). Progress was made in increasing N 2 fixation by these legumes towards obtaining economic yields without fertilizer N and contributing organic N for the benefit of subsequent cereal crops
Hess, Jennifer E.; Beck, Jeffrey L.
Wyoming big sagebrush ( Artemisia tridentata wyomingensis A. t. Nutt. ssp. wyomingensis Beetle and Young) communities provide structure and forbs and insects needed by greater sage-grouse ( Centrocercus urophasianus) for growth and survival. We evaluated forb, insect, and soil responses at six mowed and 19 prescribed burned sites compared to 25, paired and untreated reference sites. Sites were classified by treatment type, soil type, season, and decade of treatment (sites burned during 1990-1999 and sites burned or mowed during 2000-2006). Our objective was to evaluate differences in ten habitat attributes known to influence sage-grouse nesting and brood rearing to compare responses among treatment scenarios. Contrary to desired outcomes, treating Wyoming big sagebrush through prescribed burning or mowing may not stimulate cover or increase nutrition in food forbs, or increase insect abundance or indicators of soil quality compared with reference sites. In some cases, prescribed burning showed positive results compared with mowing such as greater forb crude protein content (%), ant (Hymenoptera; no./trap), beetle (Coleoptera/no./trap), and grasshopper abundance (Orthoptera; no./sweep), and total (%) soil carbon and nitrogen, but of these attributes, only grasshopper abundance was enhanced at burned sites compared with reference sites in 2008. Mowing did not promote a statistically significant increase in sage-grouse nesting or early brood-rearing habitat attributes such as cover or nutritional quality of food forbs, or counts of ants, beetles, or grasshoppers compared with reference sites.
Fauchald, Per; Langeland, Knut; Ims, Rolf A.; Yoccoz, Nigel G.; Bråthen, Kari Anne
The spatial and temporal distribution of forage quality is among the most central factors affecting herbivore habitat selection. Yet, for high latitude areas, forage quantity has been found to be more important than quality. Studies on large ungulate foraging patterns are faced with methodological challenges in both assessing animal movements at the scale of forage distribution, and in assessing forage quality with relevant metrics. Here we use first-passage time analyses to assess how reindeer movements relate to forage quality and quantity measured as the phenology and cover of growth forms along reindeer tracks. The study was conducted in a high latitude ecosystem dominated by low-palatable growth forms. We found that the scale of reindeer movement was season dependent, with more extensive area use as the summer season advanced. Small-scale movement in the early season was related to selection for younger stages of phenology and for higher abundances of generally phenologically advanced palatable growth forms (grasses and deciduous shrubs). Also there was a clear selection for later phenological stages of the most dominant, yet generally phenologically slow and low-palatable growth form (evergreen shrubs). As the summer season advanced only quantity was important, with selection for higher quantities of one palatable growth form and avoidance of a low palatable growth form. We conclude that both forage quality and quantity are significant predictors to habitat selection by a large herbivore at high latitude. The early season selectivity reflected that among dominating low palatability growth forms there were palatable phenological stages and palatable growth forms available, causing herbivores to be selective in their habitat use. The diminishing selectivity and the increasing scale of movement as the season developed suggest a response by reindeer to homogenized forage availability of low quality. PMID:24972188
Amer, I.M.; Moustafa, H.A.M.; Mansour, M.F.
Mutation breeding program has been initiated for inducing canola mutations tolerance to saline stressed conditions for growing at harsh land in Egypt. Therefore, seed lots of three cultivars and exotic variety (Bactol, Serow 4, Serow 6 and Evita) were subjected to 100,400 and 600 Gy of gamma rays. Mass selection with 20 % intensity for high number of pods per plant has been done in each treatment in M2 generation. However, individually plants with high number of pods / plant were selected from each variety in M3 generation for test under saline stressed conditions at Ras Sudr region in M4 (8600 and 8300 ppm salinity for soil and irrigation, respectively). The obtained results revealed that eight mutated families from 12- test families in M4 generation surpassed their parents in seed yield / plant and related characters ( plant height ,fruiting zone length , No. of branches , No. of pods / plant ). In addition, the mutant F93 characterized by fast growing and non shuttering pods reflecting 50.4% over Evita control in seed yield/ plant. Twelve mutant lines in M5 represented the mutant families were grown in sandy-loam soil at Inshas region. The three mutant lines (L 22, L 38 and L 45) continuously surpassed their parents in seed yield and related characters, but the increases were less than the previous generation. The increase was 22.3 %, 38.7 % and 36.7 % over seed yield of respective parents. Moreover, mutant L66 exhibited an increase in its yield components in M5 at Inshas only, suggesting that gene expression and genomic structure extremely influenced by environmental factors. Genetic stability for the obtained mutations could be done at different environmental conditions in further studies
Fox, Anthony D.; Flint, Paul L.; Hohman, William L.; Savard, Jean-Pierre L.
This paper reviews factors affecting site selection amongst waterfowl (Anatidae) during the flightless remigial moult, emphasising the roles of predation and food supply (especially protein and energy). The current literature suggests survival during flightless moult is at least as high as at other times of the annual cycle, but documented cases of predation of flightless waterfowl under particular conditions lead us to infer that habitat selection is generally highly effective in mitigating or avoiding predation. High energetic costs of feather replacement and specific amino-acid requirements for their construction imply adoption of special energetic and nutritional strategies at a time when flightlessness limits movements. Some waterfowl meet their energy needs from endogenous stores accumulated prior to remigial moult, others rely on exogenous supply, but this varies with species, age, reproductive status and site. Limited evidence suggests feather proteins are derived from endogenous and exogenous sources which may affect site selection. Remigial moult does not occur independently of other annual cycle events and is affected by reproductive investment and success. Hence, moult strategies are affected by age, sex and reproductive history, and may be influenced by the need to attain a certain internal state for the next stage in the annual cycle (e.g. autumn migration). We know little about habitat selection during moult and urge more research of this poorly known part of the annual cycle, with particular emphasis on identifying key concentrations and habitats for specific flyway populations and the effects of disturbance upon these. This knowledge will better inform conservation actions and management actions concerning waterfowl during moult and the habitats that they exploit.
Martin, Thomas E.
Resource selection specialization may increase vulnerability of populations to environmental change. One environmental change that may negatively impact some populations is the broad decline of quaking aspen Populus tremuloides, a preferred nest tree of cavity-nesting organisms who are commonly limited by nest-site availability. However, the long-term consequences of this habitat change for cavity-nesting bird populations are poorly studied.
Som, Nicholas A.; Perry, Russell W.; Jones, Edward C.; De Juilio, Kyle; Petros, Paul; Pinnix, William D.; Rupert, Derek L.
Models that formulate mathematical linkages between fish use and habitat characteristics are applied for many purposes. For riverine fish, these linkages are often cast as resource selection functions with variables including depth and velocity of water and distance to nearest cover. Ecologists are now recognizing the role that detection plays in observing organisms, and failure to account for imperfect detection can lead to spurious inference. Herein, we present a flexible N-mixture model to associate habitat characteristics with the abundance of riverine salmonids that simultaneously estimates detection probability. Our formulation has the added benefits of accounting for demographics variation and can generate probabilistic statements regarding intensity of habitat use. In addition to the conceptual benefits, model application to data from the Trinity River, California, yields interesting results. Detection was estimated to vary among surveyors, but there was little spatial or temporal variation. Additionally, a weaker effect of water depth on resource selection is estimated than that reported by previous studies not accounting for detection probability. N-mixture models show great promise for applications to riverine resource selection.
Full Text Available The objective of this research was to determine the effect of breed, feed type and sex, on the final body weight in New Zealand white and Blanc de Termonde rabbits. The experiment was conducted on a farm in the Małopolska Province in the south of Poland. Rabbits of both breeds were kept in identical conditions up to the age of 90 days. However, they were fed using two different methods – with commercial balanced (granulated feed (9.75 MJ, 155 g protein and farm-made feed (9.54 MJ, 157 g protein. Among New Zealand White rabbits, commercial balanced feed was given to 38 males and 42 females, whereas farm-made feed to 37 males and 38 females. Among Blanc de Termonde rabbits, commercial balanced feed was given to 65 males and 68 females, and farm-made feed to 54 males and 60 females. Daily gains were determined for both examined breeds divided into sexes. Then, we calculated interactions between breed and feed type, between breed and sex, as well as between feed type and sex. The mean body weights on the 90th day of fattening differed for both sexes and feed types. For both rabbit breeds, the higher mean final body weight was observed in case of feeding with the commercial balanced feed, whereas the highest body weight (2515.13 g was registered for the females of Blanc de Termonde rabbits.
de la Fuente, Ana Laura Carbajal; Dias-Lima, Artur; Lopes, Catarina Macedo; Emperaire, Laure; Walter, Annie; Ferreira, Agenor; Sherlock, Italo; Noireau, François
Triatoma pseudomaculata Corrêa and Espínola, 1964 and Triatoma juazeirensis Costa and Felix, 2007 ( = T. brasiliensis Neiva, 1911 [part]), are sylvatic vectors of Trypanosoma cruzi (Chagas, 1909), the causative agent of Chagas disease, in northeast Brazil-especially in the caatinga region. In an area of caatinga in the State of Bahia, we compared the wild and peridomestic habitats of these two species of Triatominae to assess their behavioral plasticity in relation to habitat selection in different environments. In the sylvatic environment, the habitat of these two species is never shared. T. pseudomaculata is found in trees and bird nests, but without apparent preference for any particular tree species. In contrast, T. juazeirensis is exclusively rupicolous (found among rocks). Both species invade peridomestic structures but do not display a significant ability to colonize human dwellings. In the peridomestic area, they are highly adaptable to different habitats and can occupy substrates that they do not colonize in the sylvatic environment. This behavioral plasticity seems to be more striking in T. juazeirensis-rupicolous in sylvatic environments but colonizing wooden structures in the peridomicile in >80% of cases.
Full Text Available Genetic improvement through selective breeding relies on the genetically-controlled phenotypic variability in the character of interest. Therefore, the extent of phenotypic variability in the population to be selected is an important parameter, as it potentially influences the population’s response to selection. This study was aimed to investigate the effect of inbreeding on the survivability, growth, and phenotypic variability of giant freshwater prawn (GFP, Macrobrachium rosenbergii. Two GFP populations of different inbreeding levels, namely 25% and 0%, respectively, were formed by mating of individual broodstock with known pedigree. Study was conducted for two months starting from newly hatched larvae up to nursery stage (30 day-old post larva. Phenotypic variability profile, expressed in the morphometric mean and coefficient of variation (CV of twenty one morphometric characters were measured and evaluated. Results showed that in general, the inbred populations had lower values in the mean of all characters (100%, indicating that they suffered from inbreeding depression. Similarly, a lower CV values were observed in sixteen (75% of the morphometric characters measured, indicating a potential reduced of genetic gain when they are used in selective breeding program. These results suggest the importance of controlling inbreeding level in breeding population that adverse effects resulted resulted from inbreeding can be minimized.
Full Text Available Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
Keating, Kim A.; Cherry, Steve
Logistic regression is an important tool for wildlife habitat-selection studies, but the method frequently has been misapplied due to an inadequate understanding of the logistic model, its interpretation, and the influence of sampling design. To promote better use of this method, we review its application and interpretation under 3 sampling designs: random, case-control, and use-availability. Logistic regression is appropriate for habitat use-nonuse studies employing random sampling and can be used to directly model the conditional probability of use in such cases. Logistic regression also is appropriate for studies employing case-control sampling designs, but careful attention is required to interpret results correctly. Unless bias can be estimated or probability of use is small for all habitats, results of case-control studies should be interpreted as odds ratios, rather than probability of use or relative probability of use. When data are gathered under a use-availability design, logistic regression can be used to estimate approximate odds ratios if probability of use is small, at least on average. More generally, however, logistic regression is inappropriate for modeling habitat selection in use-availability studies. In particular, using logistic regression to fit the exponential model of Manly et al. (2002:100) does not guarantee maximum-likelihood estimates, valid probabilities, or valid likelihoods. We show that the resource selection function (RSF) commonly used for the exponential model is proportional to a logistic discriminant function. Thus, it may be used to rank habitats with respect to probability of use and to identify important habitat characteristics or their surrogates, but it is not guaranteed to be proportional to probability of use. Other problems associated with the exponential model also are discussed. We describe an alternative model based on Lancaster and Imbens (1996) that offers a method for estimating conditional probability of use in
Loges, Brian W.; Lyons, James E.; Tavernia, Brian G.
The Clarence Cannon National Wildlife Refuge (CCNWR) in the Mississippi River flood plain of eastern Missouri provides high quality emergent marsh and moist-soil habitat benefitting both nesting marsh birds and migrating waterfowl. Staff of CCNWR manipulate water levels and vegetation in the 17 units of the CCNWR to provide conditions favorable to these two important guilds. Although both guilds include focal species at multiple planning levels and complement objectives to provide a diversity of wetland community types and water regimes, additional decision support is needed for choosing how much emergent marsh and moist-soil habitat should be provided through annual management actions.To develop decision guidance for balanced delivery of high-energy waterfowl habitat and breeding marsh bird habitat, two measureable management objectives were identified: nonbreeding Anas Linnaeus (dabbling duck) use-days and Rallus elegans (king rail) occupancy of managed units. Three different composite management actions were identified to achieve these objectives. Each composite management action is a unique combination of growing season water regime and soil disturbance. The three composite management actions are intense moist-soil management (moist-soil), intermediate moist-soil (intermediate), and perennial management, which idles soils disturbance (perennial). The two management objectives and three management options were used in a multi-criteria decision analysis to indicate resource allocations and inform annual decision making. Outcomes of the composite management actions were predicted in two ways and multi-criteria decision analysis was used with each set of predictions. First, outcomes were predicted using expert-elicitation techniques and a panel of subject matter experts. Second, empirical data from the Integrated Waterbird Management and Monitoring Initiative collected between 2010 and 2013 were used; where data were lacking, expert judgment was used. Also, a
de Fraga, Rafael; Moravec, Jiří; Kaefer, Igor L.; Lima, Albertina P.
The genus Scinax is one of the most specious genera of treefrogs of the family Hylidae. Despite the high number of potential new species of Scinax revealed in recent studies, the rate of species descriptions for Amazonia has been low in the last decade. A potential cause of this low rate may be the existence of morphologically cryptic species. Describing new species may not only impact the taxonomy and systematics of a group of organisms but also benefit other fields of biology. Ecological studies conducted in megadiverse regions, such as Amazonia, often meet challenging questions concerning insufficient knowledge of organismal alpha taxonomy. Due to that, detecting species-habitat associations is dependent on our ability to properly identify species. In this study, we first provide a description of a new species (including its tadpoles) of the genus Scinax distributed along heterogeneous landscapes in southern Amazonia; and secondly assess the influence of environmental heterogeneity on the new species’ abundance and distribution. Scinax ruberoculatus sp. nov. differs from all nominal congeners by its small size (SVL 22.6–25.9 mm in males and 25.4–27.5 mm in females), by having a dark brown spot on the head and scapular region shaped mainly like the moth Copiopteryx semiramis (or a human molar in lateral view, or a triangle), bicolored reddish and grey iris, snout truncate in dorsal view, bilobate vocal sac in males, by its advertisement call consisting of a single pulsed note with duration of 0.134–0.331 s, 10–23 pulses per note, and dominant frequency 1,809–1,895 Hz. Both occurrence and abundance of the new species are significantly influenced by silt content in the soil. This finding brings the first evidence that edaphic factors influence species-habitat association in Amazonian aquatic breeding frogs. PMID:29441233
Bradley C Fedy
Full Text Available Growing global energy demands ensure the continued growth of energy development. Energy development in wildlife areas can significantly impact wildlife populations. Efforts to mitigate development impacts to wildlife are on-going, but the effectiveness of such efforts is seldom monitored or assessed. Greater sage-grouse (Centrocercus urophasianus are sensitive to energy development and likely serve as an effective umbrella species for other sagebrush-steppe obligate wildlife. We assessed the response of birds within an energy development area before and after the implementation of mitigation action. Additionally, we quantified changes in habitat distribution and abundance in pre- and post-mitigation landscapes. Sage-grouse avoidance of energy development at large spatial scales is well documented. We limited our research to directly within an energy development field in order to assess the influence of mitigation in close proximity to energy infrastructure. We used nest-location data (n = 488 within an energy development field to develop habitat selection models using logistic regression on data from 4 years of research prior to mitigation and for 4 years following the implementation of extensive mitigation efforts (e.g., decreased activity, buried powerlines. The post-mitigation habitat selection models indicated less avoidance of wells (well density β = 0.18 ± 0.08 than the pre-mitigation models (well density β = -0.09 ± 0.11. However, birds still avoided areas of high well density and nests were not found in areas with greater than 4 wells per km2 and the majority of nests (63% were located in areas with ≤ 1 well per km2. Several other model coefficients differed between the two time periods and indicated stronger selection for sagebrush (pre-mitigation β = 0.30 ± 0.09; post-mitigation β = 0.82 ± 0.08 and less avoidance of rugged terrain (pre-mitigation β = -0.35 ± 0.12; post-mitigation β = -0.05 ± 0.09. Mitigation efforts
Bernal-Vasquez, Angela-Maria; Gordillo, Andres; Schmidt, Malthe; Piepho, Hans-Peter
The use of multiple genetic backgrounds across years is appealing for genomic prediction (GP) because past years' data provide valuable information on marker effects. Nonetheless, single-year GP models are less complex and computationally less demanding than multi-year GP models. In devising a suitable analysis strategy for multi-year data, we may exploit the fact that even if there is no replication of genotypes across years, there is plenty of replication at the level of marker loci. Our principal aim was to evaluate different GP approaches to simultaneously model genotype-by-year (GY) effects and breeding values using multi-year data in terms of predictive ability. The models were evaluated under different scenarios reflecting common practice in plant breeding programs, such as different degrees of relatedness between training and validation sets, and using a selected fraction of genotypes in the training set. We used empirical grain yield data of a rye hybrid breeding program. A detailed description of the prediction approaches highlighting the use of kinship for modeling GY is presented. Using the kinship to model GY was advantageous in particular for datasets disconnected across years. On average, predictive abilities were 5% higher for models using kinship to model GY over models without kinship. We confirmed that using data from multiple selection stages provides valuable GY information and helps increasing predictive ability. This increase is on average 30% higher when the predicted genotypes are closely related with the genotypes in the training set. A selection of top-yielding genotypes together with the use of kinship to model GY improves the predictive ability in datasets composed of single years of several selection cycles. Our results clearly demonstrate that the use of multi-year data and appropriate modeling is beneficial for GP because it allows dissecting GY effects from genomic estimated breeding values. The model choice, as well as ensuring
Cameron, Michael F; Frost, Kathryn J; Ver Hoef, Jay M; Breed, Greg A; Whiting, Alex V; Goodwin, John; Boveng, Peter L
The first year of life is typically the most critical to a pinniped's survival, especially for Arctic phocids which are weaned at only a few weeks of age and left to locate and capture prey on their own. Their seasonal movements and habitat selection are therefore important factors in their survival. During a cooperative effort between scientists and subsistence hunters in October 2004, 2005, and 2006, 13 female and 13 male young (i.e., age Bering Strait and into the Bering Sea where they spent the winter and early spring. The SDRs of 17 (8 female and 9 male) seals provided frequent high-quality positions in the Bering Sea; their data were used in our analysis. To investigate habitat selection, we simulated 20 tracks per seal by randomly selecting from the pooled distributions of the absolute bearings and swim speeds of the tagged seals. For each point in the observed and simulated tracks, we obtained the depth, sea-ice concentration, and the distances to sea-ice, open water, the shelf break and coastline. Using logistic regression with a stepwise model selection procedure, we compared the simulated tracks to those of the tagged seals and obtained a model for describing habitat selection. The regression coefficients indicated that the bearded seals in our study selected locations near the ice edge. In contrast, aerial surveys of the bearded seal population, predominantly composed of adults, indicated higher abundances in areas farther north and in heavier pack ice. We hypothesize that this discrepancy is the result of behavioral differences related to age. Ice concentration was also shown to be a statistically significant variable in our model. All else being equal, areas of higher ice concentration are selected for up to about 80%. The effects of sex and bathymetry were not statistically significant. The close association of young bearded seals to the ice edge in the Bering Sea is important given the likely effects of climate warming on the extent of sea-ice and
Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi
To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat ( Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598-50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.
Full Text Available To evaluate the potential of genomic selection (GS, a selection experiment with GS and phenotypic selection (PS was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench. To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598–50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.
He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin
Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
Aschenbrenner, Alexandre; Hackradt, Carlos Werner; Ferreira, Beatrice Padovani
The early life history of Lutjanus alexandrei and Lutjanus jocu in Southwestern Atlantic is still largely unknown. Habitat use of different life stages (i.e. size categories and densities) of the Brazilian snapper (L. alexandrei) and dog snapper (L. jocu) was examined in a tropical portion of NE coast of Brazil. Visual surveys were conducted in different shallow habitats (mangroves and reefs). Both snapper species showed higher densities in early life stages in mangrove habitat, with a clear increase in fish size from mangrove to adjacent reefs. Post-settler individuals were exclusively found in mangroves for both species. Juveniles of L. alexandrei were also registered only in mangroves, while sub-adult individuals were associated with both mangrove and reef habitats. Mature individuals of L. alexandrei were only observed in reef habitats. Juvenile and sub-adult individuals of the dog snapper were both associated with mangrove and reef habitats, with high densities registered in mangroves. Mature individuals of L. jocu were not registered in the study area. This pattern suggests preference for mangrove habitat in early life stages for both species. Ontogenetic movement between habitats was also recorded. This pattern denotes habitat selection across different life cycle of both species. Such information highlights the importance of directing management and conservation efforts to these habitats to secure the continuity of contribution to adult populations. Copyright © 2015 Elsevier Ltd. All rights reserved.
Full Text Available A large number of potato varieties and distinguished breeding lines disappeared as an effect of nonfavourable climatically conditions and especially by viruses diseases, as well as other biological and viruses degeneration. To avoid the negative effect of degeneration on potato varieties and distinguished breeding lines, the method of selection for maintaining and multiplication of potato is applying in Romania in the frame of National Center for Maintaining of potato varieties and distinguished breeding lines Apa Rosie, Covasna County, which belong to the Station for Research and Development of Potato, Targu Secuiesc, Covasna County.In this center are maintained and multiplied all distinguished varieties and breeding centers from Romania (National Institute for research and Development of Potato and Sugar beet Brasov, Research and Development Station for Agriculture Suceava, Research and Development Station for Potato Targu Secuiesc, Research and development Station for Potato Miercurea Ciuc.Using the method of selection for maintaining it is possible an early identification of somatic mutations, disease (especially viruses infection by visual elimination or by serological testing.The viruses’ infection of potato leads to disturbed the metabolism of plants and produces anatomical – morphological alters as: mosaic, crinkle, rolling, browning of leaves and plants deformation.The disturbing of plant metabolism has as negative effect the reduction of vegetation period, decreasing the yield capacity, depreciation of physical and chemical quality of tubers.The genetically complex structure of cultivated potato (2n = 4x = 48 and strong segregation of long – expected characters in the obtained future progeny by sexual hybridization, complicated many times by nonfavourable linkage, are the backgrounds for initiation of maintain selection.
The Wadden Sea region is one of the most important breeding areas in Western Europe for coastal breeding bird species. It is expected that management of salt marshes is important for successful conservation of breeding bird populations but the impact of management on the habitat quality for breeding birds is still not fully understood. In this study the effects of management on the three crucial habitat characteristics for breeding birds were studied on mainland salt marshes: effects of manag...
XINGBO ZHAO1∗. 1College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China ... 4Hebei Liansheng Agricultural Development Company Limited, Baoding 072750, People's Republic of China. [Chen X. ... breed population (1.76±0.03) was significantly greater than.
Full Text Available Abundance of common shrew (Sorex araneus was evaluated on selected forest sites in Moravia, Czech Republic. Six types of habitats were assessed: forest clearings and mature forests in lowlands (173 – 233 m, uplands (360 – 600 m, and mountains (600 – 1200 m. Data were collected over five‑year‑long periods; 2006 – 2010 (uplands and 2007 – 2011 (lowlands and mountains. Small terrestrial mammals were captured using snap traps laid in lines. In total, 200 individuals of common shrew were trapped. Relative abundance among different habitats was statistically evaluated. The highest relative abundance was found in mountain forest clearings (n = 132, rA = 0.719. Lower abundance was in upland forest clearings (n = 15, rA = 0.384, in mature mountain forests (n = 32, rA = 0.355, and in the lowland forest clearings (n = 9, rA = 0.109. The lowest abundance was in mature upland forests (n = 9, rA = 0.031 and in mature lowland forests (n = 3, rA = 0.011. Differences between sites were statistically significant. Among all altitudes, shrew populations in plantations were significantly more numerous than those in mature forests. Mountain forest clearings with dense herb layer proved to be the most suitable habitat while mature lowland forests with less developed herbaceous layer were the least suitable. Forest clearings proved to be an important refuge for the populations of common shrew.
Rostro-Garc?a, Susana; Kamler, Jan F.; Hunter, Luke T. B.
Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges) and 4th order (selection of kill sites within the habitats used) of a reintroduced populatio...
Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio
Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.
John W. Edwards; Susan C. Loeb; David C. Guynn
Multiple regression and use-availability analyses are two methods for examining habitat selection. Use-availability analysis is commonly used to evaluate macrohabitat selection whereas multiple regression analysis can be used to determine microhabitat selection. We compared these techniques using behavioral observations (n = 5534) and telemetry locations (n = 2089) of...
Full Text Available We examined home range characteristics and habitat selection of Daurian hedgehogs in Ikh Nart Nature Reserve, Mongolia. Home ranges of hedgehogs varied from 113.15 ha to 2,171.97 ha, and were larger in early summer than late summer. Hedgehogs showed relative preference for rocky outcrops and low-density shrub habitats, and relative avoidance of high- density shrub areas. Habitat selection also changed between early and late summer, shifting to greater use of low-density shrub areas and decreased use of forb-dominated short grass. Our baseline data on home ranges and habitat selection expand understanding of hedgehog ecology and provide guidance for future management decisions in Ikh Nart Nature Reserve and elsewhere in Mongolia.
Full Text Available Of 30 known subpopulations of Phelsuma guimbeaui, 18 are in patches of exotic forest and are predicted to disappear in the next decade. One possible means of mitigating the reduction in genetic diversity associated with the loss of subpopulations is to translocate “at risk” subpopulations to more secure habitats. Prior to any such intervention, it is important to identify a species’ basic ecological needs. We had three main objectives: to calculate home range sizes of adult geckos; characterise habitat selection among age groups; and identify the order of importance of each habitat predictor. Habitat selection of P. guimbeaui was explored at the population, home range and microhabitat levels. Males had larger home ranges than females, and overlapped temporally with more females than males. We showed that habitat selection differed between age groups. In order of importance, tree diversity, tree species, tree height, trunk dbh and cavity density were important habitat predictors. We discuss how these data can be used to inform the choice of sites for the translocation of threatened subpopulations. Our results also highlight the importance of undertaking habitat restoration for the long-term conservation of the 12 subpopulations that survive in patches of endemic forest.
Laboratory experiments with a rock-dwelling nocturnal gecko, Oedura lesueurii, showed that retreat-site selection (and other behaviours) are affected by the interplay between thermal benefits, social advantages and avoidance of predators. Velvet geckos were highly selective in habitat choice: they preferred artificial retreat-sites that mimic the thermal properties of natural rocks in full sun rather than those that mimic rocks in full shade; mature male geckos rarely shared retreat-sites with other adult males; and these lizards strongly avoided retreat-sites covered with the scent of a natural predator (the broadheaded snake, Hoplocephalus bungaroides). After documenting these preferences, we carried out additional trials in which two or more of these factors co-occurred, as is often the case in nature. Social dominance interacted with thermal benefits in determining retreat-site selection, with smaller (subordinate) males forced to use cooler retreat-sites when larger (dominant) males were present. Avoidance of predators was a higher priority than thermoregulation: the lizards would forego a warmer retreat-site with predator scent in favour of a cooler, unscented one. There was also an interplay between social dominance and predator scent: smaller males were forced to use either predator-scented retreat-sites or no retreat-site when larger males were present. General activity levels, and the frequencies of specific behavioural acts, also shifted in response to social and predator-scent cues. Our study emphasizes the complexity of habitat-selection behaviour in these lizards, and clarifies the criteria used in retreat-site selection when (as is commonly the case) the animal must choose between conflicting priorities. Copyright 1998 The Association for the Study of Animal Behaviour. Copyright 1998 The Association for the Study of Animal Behaviour.
Ela, S.W.; Anderson, M.A.; Brill, W.J.
We have increased, through screening and breeding, the ability of corn (maize, Zea mays L.) to support bacterial nitrogen fixation in or on corn roots. Isotopic N fixed from /sup 15/N/sub 2/ was found on the roots. Even though the nitrogen-fixing association depends on germ plasm from tropical corn, the activity can be bred into corn currently used in midwestern United States agriculture.
K. Anne-Isola Nekaris
Full Text Available Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective conservation surrogates especially in habitats where traditional flagship species have been extirpated.
Francisco G. Araújo
Full Text Available Distribution of anchovies (Clupeiformes, Engraulidae was described in the Sepetiba Bay, a coastal area of Southeastern Brazil, to assess eventual mechanisms of habitat selection. Two fish sampling programmes were accomplished; one using beach seine (1998/2000 to catch juveniles in sandy beaches, and the other, using seines (1999/2000 to catch adults in deeper bay areas. Six species representing 4 genera were recorded: Anchoa tricolor, Anchoa januaria, Anchoa lyolepis, Cetengraulis edentulus, Engraulis anchoita and Lycengraulis grossidens. Anchoa tricolor and A. januaria were the most abundant species, with the former peaking in the outer bay, while the latter peaking in the inner bay. Adults A. tricolor are target of heavy commercial fisheries in the bay during Spring-Summer, while E. anchoita, an abundant species in the continental shelf, was occasionally caught in large numbers during the Autumn. The habitat selection, by using two different bay areas, was developed by the two most abundant species, a probable mechanism to enable their coexistence.
Zhao, Jie; Li, Tingting; Zhu, Chao; Jiang, Xiaoling; Zhao, Yan; Xu, Zhenzhen; Yang, Shuming; Chen, Ailiang
Meat traceability based on molecular markers is exerting a great influence on food safety and will enhance its key role in the future. This study aimed to investigate and verify the polymorphism of 23 microsatellite markers and select the most suitable markers for individual identification and meat traceability of six swine breeds in the Chinese market. The mean polymorphism information content value of these 23 loci was 0.7851, and each locus exhibited high polymorphism in the pooled population. There were 10 loci showing good polymorphism in each breed, namely, Sw632, S0155, Sw2406, Sw830, Sw2525, Sw72, Sw2448, Sw911, Sw122 and CGA. When six highly polymorphic loci were combined, the match probability value for two random individual genotypes among the pig breeds (Beijing Black, Sanyuan and Taihu) was lower than 1.151 E-06. An increasing number of loci indicated a gradually decreasing match probability value and therefore enhanced traceability accuracy. The validation results of tracing 18 blood and corresponding meat samples based on five highly polymorphic loci (Sw2525, S0005, Sw0107, Sw911 and Sw857) were successful, with 100% conformation probability, which provided a foundation for establishing a traceability system for pork in the Chinese market.
Full Text Available Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5, Landrace (n = 13, and Duroc (n = 6. An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc.These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718 in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.
Rostro-García, Susana; Kamler, Jan F.; Hunter, Luke T. B.
Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges) and 4th order (selection of kill sites within the habitats used) of a reintroduced population of cheetahs Acinonyx jubatus in Phinda Private Game Reserve, South Africa. Along with landscape characteristics, we investigated if lion Panthera leo presence affected habitat selection of cheetahs. Our results indicated that cheetah habitat selection was driven by a trade-off between resource acquisition and lion avoidance, and the balance of this trade-off varied with scale: more open habitats with high prey densities were positively selected within home ranges, whereas more closed habitats with low prey densities were positively selected for kill sites. We also showed that habitat selection, feeding ecology, and avoidance of lions differed depending on the sex and reproductive status of cheetahs. The results highlight the importance of scale when investigating a species’ habitat selection. We conclude that the adaptability of cheetahs, together with the habitat heterogeneity found within Phinda, explained their success in this small fenced reserve. The results provide information for the conservation and management of this threatened species, especially with regards to reintroduction efforts in South Africa. PMID:25693067
Rostro-García, Susana; Kamler, Jan F; Hunter, Luke T B
Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges) and 4th order (selection of kill sites within the habitats used) of a reintroduced population of cheetahs Acinonyx jubatus in Phinda Private Game Reserve, South Africa. Along with landscape characteristics, we investigated if lion Panthera leo presence affected habitat selection of cheetahs. Our results indicated that cheetah habitat selection was driven by a trade-off between resource acquisition and lion avoidance, and the balance of this trade-off varied with scale: more open habitats with high prey densities were positively selected within home ranges, whereas more closed habitats with low prey densities were positively selected for kill sites. We also showed that habitat selection, feeding ecology, and avoidance of lions differed depending on the sex and reproductive status of cheetahs. The results highlight the importance of scale when investigating a species' habitat selection. We conclude that the adaptability of cheetahs, together with the habitat heterogeneity found within Phinda, explained their success in this small fenced reserve. The results provide information for the conservation and management of this threatened species, especially with regards to reintroduction efforts in South Africa.
Full Text Available Understanding how animals utilize available space is important for their conservation, as it provides insight into the ecological needs of the species, including those related to habitat, prey and inter and intraspecific interactions. We used 28 months of radio telemetry data and information from 200 kill locations to assess habitat selection at the 3rd order (selection of habitats within home ranges and 4th order (selection of kill sites within the habitats used of a reintroduced population of cheetahs Acinonyx jubatus in Phinda Private Game Reserve, South Africa. Along with landscape characteristics, we investigated if lion Panthera leo presence affected habitat selection of cheetahs. Our results indicated that cheetah habitat selection was driven by a trade-off between resource acquisition and lion avoidance, and the balance of this trade-off varied with scale: more open habitats with high prey densities were positively selected within home ranges, whereas more closed habitats with low prey densities were positively selected for kill sites. We also showed that habitat selection, feeding ecology, and avoidance of lions differed depending on the sex and reproductive status of cheetahs. The results highlight the importance of scale when investigating a species' habitat selection. We conclude that the adaptability of cheetahs, together with the habitat heterogeneity found within Phinda, explained their success in this small fenced reserve. The results provide information for the conservation and management of this threatened species, especially with regards to reintroduction efforts in South Africa.
Raabe, Ellen A.; D'Anjou, Robert; Pope, Domonique K.; Robbins, Lisa L.
This project combines underwater video with maps and descriptions to illustrate diverse seafloor habitats from Tampa Bay, Florida, to Mobile Bay, Alabama. A swath of seafloor was surveyed with underwater video to 100 meters (m) water depth in 1999 and 2000 as part of the Gulfstream Natural Gas System Survey. The U.S. Geological Survey (USGS) in St. Petersburg, Florida, in cooperation with Eckerd College and the Florida Department of Environmental Protection (FDEP), produced an archive of analog-to-digital underwater movies. Representative clips of seafloor habitats were selected from hundreds of hours of underwater footage. The locations of video clips were mapped to show the distribution of habitat and habitat transitions. The numerous benthic habitats in the northeastern Gulf of Mexico play a vital role in the region's economy, providing essential resources for tourism, natural gas, recreational water sports (fishing, boating, scuba diving), materials, fresh food, energy, a source of sand for beach renourishment, and more. These submerged natural resources are important to the economy but are often invisible to the general public. This product provides a glimpse of the seafloor with sample underwater video, maps, and habitat descriptions. It was developed to depict the range and location of seafloor habitats in the region but is limited by depth and by the survey track. It should not be viewed as comprehensive, but rather as a point of departure for inquiries and appreciation of marine resources and seafloor habitats. Further information is provided in the Resources section.
Sae-Lim, P.; Komen, J.; Kause, A.; Martin, K.E.; Crooijmans, R.P.M.A.; Arendonk, van J.A.M.; Parsons, J.E.
Enhancing selection using two-stage selection is normally implemented by pre-selection for tagging weight (BWT) and by final selection for ungutted harvest weight (BWH) and thermal growth coefficient from tagging to harvest (TGCTH). However, selection on harvest traits, i.e., gutted weight (GBWH),
Longin, C Friedrich H; Utz, H Friedrich; Reif, Jochen C; Schipprack, Wolfgang; Melchinger, Albrecht E
Optimum allocation of resources is of fundamental importance for the efficiency of breeding programs. The objectives of our study were to (1) determine the optimum allocation for the number of lines and test locations in hybrid maize breeding with doubled haploids (DHs) regarding two optimization criteria, the selection gain deltaG(k) and the probability P(k) of identifying superior genotypes, (2) compare both optimization criteria including their standard deviations (SDs), and (3) investigate the influence of production costs of DHs on the optimum allocation. For different budgets, number of finally selected lines, ratios of variance components, and production costs of DHs, the optimum allocation of test resources under one- and two-stage selection for testcross performance with a given tester was determined by using Monte Carlo simulations. In one-stage selection, lines are tested in field trials in a single year. In two-stage selection, optimum allocation of resources involves evaluation of (1) a large number of lines in a small number of test locations in the first year and (2) a small number of the selected superior lines in a large number of test locations in the second year, thereby maximizing both optimization criteria. Furthermore, to have a realistic chance of identifying a superior genotype, the probability P(k) of identifying superior genotypes should be greater than 75%. For budgets between 200 and 5,000 field plot equivalents, P(k) > 75% was reached only for genotypes belonging to the best 5% of the population. As the optimum allocation for P(k)(5%) was similar to that for deltaG(k), the choice of the optimization criterion was not crucial. The production costs of DHs had only a minor effect on the optimum number of locations and on values of the optimization criteria.
Herein I compare the relative importance of preference for structurally complex habitat against avoidance of competitors and predators in two benthic fishes common in the Gulf of Mexico. The code goby Gobiosoma robustum Ginsburg and clown goby Microgobius gulosus (Girard) are common, ecologically similar fishes found throughout the Gulf of Mexico and in the southeastern Atlantic Ocean. In Florida Bay, these fishes exhibit habitat partitioning: G. robustum is most abundant in seagrass-dominated areas while M. gulosus is most abundant in sparsely vegetated habitats. In a small-scale field survey, I documented the microhabitat use of these species where their distributions overlap. In a series of laboratory experiments, I presented each species with structured (artificial seagrass) versus nonstructured (bare sand) habitats and measured their frequency of choosing either habitat type. I then examined the use of structured versus nonstructured habitats when the two species were placed together in a mixed group. Finally, I placed a predator (Opsanus beta) in the experimental aquaria to determine how its presence influenced habitat selection. In the field, G. robustum was more abundant in seagrass and M. gulosus was more abundant in bare mud. In the laboratory, both species selected grass over sand in allopatry. However, in sympatry, M. gulosus occupied sand more often when paired with G. robustum than when alone. G. robustum appears to directly influence the habitat choice of M. gulosus: It seems that M. gulosus is pushed out of the structured habitat that is the preferred habitat of G. robustum. Thus, competition appears to modify the habitat selection of these species when they occur in sympatry. Additionally, the presence of the toadfish was a sufficient stimulus to provoke both M. gulosus and G. robustum to increase their selection for sand (compared to single-species treatments). Distribution patterns of M. gulosus and G. robustum
Full Text Available The aim of the present study was to evaluate the effect of breed on haematological and biochemical indicators in 3 dwarf rabbit breeds. In the experiment, 30 sexually intact dwarf rabbit females aged 6 mo were used. With the sole exception of white blood cells and haematocrit value, breed had the most significant effect on the majority of haematological indicators monitored. The red blood cell count was higher in the Dwarf Lop compared to the Netherland Dwarf (+1.91×1012 cells/L; P<0.05 and also the Teddy Dwarf (+1.32×1012 cells/L; P<0.05. For haemoglobin concentration, a higher value was found in the Netherland Dwarf than in the Teddy Dwarf (+39.29 g/L; P<0.05 and the Dwarf Lop (+26.36 g/L; P<0.05. For erythrocytic indicators, the highest values of mean corpuscular volume, mean corpuscular haemoglobin and mean corpuscular haemoglobin concentration were found in the Netherland Dwarf. The breed had a significant effect on the urea and potassium values. A higher value of urea was recorded in the Dwarf Lop compared to the Teddy Dwarf (+1.56 mmol/L; P<0.05. For potassium, a higher value was found in the Netherland Dwarf compared to the Teddy Dwarf (+0.85 mmol/L; P<0.05. In addition, a significantly positive correlation (P<0.05 was found between the live weight of dwarf females and values of haematocrit (0.49, albumin (0.54, alanine aminotransferase (0.51, and aspartate aminotransferase (0.41, while a significantly negative correlation (P<0.05 was found between their live weight and values of triacylglycerols (–0.44, alkaline phosphatase (–0.38 and inorganic phosphorus (–0.52.
Parsons, P A
Fitness varies nonlinearly with environmental variables such as temperature, water availability, and nutrition, with maximum fitness at intermediate levels between more stressful extremes. For environmental agents that are highly toxic at exposures that substantially exceed background levels, fitness is maximized at concentrations near zero--a phenomenon often referred to as hormesis. Two main components are suggested: (1) background hormesis, which derives from the direct adaptation of organisms to their habitats; and (2) stress-derived hormonesis, which derives from metabolic reserves that are maintained as an adaptation to environmental stresses through evolutionary time. These reserves provide protection from lesser correlated stresses. This article discusses illustrative examples, including ethanol and ionizing radiation, aimed at placing hormesis into an ecological and evolutionary context. A unifying approach comes from fitness-stress continua that underlie responses to abiotic variables, whereby selection for maximum metabolic efficiency and hence fitness in adaptation to habitats in nature underlies hormetic zones. Within this reductionist model, more specific metabolic mechanisms to explain hormesis are beginning to emerge, depending upon the agent and the taxon in question. Some limited research possibilities based upon this evolutionary perspective are indicated.
Hartati, Retno; Trianto, Agus; Widianingsih
Sea cucumbers face heavily overfished because of their high prices and very strong market demand. One effort suggested to overcome this problem is sea ranching. The objectives of present works were to determine biological, physical, and chemical characteristics of prospective location for sea ranching of sea cucumber Holothuria atra. Two location at Jepara Waters (Teluk Awur and Bandengan WateRs of Jepara Regency) were selected. The determination of chemical (salinity, temperature, dissolved oxygen of water, phosphate, nitrate, nitrite and ammonium of water and sediment, organic matters of sediment), physical (transparancy, sedimen grains size, water current direction and its velocity), biologycal characteristic (coverage of seagrass and its macroalgae associated, phytoplankton as well as chlorophyl-a and phaeopytin of water and sediment) ware determined. The result of present work showed that some characteristic were matched with requirement as sea ranching location of sea cucumber because the density of sea cucumber in the sea is a function of habitat features. For sediment feeding holothurians of the family Aspidochirotida, the biologycal characteristic act as very important considerations by providing sea cucumber food. High cholophyl-a and phaeopytin in sediment also represent a prosperous habitat for sea cucumber ranching.
Stock, K F; Distl, O
Different modes of selection in dogs were studied with a special focus on the availability of disease information. Canine hip dysplasia (CHD) in the German shepherd dog was used as an example. The study was performed using a simulation model, comparing cases when selection was based on phenotype, true or predicted breeding value, or genomic breeding value. The parameters in the simulation model were drawn from the real population data. The data on all parents and 40% of their progeny were assumed to be available for the genetic evaluation carried out by Gibbs sampling. With respect to the use of disease records on progeny, three scenarios were considered: random exclusion of disease data (no restrictions, N), general exclusion of disease data (G) and exclusion of disease data for popular sires (P). One round of selection was considered, and the response was expressed as change of mean CHD score, proportion of dogs scored as normal, proportion of dogs scored as clearly affected and true mean breeding value in progeny of popular sires in comparison with all sires. When no restrictions on data were applied, selection on breeding value was three times more efficient than when some systematic exclusion was practised. Higher selection response than in the exclusion cases was achieved by selecting on the basis of genomic breeding value and CHD score. Genomic selection would therefore be the method of choice in the future.
Adrienne C. Shelton
Full Text Available Organic growers face unique challenges when raising sweet corn, and benefit from varieties that maintain high eating quality, germinate consistently, deter insect pests, and resist diseases. Genotype by environment rank changes can occur in the performance of cultivars grown on conventional and organic farms, yet few varieties have been bred specifically for organic systems. The objective of this experiment was to evaluate the changes made to open-pollinated sweet corn populations using recurrent selection and a participatory plant breeding (PPB methodology. From 2008 to 2011, four cycles of two open-pollinated (OP sweet corn populations were selected on a certified organic farm in Minnesota using a modified ear-to-row recurrent selection scheme. Selections were made in collaboration with an organic farmer, with selection criteria based on traits identified by the farmer. In 2012 and 2013, the population cycles were evaluated in a randomized complete block design in two certified organic locations in Wisconsin, with multiple replications in each environment. Significant linear trends were found among cycles of selection for quantitative and qualitative traits, suggesting the changes were due to recurrent selection and PPB methodology for these populations. However, further improvement is necessary to satisfy the requirements for a useful cultivar for organic growers.
Som, Nicholas A.; Goodman, Damon H.; Perry, Russell W.; Hardy, Thomas B.
Previous methods for constructing univariate habitat suitability criteria (HSC) curves have ranged from professional judgement to kernel-smoothed density functions or combinations thereof. We present a new method of generating HSC curves that applies probability density functions as the mathematical representation of the curves. Compared with previous approaches, benefits of our method include (1) estimation of probability density function parameters directly from raw data, (2) quantitative methods for selecting among several candidate probability density functions, and (3) concise methods for expressing estimation uncertainty in the HSC curves. We demonstrate our method with a thorough example using data collected on the depth of water used by juvenile Chinook salmon (Oncorhynchus tschawytscha) in the Klamath River of northern California and southern Oregon. All R code needed to implement our example is provided in the appendix. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
Mauro Rezende Tavares
Full Text Available The factors that influence the selection of marine macrophytes by meso-herbivores are complex, and may include the nutritional quality of algae, the value of the habitat as a shelter, and the availability of algae in the environment. Here we investigated the existence of differential use of Sargassum filipendula C. Agardh, 1824 (Phaeophyta and Galaxaura stupocaulon Kjellman, 1900 (Rhodophyta as habitats and feeding resources by species of Hyalidae and Ampithoidae, in laboratory manipulation experiments and in an algal bed on the northern coast of the state of São Paulo, Brazil. In the field, 19 fronds were collected from each alga and the associated amphipods were identified and counted. To evaluate food preference and habitat selection by amphipods, we conducted laboratory experiments using containers containing fragments of algae and individuals of Cymadusa filosa Savigny, 1816 or Hyale nigra (Haswell, 1879. In natural conditions, the density of C. filosa was significantly higher on G. stupocaulon, while in the feeding and habitat preference experiment we found a higher density on S. filipendula. The densities of H. nigra did not differ between the algae in both experiments, probably as a result of the variety of food items in its diet, and its high mobility and wide distribution on different substrates. The different results for C. filosa suggest that the pattern of feeding and habitat selection can be affected by external characteristics of the algae; probably, refuge from predation is an important selective force acting on the use of algae by these animals.
Full Text Available The variations in ground beetles (Coleoptera: Carabidae assemblages across the three types of farmland habitats, arable land, meadows and woody vegetation were studied in relation to vegetation cover structure, intensity of agrotechnical interventions and selected soil properties. Material was pitfall trapped in 2010 and 2011 on twelve sites of the agricultural landscape in the Prešov town and its near vicinity, Eastern Slovakia. A total of 14,763 ground beetle individuals were entrapped. Material collection resulted into 92 Carabidae species, with the following six species dominating: Poecilus cupreus, Pterostichus melanarius, Pseudoophonus rufipes, Brachinus crepitans, Anchomenus dorsalis and Poecilus versicolor. Studied habitats differed significantly in the number of entrapped individuals, activity abundance as well as representation of the carabids according to their habitat preferences and ability to fly. However, no significant distinction was observed in the diversity, evenness neither dominance. The most significant environmental variables affecting Carabidae assemblages species variability were soil moisture and herb layer 0-20 cm. Another best variables selected by the forward selection were intensity of agrotechnical interventions, humus content and shrub vegetation. The other from selected soil properties seem to have just secondary meaning for the adult carabids. Environmental variables have the strongest effect on the habitat specialists, whereas ground beetles without special requirements to the habitat quality seem to be affected by the studied environmental variables just little.
Shallow water habitat, also referred to as in-stream fish habitat, refers to areas that fish and other aquatic organisms need for concealment, breeding and feeding. This includes large woody snags, boulders, rock ledges, and undercut banks.
Full Text Available Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and (initially more labor, as seen from the System of Rice Intensification (SRI, whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However, unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the
Jonas, I.; Schubert, K. A.; Reijne, A. C.; Scholte, J.; Garland, T.; Gerkema, M. P.; Scheurink, A. J. W.; Nyakas, C.; van Dijk, G.; Garland Jr., T.; Maxson, Stephen
Voluntary physical activity may be related to personality traits. Here, we investigated these relations in two mouse lines selectively bred for high voluntary wheel-running behavior and in one non-selected control line. Selection lines were more explorative and "information gathering" in the
Phocas, F; Belloc, C; Bidanel, J; Delaby, L; Dourmad, J Y; Dumont, B; Ezanno, P; Fortun-Lamothe, L; Foucras, G; Frappat, B; González-García, E; Hazard, D; Larzul, C; Lubac, S; Mignon-Grasteau, S; Moreno, C R; Tixier-Boichard, M; Brochard, M
Agroecology uses natural processes and local resources rather than chemical inputs to ensure production while limiting the environmental footprint of livestock and crop production systems. Selecting to achieve a maximization of target production criteria has long proved detrimental to fitness traits. However, since the 1990s, developments in animal breeding have also focussed on animal robustness by balancing production and functional traits within overall breeding goals. We discuss here how an agroecological perspective should further shift breeding goals towards functional traits rather than production traits. Breeding for robustness aims to promote individual adaptive capacities by considering diverse selection criteria which include reproduction, animal health and welfare, and adaptation to rough feed resources, a warm climate or fluctuating environmental conditions. It requires the consideration of genotype×environment interactions in the prediction of breeding values. Animal performance must be evaluated in low-input systems in order to select those animals that are adapted to limiting conditions, including feed and water availability, climate variations and diseases. Finally, we argue that there is no single agroecological animal type, but animals with a variety of profiles that can meet the expectations of agroecology. The standardization of both animals and breeding conditions indeed appears contradictory to the agroecological paradigm that calls for an adaptation of animals to local opportunities and constraints in weakly artificialized systems tied to their physical environment.
Oetjen, Katharina; Ferber, Steven; Dankert, Ilka; Reusch, Thorsten B. H.
Eelgrass Zostera marina is an ecosystem-engineering species of outstanding importance for coastal soft sediment habitats that lives in widely diverging habitats. Our first goal was to detect divergent selection and habitat adaptation at the molecular genetic level; hence, we compared three pairs of
Full Text Available Field studies were conducted in two years using 638 F2 and 1185 F3 lines of selected 16 F1 and 15 F2 parent lines (³80 pods plant-1 to evaluate pod number and CO2 exchange rate (CER as selection criteria. Pod and seed number, and seed weight of individual lines were observed during harvesting time, and CER of randomly selected 32 F2 and 30 F3 lines was measured at initial seed filling stage. The selection of F2 lines based on pod number to generate F3 lines increased the average of seed yield by 39%, and pod number by 77% in F3 lines compared with F2 lines. A close relationships was found between seed weight and pod or seed number per plant. Net CER responded sensitively to a reduction of light in a short-term and showed 78% of F2 lines and all F3 lines with maximum CER (Pmax³20 mmolCO2.m-2.s-1. The ratio of pod number per plant and Pmax varied between lines and were used to group lines resulting in close relationships between Pmax and pod number. It is concluded that the use of pod number and CER (Pmax as selection criteria offers an alternative approach in soybean breeding for high yield.
Brock M Huntsman
Full Text Available Density-dependent (DD and density-independent (DI habitat selection is strongly linked to a species' evolutionary history. Determining the relative importance of each is necessary because declining populations are not always the result of altered DI mechanisms but can often be the result of DD via a reduced carrying capacity. We developed spatially and temporally explicit models throughout the Chena River, Alaska to predict important DI mechanisms that influence Chinook salmon spawning success. We used resource-selection functions to predict suitable spawning habitat based on geomorphic characteristics, a semi-distributed water-and-energy balance hydrologic model to generate stream flow metrics, and modeled stream temperature as a function of climatic variables. Spawner counts were predicted throughout the core and periphery spawning sections of the Chena River from escapement estimates (DD and DI variables. Additionally, we used isodar analysis to identify whether spawners actively defend spawning habitat or follow an ideal free distribution along the riverscape. Aerial counts were best explained by escapement and reference to the core or periphery, while no models with DI variables were supported in the candidate set. Furthermore, isodar plots indicated habitat selection was best explained by ideal free distributions, although there was strong evidence for active defense of core spawning habitat. Our results are surprising, given salmon commonly defend spawning resources, and are likely due to competition occurring at finer spatial scales than addressed in this study.
Indicators of breed composition such as hair color and ear length often result in increased or decreased prices of young calves marketed into feedlots. Similarly, feedlot research trials are often initiated with blended cattle from multiple sources with little more than coat color used as a blockin...
Qu, Luping; Widrlechner, Mark P
Strong seed dormancy has been an obstacle for field production of Echinacea species. Previous research on overcoming Echinacea seed dormancy has been extensive and focused on treatment methods, which involve time and expense, and are incompatible with organic production if synthetic chemicals are used. We have attempted to genetically reduce seed dormancy through selection and breeding in Echinacea, by using E. pallida as a model species. Three accessions were used in this study. Nine parent plants of each accession selected from early, in-dark germinated seeds (in-dark plants) or from late, in-light seeds (in-light plants) were planted and grouped by accession and germination treatment method for seed production through a polycross method. Germination tests indicated that these in-dark plants produced seed (in-dark seed) with significantly reduced seed dormancy when tested under light or dark conditions in comparison to the seed of the in-light plants (in-light seed). Among the three accessions, the in-dark seed germinated at much higher rates than did the in-light seed, more than 2× at 25°C under light and up to an 83× increase in darkness, and up to an 8× increase over the corresponding parental seed lots under comparable germination conditions. In addition to these increases in germination, the in-dark seed showed early and synchronized germination as compared to the in-light seed. Since these results were achieved through only one cycle of selection and breeding, they strongly suggest that we have developed a very effective method for modifying seed dormancy in Echinacea.
Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio
Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity. PMID:23985993
Pan, Yen-Ju; Souissi, Anissa; Sadovskaya, Irina
In this study, we conducted a novel approach of selective breeding by using temperature acclimation to enhance the aquaculture potential of the tropical cyclopoid copepod Apocyclops royi. Two copepod culture strains were acclimated separately at high (28°C, control strain) and low (18°C, selective...
Sogge, Mark K.; Marshall, Robert M.; Finch, Deborah M.; Stoleson, Scott H.
The distribution and abundance of a species across a landscape depends, in part, on the distribution and abundance of appropriate habitat. If basic resource needs such as food, water, and cover are not present, then that species is excluded from the area. Scarcity of appropriate habitat is generally the key reason for the status of most rare and endangered species. An understanding of an endangered species’ habitat characteristics is crucial to effective management, conservation and recovery.
Full Text Available Feeding stations are commonly used to sustain conservation programs of scavengers but their impact on behaviour is still debated. They increase the temporal and spatial predictability of food resources while scavengers have supposedly evolved to search for unpredictable resources. In the Grands Causses (France, a reintroduced population of Griffon vultures Gyps fulvus can find carcasses at three types of sites: 1. "light feeding stations", where farmers can drop carcasses at their farm (spatially predictable, 2. "heavy feeding stations", where carcasses from nearby farms are concentrated (spatially and temporally predictable and 3. open grasslands, where resources are randomly distributed (unpredictable. The impact of feeding stations on vulture's foraging behaviour was investigated using 28 GPS-tracked vultures. The average home range size was maximal in spring (1272 ± 752 km(2 and minimal in winter (473 ± 237 km(2 and was highly variable among individuals. Analyses of home range characteristics and feeding habitat selection via compositional analysis showed that feeding stations were always preferred compared to the rest of the habitat where vultures can find unpredictable resources. Feeding stations were particularly used when resources were scarce (summer or when flight conditions were poor (winter, limiting long-ranging movements. However, when flight conditions were optimal, home ranges also encompassed large areas of grassland where vultures could find unpredictable resources, suggesting that vultures did not lose their natural ability to forage on unpredictable resources, even when feeding stations were available. However during seasons when food abundance and flight conditions were not limited, vultures seemed to favour light over heavy feeding stations, probably because of the reduced intraspecific competition and a pattern closer to the natural dispersion of resources in the landscape. Light feeding stations are interesting tools
Waddle, H.R.; Coutant, C.C.; Wilson, J.L.
Summer habitat selection patterns of 18 adult striped bass (Morone saxatilis) in Cherokee Reservoir were monitored with externally attached temperature-sensing acoustic or radio transmitters from June through September 1977. Mortalities of adult striped bass in this reservoir were hypothesized to be related to high summer temperatures and low dissolved oxygen (DO). The inhabited areas or refuges differed from noninhabited areas by maintaining temperatures less than or equal to 22 C and DO concentrations greater than 5 mg/liter. Total water hardness, pH, and water transparency were not significantly different among refuges and noninhabited areas. Movement of fish outside refuges occurred more frequently and for longer periods during June when the summer pattern of high temperatures and low DO was less severe. Fish experienced temperatures between 15 and 27 C with mean temperatures of individuals ranging from 18.5 to 22.0 C. Several tagged fish migrated outside the refuges and selected the lowest available temperature, generally near 21 C, even though DO concentrations at these temperatures were 3 mg/liter or less. Long-term survival of tagged and nontagged fish outside refuges was undetermined because no fish were tracked outside a refuge for more than 12 days without being lost. This study indicates that temperature strongly influences the behavior of striped bass and that adults of this species may have a thermal preferendum of approximately 21 C.
Windig, J.J.; Hoving, A.H.
National legislation to breed for scrapie resistence was changed in 2007. The obligatory use of ARR/ARR rams was suspended in that year. Breeding for scrapie resistance is, however, still stimulated and not suspended. In this report a general advice on how to continue breeding for scrapie resistance
Selection and Breeding of Cattle in Asia: Strategies and Criteria for Improved Breeding. Prepared under the Framework of an RCA Project with the Technical Support of the Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture
The International Atomic Energy Agency (IAEA) and the Regional Cooperative Agreement for Asia and the Pacific Region (RCA), with the technical support of the Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, implemented a Technical Cooperation (TC) project entitled Integrated Approach for Improving Livestock Production Using Indigenous Resources and Conserving the Environment (RAS/5/044). The 23 project counterparts and the IAEA technical officer, based on the lack of standard practices in the region with regard to selection of cattle for breeding purposes, and the need to properly manage the genetic resources within each country for improving the productivity of the existing stock while maintaining the unique and beneficial genetic characteristics of the indigenous breeds, agreed during the first meeting to request the IAEA to recruit a group of experts with the task of preparing guidelines for the selection and breeding of cattle and buffalo on the Asian continent. To address these recommendations, an experts meeting on Selection Criteria for Breeding Heifers was organized and held in Mymensingh, Bangladesh. The meeting was hosted by the Faculty of Veterinary Science of the Bangladesh Agricultural University (BAU) from 6 to 10 February 2006. It was attended by six foreign experts and two local experts, and was supported by the technical officer of RAS/5/044. The experts from countries participating in RAS/5/044 gave presentations on the current state of cattle breeding in their countries and two experts working in industrialized countries within the region (New Zealand and Australia) informed the participants about the existing cattle breeding programmes in their respective countries and offered their perspectives on how similar approaches could be transferred to the Member States participating in RAS/5/044. All experts also made a field visit to a prominent dairy-producing region, to experience at first-hand some of the current programmes
Two generations of selection on restricted BLUP breeding values were applied in an experiment with laying hens. Selection had been on phenotype of income minus feed cost (IFC) between 21 and 40 wk of age in the previous five generations. The restriction of no genetic change in egg weight was included in the EBV for power-transformed IFC (i.e., IFCt, with t-values of 3.7 and 3.6 in the two generations, respectively). The experiment consisted of two selection lines plus a randomly bred control of 20 male and 80 female breeders each. Observations on 8,844 survivors to 40 wk were available. Relative to the base population average, the restriction reduced genetic gain in IFC from 4.1 and 3.9% to 2.0 and 2.2% per generation in the two selection lines, respectively. Average EBV for egg weight remained nearly constant after a strong increase in the previous five generations. Rates of genetic gain for egg number, body weight, and feed conversion (feed/egg mass) were not affected significantly. In the seventh generation, a genetic gain in feed conversion of 10.3% relative to the phenotypic mean of the base population was obtained.
Alcinei Mistico Azevedo
Full Text Available The efficiency of artificial neural networks (ANN to model complex problems may enable the prediction of characteristics that are hard to measure, providing better results than the traditional indirect selection. Thus, this study aimed to investigate the potential of using artificial neural networks (ANN for indirect selection against early flowering in lettuce, identify the influence of genotype by environment interaction in this strategy and compare your results with the traditional indirect selection. The number of days to anthesis were used as the desired output and the information of six characteristics (fresh weight of shoots, mass of marketable fresh matter of shoots, commercial dry matter of shoots, average diameter of the head, head circumference and leaf number as input file for the training of the ANN-MLP (Perceptron Multi-Layer. The use of ANN has great potential adjustment for indirect selection for genetic improvement of lettuce against early flowering. The selection based on the predicted values by network provided estimates of gain selection largest that traditional indirect selection. The ANN trained with data from an experiment have low power extrapolation to another experiment, due to effect of interaction genotype by environment. The ANNs trained simultaneously with data from different experiments presented greater predictive power and extrapolation.
Pigeon, Karine E; Cardinal, Etienne; Stenhouse, Gordon B; Côté, Steeve D
To fulfill their needs, animals are constantly making trade-offs among limiting factors. Although there is growing evidence about the impact of ambient temperature on habitat selection in mammals, the role of environmental conditions and thermoregulation on apex predators is poorly understood. Our objective was to investigate the influence of ambient temperature on habitat selection patterns of grizzly bears in the managed landscape of Alberta, Canada. Grizzly bear habitat selection followed a daily and seasonal pattern that was influenced by ambient temperature, with adult males showing stronger responses than females to warm temperatures. Cutblocks aged 0-20 years provided an abundance of forage but were on average 6 °C warmer than mature conifer stands and 21- to 40-year-old cutblocks. When ambient temperatures increased, the relative change (odds ratio) in the probability of selection for 0- to 20-year-old cutblocks decreased during the hottest part of the day and increased during cooler periods, especially for males. Concurrently, the probability of selection for 21- to 40-year-old cutblocks increased on warmer days. Following plant phenology, the odds of selecting 0- to 20-year-old cutblocks also increased from early to late summer while the odds of selecting 21- to 40-year-old cutblocks decreased. Our results demonstrate that ambient temperatures, and therefore thermal requirements, play a significant role in habitat selection patterns and behaviour of grizzly bears. In a changing climate, large mammals may increasingly need to adjust spatial and temporal selection patterns in response to thermal constraints.
V. K. Cherkasova; O. N. Shabetya
12 samples of carrot were analyzed for biochemical components in roots. 5 genotypes with high content of vitamin C, β-carotene, and total sugar were selected as genetic sources of high biochemical components.
Henryon, M; Berg, P; Sørensen, A C
We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stoch......We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis...
Brown, Matthew B G J; Gemmill, Chrissen E C; Miller, Steven; Wehi, Priscilla M
Insects are important but overlooked components of forest ecosystems in New Zealand. For many insect species, information on foraging patterns and trophic relationships is lacking. We examined diet composition and selectivity in a large-bodied insect, the Auckland tree wētā Hemideina thoracica , in three habitat zones in a lowland New Zealand forest. We asked whether H. thoracica selectively forage from available plant food sources, and whether these choices were lipid-rich compared to nonpreferred available plants. We also identified the proportion of invertebrates in their frass as a proxy for omnivory. From reconnaissance plot sampling, together with fecal fragment analysis, we report that more than 93% of individual tree wētā had eaten invertebrates before capture. Additionally, wētā in the highest elevation hillslope habitat zone consumed significantly fewer species of plants on average than wētā on the low-elevation terrace habitat. Upper hillslope wētā also had the highest average number of invertebrate fragments in their frass, significantly more than wētā in the low-elevation terrace habitat zone. Wētā showed high variability in the consumption of fruit and seeds across all habitat zones. Generally, we did not observe diet differences between the sexes (although it appears that male wētā in the mid-hillslope habitat ate fruits and seeds more voraciously than females), suggesting that the sexes have similar niche breadths and display similar degrees of omnivorous behavior. Extraction of leaf lipids demonstrated a range of lipid content values in available plants, and Ivlev's Electivity Index indicated that plant species which demonstrated high electivity tended to have higher concentrations of lipids in their leaves. Our findings indicate that H. thoracica forage omnivorously and selectively, and hence play multiple roles in native ecosystems and food webs.
Bhering, L L; Junqueira, V S; Peixoto, L A; Cruz, C D; Laviola, B G
The aim of this study was to evaluate different methods used in genomic selection, and to verify those that select a higher proportion of individuals with superior genotypes. Thus, F2 populations of different sizes were simulated (100, 200, 500, and 1000 individuals) with 10 replications each. These consisted of 10 linkage groups (LG) of 100 cM each, containing 100 equally spaced markers per linkage group, of which 200 controlled the characteristics, defined as the 20 initials of each LG. Genetic and phenotypic values were simulated assuming binomial distribution of effects for each LG, and the absence of dominance. For phenotypic values, heritabilities of 20, 50, and 80% were considered. To compare methodologies, the analysis processing time, coefficient of coincidence (selection of 5, 10, and 20% of superior individuals), and Spearman correlation between true genetic values, and the genomic values predicted by each methodology were determined. Considering the processing time, the three methodologies were statistically different, rrBLUP was the fastest, and Bayesian LASSO was the slowest. Spearman correlation revealed that the rrBLUP and GBLUP methodologies were equivalent, and Bayesian LASSO provided the lowest correlation values. Similar results were obtained in coincidence variables among the individuals selected, in which Bayesian LASSO differed statistically and presented a lower value than the other methodologies. Therefore, for the scenarios evaluated, rrBLUP is the best methodology for the selection of genetically superior individuals.
Andrew L. Rypel; David R. Bayne
Large-scale habitat preferences of riverine taxa are not always revealed by examining community data. Here, we show how lipid and growth can be used to evaluate hydrologic habitat preferences of fishes resilient to river fragmentation (i.e. species that can tolerate river fragmentation by dams, but not collapse). Lipid content was examined for seven fishes in a major...
Jason W. Scott; Susan E. Meyer; Keith R. Merrill; Val J. Anderson
A central question of invasion biology is how an exotic species invades new habitats following its initial establishment. Three hypotheses to explain this expansion are: (1) the existence of 'general purpose' genotypes, (2) the in situ evolution of novel genotypes, and (3) the dispersal of existing specialized genotypes into habitats for which they are pre-...
Full Text Available Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.
V. K. Cherkasova
Full Text Available 12 samples of carrot were analyzed for biochemical components in roots. 5 genotypes with high content of vitamin C, β-carotene, and total sugar were selected as genetic sources of high biochemical components.
Nielsen, H.M.; Christensen, L.G.; Groen, A.F.
The objective was to present 2 methods for the derivation of nonmarket values for functional traits in dairy cattle using deterministic simulation and selection index theory. A nonmarket value can be a value representing animal welfare and societal influences for animal production, which can be
El-Kareem Ismail, Tarek Gad
The present work aims to assess the spatial distribution, analyze shell utilization, shell fitness and determine the effect of coexistence of two hermit crabs Calcinus latens and Clibanarius signatus on used shell resources in various habitats on the Red Sea Coast. Also, to determine the choice of shells and investigate the shell species preference of C. latens and C. signatus in the laboratory. The hermit crabs C. latens and C. signatus were found to occupy shells of 39 gastropod species. The most commonly occupied gastropod shells are those belonging to genera Strombus, Nerita, Cerithium and Planaxis. The results showed that crab individuals utilized mainly the shell with elongate aperture. Laboratory experiments showed that two crab species preferred shells of Strombus followed by Cerithium and Nerita when offered shells of nearly similar size (optimal). Crab individuals showed a significant preference for optimal sized shells when given suboptimal shells as an alternative choice. Also, the hermit crabs avoid damaged shells when given a choice of optimal sized damaged shell and optimal sized intact one. In addition, two hermit crab species chose shells of smaller than optimal size when given a choice of damaged optimal sized shells and smaller intact ones. On the other hand, field observations showed that most crab individuals lived in adequate sized shells. The present data conclude that shell selection by hermit crabs C. latens and C. signatus depends mostly on shell internal volume, shell quality and shell aperture size than other factors, because they provide a maximum protection for hermit crabs.
Howard B. Stauffer; Cynthia J. Zabel; Jeffrey R. Dunk
We compared a set of competing logistic regression habitat selection models for Northern Spotted Owls (Strix occidentalis caurina) in California. The habitat selection models were estimated, compared, evaluated, and tested using multiple sample datasets collected on federal forestlands in northern California. We used Bayesian methods in interpreting...
Full Text Available Abstract Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers. The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.
Koehler, D.K.; Anderson, S.H.
Research has been conducted on various aspects of the ecology of wildlife residing on and adjacent to the Subsurface Disposal Area (SDA) and one other low-level radioactive waste disposal site on the Idaho National Engineering Laboratory (INEL) in southeastern Idaho. Habitat use and food selection data were collected for deer mice (Peromyscus maniculatus), montane voles (Microtus montanus), Ord's kangaroo rats (Dipodomys ordii), and Townsend's ground squirrels (Spermophilus townsendii) near a sagebrush (Artemisia tridentata)/crested wheatgrass (Agropyron cristatum) interface. Significantly more captures occurred in the native sagebrush habitat than in areas planted in crested wheatgrass or in disturbed sites. Crested wheatgrass, a prolific seed producer, still accounted for over 30% of the total captures. Montane voles and Townsend's ground squirrels (during periods of aboveground activity) used the crested wheatgrass habitat throughout the summer, while deer mice and Ord's kangaroo rats exhibited heavy use after seed set
Gylander, Tim; Hamann, Andreas; Brouard, Jean S.; Thomas, Barb R.
Background Aspen naturally grows in large, single-species, even-aged stands that regenerate clonally after fire disturbance. This offers an opportunity for an intensive clonal forestry system that closely emulates the natural life history of the species. In this paper, we assess the potential of genetic tree improvement and clonal deployment to enhance the productivity of aspen forests in Alberta. We further investigate geographic patterns of genetic variation in aspen and infer forest management strategies under uncertain future climates. Methodology/Principal Findings Genetic variation among 242 clones from Alberta was evaluated in 13 common garden trials after 5–8 growing seasons in the field. Broad-sense heritabilities for height and diameter at breast height (DBH) ranged from 0.36 to 0.64, allowing 5–15% genetic gains in height and 9–34% genetic gains in DBH. Geographic partitioning of genetic variance revealed predominant latitudinal genetic differentiation. We further observed that northward movement of clones almost always resulted in increased growth relative to local planting material, while southward movement had a strong opposite effect. Conclusion/Significance Aspen forests are an important natural resource in western Canada that is used for pulp and oriented strandboard production, accounting for ∼40% of the total forest harvest. Moderate to high broad-sense heritabilities in growth traits suggest good potential for a genetic tree improvement program with aspen. Significant productivity gains appear possible through clonal selection from existing trials. We propose two breeding regions for Alberta, and suggest that well-tested southern clones may be used in the northern breeding region, accounting for a general warming trend observed over the last several decades in Alberta. PMID:22957006
Zhou, Muchu; Fuller, Rebecca C.
Abstract Elaborate, sexually dimorphic traits are widely thought to evolve under sexual selection through female preference, male?male competition, or both. The orangethroat darter (Etheostoma spectabile) is a sexually dichromatic fish in which females exhibit no preferences for male size or coloration. We tested whether these traits affect individual reproductive success in E.?spectabile when multiple males are allowed to freely compete for a female. The quality and quantity of male colorati...
Blask, Katarina; Walther, Eva; Frings, Christian
We investigated in two experiments whether selective attention processes modulate evaluative conditioning (EC). Based on the fact that the typical stimuli in an EC paradigm involve an affect-laden unconditioned stimulus (US) and a neutral conditioned stimulus (CS), we started from the assumption that learning might depend in part upon selective attention to the US. Attention to the US was manipulated by including a variant of the Eriksen flanker task in the EC paradigm. Similarly to the original Flanker paradigm, we implemented a target-distracter logic by introducing the CS as the task-relevant stimulus (i.e. the target) to which the participants had to respond and the US as a task-irrelevant distracter. Experiment 1 showed that CS-US congruence modulated EC if the CS had to be selected against the US. Specifically, EC was more pronounced for congruent CS-US pairs as compared to incongruent CS-US pairs. Experiment 2 disentangled CS-US congruence and CS-US compatibility and suggested that it is indeed CS-US stimulus congruence rather than CS-US response compatibility that modulates EC.
Bøcher, Peder Klith; Root-Bernstein, Meredith; Svenning, Jens-Christian
After centuries of range contraction, many megafauna species are recolonizing parts of Europe. One example is the red deer (Cervus elaphus), which was able to expand its range and is now found in half the areas it inhabited in the beginning of the 19th century. Herbivores are important ecosystem engineers, influencing e.g. vegetation. Knowledge on their habitat selection and their influence on ecosystems might be crucial for future landscape management, especially for hybrid and novel ecosystems emerging in post-industrial landscapes. In this study, red deer habitat selection was studied in a former brown-coal mining area in Denmark. Here, natural settings were severely changed during the mining activity and its current landscape is in large parts managed by hunters as suitable deer habitat. We assessed red deer habitat preferences through feces presence and camera traps combined with land cover data from vegetation sampling, remote sensing and official geographic data. Red deer occurrence was negatively associated with human disturbance and positively associated with forage availability, tree cover and mean terrain height. Apparently, red deer are capable of recolonizing former industrial landscapes quite well if key conditions such as forage abundance and cover are appropriate. In the absence of carnivores, human disturbance, such as a hunting regime is a main reason why deer avoid certain areas. The resulting spatial heterogeneity red deer showed in their habitat use of the study area might be a tool to preserve mosaic landscapes of forest and open habitats and thus promote biodiversity in abandoned post-industrial landscapes. PMID:28505192
Longin, C Friedrich H; Utz, H Friedrich; Melchinger, Albrecht E; Reif, Jochen C
Optimum allocation of test resources is of crucial importance for the efficiency of breeding programs. Our objectives were to (1) determine the optimum allocation of the number of lines, test locations, as well as number and type of testers in hybrid maize breeding using doubled haploids with two breeding strategies for improvement of general combining ability (GCA), (2) compare the maximum selection gain (DeltaG) achievable under both strategies, and (3) give recommendations for the optimum implementation of doubled haploids in commercial hybrid maize breeding. We calculated DeltaG by numerical integration for two two-stage selection strategies with evaluation of (1) testcross performance in both stages (BS1) or (2) line per se performance in the first stage followed by testcross performance in the second stage (BS2). Different assumptions were made regarding the budget, variance components (VCs), and the correlation between line per se performance and GCA. Selection gain for GCA increased with a broader genetic base of the tester. Hence, testers combining a large number of divergent lines are advantageous. However, in applied breeding programs, the use of single- or double-cross testers in the first and inbred testers in the second selection stage may be a good compromise between theoretical and practical requirements. With a correlation between line per se performance and GCA of 0.50, DeltaG for BS1 is about 5% higher than for BS2, if an economic weight of line per se performance is neglected. With increasing economic weight of line per se performance, relative efficiency of BS2 increased rapidly resulting in a superiority of BS2 over BS1 already for an economic weight for line per se performance larger than 0.1. Considering the importance of an economic seed production, an economic weight larger than 0.1 seems realistic indicating the necessity of separate breeding strategies for seed and pollen parent heterotic groups.
Deperno, Christopher Shannon
Habitat selection, survival rates, the Black Hills National Forest Habitat Capability Model (HABCAP), and the USDA Forest Service Geographic Information System (GIS) data base were evaluated for a declining white-tailed deer (Odocoileus virginianus dacotensis) herd in the central Black Hills of South Dakota and Wyoming. From July 1993 through July 1996, 73 adult and yearling female and 12 adult and yearling male white-tailed deer were radiocollared and visually monitored. Habitat information was collected at 4,662 white-tailed deer locations and 1,087 random locations. Natural mortality (71%) was the primary cause of female mortality, followed by harvest (22.5%) and accidental causes (6.5%). More females died in spring (53.2%) than in fall (22.6%), winter (14.5%), or summer (9.7%). Male mortality resulted from hunting in fall (66.7%) and natural causes in spring (33.3%). Survival rates for all deer by year were 62.1% in 1993, 51.1% in 1994, 56.4% in 1995, and 53.9% in 1996 and were similar (P = 0.691) across years. During winter, white-tailed deer selected ponderosa pine- (Pinus ponderosa ) deciduous and burned pine cover types. Overstory-understory habitats selected included pine/grass-forb, pine/bearberry (Arctostaphylos uva-ursi), pine/snowberry (Symphoricarpos albus), burned pine/grass-forb, and pine/shrub habitats. Structural stages selected included sapling-pole pine stands with >70% canopy cover, burned pine sapling-pole and saw-timber stands with 40% canopy cover and all sapling-pole pine structural stages; sapling-pole stands with >70% canopy cover received the greatest use. White-tailed deer primarily fed in pine saw-timber structural stage with less than 40% canopy cover. Overall, selected habitats contained lower amounts of grass/forb, shrubs, and litter than random locations. Male and female deer generally bedded in areas that were characterized by greater horizontal cover than feeding and random sites. When feeding and bedding sites were combined
Sollero, Bruna P; Junqueira, Vinícius S; Gomes, Cláudia C G; Caetano, Alexandre R; Cardoso, Fernando F
Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset. BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil. To estimate the combined effect of a genomic region that is potentially associated with quantitative trait loci (QTL), 2519 non-overlapping 1-Mb windows that varied in SNP number were defined, with the top 48 windows including 914 SNPs and explaining more than 20% of the estimated genetic variance for tick resistance. Subsequently, the most informative SNPs were selected based on Bayesian parameters (model frequency and t-like statistics), linkage disequilibrium and minor allele frequency to propose a very low-density 58-SNP panel. Some of these tag SNPs mapped close to or within genes and pseudogenes that are functionally related to tick resistance. Prediction ability of this SNP panel was investigated by cross-validation using K-means and random clustering and a BayesA model to predict direct genomic values. Accuracies from these cross-validations were 0.27 ± 0.09 and 0.30 ± 0.09 for the K-means and random clustering groups, respectively, compared to respective values of 0.37 ± 0.08 and 0.43 ± 0.08 when using all 41,045 SNPs and BayesB with π = 0.99, or of 0.28 ± 0.07 and 0.40 ± 0.08 with π = 0.999. Bayesian GWAS model parameters can be used to select tag SNPs for a very low-density panel, which will include SNPs that are potentially linked to functional genes. It can be useful for cost
Shive, J.P.; Pilliod, D.S.; Peterson, C.R.
Wildlife managers increasingly are using remotely sensed imagery to improve habitat delineations and sampling strategies. Advances in remote sensing technology, such as hyperspectral imagery, provide more information than previously was available with multispectral sensors. We evaluated accuracy of high-resolution hyperspectral image classifications to identify wetlands and wetland habitat features important for Columbia spotted frogs (Rana luteiventris) and compared the results to multispectral image classification and United States Geological Survey topographic maps. The study area spanned 3 lake basins in the Salmon River Mountains, Idaho, USA. Hyperspectral data were collected with an airborne sensor on 30 June 2002 and on 8 July 2006. A 12-year comprehensive ground survey of the study area for Columbia spotted frog reproduction served as validation for image classifications. Hyperspectral image classification accuracy of wetlands was high, with a producer's accuracy of 96 (44 wetlands) correctly classified with the 2002 data and 89 (41 wetlands) correctly classified with the 2006 data. We applied habitat-based rules to delineate breeding habitat from other wetlands, and successfully predicted 74 (14 wetlands) of known breeding wetlands for the Columbia spotted frog. Emergent sedge microhabitat classification showed promise for directly predicting Columbia spotted frog egg mass locations within a wetland by correctly identifying 72 (23 of 32) of known locations. Our study indicates hyperspectral imagery can be an effective tool for mapping spotted frog breeding habitat in the selected mountain basins. We conclude that this technique has potential for improving site selection for inventory and monitoring programs conducted across similar wetland habitat and can be a useful tool for delineating wildlife habitats. ?? 2010 The Wildlife Society.
Grattapaglia, D; Ribeiro, V J; Rezende, G D S P
revitalization of the orchard. An average realized gain of 24.3% in volume growth was obtained from the selection of parents as measured in forest stands at age 2-4 years. The marker-assisted tree-breeding tactic presented herein efficiently identified top parents in a seed orchard and resulted in an improved seed variety. It should be applicable for rapidly improving the output quality of seed orchards, especially when an emergency demand for improved seed is faced by the breeder.
Social evolution has influenced every aspect of contemporary honey bee biology, but the details are difficult to reconstruct. The reproductive ground plan hypothesis of social evolution proposes that central regulators of the gonotropic cycle of solitary insects have been coopted to coordinate social complexity in honey bees, such as the division of labor among workers. The predicted trait associations between reproductive physiology and social behavior have been identified in the context of the pollen hoarding syndrome, a larger suite of interrelated traits. The genetic architecture of this syndrome is characterized by a partially overlapping genetic architecture with several consistent, pleiotropic QTL. Despite these central QTL and an integrated hormonal regulation, separate aspects of the pollen hoarding syndrome may evolve independently due to peripheral QTL and additionally segregating genetic variance. The characterization of the pollen hoarding syndrome has also demonstrated that this syndrome involves many non-behavioral traits, which may be the case for numerous "behavioral" syndromes. Furthermore, the genetic architecture of the pollen hoarding syndrome has implications for breeding programs for improving honey health and other desirable traits: If these traits are comparable to the pollen hoarding syndrome, consistent pleiotropic QTL will enable marker assisted selection, while sufficient additional genetic variation may permit the dissociation of trade-offs for efficient multiple trait selection.
Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.
Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.
Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.
Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.
Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines
Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273
Curran, Janet H.; Rice, William J.
Small streams in the rapidly developing Matanuska-Susitna Valley in south-central Alaska are known to support anadromous and resident fish but little is known about their hydrologic and riparian conditions, or their sensitivity to the rapid development of the area or climate variability. To help address this need, channel geometry and aquatic habitat data were collected in 2005 as a baseline of stream conditions for selected streams. Three streams were selected as representative of various stream types, and one drainage network, the Big Lake drainage basin, was selected for a systematic assessment. Streams in the Big Lake basin were drawn in a Geographic Information System (GIS), and 55 reaches along 16 miles of Meadow Creek and its primary tributary Little Meadow Creek were identified from orthoimagery and field observations on the basis of distinctive physical and habitat parameters, most commonly gradient, substrate, and vegetation. Data-collection methods for sites at the three representative reaches and the 55 systematically studied reaches consisted of a field survey of channel and flood-plain geometry and collection of 14 habitat attributes using published protocols or slight modifications. Width/depth and entrenchment ratios along the Meadow-Little Meadow Creek corridor were large and highly variable upstream of Parks Highway and lower and more consistent downstream of Parks Highway. Channel width was strongly correlated with distance, increasing downstream in a log-linear relation. Runs formed the most common habitat type, and instream vegetation dominated the habitat cover types, which collectively covered 53 percent of the channel. Gravel suitable for spawning covered isolated areas along Meadow Creek and about 29 percent of Little Meadow Creek. Broad wetlands were common along both streams. For a comprehensive assessment of small streams in the Mat-Su Valley, critical additional data needs include hydrologic, geologic and geomorphic, and biologic data
Cotes, Belén; Rännbäck, Linda Marie; Björkman, Maria
To locate and evaluate host patches before oviposition, parasitoids of herbivorous insects utilize plant volatiles and host-derived cues, but also evaluate predator-derived infochemicals to reduce predation risks. When foraging in host habitats infested with entomopathogenic fungi that can infect...... both a parasitoid and its host, parasitoids may reduce the risk of intraguild predation (IGP) by avoiding such patches. In this study, we examined whether the presence of the entomopathogenic fungi Metarhizium brunneum and Beauveria bassiana in soil habitats of a root herbivore, Delia radicum, affects...... the behavior of Trybliographa rapae, a parasitoid of D. radicum. Olfactometer bioassays revealed that T. rapae avoided fungal infested host habitats and that this was dependent on fungal species and density. In particular, the parasitoid avoided habitats with high densities of the more virulent fungus, M...
Lopez-Cruz, Marco; Crossa, Jose; Bonnett, David; Dreisigacker, Susanne; Poland, Jesse; Jannink, Jean-Luc; Singh, Ravi P; Autrique, Enrique; de los Campos, Gustavo
Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates of selection. Originally, these models were developed without considering genotype × environment interaction(G×E). Several authors have proposed extensions of the single-environment GS model that accommodate G×E using either covariance functions or environmental covariates. In this study, we model G×E using a marker × environment interaction (M×E) GS model; the approach is conceptually simple and can be implemented with existing GS software. We discuss how the model can be implemented by using an explicit regression of phenotypes on markers or using co-variance structures (a genomic best linear unbiased prediction-type model). We used the M×E model to analyze three CIMMYT wheat data sets (W1, W2, and W3), where more than 1000 lines were genotyped using genotyping-by-sequencing and evaluated at CIMMYT's research station in Ciudad Obregon, Mexico, under simulated environmental conditions that covered different irrigation levels, sowing dates and planting systems. We compared the M×E model with a stratified (i.e., within-environment) analysis and with a standard (across-environment) GS model that assumes that effects are constant across environments (i.e., ignoring G×E). The prediction accuracy of the M×E model was substantially greater of that of an across-environment analysis that ignores G×E. Depending on the prediction problem, the M×E model had either similar or greater levels of prediction accuracy than the stratified analyses. The M×E model decomposes marker effects and genomic values into components that are stable across environments (main effects) and others that are environment-specific (interactions). Therefore, in principle, the interaction model could shed light over which variants have effects that are stable across environments and which ones are responsible for G×E. The data set and the scripts required to reproduce the analysis are
Full Text Available Organic breeding is a new trend in plant breeding aimed at breeding of organic cultivars adapted to conditions and expectations of organic plant production. The best proof for the need of organic cultivars is the existence of interaction between the performances of genotypes with the kind of production (conventional or organic (graph. 1. The adaptation to low-input conditions of organic production by more eddicient uptake and utilization of plant nutrients is especially important for organic cultivars. One of the basic mechanism of weed control in organic production is the competition of organic cultivars and weeds i.e. the enhanced ability of organic cultivars to suppress the weeds. Resistance/tolerance to diseases and pests is among the most important expectations toward the organic cultivars. In comparison with the methods of conventional plant breeding, in case of organic plant breeding limitations exist in choice of methods for creation of variability and selection classified as permitted, conditionally permitted and banned. The use of genetically modified organisms and their derivated along with induced mutations is not permitted in organic production. The use of molecular markers in organic plant breeding is the only permitted modern method of biotechnology. It is not permitted to patent the breeding material of organic plant breeding or the organic cultivars. .
Longin, C Friedrich H; Utz, H Friedrich; Reif, Jochen C; Wegenast, Thilo; Schipprack, Wolfgang; Melchinger, Albrecht E
Early testing prior to doubled haploid (DH) production is a promising approach in hybrid maize breeding. We (1) determined the optimum allocation of the number of S(1) families, DH lines, and test locations for two different breeding schemes, (2) compared the maximum selection gain achievable under both breeding schemes, and (3) investigated limitations in the current method of DH production. Selection gain was calculated by numerical integration in two-stage breeding schemes with evaluation of testcross progenies of (1) DH lines in both stages (DHTC), or (2) S(1) families in the first and DH lines within S(1) families in the second stage (S(1)TC-DHTC). Different assumptions were made regarding the budget, variance components, and time of DH production within S(1) families. Maximum selection gain in S(1)TC-DHTC was about 10% larger than in DHTC, indicating the large potential of early testing prior to DH production. The optimum allocation of test resources in S(1)TC-DHTC involved similar numbers of test locations and test candidates in both stages resulting in a large optimum number of S(1) families in the first stage and DH lines within the best two S(1) families in the second stage. The longer cycle length of S(1)TC-DHTC can be compensated by haploid induction of individual S(1) plants instead of S(1) families. However, this reduces selection gain largely due to the current limitations in the DH technique. Substantial increases in haploid induction and chromosome doubling rates as well as reduction in costs of DH production would allow early testing of S(1) lines and subsequent production and testing of DH lines in a breeding scheme that combines high selection gain with a short cycle length.
Steensels, Jan; Meersman, Esther; Snoek, Tim; Saels, Veerle; Verstrepen, Kevin J
The concentrations and relative ratios of various aroma compounds produced by fermenting yeast cells are essential for the sensory quality of many fermented foods, including beer, bread, wine, and sake. Since the production of these aroma-active compounds varies highly among different yeast strains, careful selection of variants with optimal aromatic profiles is of crucial importance for a high-quality end product. This study evaluates the production of different aroma-active compounds in 301 different Saccharomyces cerevisiae, Saccharomyces paradoxus, and Saccharomyces pastorianus yeast strains. Our results show that the production of key aroma compounds like isoamyl acetate and ethyl acetate varies by an order of magnitude between natural yeasts, with the concentrations of some compounds showing significant positive correlation, whereas others vary independently. Targeted hybridization of some of the best aroma-producing strains yielded 46 intraspecific hybrids, of which some show a distinct heterosis (hybrid vigor) effect and produce up to 45% more isoamyl acetate than the best parental strains while retaining their overall fermentation performance. Together, our results demonstrate the potential of large-scale outbreeding to obtain superior industrial yeasts that are directly applicable for commercial use. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Puddhanon, Prawit; Pintanon, Prateep; Chaithep, Waree; Songjuntuke, Ksan
Full text: Effects of 80 keV ion beam (10 16 ion/cm 2 on mutations of RD6 and Sanpatong 1 rice varieties were studied in 2006. In order to obtain the phenotypic mutants, each variety was sown in the laboratory and under field conditions at Maejo University in 2007 dry season. Seed germination noticeably declined. For RD6, only 45.1% germinated in the laboratory, and 18.1% were established under the field condition. Similarly, 62.3% of Sanpatong 1 germinated in the laboratory and 31.4% established in the field. No phenotypic mutants were observed in the first generation (M 1 ). The M2 seeds were harvested separately from 3 panicles of each M plant in RD6 and Sanpatong1, totaling 810 and 1,878 lines, respectively. In 2007 rainy season, they were planted on a panicle to row basis. It was found that more phenotypic mutants were observed in the M 2 for Sanpatong 1 than for RD6. The mutant characters included dwarf plants, early maturity, male sterility and larger panicle sizes. As a result, about 420 within line selections were collected and the M 3 seeds were harvested for further field condition and gene markers evaluations
Tracey, Jeff A.; Madden, Melanie C.; Bloom, Peter H.; Katzner, Todd E.; Fisher, Robert N.
Beginning in 2014, the U.S. Geological Survey, in collaboration with Bloom Biological, Inc., began telemetry research on golden eagles (Aquila chrysaetos) captured in the San Diego, Orange, and western Riverside Counties of southern California. This work was supported by the San Diego Association of Governments, California Department of Fish and Wildlife, the U.S. Fish and Wildlife Service, the Bureau of Land Management, and the U.S. Geological Survey. Since 2014, we have tracked more than 40 eagles, although this report focuses only on San Diego County eagles.An important objective of this research is to develop habitat selection models for golden eagles. Here we provide predictions of population-level habitat selection for golden eagles in San Diego County based on environmental covariates related to land use and terrain.
Full Text Available Genetic improvement of the African catfish (Clarias gariepinus in Indonesia for increasing growth performance has been conducted by Research Institute for Fish Breeding at Sukamandi through mass selection. Collection and characterizations of the founder populations, building the synthetic base population, first generation and second generation through mass selection were conducted during 2010-2013. Later, in 2014 it was followed by building the third generation. The present study aimed to find out the genetic gain in the third generation in term of response to selection for body weight. Fifty-two pairs of the selected (fast growing individuals from the second generation were mated to produce the third generation. As a comparison, five pairs of average-sized individuals were mated to produce the control population, as a second generation representative. Larval rearing, nursery and grow-out phases were respectively held for 25 days in the aquaria, 30 days in the concrete ponds and 60 days in the concrete ponds. At the end of each phase, individual samplings of body weight were undertaken. The results showed that mean body weight of the third generation was higher than that of control population at the end of larval rearing phase (0.21 ± 0.26 g versus 0.20 ± 0.15 g, nursery phase (6.12 ± 2.93 g versus 5.80 ± 3.50 g and grow-out phase (198.67 ± 82.82 g versus 165.22 ± 71.09 g. Those results revealed that response to selection for body weight of the third generation was positive, i.e. about 20.24% (33.45 g.
Sarkar, Mriganka Shekhar; Krishnamurthy, Ramesh; Johnson, Jeyaraj A; Sen, Subharanjan; Saha, Goutam Kumar
Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals' ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger ( Panthera tigris ), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly's selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D 2 method and the Boyce index. There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Based on threshold limits
Mriganka Shekhar Sarkar
Full Text Available Background Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals’ ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris, which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. Methods We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly’s selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D2 method and the Boyce index. Results There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory
Sarkar, Mriganka Shekhar; Johnson, Jeyaraj A.; Sen, Subharanjan
Background Large carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals’ ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale. Methods We studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly’s selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D2 method and the Boyce index. Results There was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods