ALIEN SPECIES: THEIR ROLE IN AMPHIBIAN POPULATION DECLINES AND RESTORATION

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Alien species (also referred to as exotic, invasive, introduced, or normative species) have been implicated as causal agents in population declines of many amphibian species. Herein, we evaluate the relative contributions of alien species and other factors in adversely affecting ...

Climate Change and Genetic Structure of Leading Edge and Rear End Populations in a Northwards Shifting Marine Fish Species, the Corkwing Wrasse (Symphodus melops).

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Knutsen, Halvor; Jorde, Per Erik; Gonzalez, Enrique Blanco; Robalo, Joana; Albretsen, Jon; Almada, Vitor

2013-01-01

One mechanism by which marine organisms may respond to climate shifts is range shifts. The corkwing wrasse (Symphodus melops) is a temperate fish species, inhabiting the coasts of Europe, that show strong indications of current as well as historical (ice-age) range shifts towards the north. Nine neutral microsatellite DNA markers were screened to study genetic signatures and spatial population structure over the entire geographic and thermal gradient of the species from Portugal to Norway. A major genetic break (F ST  = 0.159 average among pairs) was identified between Scandinavian and more southern populations, with a marked reduction (30% or more) in levels of genetic variability in Scandinavia. The break is probably related to bottleneck(s) associated with post-glacial colonization of the Scandinavian coasts, and indicates a lack of present gene flow across the North Sea. The lack of gene flow can most likely be attributed to the species' need for rocky substrate for nesting and a relatively short pelagic larval phase, limiting dispersal by ocean currents. These findings demonstrate that long-distance dispersal may be severely limited in the corkwing wrasse, and that successful range-shifts following present climate change may be problematic for this and other species with limited dispersal abilities, even in the seemingly continuous marine environment.

Population dynamics of Pseudo-nitzschia species ...

African Journals Online (AJOL)

The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es Salaam. Samples ...

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico

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Ceballos-Vázquez, Bertha P.; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J.; Culver, Melanie; Reyes-Bonilla, Hector

2018-01-01

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O

Species conservation and natural variation among populations [Chapter 5

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Leonard F. Ruggiero; Michael K. Schwartz; Keith B. Aubry; Charles J. Krebs; Amanda Stanley; Steven W. Buskirk

2000-01-01

In conservation planning, the importance of natural variation is often given inadequate consideration. However, ignoring the implications of variation within species may result in conservation strategies that jeopardize, rather than conserve, target species (see Grieg 1979; Turcek 1951; Storfer 1999). Natural variation in the traits of individuals and populations is...

Population ecology of turbot and brill: What can we learn from two rare flatfish species?

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van der Hammen, Tessa; Poos, Jan Jaap; van Overzee, Harriët M. J.; Heessen, Henk J. L.; Magnusson, Arni; Rijnsdorp, Adriaan D.

2013-11-01

Turbot and brill are widely distributed in the Northeast Atlantic but occur at low abundance. They are ecologically very similar and closely related. The low abundance and the similarities make them particularly interesting to study the population dynamics because it raises the questions how the populations can sustain themselves at low abundances and how turbot and brill avoid strong interspecific competition. Knowledge of both species is hampered by lack of analysed data. The main objective of this study is therefore to increase the knowledge of turbot and brill and in particular to compare the two species in order to address the above questions. Based on biological samples collected in the North Sea, we calculated seasonal von Bertalanffy growth parameters, maturity ogives, monthly gonado-somatic indices (GSI) and condition factors (Fulton's K) and indices of inter- and intraspecific mean crowding and compared the results for turbot and brill. The main differences between the two species were found in their spawning period, with brill having a more protracted spawning period. Brill also showed an earlier peak in their GSI values, suggesting an earlier start of their spawning period. The mean crowding showed that interspecific competition was lower than intraspecific competition. The exploitation pattern was also studied. Turbot and brill are exploited as a bycatch species in the mixed demersal fishery. We found that productivity is highest in areas where the maximum temperature is close to the optimal temperature for growth (16-18 °C) and landings decrease where salinity falls below ~ 5 psu (turbot) and ~ 15 psu (brill). Recent fishing mortality rates of North Sea turbot are around 0.5-0.7, but there is no indication that recruitment is impaired at low levels of spawning stock biomass. We conclude that although both species have similar ecological characteristics, differences may reduce inter-specific competition.

[Urbanization mechanisms in bird species: population systems transformations or adaptations at the individual level?].

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Fridman, V S; Eremkin, G S; Zakharova-Kubareva, N Iu

2008-01-01

The present research deals with urbanization of wild bird and mammal species. Forms and mechanisms of population steadiness in the urban landscape have been examined. The urbanization process turned out to be a directed change of the population system forming de novo in the urbolandscape leading to a sustainable organization peculiar for the particular environment. The population organization of different types in urbolandscape is found to provide its stability under conditions of directed and fast changes accompanied with instability and heterogenous structure of habitats. It is shown that the same type of population organization meets the corresponding demands among different species settling in the urban environment. Its features are "openness" and "flowage" of the groups, far order of settlement levels and other units of population system, constant movements of the individuals between the groups as a respond to the signals of urboenvironment significant changes. The "urban" variant of the population system organization turns out to be opposite to that of the same species in the non-urban habitats. After formation of the urban types by the species and successful developing of the town, the urban population becomes separated from the maternal local population and begins to exist independently in the urban landscape. The variety of adaptation aberrations in ecology, behavior, and mode of life of urban birds is the population system stability function in the urban landscape and is not a results of individual selection. It is shown that the urbanization process of the species goes firstly on the population level being the system structure transformation developed by the species towards the most stable state in the town (city) territory. Only after the appearance of stable urban population, the urban individuals show the rapid growth of different changes in ecology, behavior, mode of life that was traditionally described by naturalists as species adaptation to the

General two-species interacting Lotka-Volterra system: Population dynamics and wave propagation

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Zhu, Haoqi; Wang, Mao-Xiang; Lai, Pik-Yin

2018-05-01

The population dynamics of two interacting species modeled by the Lotka-Volterra (LV) model with general parameters that can promote or suppress the other species is studied. It is found that the properties of the two species' isoclines determine the interaction of species, leading to six regimes in the phase diagram of interspecies interaction; i.e., there are six different interspecific relationships described by the LV model. Four regimes allow for nontrivial species coexistence, among which it is found that three of them are stable, namely, weak competition, mutualism, and predator-prey scenarios can lead to win-win coexistence situations. The Lyapunov function for general nontrivial two-species coexistence is also constructed. Furthermore, in the presence of spatial diffusion of the species, the dynamics can lead to steady wavefront propagation and can alter the population map. Propagating wavefront solutions in one dimension are investigated analytically and by numerical solutions. The steady wavefront speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. In addition to the inter- and intraspecific interaction parameters, the intrinsic speed parameters of each species play a decisive role in species populations and wave properties. In some regimes, both species can copropagate with the same wave speeds in a finite range of parameters. Our results are further discussed in the light of possible biological relevance and ecological implications.

Prioritizing Avian Species for Their Risk of Population-Level Consequences from Wind Energy Development.

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Julie A Beston

Full Text Available Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species' distributions relative to turbine locations, number of suitable habitat types, and species' conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson's hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future

Prioritizing Avian Species for Their Risk of Population-Level Consequences from Wind Energy Development.

Science.gov (United States)

Beston, Julie A; Diffendorfer, Jay E; Loss, Scott R; Johnson, Douglas H

2016-01-01

Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species' distributions relative to turbine locations, number of suitable habitat types, and species' conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories) for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson's hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future study and management

The effects of spatial and temporal heterogeneity on the population dynamics of four animal species in a Danish landscape

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Forchhammer Mads C

2009-06-01

Full Text Available Abstract Background Variation in carrying capacity and population return rates is generally ignored in traditional studies of population dynamics. Variation is hard to study in the field because of difficulties controlling the environment in order to obtain statistical replicates, and because of the scale and expense of experimenting on populations. There may also be ethical issues. To circumvent these problems we used detailed simulations of the simultaneous behaviours of interacting animals in an accurate facsimile of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of skylarks Alauda arvensis, voles Microtus agrestis, a ground beetle Bembidion lampros and a linyphiid spider Erigone atra. This allows us to quantify and evaluate the importance of spatial and temporal heterogeneity on the population dynamics of the four species. Results Both spatial and temporal heterogeneity affected the relationship between population growth rate and population density in all four species. Spatial heterogeneity accounted for 23–30% of the variance in population growth rate after accounting for the effects of density, reflecting big differences in local carrying capacity associated with the landscape features important to individual species. Temporal heterogeneity accounted for 3–13% of the variance in vole, skylark and spider, but 43% in beetles. The associated temporal variation in carrying capacity would be problematic in traditional analyses of density dependence. Return rates were less than one in all species and essentially invariant in skylarks, spiders and beetles. Return rates varied over the landscape in voles, being slower where there were larger fluctuations in local population sizes. Conclusion Our analyses estimated the traditional parameters of carrying capacities and return rates, but these are now seen as varying continuously over the landscape depending on habitat quality and the mechanisms

Efficiency of green manure species on the population of reniform nematode

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Cristiane Gonçalves Gardiano

2014-02-01

Full Text Available The objective of this study was to evaluate the growing of soil improving crops on the population of Rotylenchulus reniformis in naturally infested soil. It was evaluated the effect of 6 species of plants as cover crops in winter and 13 summer species and a fallow treatment on the nematode population under greenhouse. After 60 days, the root system was collected. Then, a sample of soil was taken in order to extract juveniles from the soil and quantification the final population of the pathogen in each pot for determining of the reproduction factor (RF. Fallow and all winter species of green manure, except hairy vetch, reduced the population of R. reniformis after cultivation in infested soil, in comparison to the control. Regarding summer cover crops, it was observed that sorghum ‘SI03204’ (Sorghum vulgare, millet ‘BRS1501’ (Pennisetum glaucum, Brachiaria ruziziensis, finger millet (Eleusine coracana, estylo ‘Campo Grande’ (Stylosanthes capitata x S. macrocephala, peanut ‘IAC Tatu ST’ (Arachis hypogaea and dwarf velvet bean (Mucuna deeringiana reduced the population of R. reniformis, when compared to the control, could be used in the management of this nematode.

Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert

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Richmond, Jonathan Q.; Wood, Dustin A.; Westphal, Michael F.; Vandergast, Amy; Leache, Adam D.; Saslaw, Lawrence; Butterfield, H. Scott; Fisher, Robert N.

2017-01-01

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes.

Using citizen science butterfly counts to predict species population trends.

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Dennis, Emily B; Morgan, Byron J T; Brereton, Tom M; Roy, David B; Fox, Richard

2017-12-01

Citizen scientists are increasingly engaged in gathering biodiversity information, but trade-offs are often required between public engagement goals and reliable data collection. We compared population estimates for 18 widespread butterfly species derived from the first 4 years (2011-2014) of a short-duration citizen science project (Big Butterfly Count [BBC]) with those from long-running, standardized monitoring data collected by experienced observers (U.K. Butterfly Monitoring Scheme [UKBMS]). BBC data are gathered during an annual 3-week period, whereas UKBMS sampling takes place over 6 months each year. An initial comparison with UKBMS data restricted to the 3-week BBC period revealed that species population changes were significantly correlated between the 2 sources. The short-duration sampling season rendered BBC counts susceptible to bias caused by interannual phenological variation in the timing of species' flight periods. The BBC counts were positively related to butterfly phenology and sampling effort. Annual estimates of species abundance and population trends predicted from models including BBC data and weather covariates as a proxy for phenology correlated significantly with those derived from UKBMS data. Overall, citizen science data obtained using a simple sampling protocol produced comparable estimates of butterfly species abundance to data collected through standardized monitoring methods. Although caution is urged in extrapolating from this U.K. study of a small number of common, conspicuous insects, we found that mass-participation citizen science can simultaneously contribute to public engagement and biodiversity monitoring. Mass-participation citizen science is not an adequate replacement for standardized biodiversity monitoring but may extend and complement it (e.g., through sampling different land-use types), as well as serving to reconnect an increasingly urban human population with nature. © 2017 The Authors. Conservation Biology published

Lack of Population Genetic Structuring in Ocelots (Leopardus pardalis in a Fragmented Landscape

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Marina G. Figueiredo

2015-07-01

Full Text Available Habitat fragmentation can promote patches of small and isolated populations, gene flow disruption between those populations, and reduction of local and total genetic variation. As a consequence, these small populations may go extinct in the long-term. The ocelot (Leopardus pardalis, originally distributed from Texas to southern Brazil and northern Argentina, has been impacted by habitat fragmentation throughout much of its range. To test whether habitat fragmentation has already induced genetic differentiation in an area where this process has been documented for a larger felid (jaguars, we analyzed molecular variation in ocelots inhabiting two Atlantic Forest fragments, Morro do Diabo (MD and Iguaçu Region (IR. Analyses using nine microsatellites revealed mean observed and expected heterozygosity of 0.68 and 0.70, respectively. The MD sampled population showed evidence of a genetic bottleneck under two mutational models (TPM = 0.03711 and SMM = 0.04883. Estimates of genetic structure (FST = 0.027; best fit of k = 1 with STRUCTURE revealed no meaningful differentiation between these populations. Thus, our results indicate that the ocelot populations sampled in these fragments are still not significantly different genetically, a pattern that strongly contrasts with that previously observed in jaguars for the same comparisons. This observation is likely due to a combination of two factors: (i larger effective population size of ocelots (relative to jaguars in each fragment, implying a slower effect of drift-induced differentiation; and (ii potentially some remaining permeability of the anthropogenic matrix for ocelots, as opposed to the observed lack of permeability for jaguars. The persistence of ocelot gene flow between these areas must be prioritized in long-term conservation planning on behalf of these felids.

Varying Herbivore Population Structure Correlates with Lack of Local Adaptation in a Geographic Variable Plant-Herbivore Interaction

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Cogni, Rodrigo; Trigo, José R.; Futuyma, Douglas J.

2011-01-01

Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries) vary at the regional scale, while other traits (trichomes and nitrogen content) just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation. PMID:22220208

Varying herbivore population structure correlates with lack of local adaptation in a geographic variable plant-herbivore interaction.

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Rodrigo Cogni

Full Text Available Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries vary at the regional scale, while other traits (trichomes and nitrogen content just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation.

Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae).

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González-Castro, Mariano; Rosso, Juan José; Mabragaña, Ezequiel; Díaz de Astarloa, Juan Martín

2016-01-01

Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Prioritizing avian species for their risk of population-level consequences from wind energy development

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Beston, Julie A.; Diffendorfer, James E.; Loss, Scott; Johnson, Douglas H.

2016-01-01

Recent growth in the wind energy industry has increased concerns about its impacts on wildlife populations. Direct impacts of wind energy include bird and bat collisions with turbines whereas indirect impacts include changes in wildlife habitat and behavior. Although many species may withstand these effects, species that are long-lived with low rates of reproduction, have specialized habitat preferences, or are attracted to turbines may be more prone to declines in population abundance. We developed a prioritization system to identify the avian species most likely to experience population declines from wind facilities based on their current conservation status and their expected risk from turbines. We developed 3 metrics of turbine risk that incorporate data on collision fatalities at wind facilities, population size, life history, species’ distributions relative to turbine locations, number of suitable habitat types, and species’ conservation status. We calculated at least 1 measure of turbine risk for 428 avian species that breed in the United States. We then simulated 100,000 random sets of cutoff criteria (i.e., the metric values used to assign species to different priority categories) for each turbine risk metric and for conservation status. For each set of criteria, we assigned each species a priority score and calculated the average priority score across all sets of criteria. Our prioritization system highlights both species that could potentially experience population decline caused by wind energy and species at low risk of population decline. For instance, several birds of prey, such as the long-eared owl, ferruginous hawk, Swainson’s hawk, and golden eagle, were at relatively high risk of population decline across a wide variety of cutoff values, whereas many passerines were at relatively low risk of decline. This prioritization system is a first step that will help researchers, conservationists, managers, and industry target future study and

Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

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Conor P. McGowan

2017-10-01

Full Text Available Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises in transparent and explicit ways tailored to support decision making processes related to endangered species.

Incorporating population viability models into species status assessment and listing decisions under the U.S. Endangered Species Act

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McGowan, Conor P.; Allan, Nathan; Servoss, Jeff; Hedwall, Shaula J.; Wooldridge, Brian

2017-01-01

Assessment of a species' status is a key part of management decision making for endangered and threatened species under the U.S. Endangered Species Act. Predicting the future state of the species is an essential part of species status assessment, and projection models can play an important role in developing predictions. We built a stochastic simulation model that incorporated parametric and environmental uncertainty to predict the probable future status of the Sonoran desert tortoise in the southwestern United States and North Central Mexico. Sonoran desert tortoise was a Candidate species for listing under the Endangered Species Act, and decision makers wanted to use model predictions in their decision making process. The model accounted for future habitat loss and possible effects of climate change induced droughts to predict future population growth rates, abundances, and quasi-extinction probabilities. Our model predicts that the population will likely decline over the next few decades, but there is very low probability of quasi-extinction less than 75 years into the future. Increases in drought frequency and intensity may increase extinction risk for the species. Our model helped decision makers predict and characterize uncertainty about the future status of the species in their listing decision. We incorporated complex ecological processes (e.g., climate change effects on tortoises) in transparent and explicit ways tailored to support decision making processes related to endangered species.

Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species.

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Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

2017-01-01

Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis , which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

Phenotypic plasticity and population differentiation in an ongoing species invasion.

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Silvia Matesanz

Full Text Available The ability to succeed in diverse conditions is a key factor allowing introduced species to successfully invade and spread across new areas. Two non-exclusive factors have been suggested to promote this ability: adaptive phenotypic plasticity of individuals, and the evolution of locally adapted populations in the new range. We investigated these individual and population-level factors in Polygonum cespitosum, an Asian annual that has recently become invasive in northeastern North America. We characterized individual fitness, life-history, and functional plasticity in response to two contrasting glasshouse habitat treatments (full sun/dry soil and understory shade/moist soil in 165 genotypes sampled from nine geographically separate populations representing the range of light and soil moisture conditions the species inhabits in this region. Polygonum cespitosum genotypes from these introduced-range populations expressed broadly similar plasticity patterns. In response to full sun, dry conditions, genotypes from all populations increased photosynthetic rate, water use efficiency, and allocation to root tissues, dramatically increasing reproductive fitness compared to phenotypes expressed in simulated understory shade. Although there were subtle among-population differences in mean trait values as well as in the slope of plastic responses, these population differences did not reflect local adaptation to environmental conditions measured at the population sites of origin. Instead, certain populations expressed higher fitness in both glasshouse habitat treatments. We also compared the introduced-range populations to a single population from the native Asian range, and found that the native population had delayed phenology, limited functional plasticity, and lower fitness in both experimental environments compared with the introduced-range populations. Our results indicate that the future spread of P. cespitosum in its introduced range will likely be

Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert.

Science.gov (United States)

Richmond, Jonathan Q; Wood, Dustin A; Westphal, Michael F; Vandergast, Amy G; Leaché, Adam D; Saslaw, Lawrence R; Butterfield, H Scott; Fisher, Robert N

2017-07-01

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt-nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site-associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid-adapted taxa in one of the world's most compromised landscapes. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels.

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Settepani, V; Schou, M F; Greve, M; Grinsted, L; Bechsgaard, J; Bilde, T

2017-08-01

Across several animal taxa, the evolution of sociality involves a suite of characteristics, a "social syndrome," that includes cooperative breeding, reproductive skew, primary female-biased sex ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genomewide diversity in spider species that differ in level of sociality, reproductive skew and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within-population diversity were sixfold to 10-fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genomewide diversity, likely to limit their evolutionary potential. © 2017 John Wiley & Sons Ltd.

Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species

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AB Choupina

Full Text Available Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia, are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal, there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates, as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as “glochidia” hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

Genetic variations in two seahorse species (Hippocampus mohnikei and Hippocampus trimaculatus): evidence for middle Pleistocene population expansion.

Science.gov (United States)

Zhang, Yanhong; Pham, Nancy Kim; Zhang, Huixian; Lin, Junda; Lin, Qiang

2014-01-01

Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb) and control region (CR) were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA) diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ) tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML) tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments.

Population Genetic Structure and Species Status of Asiatic Toads (Bufo gargarizans) in Western China.

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Wen, Guannan; Yang, Weizhao; Fu, Jinzhong

2015-10-01

We investigated the population genetic structure of Asiatic toads (Bufo gargarizans) from the mountains of western China to determine their species status, using genotypic data of ten microsatellite DNA loci and DNA sequences from one mitochondrial gene. A total of 197 samples from eight sites were examined, which cover a large range of elevations (559-3457 m), as well as all three traditionally defined species (or subspecies). AMOVA did not reveal any particularly large among-groups structure, whether the sites were grouped by drainage, elevation, region, or species (subspecies). Individual assignment tests placed all samples into two genetic clusters, which largely corresponded to their geographic locations. An isolation-by-distance pattern was also detected when an outlier population (site 3) was excluded. Furthermore, a mitochondrial gene tree revealed deep divergence among haplotypes, sometimes within the same site. The clade patterns were partially associated with geographic distribution but had no resemblance to the traditional 2- or 3-species classification. Overall, these toad populations harbor a large amount of genetic diversity and have very high population differentiation, but taken together the evidence suggests that all populations belong to a single species. Our results are consistent with most previous molecular studies, and we recommend using Bufo gargarizans to represent all Asiatic toad populations from western China without subspecies division.

Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation.

Science.gov (United States)

Muller, Mischa F; Barnes, Irene; Kunene, Ncobile T; Crampton, Bridget G; Bluhm, Burton H; Phillips, Sonia M; Olivier, Nicholas A; Berger, Dave K

2016-10-01

South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The

Environmental variability uncovers disruptive effects of species' interactions on population dynamics.

Science.gov (United States)

Gudmundson, Sara; Eklöf, Anna; Wennergren, Uno

2015-08-07

How species respond to changes in environmental variability has been shown for single species, but the question remains whether these results are transferable to species when incorporated in ecological communities. Here, we address this issue by analysing the same species exposed to a range of environmental variabilities when (i) isolated or (ii) embedded in a food web. We find that all species in food webs exposed to temporally uncorrelated environments (white noise) show the same type of dynamics as isolated species, whereas species in food webs exposed to positively autocorrelated environments (red noise) can respond completely differently compared with isolated species. This is owing to species following their equilibrium densities in a positively autocorrelated environment that in turn enables species-species interactions to come into play. Our results give new insights into species' response to environmental variation. They especially highlight the importance of considering both species' interactions and environmental autocorrelation when studying population dynamics in a fluctuating environment. © 2015 The Author(s).

Net Effects of Ecotourism on Threatened Species Survival.

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Ralf C Buckley

Full Text Available Many threatened species rely on ecotourism for conservation funding, but simultaneously suffer direct ecological impacts from ecotourism. For a range of IUCN-Redlisted terrestrial and marine bird and mammal species worldwide, we use population viability analyses to calculate the net effects of ecotourism on expected time to extinction, in the presence of other anthropogenic threats such as poaching, primary industries and habitat loss. Species for which these calculations are currently possible, for one or more subpopulations, include: orangutan, hoolock gibbon, golden lion tamarin, cheetah, African wild dog, New Zealand sealion, great green macaw, Egyptian vulture, and African penguin. For some but not all of these species, tourism can extend expected survival time, i.e., benefits outweigh impacts. Precise outcomes depend strongly on population parameters and starting sizes, predation, and ecotourism scale and mechanisms. Tourism does not currently overcome other major conservation threats associated with natural resource extractive industries. Similar calculations for other threatened species are currently limited by lack of basic population data.

Net Effects of Ecotourism on Threatened Species Survival.

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Buckley, Ralf C; Morrison, Clare; Castley, J Guy

2016-01-01

Many threatened species rely on ecotourism for conservation funding, but simultaneously suffer direct ecological impacts from ecotourism. For a range of IUCN-Redlisted terrestrial and marine bird and mammal species worldwide, we use population viability analyses to calculate the net effects of ecotourism on expected time to extinction, in the presence of other anthropogenic threats such as poaching, primary industries and habitat loss. Species for which these calculations are currently possible, for one or more subpopulations, include: orangutan, hoolock gibbon, golden lion tamarin, cheetah, African wild dog, New Zealand sealion, great green macaw, Egyptian vulture, and African penguin. For some but not all of these species, tourism can extend expected survival time, i.e., benefits outweigh impacts. Precise outcomes depend strongly on population parameters and starting sizes, predation, and ecotourism scale and mechanisms. Tourism does not currently overcome other major conservation threats associated with natural resource extractive industries. Similar calculations for other threatened species are currently limited by lack of basic population data.

The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

OpenAIRE

Zhang, Yi; Zhang, Qiaoling; Li, Jinghao; Zhang, Qingling

2014-01-01

The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity ind...

Population dynamics along a primary succession gradient: do alpine species fit into demographic succession theory?

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Marcante, Silvia; Winkler, Eckart; Erschbamer, Brigitta

2009-05-01

Understanding processes and mechanisms governing changes in plant species along primary successions has been of major importance in ecology. However, to date hardly any studies have focused on the complete life cycle of species along a successional gradient, comparing pioneer, early and late-successional species. In this study it is hypothesized that pioneer species should initially have a population growth rate, lambda, greater than one with high fecundity rates, and declining growth rates when they are replaced by late-successional species. Populations of late-successional species should also start, at the mid-successional stage (when pioneer species are declining), with growth rates greater than one and arrive at rates equal to one at the late successional stage, mainly due to higher survival rates that allow these species to persist for a long time. The demography of pioneer- (Saxifraga aizoides), early (Artemisia genipi) and late-successional species (Anthyllis vulneraria ssp. alpicola) was investigated together with that of a ubiquitous species (Poa alpina) along the Rotmoos glacier foreland (2300-2400 m a.s.l., Central Alps, Austria) over 3 years. A matrix modelling approach was used to compare the main demographic parameters. Elasticity values were plotted in a demographic triangle using fecundity, individual growth and survival as vital rates contributing to the population growth rates. The results largely confirmed the predictions for population growth rates during succession. However, high survival rates of larger adults characterized all species, regardless of where they were growing along the succession. At the pioneer site, high mortality rates of seedlings, plantlets and young individuals were recorded. Fecundity was found to be of minor relevance everywhere, but it was nevertheless sufficient to increase or maintain the population sizes. Demographically, all the species over all sites behaved like late-successional or climax species in secondary

The Bifurcation and Control of a Single-Species Fish Population Logistic Model with the Invasion of Alien Species

Directory of Open Access Journals (Sweden)

Yi Zhang

2014-01-01

Full Text Available The objective of this paper is to study systematically the bifurcation and control of a single-species fish population logistic model with the invasion of alien species based on the theory of singular system and bifurcation. It regards Spartina anglica as an invasive species, which invades the fisheries and aquaculture. Firstly, the stabilities of equilibria in this model are discussed. Moreover, the sufficient conditions for existence of the trans-critical bifurcation and the singularity induced bifurcation are obtained. Secondly, the state feedback controller is designed to eliminate the unexpected singularity induced bifurcation by combining harvested effort with the purification capacity. It obviously inhibits the switch of population and makes the system stable. Finally, the numerical simulation is proposed to show the practical significance of the bifurcation and control from the biological point of view.

POPULATION SYNCHRONY WITHIN AND AMONG LEPIDOPTERA SPECIES IN RELATION TO WEATHER, PHYLOGENY, AND LARVEL PHENOLOGY

Science.gov (United States)

1. The population dynamics of native herbivore species in central Appalachian deciduous forests were studied by analysing patterns of synchrony among intra- and interspecific populations and weather. 2. Spatial synchrony of 10 Lepidoptera species and three weather variables (min...

Genetic variations in two seahorse species (Hippocampus mohnikei and Hippocampus trimaculatus: evidence for middle Pleistocene population expansion.

Directory of Open Access Journals (Sweden)

Yanhong Zhang

Full Text Available Population genetic of seahorses is confidently influenced by their species-specific ecological requirements and life-history traits. In the present study, partial sequences of mitochondrial cytochrome b (cytb and control region (CR were obtained from 50 Hippocampus mohnikei and 92 H. trimaculatus from four zoogeographical zones. A total of 780 base pairs of cytb gene were sequenced to characterize mitochondrial DNA (mtDNA diversity. The mtDNA marker revealed high haplotype diversity, low nucleotide diversity, and a lack of population structure across both populations of H. mohnikei and H. trimaculatus. A neighbour-joining (NJ tree of cytb gene sequences showed that H. mohnikei haplotypes formed one cluster. A maximum likelihood (ML tree of cytb gene sequences showed that H. trimaculatus belonged to one lineage. The star-like pattern median-joining network of cytb and CR markers indicated a previous demographic expansion of H. mohnikei and H. trimaculatus. The cytb and CR data sets exhibited a unimodal mismatch distribution, which may have resulted from population expansion. Mismatch analysis suggested that the expansion was initiated about 276,000 years ago for H. mohnikei and about 230,000 years ago for H. trimaculatus during the middle Pleistocene period. This study indicates a possible signature of genetic variation and population expansion in two seahorses under complex marine environments.

Genetic Differentiations among the Populations of Salvia japonica (Lamiaceae and Its Related Species

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SUDARMONO

2008-03-01

Full Text Available Morphological and genetic variations within Salvia japonica (Lamiaceae and its related species in Japan were analyzed for clarifying their taxonomic significance. The genetic variations were explored through chloroplast and nuclear ribosomal DNA sequences and allozyme polymorphisms. Since chromosome numbers characterized the genus of Salvia, we also examined whether the karyotypes were different. We examined 58 populations of S. japonica and 14 populations of others species of Salvia. Among the populations of S. japonica represented four forms (f. japonica, f. longipes, f. lanuginosa and f. albiflora. The size of chromosomes were various among Salvia spp. Based on the allozyme as well as the DNA sequence, the populations of S. japonica separated from the others Salvia species. The populations of S. japonica exhibited four combinations of the morphological characters. However, these combinations did not correlate to the four forms of S. japonica. In addition, the morphological variations did not correlate to the allozyme and DNA sequences. It is suggested that the four morphological variations as well as the four form of S. japonica should not considered to be a taxonomic unit; accordingly, S. japonica were considered to be still at the early stage of speciation process.

Phylogeny of Fomitopsis pinicola: A species complex

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John Haight; Gary A. Laursen; Jessie A. Glaeser; D. Lee. Taylor

2016-01-01

Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an...

Individualistic population responses of five frog species in two changing tropical environments over time.

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Mason J Ryan

Full Text Available Roughly 40% of amphibian species are in decline with habitat loss, disease, and climate change being the most cited threats. Heterogeneity of extrinsic (e.g. climate and intrinsic (e.g. local adaptations factors across a species' range should influence population response to climate change and other threats. Here we examine relative detectability changes for five direct-developing leaf litter frogs between 42-year sampling periods at one Lowland Tropical Forest site (51 m.a.s.l. and one Premontane Wet Forest site (1100 m.a.s.l. in southwest Costa Rica. We identify individualistic changes in relative detectability among populations between sampling periods at different elevations. Both common and rare species showed site-specific declines, and no species exhibited significant declines at both sites. Detection changes are correlated with changes in temperature, dry season rainfall, and leaf litter depth since 1969. Our study species share Least Concern conservation status, life history traits, and close phylogenetic relationship, yet their populations changed individualistically both within and among species. These results counter current views of the uniformity or predictability of amphibian decline response and suggest additional complexity for conservation decisions.

Population Viability of Avian Endangered Species: the PVAvES Program

National Research Council Canada - National Science Library

Melton, Robert

2001-01-01

.... The program is designed to assess the viability of endangered bird species populations on U.S. Army lands. It also facilitates the comparison of alternative ecological scenarios based on different assumptions about the effects of natural or human...

Determinants of bird conservation-action implementation and associated population trends of threatened species.

Science.gov (United States)

Luther, David A; Brooks, Thomas M; Butchart, Stuart H M; Hayward, Matt W; Kester, Marieke E; Lamoreux, John; Upgren, Amy

2016-12-01

Conservation actions, such as habitat protection, attempt to halt the loss of threatened species and help their populations recover. The efficiency and the effectiveness of actions have been examined individually. However, conservation actions generally occur simultaneously, so the full suite of implemented conservation actions should be assessed. We used the conservation actions underway for all threatened and near-threatened birds of the world (International Union for Conservation of Nature Red List of Threatened Species) to assess which biological (related to taxonomy and ecology) and anthropogenic (related to geoeconomics) factors were associated with the implementation of different classes of conservation actions. We also assessed which conservation actions were associated with population increases in the species targeted. Extinction-risk category was the strongest single predictor of the type of conservation actions implemented, followed by landmass type (continent, oceanic island, etc.) and generation length. Species targeted by invasive nonnative species control or eradication programs, ex situ conservation, international legislation, reintroduction, or education, and awareness-raising activities were more likely to have increasing populations. These results illustrate the importance of developing a predictive science of conservation actions and the relative benefits of each class of implemented conservation action for threatened and near-threatened birds worldwide. © 2016 Society for Conservation Biology.

Population dynamics in changing environments: the case of an eruptive forest pest species.

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Kausrud, Kyrre; Okland, Bjørn; Skarpaas, Olav; Grégoire, Jean-Claude; Erbilgin, Nadir; Stenseth, Nils Chr

2012-02-01

In recent decades we have seen rapid and co-occurring changes in landscape structure, species distributions and even climate as consequences of human activity. Such changes affect the dynamics of the interaction between major forest pest species, such as bark beetles (Coleoptera: Curculionidae, Scolytinae), and their host trees. Normally breeding mostly in broken or severely stressed spruce; at high population densities some bark beetle species can colonise and kill healthy trees on scales ranging from single trees in a stand to multi-annual landscape-wide outbreaks. In Eurasia, the largest outbreaks are caused by the spruce bark beetle, Ips typographus (Linnaeus), which is common and shares a wide distribution with its main host, Norway spruce (Picea abies Karst.). A large literature is now available, from which this review aims to synthesize research relevant for the population dynamics of I. typographus and co-occurring species under changing conditions. We find that spruce bark beetle population dynamics tend to be metastable, but that mixed-species and age-heterogeneous forests with good site-matching tend to be less susceptible to large-scale outbreaks. While large accumulations of logs should be removed and/or debarked before the next swarming period, intensive removal of all coarse dead wood may be counterproductive, as it reduces the diversity of predators that in some areas may play a role in keeping I. typographus populations below the outbreak threshold, and sanitary logging frequently causes edge effects and root damage, reducing the resistance of remaining trees. It is very hard to predict the outcome of interspecific interactions due to invading beetle species or I. typographus establishing outside its current range, as they can be of varying sign and strength and may fluctuate depending on environmental factors and population phase. Most research indicates that beetle outbreaks will increase in frequency and magnitude as temperature, wind speed and

Disjunct populations of European vascular plant species keep the same climatic niches

DEFF Research Database (Denmark)

Wasof, Safaa; Lenoir, Jonathan; Aarrestad, Per Arild

2015-01-01

separated for thousands of years. Location: European Alps and Fennoscandia. Methods: Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly......Aim: Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been...... to be largely valid for arctic-alpine plants....

Temporal variation in population size of European bird species: effects of latitude and marginality of distribution.

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José J Cuervo

Full Text Available In the Northern Hemisphere, global warming has been shown to affect animal populations in different ways, with southern populations in general suffering more from increased temperatures than northern populations of the same species. However, southern populations are also often marginal populations relative to the entire breeding range, and marginality may also have negative effects on populations. To disentangle the effects of latitude (possibly due to global warming and marginality on temporal variation in population size, we investigated European breeding bird species across a latitudinal gradient. Population size estimates were regressed on years, and from these regressions we obtained the slope (a proxy for population trend and the standard error of the estimate (SEE (a proxy for population fluctuations. The possible relationships between marginality or latitude on one hand and slopes or SEE on the other were tested among populations within species. Potentially confounding factors such as census method, sampling effort, density-dependence, habitat fragmentation and number of sampling years were controlled statistically. Population latitude was positively related to regression slopes independent of marginality, with more positive slopes (i.e., trends in northern than in southern populations. The degree of marginality was positively related to SEE independent of latitude, with marginal populations showing larger SEE (i.e., fluctuations than central ones. Regression slopes were also significantly related to our estimate of density-dependence and SEE was significantly affected by the census method. These results are consistent with a scenario in which southern and northern populations of European bird species are negatively affected by marginality, with southern populations benefitting less from global warming than northern populations, thus potentially making southern populations more vulnerable to extinction.

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

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Yan, Yu-Bin; Duke, Norm C; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata , and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa , suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance.

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Gail S Robertson

Full Text Available Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis. With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes

Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

KAUST Repository

Pailles, Yveline

2017-02-15

Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane

Science.gov (United States)

Gerber, Brian D.; Kendall, William L.

2016-01-01

The importance of transient dynamics of structured populations is increasingly recognized in ecology, yet these implications are not largely considered in conservation practices. We investigate transient and long-term population dynamics to demonstrate the process and utility of incorporating transient dynamics into conservation research and to better understand the population management of slow life-history species; these species can be theoretically highly sensitive to short- and long-term transient effects. We are specifically interested in the effects of anthropogenic removal of individuals from populations, such as caused by harvest, poaching, translocation, or incidental take. We use the sandhill crane (Grus canadensis) as an exemplar species; it is long-lived, has low reproduction, late maturity, and multiple populations are subject to sport harvest. We found sandhill cranes to have extremely high potential, but low likelihood for transient dynamics, even when the population is being harvested. The typically low population growth rate of slow life-history species appears to buffer against many perturbations causing large transient effects. Transient dynamics will dominate population trajectories of these species when stage structures are highly biased towards the younger and non-reproducing individuals, a situation that may be rare in established populations of long-lived animals. However, short-term transient population growth can be highly sensitive to vital rates that are relatively insensitive under equilibrium, suggesting that stage structure should be known if perturbation analysis is used to identify effective conservation strategies. For populations of slow life-history species that are not prone to large perturbations to their most productive individuals, population growth may be approximated by equilibrium dynamics.

De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei and the Development of Molecular Markers for Population Genetics.

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Qiang Lin

Full Text Available Seahorse conservation has been performed utilizing various strategies for many decades, and the deeper understanding of genomic information is necessary to more efficiently protect the germplasm resources of seahorse species. However, little genetic information about seahorses currently exists in the public databases. In this study, high-throughput RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 unigenes for H. mohnikei. Among them, 17,338 (46.23% unigenes for H. erectus and 17,900 (49.57% for H. mohnikei were successfully annotated based on the information available from the public databases. Through comparing the unigenes of two seahorse species, 7,802 candidate orthologous genes were identified and 5,268 genes among them could be annotated. In addition, gene ontology analysis of two species was similarly performed on biological processes, cellular components, and molecular functions. Twenty-four and twenty-one unigenes in H. erectus and H. mohnikei were annotated in the biosynthesis of unsaturated fatty acids pathways, and both seahorses lacked the Δ12 and Δ15 desaturases. Total of 8,992 and 9,116 SSR loci were obtained from H. erectus and H. mohnikei unigenes, respectively. Dozens of SSR were developed and then applied to assess the population genetic diversity, as well as cross-amplified in a related species, H. trimaculatus. The HO and HE values of the tested populations for H. erectus, H. mohnikei, and H. trimaculatus were medium. These resources would facilitate the conservation of the species through a better understanding of the genomics and comparative genome analysis within the Hippocampus genus.

De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population Genetics.

Science.gov (United States)

Lin, Qiang; Luo, Wei; Wan, Shiming; Gao, Zexia

2016-01-01

Seahorse conservation has been performed utilizing various strategies for many decades, and the deeper understanding of genomic information is necessary to more efficiently protect the germplasm resources of seahorse species. However, little genetic information about seahorses currently exists in the public databases. In this study, high-throughput RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 unigenes for H. mohnikei. Among them, 17,338 (46.23%) unigenes for H. erectus and 17,900 (49.57%) for H. mohnikei were successfully annotated based on the information available from the public databases. Through comparing the unigenes of two seahorse species, 7,802 candidate orthologous genes were identified and 5,268 genes among them could be annotated. In addition, gene ontology analysis of two species was similarly performed on biological processes, cellular components, and molecular functions. Twenty-four and twenty-one unigenes in H. erectus and H. mohnikei were annotated in the biosynthesis of unsaturated fatty acids pathways, and both seahorses lacked the Δ12 and Δ15 desaturases. Total of 8,992 and 9,116 SSR loci were obtained from H. erectus and H. mohnikei unigenes, respectively. Dozens of SSR were developed and then applied to assess the population genetic diversity, as well as cross-amplified in a related species, H. trimaculatus. The HO and HE values of the tested populations for H. erectus, H. mohnikei, and H. trimaculatus were medium. These resources would facilitate the conservation of the species through a better understanding of the genomics and comparative genome analysis within the Hippocampus genus.

Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico.

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Baptiste Faure

Full Text Available Hydrocarbon seepage is widespread and patchy in the Gulf of Mexico, and six species of symbiont containing bathymodiolin mussels are found on active seeps over wide and overlapping depth and geographic ranges. We use mitochondrial genes to discriminate among the previously known and a newly discovered species and to assess the connectivity among populations of the same species in the northern Gulf of Mexico (GoM. Our results generally validate the morphologically based distribution of the three previously known GoM species of Bathymodiolus, although we found that approximately 10% of the morphologically based identifications were incorrect and this resulted in some inaccuracies with respect to their previously assigned depth and geographical distribution patterns. These data allowed us to confirm that sympatry of two species of Bathymodiolus within a single patch of mussels is common. A new species of bathymodiolin, Bathymodiolus sp. nov., closely related to B. heckerae was also discovered. The two species live at the same depths but have not been found in sympatry and both have small effective population sizes. We found evidence for genetic structure within populations of the three species of Bathymodiolinae for which we had samples from multiple sites and suggest limited connectivity for populations at some sites. Despite relatively small sample sizes, genetic diversity indices suggest the largest population sizes for B. childressi and Tamu fisheri and the smallest for B. heckerae and B. sp. nov. among the GoM bathymodiolins. Moreover, we detected an excess of rare variants indicating recent demographic changes and population expansions for the four species of bathymodiolins from the Gulf of Mexico.

High prices for rare species can drive large populations extinct: the anthropogenic Allee effect revisited.

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Holden, Matthew H; McDonald-Madden, Eve

2017-09-21

Consumer demand for plant and animal products threatens many populations with extinction. The anthropogenic Allee effect (AAE) proposes that such extinctions can be caused by prices for wildlife products increasing with species rarity. This price-rarity relationship creates financial incentives to extract the last remaining individuals of a population, despite higher search and harvest costs. The AAE has become a standard approach for conceptualizing the threat of economic markets on endangered species. Despite its potential importance for conservation, AAE theory is based on a simple graphical model with limited analysis of possible population trajectories. By specifying a general class of functions for price-rarity relationships, we show that the classic theory can understate the risk of species extinction. AAE theory proposes that only populations below a critical Allee threshold will go extinct due to increasing price-rarity relationships. Our analysis shows that this threshold can be much higher than the original theory suggests, depending on initial harvest effort. More alarmingly, even species with population sizes above this Allee threshold, for which AAE predicts persistence, can be destined to extinction. Introducing even a minimum price for harvested individuals, close to zero, can cause large populations to cross the classic anthropogenic Allee threshold on a trajectory towards extinction. These results suggest that traditional AAE theory may give a false sense of security when managing large harvested populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sharing the Planet. Population - Consumption - Species. Science and Ethics for a Sustainable and Equitable World

Energy Technology Data Exchange (ETDEWEB)

Van der Zwaan, B.; Petersen, A. (eds.)

2003-11-01

The world is going through the profound changes of a demographic transition. Population growth is best taken care of when women and men are able to choose freely and responsibly their number of children. The most important aspects are the availability of reliable and safe means and the access women have to knowledge, resources and decision power. General education is a prerequisite. (Groningen Manifesto, statement no. 7). The current international, political, economic and financial order still primarily reflects the claims of international trade. There is a lack of public awareness as to the inescapable limits of the planet's resources and we hardly seem to be moving towards a sustainable and equitable world. The contributors to this volume provide an up-to-date and forceful exposition of this problematique. In the aftermath of the World Summit on Sustainable Development held in Johannesburg, they suggest topical ways to alter the world's course. The keys to reaching a sustainable world, in which the planet is equitably shared among humans and other species, are to consider the impact of our collective actions at longer timescales and to deal head-on with the interconnected issues of population pressure, consumption volume and species loss. The volume displays a multidisciplinary and multicultural approach involving both scientific and ethical arguments. It is of interest to a wide audience of scholars and concerned citizens. With contributions by: Ernst Ulrich von Weizsaecker, Friedrich Schmidt-Bleek, Johan van Klinken, Anne Ehrlich, Sergey Kapitza, Roefie Hueting, Jan van Hooff, Lucas Reijnders, Arthur Petersen, Bob van der Zwaan, Vandana Shiva, Radha Holla, Koo van der Wal, Bas de Gaay Fortman, Atiq Rahman and Jane Goodall.

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

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Yu-Bin Yan

2016-09-01

Full Text Available Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, R. mucronata, and R. stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the

Toward reassessing data-deficient species.

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Bland, Lucie M; Bielby, Jon; Kearney, Stephen; Orme, C David L; Watson, James E M; Collen, Ben

2017-06-01

One in 6 species (13,465 species) on the International Union for Conservation of Nature (IUCN) Red List is classified as data deficient due to lack of information on their taxonomy, population status, or impact of threats. Despite the chance that many are at high risk of extinction, data-deficient species are typically excluded from global and local conservation priorities, as well as funding schemes. The number of data-deficient species will greatly increase as the IUCN Red List becomes more inclusive of poorly known and speciose groups. A strategic approach is urgently needed to enhance the conservation value of data-deficient assessments. To develop this, we reviewed 2879 data-deficient assessments in 6 animal groups and identified 8 main justifications for assigning data-deficient status (type series, few records, old records, uncertain provenance, uncertain population status or distribution, uncertain threats, taxonomic uncertainty, and new species). Assigning a consistent set of justification tags (i.e., consistent assignment to assessment justifications) to species classified as data deficient is a simple way to achieve more strategic assessments. Such tags would clarify the causes of data deficiency; facilitate the prediction of extinction risk; facilitate comparisons of data deficiency among taxonomic groups; and help prioritize species for reassessment. With renewed efforts, it could be straightforward to prevent thousands of data-deficient species slipping unnoticed toward extinction. © 2016 Society for Conservation Biology.

Fish population studies using parasites from the Southeastern Pacific Ocean: considering host population changes and species body size as sources of variability of parasite communities.

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George-Nascimento, Mario; Oliva, Marcelo

2015-01-01

Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae, Rhodophyta) from New Zealand.

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Muangmai, Narongrit; Fraser, Ceridwen I; Zuccarello, Giuseppe C

2015-06-01

Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct "cryptic" species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa. © 2015 Phycological Society of America.

On the surprising lack of differences between two congeneric calanoid copepod species, Calanus finmarchicus and C. helgolandicus

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Wilson, Robert J.; Speirs, Douglas C.; Heath, Michael R.

2015-05-01

as a result of an inability to diapause for significant periods. This synthesised view of each species' respective life cycle traits is that response of growth and development to temperature is the only known difference between each species, which indicates a promising direction for the extension of population models of C. finmarchicus to C. helgolandicus.

Helminth species richness of introduced and native grey mullets (Teleostei: Mugilidae).

Science.gov (United States)

Sarabeev, Volodimir

2015-08-01

Quantitative complex analyses of parasite communities of invaders across different native and introduced populations are largely lacking. The present study provides a comparative analysis of species richness of helminth parasites in native and invasive populations of grey mullets. The local species richness differed between regions and host species, but did not differ when compared with invasive and native hosts. The size of parasite assemblages of endohelminths was higher in the Mediterranean and Azov-Black Seas, while monogeneans were the most diverse in the Sea of Japan. The helminth diversity was apparently higher in the introduced population of Liza haematocheilus than that in their native habitat, but this trend could not be confirmed when the size of geographic range and sampling efforts were controlled for. The parasite species richness at the infracommunity level of the invasive host population is significantly lower compared with that of the native host populations that lends support to the enemy release hypothesis. A distribution pattern of the infracommunity richness of acquired parasites by the invasive host can be characterized as aggregated and it is random in native host populations. Heterogeneity in the host susceptibility and vulnerability to acquired helminth species was assumed to be a reason of the aggregation of species numbers in the population of the invasive host. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Optimizing conservation of migratory species over their full annual cycle in the Western Hemisphere

OpenAIRE

Bennett, Joseph; Auer, Tom; Fink, Daniel; Arcese, Peter; Rodewald, Amanda; Wilson, Scott; Schuster, Richard

2018-01-01

Strategic plans to conserve migratory species require detailed knowledge on species distribution, abundance, and habitat use over the annual cycle, but such data are lacking for most species. We developed a hemispheric approach to planning using spatiotemporally explicit species abundance models to prioritize land needed to conserve ≥17% of the global populations of 109 species of Neotropical migratory birds. The efficiency of annual cycle plans was evaluated in comparisons to single-season p...

Population dynamics model for plasmid bearing and plasmid lacking ...

African Journals Online (AJOL)

Streptokinase production in bioreactor is well associated to cell population dynamics. It is an established fact that two types of cell populations are found to emerge from the initial pool of recombinant cell population. This phenomenon leads to an undesired loss in yield of the product. Primary metabolites, like acetic acid etc ...

Population genetics of four heavily exploited shark species around the Arabian Peninsula

KAUST Repository

Spaet, Julia L.Y.

2015-05-01

The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.

Conservation state of populations of rare plant species in highly transformed meadow steppes of Southern Opillya

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I. I. Dmytrash-Vatseba

2016-09-01

Full Text Available Degradation of natural habitats causes rapid extinction of rare plant populations. The diversity of rare plant species in the meadow steppes of Southern Opillya (Western Ukraine depends strongly on patch area, pasture digression of vegetation and a variety of eco-coenotical conditions. The main threats for the rare components of the meadow steppe flora are reduction of habitat and overgrazing. Spatial connections between sites are unable to support a constant rare plant population. The analysis of the composition of rare plant meadow-steppe species indicated that habitats with similar rare species composition usually have similar parameters of area, stages of pasture digression and eco-coenotical conditions. Spatial connectivity of patches does not ensure species similarity of rare components of the flora. Rare plant species were grouped according to their preferences for habitat , area and condition. In small patches subject to any stage of pasture digression grow populations of Adonis vernalis L., Pulsatilla patens (L. Mill., P. grandis Wender., Stipa capillata L., S. рennata L., Chamaecytisus blockianus (Pawł. Klásková etc. On the contrary, populations of other species (Carlina onopordifolia Besser. ex Szafer., Kuecz. et Pawł., Adenophora liliifolia (L. Ledeb. ex A. DC., Crambe tataria Sebeók, Euphorbia volhynica Besser ex Racib., Stipa tirsa Stev. etc. prefer large habitats, not changed by pasture digression. Prevention of reduction of rare species diversity requires preservation (also extension of patch area and regulation of grazing intensity.

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

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Maslov, Sergei; Sneppen, Kim

2017-01-01

Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

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Brewer Marin

2010-09-01

Full Text Available Abstract Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated. Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern

Climate, invasive species and land use drive population dynamics of a cold-water specialist

Science.gov (United States)

Kovach, Ryan P.; Al-Chokhachy, Robert K.; Whited, Diane C.; Schmetterling, David A.; Dux, Andrew M; Muhlfeld, Clint C.

2017-01-01

Climate change is an additional stressor in a complex suite of threats facing freshwater biodiversity, particularly for cold-water fishes. Research addressing the consequences of climate change on cold-water fish has generally focused on temperature limits defining spatial distributions, largely ignoring how climatic variation influences population dynamics in the context of other existing stressors.We used long-term data from 92 populations of bull trout Salvelinus confluentus – one of North America's most cold-adapted fishes – to quantify additive and interactive effects of climate, invasive species and land use on population dynamics (abundance, variability and growth rate).Populations were generally depressed, more variable and declining where spawning and rearing stream habitat was limited, invasive species and land use were prevalent and stream temperatures were highest. Increasing stream temperature acted additively and independently, whereas land use and invasive species had additive and interactive effects (i.e. the impact of one stressor depended on exposure to the other stressor).Most (58%–78%) of the explained variation in population dynamics was attributed to the presence of invasive species, differences in life history and management actions in foraging habitats in rivers, lakes and reservoirs. Although invasive fishes had strong negative effects on populations in foraging habitats, proactive control programmes appeared to effectively temper their negative impact.Synthesis and applications. Long-term demographic data emphasize that climate warming will exacerbate imperilment of cold-water specialists like bull trout, yet other stressors – especially invasive fishes – are immediate threats that can be addressed by proactive management actions. Therefore, climate-adaptation strategies for freshwater biodiversity should consider existing abiotic and biotic stressors, some of which provide potential and realized opportunity for conservation

Population assessment and degree of threat of chalybea Macrocarpa (Melastomataceae) endemic species from Colombia

International Nuclear Information System (INIS)

Gil Leguizamon, Pablo Andres; Morales Puentes, Maria Eugenia; Diaz Perez, Carlos Nelson

2014-01-01

Population assessment results from chalybea macrocarpaare shown, the specie is considerate ENDANGERED (EN) by its restricted area, threatened is generated by crops and extensive cattle farming. the study was conducted in the Boyaca Department (Colombia), Municipality of Arcabuco, in three established localities using herbarium and literature information; field work made possible identified distribution, density and phenology like sub criteria, allowing identify the presence extension and occupancy area. We took structural data (height, coverage and DBH) to determinate the population age's classes. Which the gathered information and the associated vegetation, the specie is re-categorized which the b IUCN criteria. It is distributed to the northwest and southern in Arcabuco, in an area of 59.9 km"2, 4 km"2 of occupancy and a population density of 50 individual/km"2. Flowering and fruiting is continuous through the year, however, most of the flowering is from March to August and fruiting from September to February. Age structure allows identified ten species between seedlings, juveniles and adults. Population is represented by few seedling individuals (10.6 %) and juveniles (20.9 %) versus adults (68.5 %). finally, C. macrocarpais upgraded to Critical Risk (CR B1ab (iii)).

Fire management strategies to maintain species population processes in a fragmented landscape of fire-interval extremes.

Science.gov (United States)

Tulloch, Ayesha I T; Pichancourt, Jean-Baptiste; Gosper, Carl R; Sanders, Angela; Chadès, Iadine

2016-10-01

Changed fire regimes have led to declines of fire-regime-adapted species and loss of biodiversity globally. Fire affects population processes of growth, reproduction, and dispersal in different ways, but there is little guidance about the best fire regime(s) to maintain species population processes in fire-prone ecosystems. We use a process-based approach to determine the best range of fire intervals for keystone plant species in a highly modified Mediterranean ecosystem in southwestern Australia where current fire regimes vary. In highly fragmented areas, fires are few due to limited ignitions and active suppression of wildfire on private land, while in highly connected protected areas fires are frequent and extensive. Using matrix population models, we predict population growth of seven Banksia species under different environmental conditions and patch connectivity, and evaluate the sensitivity of species survival to different fire management strategies and burning intervals. We discover that contrasting, complementary patterns of species life-histories with time since fire result in no single best fire regime. All strategies result in the local patch extinction of at least one species. A small number of burning strategies secure complementary species sets depending on connectivity and post-fire growing conditions. A strategy of no fire always leads to fewer species persisting than prescribed fire or random wildfire, while too-frequent or too-rare burning regimes lead to the possible local extinction of all species. In low landscape connectivity, we find a smaller range of suitable fire intervals, and strategies of prescribed or random burning result in a lower number of species with positive growth rates after 100 years on average compared with burning high connectivity patches. Prescribed fire may reduce or increase extinction risk when applied in combination with wildfire depending on patch connectivity. Poor growing conditions result in a significantly

Population dynamics of three songbird species in a nestbox population in Central Europe show effects of density, climate and competitive interactions

NARCIS (Netherlands)

Smallegange, I.M.; van der Meer, J.; Fiedler, W.

2011-01-01

Unravelling the contributions of density-dependent and density-independent factors in determining species population dynamics is a challenge, especially if the two factors interact. One approach is to apply stochastic population models to long-term data, yet few studies have included interactions

Wild Plant Species with Extremely Small Populations Require Conservation and Reintroduction in China

Science.gov (United States)

Hai Ren; Qianmei Zhang; Hongfang Lu; Hongxiao Liu; Qinfeng Guo; Jun Wang; Shuguang Jian; Hai’ou Bao

2012-01-01

China is exceptionally rich in biodiversity, with more than 30000 vascular plant species that include many endemic genera, species of ancient origin, and cultivated plants (Yang et al. 2005). Because of rapid economic development, population growth, pollution, and continuing resource exploitation, China’s plant diversity faces severe threats. According to the Chinese...

Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

Science.gov (United States)

Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

2018-02-01

The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

Monitoring of fish species in the Lamone river: distribution and morphometric measures of the populations

Directory of Open Access Journals (Sweden)

Riccardo Bozzi

2010-01-01

Full Text Available Fish samplings were carried out monthly from spring to autumn during 2008, on the Lamone river and the Campigno stream by an electrofishing, in order to verify the presence of fish populations and the most common species represented. Barb, Barbus plebejus, Blageon, Leuciscus muticellus, Chub, Leuciscus cephalus, South European Nase, Chondrostoma genei were identified. A small population of Brown trout, Salmo trutta fario was also recognized. Barb is the most represented species in all the sites. The samplings highlight that Lamone river presented conditions suitable to fully guarantee the life of the fish populations.

Crater Lake Apoyo Revisited - Population Genetics of an Emerging Species Flock

Science.gov (United States)

Geiger, Matthias F.; McCrary, Jeffrey K.; Schliewen, Ulrich K.

2013-01-01

The polytypic Nicaraguan Midas cichlids ( Amphilophus cf. citrinellus) have been established as a model system for studying the mechanisms of speciation and patterns of diversification in allopatry and sympatry. The species assemblage in Crater Lake Apoyo has been accepted as a textbook example for sympatric speciation. Here, we present a first comprehensive data set of population genetic (mtDNA & AFLPs) proxies of species level differentiation for a representative set of individuals of all six endemic Amphilophus species occurring in Crater Lake Apoyo. AFLP genetic differentiation was partitioned into a neutral and non-neutral component based on outlier-loci detection approaches, and patterns of species divergence were explored with Bayesian clustering methods. Substantial levels of admixture between species were detected, indicating different levels of reproductive isolation between the six species. Analysis of neutral genetic variation revealed several A . zaliosus as being introgressed by an unknown contributor, hereby rendering the sympatrically evolving L. Apoyo flock polyphyletic. This is contrasted by the mtDNA analysis delivering a clear monophyly signal with Crater Lake Apoyo private haplotypes characterising all six described species, but also demonstrating different demographic histories as inferred from pairwise mismatch distributions. PMID:24086393

Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

Science.gov (United States)

Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

2005-04-01

Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

76 FR 77465 - Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of...

Science.gov (United States)

2011-12-13

... Population Segments of the Bearded Seal AGENCY: National Marine Fisheries Service (NMFS), National Oceanic... population segments (DPS) of the bearded seal (Erignathus barbatus) as threatened species under the... posed to this population by the projected habitat changes. Extension of Final Listing Determination The...

Population Development of Several Species of Ants on the Cocoa Trees in South Sulawesi

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Fatahuddin Fatahuddin

2010-08-01

Full Text Available Several species of ants with different behavior have been found in cocoa plantations and their behavior is important to be considered because it might be correlated with the degree of protection of cocoa plant from cocoa pests. The aim of this research is to manipulate and to develop ants population in environment, so they are able to establish permanently in cocoa trees. This research was conducted in Papakaju Regions Luwu Regency in Juli to November 2009. In this study, 10 cocoa trees with ants were sampled (each species of ant in 10 cocoa trees. A control of 10 tree samples without ant was also taken. In order to assess the abundance of ant population, it was grouped based on scoring, which score 1 for less than 20 ants, score 2 for 21–50 ants, score 3 for 51–200 ants, score 4 for 201–1000 ants, and score 5 for more than 1000 per tree. The results indicated that average of population score of the three ants species reached the highest population for the Oecophylla. smaragdina with average score 4.85 (>1000 ants, Dolichoderus thoracicus, with average score 3.90 (> 200 ants and Crematogaster. difformis with average score 3.10 (>200 ants. This research indicated that three species of ants, Oecophylla smaragdina (weaver ant, Dolichoderus thoracicus (cocoa black ant and Crematogaster difformis (cracking ant. in farmer cocoa plantations in South Sulawesi giving better performance against major pests of cocoa in particular cocoa pod borer (CPB. Key words: Ant Population, Oecophylla smaragdina, Dolichoderus thoracicus, Crematogaster difformis, artificial nest, cocoa.

Fatalities at wind turbines may threaten population viability of a migratory bat

Science.gov (United States)

W.F. Frick; E.F. Baerwald; J.F. Pollock; R.M.R. Barclay; J.A. Szymanski; Ted Weller; A.L. Russell; Susan Loeb; R.A. Medellin; L.P. McGuire

2017-01-01

Large numbers of migratory bats are killed every year at wind energy facilities. However, population-level impacts are unknown as we lack basic demographic information about these species. We investigated whether fatalities at wind turbines could impact population viability of migratory bats, focusing on the hoary bat (Lasiurus cinereus),...

Evaluating population connectivity for species of conservation concern in the American Great Plains

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Samuel A. Cushman; Erin L. Landguth; Curtis H. Flather

2013-01-01

Habitat loss and fragmentation are widely recognized as among the most important threats to global biodiversity. New analytical approaches are providing an improved ability to predict the effects of landscape change on population connectivity at vast spatial extents. This paper presents an analysis of population connectivity for three species of conservation concern [...

Selection for life-history traits to maximize population growth in an invasive marine species

DEFF Research Database (Denmark)

Jaspers, Cornelia; Marty, Lise; Kiørboe, Thomas

2018-01-01

Species establishing outside their natural range, negatively impacting local ecosystems, are of increasing global concern. They often display life-history features characteristic for r-selected populations with fast growth and high reproduction rates to achieve positive population growth rates (r...

Differences in the Aerobic Capacity of Flight Muscles between Butterfly Populations and Species with Dissimilar Flight Abilities

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Rauhamäki, Virve; Wolfram, Joy; Jokitalo, Eija; Hanski, Ilkka; Dahlhoff, Elizabeth P.

2014-01-01

Habitat loss and climate change are rapidly converting natural habitats and thereby increasing the significance of dispersal capacity for vulnerable species. Flight is necessary for dispersal in many insects, and differences in dispersal capacity may reflect dissimilarities in flight muscle aerobic capacity. In a large metapopulation of the Glanville fritillary butterfly in the Åland Islands in Finland, adults disperse frequently between small local populations. Individuals found in newly established populations have higher flight metabolic rates and field-measured dispersal distances than butterflies in old populations. To assess possible differences in flight muscle aerobic capacity among Glanville fritillary populations, enzyme activities and tissue concentrations of the mitochondrial protein Cytochrome-c Oxidase (CytOx) were measured and compared with four other species of Nymphalid butterflies. Flight muscle structure and mitochondrial density were also examined in the Glanville fritillary and a long-distance migrant, the red admiral. Glanville fritillaries from new populations had significantly higher aerobic capacities than individuals from old populations. Comparing the different species, strong-flying butterfly species had higher flight muscle CytOx content and enzymatic activity than short-distance fliers, and mitochondria were larger and more numerous in the flight muscle of the red admiral than the Glanville fritillary. These results suggest that superior dispersal capacity of butterflies in new populations of the Glanville fritillary is due in part to greater aerobic capacity, though this species has a low aerobic capacity in general when compared with known strong fliers. Low aerobic capacity may limit dispersal ability of the Glanville fritillary. PMID:24416122

Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

Science.gov (United States)

Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

2018-04-23

The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure

Genetic Diversity and Population Structure of Varronia curassavica: A Medicinal Polyploid Species in a Threatened Ecosystem.

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Hoeltgebaum, Marcia Patricia; Dos Reis, Maurício Sedrez

2017-06-01

Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level, and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44% of the alleles occurred at low frequency in adults of all populations and 41% in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Communities, populations and individuals of arbuscular mycorrhizal fungi

DEFF Research Database (Denmark)

Rosendahl, Søren

2008-01-01

Arbuscular mycorrhizal fungi in the phylum Glomeromycota are found globally in most vegetation types, where they form a mutualistic symbiosis with plant roots. Despite their wide distribution, only relatively few species are described. The taxonomy is based on morphological characters...... of the asexual resting spores, but molecular approaches to community ecology have revealed a considerable unknown diversity from colonized roots. Although the lack of genetic recombination is not unique in the fungal kingdom, arbuscular mycorrhizal fungi are probably ancient asexuals. The long asexual evolution...... of the fungi has resulted in considerable genetic diversity within morphologically recognizable species, and challenges our concepts of individuals and populations. This review critically examines the concepts of species, communities, populations and individuals of arbuscular mycorrhizal fungi....

Long-term species balance in sympatric populations: implications for Atlantic salmon and brown trout

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Jose Luis Horreo

2014-09-01

Full Text Available The factors determining regional adaptation in salmonids are still unclear, but it is known that changes in their habitat imply changes in their population structure. In this preliminary study we integrate habitat data, molecular analyses (from both nuclear microsatellite and mitochondrial loci and life-history traits (measured on archaeological vertebrae and modern scales of two sympatric salmonid species: Atlantic salmon and brown trout. We propose that water temperature and geological characteristics changed the biogeographic patterns of these species through asymmetric migration and different (but complementary population growth rates. As a consequence, differences in a life-history trait (mean number of years at sea and population sizes were detected between regions, suggesting a process of substitution of Atlantic salmon by brown trout.

Effects of white-nose syndrome on regional population patterns of 3 hibernating bat species.

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Ingersoll, Thomas E; Sewall, Brent J; Amelon, Sybill K

2016-10-01

Hibernating bats have undergone severe recent declines across the eastern United States, but the cause of these regional-scale declines has not been systematically evaluated. We assessed the influence of white-nose syndrome (an emerging bat disease caused by the fungus Pseudogymnoascus destructans, formerly Geomyces destructans) on large-scale, long-term population patterns in the little brown myotis (Myotis lucifugus), the northern myotis (Myotis septentrionalis), and the tricolored bat (Perimyotis subflavus). We modeled population trajectories for each species on the basis of an extensive data set of winter hibernacula counts of more than 1 million individual bats from a 4-state region over 13 years and with data on locations of hibernacula and first detections of white-nose syndrome at each hibernaculum. We used generalized additive mixed models to determine population change relative to expectations, that is, how population trajectories differed with a colony's infection status, how trajectories differed with distance from the point of introduction of white-nose syndrome, and whether declines were concordant with first local observation of the disease. Population trajectories in all species met at least one of the 3 expectations, but none met all 3. Our results suggest, therefore, that white-nose syndrome has affected regional populations differently than was previously understood and has not been the sole cause of declines. Specifically, our results suggest that in some areas and species, threats other than white-nose syndrome are also contributing to population declines, declines linked to white-nose syndrome have spread across large geographic areas with unexpected speed, and the disease or other threats led to declines in bat populations for years prior to disease detection. Effective conservation will require further research to mitigate impacts of white-nose syndrome, renewed attention to other threats to bats, and improved surveillance efforts to ensure

76 FR 14883 - Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of...

Science.gov (United States)

2011-03-18

...-XZ58 Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of..., published a proposed rule to list the Beringia and Okhotsk Distinct Population Segments (DPSs) of the... published a proposed rule to list the Beringia and Okhotsk Distinct Population Segments (DPSs) of the...

The extent of population genetic subdivision differs among four co-distributed shark species in the Indo-Australian archipelago

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Giles Jenny

2009-02-01

Full Text Available Abstract Background The territorial fishing zones of Australia and Indonesia are contiguous to the north of Australia in the Timor and Arafura Seas and in the Indian Ocean to the north of Christmas Island. The area surrounding the shared boundary consists of a variety of bio-diverse marine habitats including shallow continental shelf waters, oceanic trenches and numerous offshore islands. Both countries exploit a variety of fisheries species, including whaler (Carcharhinus spp. and hammerhead sharks (Sphyrna spp.. Despite their differences in social and financial arrangements, the two countries are motivated to develop complementary co-management practices to achieve resource sustainability. An essential starting point is knowledge of the degree of population subdivision, and hence fisheries stock status, in exploited species. Results Populations of four commercially harvested shark species (Carcharhinus obscurus, Carcharhinus sorrah, Prionace glauca, Sphyrna lewini were sampled from northern Australia and central Indonesia. Neutral genetic markers (mitochondrial DNA control region sequence and allelic variation at co-dominant microsatellite loci revealed genetic subdivision between Australian and Indonesian populations of C. sorrah. Further research is needed to address the possibility of genetic subdivision among C. obscurus populations. There was no evidence of genetic subdivision for P. glauca and S. lewini populations, but the sampling represented a relatively small part of their distributional range. For these species, more detailed analyses of population genetic structure is recommended in the future. Conclusion Cooperative management between Australia and Indonesia is the best option at present for P. glauca and S. lewini, while C. sorrah and C. obscurus should be managed independently. On-going research on these and other exploited shark and ray species is strongly recommended. Biological and ecological similarity between species may

Host plant adaptation in Drosophila mettleri populations.

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Sergio Castrezana

Full Text Available The process of local adaptation creates diversity among allopatric populations, and may eventually lead to speciation. Plant-feeding insect populations that specialize on different host species provide an excellent opportunity to evaluate the causes of ecological specialization and the subsequent consequences for diversity. In this study, we used geographically separated Drosophila mettleri populations that specialize on different host cacti to examine oviposition preference for and larval performance on an array of natural and non-natural hosts (eight total. We found evidence of local adaptation in performance on saguaro cactus (Carnegiea gigantea for populations that are typically associated with this host, and to chemically divergent prickly pear species (Opuntia spp. in a genetically isolated population on Santa Catalina Island. Moreover, each population exhibited reduced performance on the alternative host. This finding is consistent with trade-offs associated with adaptation to these chemically divergent hosts, although we also discuss alternative explanations for this pattern. For oviposition preference, Santa Catalina Island flies were more likely to oviposit on some prickly pear species, but all populations readily laid eggs on saguaro. Experiments with non-natural hosts suggest that factors such as ecological opportunity may play a more important role than host plant chemistry in explaining the lack of natural associations with some hosts.

Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae: Insights from RAPD and ISSR Variation

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Pei-Luen Lu

2016-08-01

Full Text Available The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis, endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD and inter simple sequence repeats (ISSR to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon’s index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested.

Assumption-versus data-based approaches to summarizing species' ranges.

Science.gov (United States)

Peterson, A Townsend; Navarro-Sigüenza, Adolfo G; Gordillo, Alejandro

2018-06-01

For conservation decision making, species' geographic distributions are mapped using various approaches. Some such efforts have downscaled versions of coarse-resolution extent-of-occurrence maps to fine resolutions for conservation planning. We examined the quality of the extent-of-occurrence maps as range summaries and the utility of refining those maps into fine-resolution distributional hypotheses. Extent-of-occurrence maps tend to be overly simple, omit many known and well-documented populations, and likely frequently include many areas not holding populations. Refinement steps involve typological assumptions about habitat preferences and elevational ranges of species, which can introduce substantial error in estimates of species' true areas of distribution. However, no model-evaluation steps are taken to assess the predictive ability of these models, so model inaccuracies are not noticed. Whereas range summaries derived by these methods may be useful in coarse-grained, global-extent studies, their continued use in on-the-ground conservation applications at fine spatial resolutions is not advisable in light of reliance on assumptions, lack of real spatial resolution, and lack of testing. In contrast, data-driven techniques that integrate primary data on biodiversity occurrence with remotely sensed data that summarize environmental dimensions (i.e., ecological niche modeling or species distribution modeling) offer data-driven solutions based on a minimum of assumptions that can be evaluated and validated quantitatively to offer a well-founded, widely accepted method for summarizing species' distributional patterns for conservation applications. © 2016 Society for Conservation Biology.

Plastic responses to elevated temperature in low and high elevation populations of three grassland species.

Science.gov (United States)

Frei, Esther R; Ghazoul, Jaboury; Pluess, Andrea R

2014-01-01

Local persistence of plant species in the face of climate change is largely mediated by genetic adaptation and phenotypic plasticity. In species with a wide altitudinal range, population responses to global warming are likely to differ at contrasting elevations. In controlled climate chambers, we investigated the responses of low and high elevation populations (1200 and 1800 m a.s.l.) of three nutrient-poor grassland species, Trifolium montanum, Ranunculus bulbosus, and Briza media, to ambient and elevated temperature. We measured growth-related, reproductive and phenological traits, evaluated differences in trait plasticity and examined whether trait values or plasticities were positively related to approximate fitness and thus under selection. Elevated temperature induced plastic responses in several growth-related traits of all three species. Although flowering phenology was advanced in T. montanum and R. bulbosus, number of flowers and reproductive allocation were not increased under elevated temperature. Plasticity differed between low and high elevation populations only in leaf traits of T. montanum and B. media. Some growth-related and phenological traits were under selection. Moreover, plasticities were not correlated with approximate fitness indicating selectively neutral plastic responses to elevated temperature. The observed plasticity in growth-related and phenological traits, albeit variable among species, suggests that plasticity is an important mechanism in mediating plant responses to elevated temperature. However, the capacity of species to respond to climate change through phenotypic plasticity is limited suggesting that the species additionally need evolutionary adaptation to adjust to climate change. The observed selection on several growth-related and phenological traits indicates that the study species have the potential for future evolution in the context of a warming climate.

Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd.

Science.gov (United States)

Peng, Yan Qun; Fan, Ling Ling; Mao, Fu Ying; Zhao, Yun Sheng; Xu, Rui; Yin, Yu Jie; Chen, Xin; Wan, De Guang; Zhang, Xin Hui

2018-03-01

Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Overcoming challenges to the recovery of declining amphibian populations in the United States

Science.gov (United States)

Walls, Susan; Ball, Lianne C.; Barichivich, William J.; Dodd, Kenneth; Enge, Kevin M; Gorman, Thomas A.; O'Donnell, Katherine; Palis, John G; Semlitsch, Raymond D.

2016-01-01

The US Endangered Species Act of 1973 (ESA) affords many potential benefits to species threatened with extinction. However, most at-risk amphibians—one of the most imperiled vertebrate groups—remain unlisted under the provisions of the ESA, and many impediments to recovery exist for those species that have been listed. Of the 35 US amphibian species and distinct population segments (“taxa”) listed under the ESA, 40% currently lack a final (completed) recovery plan, 28.6% lack designated critical habitat, and 8.6% lack both. For taxa that have recovery plans, the time between their listing and the development of those plans was from 2 to 29 years, and the time between their listing and the designation of critical habitat ranged from 0 to 14 years. The underlying causes of such delays in protection are complex and constitute obstacles to recovery of imperiled species. We outline a series of strategic actions by which these challenges may be overcome.

Addressing potential local adaptation in species distribution models: implications for conservation under climate change

Science.gov (United States)

Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

2016-01-01

Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

Response of different populations of seven lady beetle species to lambda-cyhalothrin with record of resistance.

Science.gov (United States)

Rodrigues, Agna R S; Spindola, Aline F; Torres, Jorge B; Siqueira, Herbert A A; Colares, Felipe

2013-10-01

Simultaneous use of biological and chemical controls is a valued and historic goal of integrated pest management, but has rarely been achieved. One explanation for this failure may be the inadequate documentation of field populations of natural enemies for insecticide tolerance or resistance because natural enemies surviving insecticide application do not create problems like resistant pest species. Therefore, this study investigated 31 populations of lady beetles (Coleoptera: Coccinellidae) regarding their susceptibility to lambda-cyhalothrin, a pyrethroid insecticide that is widely used in cotton and other crops to control lepidopteran and coleopteran pests that are not targeted as prey by lady beetles. The study focused on seven coccinellid species common in cotton fields Coleomegilla maculata De Geer, Cycloneda sanguinea (L.), Eriopis connexa Germar, Harmonia axyridis (Pallas), Hippodamia convergens Guérin-Méneville, Olla v-nigrum (Mulsant), and Brumoides foudrasi (Mulsant) and one lady beetle species [Curinus coeruleus Mulsant] from a non-cotton ecosystem for comparisons. Dose-mortality curves were estimated after topical treatment of adult lady beetles with lambda-cyhalothrin. Statistically significant variations in lady beetle susceptibility were observed between species and between populations of a given species. Seven and eighteen populations of lady beetles exhibited greater values of LD50 and LD90, respectively, than the highest recommended field rate of lambda-cyhalothrin (20g a.i./hectare≈0.2g a.i./L) for cotton fields in Brazil. Furthermore, based on LD50 values, 29 out of 30 tested populations of lady beetles exhibited ratios of relative tolerance varying from 2- to 215-fold compared to the toxicity of lambda-cyhalothrin to the boll weevil, Anthonomus grandis Boh. (Coleoptera: Curculionidae). Four populations of E. connexa were 10.5-37.7 times more tolerant than the most susceptible population and thus were considered to be resistant to lambda

Habitat shift in invading species: Zebra and quagga mussel population characteristics on shallow soft substrates

Science.gov (United States)

Berkman, P.A.; Garton, D.W.; Haltuch, M.A.; Kennedy, G.W.; Febo, L.R.

2000-01-01

Unexpected habitat innovations among invading species are illustrated by the expansion of dreissenid mussels across sedimentary environments in shallow water unlike the hard substrates where they are conventionally known. In this note, records of population characteristics of invading zebra (Dreissena polymorpha) and quagga (Dreissena bugensis) mussels from 1994 through 1998 are reported from shallow (less than 20 m) sedimentary habitats in western Lake Erie. Haphazard SCUBA collections of these invading species indicated that combined densities of zebra and quagga mussels ranged from 0 to 32,500 individuals per square meter between 1994 and 1998, with D. polymorpha comprising 75-100% of the assemblages. These mixed mussel populations, which were attached by byssal threads to each other and underlying sand-grain sediments, had size-frequency distributions that were typical of colonizing populations on hard substrates. Moreover, the presence of two mussel cohorts within the 1994 samples indicated that these species began expanding onto soft substrates not later than 1992, within 4 years of their initial invasion in western Lake Erie. Such historical data provide baselines for interpreting adaptive innovations, ecological interactions and habitat shifts among the two invading dreissenid mussel species in North America.

Understanding and estimating effective population size for practical application in marine species management.

Science.gov (United States)

Hare, Matthew P; Nunney, Leonard; Schwartz, Michael K; Ruzzante, Daniel E; Burford, Martha; Waples, Robin S; Ruegg, Kristen; Palstra, Friso

2011-06-01

Effective population size (N(e)) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N(e) is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population's current and future viability. Nevertheless, compared with ecological and demographic parameters, N(e) has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved N(e) estimation; however, some obstacles remain for the practical application of N(e) estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of N(e) over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary N(e) estimates and suggest that different sampling designs can be combined to compare largely independent measures of N(e) for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary N(e) and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating N(e) by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating N(e) estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in N(e) from hatchery-based population

Invasive rats on tropical islands: Their population biology and impacts on native species

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Grant A. Harper

2015-01-01

Full Text Available The three most invasive rat species, black or ship rat Rattus rattus, brown or Norway rats, R. norvegicus and Pacific rat, R. exulans have been incrementally introduced to islands as humans have explored the world’s oceans. They have caused serious deleterious effects through predation and competition, and extinction of many species on tropical islands, many of which are biodiversity hotspots. All three rat species are found in virtually all habitat types, including mangrove and arid shrub land. Black rats tend to dominate the literature but despite this the population biology of invasive rats, particularly Norway rats, is poorly researched on tropical islands. Pacific rats can often exceed population densities of well over 100 rats ha−1 and black rats can attain densities of 119 rats ha−1, which is much higher than recorded on most temperate islands. High densities are possibly due to high recruitment of young although the data to support this are limited. The generally aseasonally warm climate can lead to year-round breeding but can be restricted by either density-dependent effects interacting with resource constraints often due to aridity. Apparent adverse impacts on birds have been well recorded and almost all tropical seabirds and land birds can be affected by rats. On the Pacific islands, black rats have added to declines and extinctions of land birds caused initially by Pacific rats. Rats have likely caused unrecorded extinctions of native species on tropical islands. Further research required on invasive rats on tropical islands includes the drivers of population growth and carrying capacities that result in high densities and how these differ to temperate islands, habitat use of rats in tropical vegetation types and interactions with other tropical species, particularly the reptiles and invertebrates, including crustaceans.

Predicted sub-populations in a marine shrimp proteome as revealed by combined EST and cDNA data from multiple Penaeus species

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Kotewong Rattanawadee

2010-11-01

Full Text Available Abstract Background Many species of marine shrimp in the Family Penaeidae, viz. Penaeus (Litopenaeus vannamei, Penaeus monodon, Penaeus (Fenneropenaeus chinensis, and Penaeus (Marsupenaeus japonicus, are animals of economic importance in the aquaculture industry. Yet information about their DNA and protein sequences is lacking. In order to predict their collective proteome, we combined over 270,000 available EST and cDNA sequences from the 4 shrimp species with all protein sequences of Drosophila melanogaster and Caenorhabditis elegans. EST data from 4 other crustaceans, the crab Carcinus maenas, the lobster Homarus americanus (Decapoda, the water flea Daphnia pulex, and the brine shrimp Artemia franciscana were also used. Findings Similarity searches from EST collections of the 4 shrimp species matched 64% of the protein sequences of the fruit fly, but only 45% of nematode proteins, indicating that the shrimp proteome content is more similar to that of an insect than a nematode. Combined results with 4 additional non-shrimp crustaceans increased matching to 78% of fruit fly and 56% of nematode proteins, suggesting that present shrimp EST collections still lack sequences for many conserved crustacean proteins. Analysis of matching data revealed the presence of 4 EST groups from shrimp, namely sequences for proteins that are both fruit fly-like and nematode-like, fruit fly-like only, nematode-like only, and non-matching. Gene ontology profiles of proteins for the 3 matching EST groups were analyzed. For non-matching ESTs, a small fraction matched protein sequences from other species in the UniProt database, including other crustacean-specific proteins. Conclusions Shrimp ESTs indicated that the shrimp proteome is comprised of sub-populations of proteins similar to those common to both insect and nematode models, those present specifically in either model, or neither. Combining small EST collections from related species to compensate for their

Genetic structure and effective population size through time: a tale on two coastal marine species with contrasting life-history patterns

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Sara Martins Francisco

2015-12-01

Full Text Available Species with dispersal mediated by planktonic larvae are expected to be more likely to show temporal genetic variation, due to differences in larval mortality and dispersal ability. The shanny Lipophrys pholis is a typical benthic rocky intertidal fish and its dispersion is limited to its long larval stage. In contrast, the sand-smelt Atherina presbyter has a very short planktonic life, small size and weak swimming capabilities, which translates into reduced dispersion potential. A total of 226 specimens of L. pholis (collected in 2003, 2013 and 2014 and 281 of A. presbyter (collected in 2005, 2012, 2013 and 2014 were screened for genetic variation using the mitochondrial control region. Only 12 (out of 171 and 25 (out of 155 haplotypes found were shared between sampling periods for the shanny and the sand smelt, respectively. For both species, haplotype networks showed a deep genealogy with multiple levels of diversification and no temporal structure. Interestingly, some of the previously inferred missing haplotypes were sampled in more recent years. The genetic diversity indices showed little variation among sampling periods and were generally high. For L. pholis significant genetic differentiation was detected between 2013 and 2014, while no significant differences were detected between sampling periods in A. presbyter. The shanny showed lower effective population size per generation when compared to the sand-smelt (which yielded lack of evidence for genetic drift for the first and second period of the study. These results highlight the fact that temporal changes in the gene pool composition need to be considered when evaluating population structure, especially for species with long pelagic larval dispersion, more vulnerable to fluctuations in the recruitment.

Geometric and morphometric analysis of fish scales to identity genera, species and populations case study: the Cyprinid family

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Seyedeh Narjes Tabatabei

2014-01-01

Full Text Available Using fish scale to identity species and population is a rapid, safe and low cost method. Hence, this study was carried out to investigate the possibility of using geometric and morphometric methods in fish scales for rapid identification of species and populations and compare the efficiency of applying few and/or high number of landmark points. For this purpose, scales of one population of Luciobarbus capito, four populations of Alburnoides eichwaldii and two populations of Rutilus frisii kutum, all belonging to cyprinid family, were examined. On two-dimensional images of the scales 7 and 23 landmark points were digitized in two separate times using TpsDig2, respectively. Landmark data after generalized procrustes analysis were analyzed using Principal Component Analysis (PCA, Canonical Variate Analysis (CVA and Cluster Analysis. The results of both methods (using 7 and 23 landmark points showed significant differences of the shape of scales among the three species studied (P0.05. The results also showed that few number of landmarks could display the differences between scale shapes. According to the results of this study, it could be stated that the scale of each species had unique shape patterns which could be utilized as a species identification key.

[Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants].

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Boronnikova, S V; Kalendar', R N

2010-01-01

Species-specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm' region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP-markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago.

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Legrand, Delphine; Vautrin, Dominique; Lachaise, Daniel; Cariou, Marie-Louise

2011-07-01

Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

Emergence of target waves in paced populations of cyclically competing species

Energy Technology Data Exchange (ETDEWEB)

Jiang Luoluo; Zhou Tao; Wang Binghong [Department of Modern Physics, University of Science and Technology of China, Hefei 230026 (China); Perc, Matjaz [Department of Physics, Faculty of Natural Sciences and Mathematics, University of Maribor, Koroska cesta 160, SI-2000 Maribor (Slovenia); Huang Xin [Department of Physics, University of Science and Technology of China, Hefei 230026 (China)], E-mail: jiangluo@mail.ustc.edu.cn, E-mail: zhutou@ustc.edu, E-mail: matjaz.perc@uni-mb.si, E-mail: bhwang@ustc.edu.cn

2009-10-15

We investigate the emergence of target waves in a cyclic predator-prey model incorporating a periodic current of the three competing species in a small area situated at the center of a square lattice. The periodic current acts as a pacemaker, trying to impose its rhythm on the overall spatiotemporal evolution of the three species. We show that the pacemaker is able to nucleate target waves that eventually spread across the whole population, whereby three routes leading to this phenomenon can be distinguished depending on the mobility of the three species and the oscillation period of the localized current. First, target waves can emerge due to the synchronization between the periodic current and oscillations of the density of the three species on the spatial grid. The second route is similar to the first, the difference being that the synchronization sets in only intermittently. Finally, the third route toward target waves is realized when the frequency of the pacemaker is much higher than that characterizing the oscillations of the overall density of the three species. By considering the mobility and frequency of the current as variable parameters, we thus provide insights into the mechanisms of pattern formation resulting from the interplay between local and global dynamics in systems governed by cyclically competing species.

The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability.

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Pennington, R Toby; Lavin, Matt

2016-04-01

A fundamental premise of this review is that distinctive phylogenetic and biogeographic patterns in clades endemic to different major biomes illuminate the evolutionary process. In seasonally dry tropical forests (SDTFs), phylogenies are geographically structured and multiple individuals representing single species coalesce. This pattern of monophyletic species, coupled with their old species stem ages, is indicative of maintenance of small effective population sizes over evolutionary timescales, which suggests that SDTF is difficult to immigrate into because of persistent resident lineages adapted to a stable, seasonally dry ecology. By contrast, lack of coalescence in conspecific accessions of abundant and often widespread species is more frequent in rain forests and is likely to reflect large effective population sizes maintained over huge areas by effective seed and pollen flow. Species nonmonophyly, young species stem ages and lack of geographical structure in rain forest phylogenies may reflect more widespread disturbance by drought and landscape evolution causing resident mortality that opens up greater opportunities for immigration and speciation. We recommend full species sampling and inclusion of multiple accessions representing individual species in phylogenies to highlight nonmonophyletic species, which we predict will be frequent in rain forest and savanna, and which represent excellent case studies of incipient speciation. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Population Trends of Central European Montane Birds Provide Evidence for Adverse Impacts of Climate Change on High-Altitude Species.

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Jiří Flousek

Full Text Available Climate change is among the most important global threats to biodiversity and mountain areas are supposed to be under especially high pressure. Although recent modelling studies suggest considerable future range contractions of montane species accompanied with increased extinction risk, data allowing to test actual population consequences of the observed climate changes and identifying traits associated to their adverse impacts are very scarce. To fill this knowledge gap, we estimated long-term population trends of montane birds from 1984 to 2011 in a central European mountain range, the Giant Mountains (Krkonoše, where significant warming occurred over this period. We then related the population trends to several species' traits related to the climate change effects. We found that the species breeding in various habitats at higher altitudes had more negative trends than species breeding at lower altitudes. We also found that the species moved upwards as a response to warming climate, and these altitudinal range shifts were associated with more positive population trends at lower altitudes than at higher altitudes. Moreover, long-distance migrants declined more than residents or species migrating for shorter distances. Taken together, these results indicate that the climate change, besides other possible environmental changes, already influences populations of montane birds with particularly adverse impacts on high-altitude species such as water pipit (Anthus spinoletta. It is evident that the alpine species, predicted to undergo serious climatically induced range contractions due to warming climate in the future, already started moving along this trajectory.

Reproductive characteristics and population decline of four species of skate (Rajidae) off the eastern coast of Canada.

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Mcphie, R P; Campana, S E

2009-07-01

Four of the most common species of skate (Rajidae) were studied off eastern Canada to determine if their reproductive characteristics were linked to their population trajectories. The fecundity of the winter skate Leucoraja ocellata, the little skate Leucoraja erinacea, the thorny skate Amblyraja radiata and the smooth skate Malacoraja senta averaged between 41 and 56 egg cases per year for each species. For all species but L. ocellata, males matured at larger sizes and at later ages than females. Theoretical rates of population increase for non-equilibrium populations of L. ocellata (c. 0.07), M. senta (c. 0.14) and L. erinacea and A. radiata (c. 0.20) were low compared to most fishes, indicating that north-west Atlantic skates are intrinsically unproductive, yet are theoretically capable of supporting low-level fisheries. Nevertheless, the results of 36 years of research surveys indicate that the abundance of mature L. ocellata, A. radiata and M. senta all decreased by >90% since 1970, indicating that past fishing mortality (both directed and undirected) has outstripped the net productivity of the skate populations on the eastern Scotian Shelf. The relationship between maximum age (t(max)) and age of maturity (t(mat)) was a better predictor of population growth rate than was body size, with the species exhibiting the highest ratios of t(mat) :t(max) (L. ocellata = 0.68, M. senta = 0.66) having the lowest predicted population growth rates. L. ocellata appears to have the lowest productivity and has experienced the greatest population decline, thus raising concerns over its future status.

Gene flow among established Puerto Rican populations of the exotic tree species, Albizia lebbeck.

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Dunphy, B K; Hamrick, J L

2005-04-01

We estimate gene flow and patterns of genetic diversity in Albizia lebbeck, an invasive leguminous tree in the dry forest of southwestern Puerto Rico. Genetic diversity estimates calculated for 10 populations of 24 trees each indicated that these populations may have been formed from multiple introductions. The presence of unique genotypes in the northernmost populations suggests that novel genotypes are still immigrating into the area. This combination of individuals from disparate locations led to high estimates of genetic diversity (He = 0.266, P = 0.67). Indirect estimates of gene flow indicate that only 0.69 migrants per generation move between populations, suggesting that genetic diversity within populations should decrease due to genetic drift. Since migration-drift equilibrium was not found, however, this estimate needs to be viewed with caution. The regular production of pods in this outcrossing species (tm = 0.979) indicates that sufficient outcross pollen is received to insure successful reproduction. Direct estimates of gene flow indicate that between 44 and 100% of pollen received by trees in four small stands of trees (n < 11) was foreign. The role of gene flow in facilitating the spread of this invasive plant species is discussed.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

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Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or

Clutch size in populations and species of cnemidophorines (Squamata: Teiidae on the eastern coast of Brazil

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VANDERLAINE A. MENEZES

2014-06-01

Full Text Available We analyzed some reproductive aspects of 16 coastal populations, belonging to five lizard species (A. ocellifera, A. abaetensis, A. nativo, A. littoralis and C. lacertoides from different restinga habitats along the eastern coast of Brazil. This study aimed to evaluate to what extent the reproductive aspects vary geographically and among species. For each female, we recorded the number of vitellogenic follicles, size and color of the largest follicle, presence and size of corpora lutea, and number and size of oviductal eggs. Clutch size of almost all coastal populations/species of Ameivula had little variation and most clutches were composed of two eggs. There was a significant relationship between female size and the mean clutch size when females from different species were pooled. Mean egg volume, among species, varied from 420 to 655 mm3. Relative clutch mass varied from 0.129 to 0.159 and did not differ significantly among species. We concluded that the five coastal species studied (four bisexuals and one parthenogenetic had similar reproductive characteristics. Most of them presented multiple clutches, low clutch size and low relative clutch mass, similar to other species in the genus and to unisexual and bisexual species of the Teiidae family.

Threatened species richness along a Himalayan elevational gradient: quantifying the influences of human population density, range size, and geometric constraints.

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Paudel, Prakash Kumar; Sipos, Jan; Brodie, Jedediah F

2018-02-07

A crucial step in conserving biodiversity is to identify the distributions of threatened species and the factors associated with species threat status. In the biodiversity hotspot of the Himalaya, very little is known about which locations harbour the highest diversity of threatened species and whether diversity of such species is related to area, mid-domain effects (MDE), range size, or human density. In this study, we assessed the drivers of variation in richness of threatened birds, mammals, reptiles, actinopterygii, and amphibians along an elevational gradient in Nepal Himalaya. Although geometric constraints (MDE), species range size, and human population density were significantly related to threatened species richness, the interaction between range size and human population density was of greater importance. Threatened species richness was positively associated with human population density and negatively associated with range size. In areas with high richness of threatened species, species ranges tend to be small. The preponderance of species at risk of extinction at low elevations in the subtropical biodiversity hotspot could be due to the double impact of smaller range sizes and higher human density.

76 FR 15932 - Endangered and Threatened Species; Proposed Listing of Nine Distinct Population Segments of...

Science.gov (United States)

2011-03-22

... Loggerhead Sea Turtles as Endangered or Threatened AGENCIES: National Marine Fisheries Service (NMFS... Distinct Population Segments (DPS) of loggerhead sea turtles, Caretta caretta, as endangered or threatened... populations of loggerhead sea turtle'' as an endangered species under the ESA. NMFS published a notice in the...

Disparity in population differentiation of sex-linked and autosomal variation in sibling species of the Jaera albifrons (Isopoda) complex

DEFF Research Database (Denmark)

Siegismund, H R

2003-01-01

The genetic variation at four enzyme loci is described for 22 populations of three Jaera species--J. albifrons, J. ischiosetosa, and J. praehirsuta--in the J. albifrons complex (Crustacea, Isopoda) in Denmark. The variation at three of the loci is similar, with the allele frequency spectra close...... to each other in all three species. An evolutionary tree based on the variation at these three loci revealed that the populations from the different species are completely intermixed in the tree. This was supported by hierarchical F-statistics where the between-species component was zero. At a fourth....... An evolutionary tree for this locus partitions the populations into separate groups and a hierarchical F-statistic has a between-species component of about 50%. The results are attributed to introgression with a higher rate for autosomes than for sex chromosomes....

Comparing climate change and species invasions as drivers of coldwater fish population extirpations.

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Sapna Sharma

Full Text Available Species are influenced by multiple environmental stressors acting simultaneously. Our objective was to compare the expected effects of climate change and invasion of non-indigenous rainbow smelt (Osmerus mordax on cisco (Coregonus artedii population extirpations at a regional level. We assembled a database of over 13,000 lakes in Wisconsin, USA, summarising fish occurrence, lake morphology, water chemistry, and climate. We used A1, A2, and B1 scenarios from the Intergovernmental Panel on Climate Change (IPCC of future temperature conditions for 15 general circulation models in 2046-2065 and 2081-2100 totalling 78 projections. Logistic regression indicated that cisco tended to occur in cooler, larger, and deeper lakes. Depending upon the amount of warming, 25-70% of cisco populations are predicted to be extirpated by 2100. In addition, cisco are influenced by the invasion of rainbow smelt, which prey on young cisco. Projecting current estimates of rainbow smelt spread and impact into the future will result in the extirpation of about 1% of cisco populations by 2100 in Wisconsin. Overall, the effect of climate change is expected to overshadow that of species invasion as a driver of coldwater fish population extirpations. Our results highlight the potentially dominant role of climate change as a driver of biotic change.

Estimating open population site occupancy from presence-absence data lacking the robust design.

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Dail, D; Madsen, L

2013-03-01

Many animal monitoring studies seek to estimate the proportion of a study area occupied by a target population. The study area is divided into spatially distinct sites where the detected presence or absence of the population is recorded, and this is repeated in time for multiple seasons. However, when occupied sites are detected with probability p Ecology 84, 2200-2207) developed a multiseason model for estimating seasonal site occupancy (ψt ) while accounting for unknown p. Their model performs well when observations are collected according to the robust design, where multiple sampling occasions occur during each season; the repeated sampling aids in the estimation p. However, their model does not perform as well when the robust design is lacking. In this paper, we propose an alternative likelihood model that yields improved seasonal estimates of p and Ψt in the absence of the robust design. We construct the marginal likelihood of the observed data by conditioning on, and summing out, the latent number of occupied sites during each season. A simulation study shows that in cases without the robust design, the proposed model estimates p with less bias than the MacKenzie et al. model and hence improves the estimates of Ψt . We apply both models to a data set consisting of repeated presence-absence observations of American robins (Turdus migratorius) with yearly survey periods. The two models are compared to a third estimator available when the repeated counts (from the same study) are considered, with the proposed model yielding estimates of Ψt closest to estimates from the point count model. Copyright © 2013, The International Biometric Society.

Lack of genetic polymorphism among peregrine falcons Falco peregrinus of Fiji

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Talbot, Sandra; Palmer, Angela G.; Sage, George K.; Sonsthagen, Sarah A.; Swem, Ted; Brimm, Daniel J.; White, Clayton M

2014-01-01

We compared levels of genetic diversity and isolation among peregrine falcons Falco peregrinus from two South Pacific island complexes (Fiji and Vanuatu: F. p. nesiotes), relative to other island and mainland populations. Fragment data from 12 microsatellite loci and sequence information from the control region of the mitochondrial DNA indicated levels of genetic variation in the South Pacific populations were lower than other island and mainland populations. Indeed, diversity varied from extremely low (Vanuatu) to completely absent (Fiji). We find little support for a hypothesis that populations on Fiji or Vanuatu were colonized via Australia. The complete lack of polymorphism in peregrine falcons of Fiji is remarkable, and to our knowledge has not been observed in a natural avian population. This lack of polymorphism, and the inability to test for decrease in polymorphism using museum samples, precludes testing whether the lack of genetic diversity in the population on Fiji is due to a recent bottleneck, or sustained isolation over evolutionary time. Increased fertility in eggs of Fiji peregrines upon outbreeding with males from other areas is consistent with inbreeding depression within a population typified by heterozygote deficiency.

Evidence of population resistance to extreme low flows in a fluvial-dependent fish species

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Katz, Rachel A.; Freeman, Mary C.

2015-01-01

Extreme low streamflows are natural disturbances to aquatic populations. Species in naturally intermittent streams display adaptations that enhance persistence during extreme events; however, the fate of populations in perennial streams during unprecedented low-flow periods is not well-understood. Biota requiring swift-flowing habitats may be especially vulnerable to flow reductions. We estimated the abundance and local survival of a native fluvial-dependent fish species (Etheostoma inscriptum) across 5 years encompassing historic low flows in a sixth-order southeastern USA perennial river. Based on capturemark-recapture data, the study shoal may have acted as a refuge during severe drought, with increased young-of-the-year (YOY) recruitment and occasionally high adult immigration. Contrary to expectations, summer and autumn survival rates (30 days) were not strongly depressed during low-flow periods, despite 25%-80% reductions in monthly discharge. Instead, YOY survival increased with lower minimum discharge and in response to small rain events that increased low-flow variability. Age-1+ fish showed the opposite pattern, with survival decreasing in response to increasing low-flow variability. Results from this population dynamics study of a small fish in a perennial river suggest that fluvial-dependent species can be resistant to extreme flow reductions through enhanced YOY recruitment and high survival

Using species abundance distribution models and diversity indices for biogeographical analyses

Science.gov (United States)

Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

2016-01-01

We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae occurring sympatrically in the Red River region of China

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Liu eJian

2015-09-01

Full Text Available Delimitating species boundaries could be of critical importance when evaluating the species’ evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH and trnL-rps4 and two single copy nuclear (RPB1 and SmHP DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into Yuanjiang-Nanhun basin and Ejia-Jiepai basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the

Morphological and genetic evolution in eastern populations of the Macrhybopsis aestivalis complex (Cypriniformes: Cyprinidae), with the descriptions of four new species.

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Gilbert, Carter R; Mayden, Richard L; Powers, Steven L

2017-03-30

For many years the North American cyprinid fish Macrhybopsis aestivalis (common name: Speckled Chub) was regarded as a single widespread and morphologically variable species, occurring in rivers throughout much of the Mississippi Valley and geographically adjacent eastern Gulf slope drainages, west to the Rio Grande basin in Texas, New Mexico, and Mexico. Eisenhour (1997) completed a morphological study of western populations of the Speckled Chub, the results of which appeared thereafter in published form (Eisenhour 1999, 2004). He demonstrated the existence of five valid species west of the Mississippi River (aestivalis, marconis, australis, tetranema, hyostoma), of which the name aestivalis was shown to be restricted to the population occurring in the Rio Grande and the geographically adjacent Rio San Fernando system, in northeastern Mexico. Eisenhour (2004) considered populations throughout the middle Mississippi Valley and its major tributaries to be a single morphologically variable species (hyostoma), and he also indicated that populations of Macrhybopsis from eastern Gulf slope drainages may represent a complex of species. Genetic confirmation of Eisenhour's conclusions regarding western species appeared in the publication by Underwood et al. (2003), who also showed that western populations of M. hyostoma, as presently recognized, are genetically much more complex than previously considered.     Meanwhile, the present authors were involved in a companion study of eastern populations of Macrhybopsis, for which a genetic summary of the eastern Gulf coast species was published by Mayden & Powers (2004). Based on their findings, four species were recognized from southeastern drainages (identified as species A-D), although no formal taxonomic descriptions were included. Their genetic data, in combination with meristic, morphometric and other morphological data presented herein, form the basis for a revised classification of eastern Macrhybopsis populations

A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

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Buckley, Ralf C; Castley, J Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C; Steven, Rochelle

2012-01-01

Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

A Population Accounting Approach to Assess Tourism Contributions to Conservation of IUCN-Redlisted Mammal Species

Science.gov (United States)

Buckley, Ralf C.; Castley, J. Guy; Pegas, Fernanda de Vasconcellos; Mossaz, Alexa C.; Steven, Rochelle

2012-01-01

Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥5% for over half of the species where relevant data exist, ≥15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg) or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species. PMID:22984467

A population accounting approach to assess tourism contributions to conservation of IUCN-redlisted mammal species.

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Ralf C Buckley

Full Text Available Over 1,000 mammal species are red-listed by IUCN, as Critically Endangered, Endangered or Vulnerable. Conservation of many threatened mammal species, even inside protected areas, depends on costly active day-to-day defence against poaching, bushmeat hunting, invasive species and habitat encroachment. Many parks agencies worldwide now rely heavily on tourism for routine operational funding: >50% in some cases. This puts rare mammals at a new risk, from downturns in tourism driven by external socioeconomic factors. Using the survival of individual animals as a metric or currency of successful conservation, we calculate here what proportions of remaining populations of IUCN-redlisted mammal species are currently supported by funds from tourism. This proportion is ≥ 5% for over half of the species where relevant data exist, ≥ 15% for one fifth, and up to 66% in a few cases. Many of these species, especially the most endangered, survive only in one single remaining subpopulation. These proportions are not correlated either with global population sizes or recognition as wildlife tourism icons. Most of the more heavily tourism-dependent species, however, are medium sized (>7.5 kg or larger. Historically, biological concern over the growth of tourism in protected areas has centered on direct disturbance to wildlife. These results show that conservation of threatened mammal species has become reliant on revenue from tourism to a previously unsuspected degree. On the one hand, this provides new opportunities for conservation funding; but on the other, dependence on such an uncertain source of funding is a new, large and growing threat to red-listed species.

A new species of Silvinichthys (Siluriformes, Trichomycteridae) lacking pelvic fins from mid-elevation localities of the southern Andes, with comments on the genus.

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Fernández, L; Sanabria, E A; Quiroga, L B; Vari, R P

2014-02-01

Silvinichthys huachi new species, is described from a stream along the lower slope of the Andean Cordillera in the Provincia de San Juan, Argentina. It shares the distinctive modifications characteristic of Silvinichthys, but is distinguished from the four previously described congeners by the combination of a lack of the pelvic fin and the pelvic girdle, details of pigmentation and various meristic and morphometric features. Silvinichthys huachi is apparently endemic to the type locality situated within an arid region of western central Argentina in the Andino Cuyana Province. Major gaps in the range of species of Silvinichthys may indicate that the origin of the genus predates the uplift events that subdivided drainages along the eastern slopes of the Andean Cordillera in west central Argentina. Silvinichthys huachi is hypothesized to be the sister species of Silvinichthys bortayro. © 2014 The Fisheries Society of the British Isles.

Estimating age composition in Alpine native populations of Austropotamobius pallipes complex

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Daniela Ghia

2015-03-01

Full Text Available Assessing the population structure and understanding growth patterns is crucial to manage freshwater resources and to solve fundamental questions concerning endangered species conservation. Austropotamobius pallipes (Lereboullet, 1858 species complex has been declining on a widespread basis in Europe, including Italy, but detailed data on population structure and growth are lacking. In four mountain streams populated by the species, water temperature data were collected by data-loggers. In July 2012, a total of 746 crayfish were collected at night and their length was measured. Females and males size distributions were analysed separately for each stream using Bhattacharya’s Method. Age was assigned to each length class. The mean values of the age classes were used to evaluate the growth rate of Von Bertalanffy, by the seasonalized equation. Up to six age classes were identified in two populations. Results show that three out of four populations are well-structured, and they confirm that A. pallipes complex is a K-selected species. We stress the need for long-term monitoring and the importance of obtained results in development of conservation plans of endangered crayfish.

EXTINCTION RISK OR LACK OF SAMPLING IN A THREATENED SPECIES: GENETIC STRUCTURE AND ENVIRONMENTAL SUITABILITY OF THE NEOTROPICAL FROG PRISTIMANTIS PENELOPUS (ANURA: CRAUGASTORIDAE

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ADRIANA RESTREPO

Full Text Available ABSTRACT IUCN Red Lists have been a valuable tool to prioritize conservation plans in endemic neotropical frogs. However, many areas in this region are poorly known in terms of their diversity and endemism. Based on examined museum specimens of the threatened species Pristimantis penelopus we revised its geographic distribution and determined the habitat suitability using niche modeling techniques. Using a mitochondrial fragment of COI gene, we determine the phylogenetic position and the extent of the genetic variation across its distribution in Colombia. We present the first records of P. penelopus for the Cordillera Oriental, the western versant of Cordillera Occidental and the northern portion of the Cauca river basin. Based on the molecular phylogenetic analysis, Pristimantis penelopus belongs to the P. ridens series sensu (Padial et al., 2014. The mean of intraspecific genetic variation is 2.1% and the variation among population ranges between 2.3 and 3.5%. The genetic distance between the western populations and the Magdalena Valley populations suggests a potential phylogeographic break in northwestern Antioquia. We expand the realized distribution by 258 kilometers north, 200 km east and 223 km northwest. Based on our results and according to the IUCN criteria we propose a new category for the species and highlight the need to increase the surveys in poorly known regions to better understand the geographic distribution and conservation status of listed species.

Population genetics of the potentially invasive African fruit fly species, Ceratitis rosa and Ceratitis fasciventris (Diptera: Tephritidae).

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Baliraine, F N; Bonizzoni, M; Guglielmino, C R; Osir, E O; Lux, S A; Mulaa, F J; Gomulski, L M; Zheng, L; Quilici, S; Gasperi, G; Malacrida, A R

2004-03-01

A set of 10 microsatellite markers was used to survey the levels of genetic variability and to analyse the genetic aspects of the population dynamics of two potentially invasive pest fruit fly species, Ceratitis rosa and C. fasciventris, in Africa. The loci were derived from the closely related species, C. capitata. The degree of microsatellite polymorphism in C. rosa and C. fasciventris was extensive and comparable to that of C. capitata. In C. rosa, the evolution of microsatellite polymorphism in its distribution area reflects the colonization history of this species. The mainland populations are more polymorphic than the island populations. Low levels of differentiation were found within the Africa mainland area, while greater levels of differentiation affect the islands. Ceratitis fasciventris is a central-east African species. The microsatellite data over the Uganda/Kenya spatial scale suggest a recent expansion and possibly continuing gene flow within this area. The microsatellite variability data from C. rosa and C. fasciventris, together with those of C. capitata, support the hypothesis of an east African origin of the Ceratitis spp.

The Canarian Camel: A Traditional Dromedary Population

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Ursula Schulz

2010-04-01

Full Text Available The domestic camel (dromedary is the most important livestock species in the Canary Islands and the most important autochthonous European camel population. After six centuries of a successful adaptation process to the particular environment of the Canary Islands, the abandonment of traditional agriculture has led this population to a major bottleneck. Along with a lack of foreign genetic interchanges, this could lead the population to the brink of extinction. Genetic analysis using 13 microsatellites showed the closest genetic proximity to the North African (Tindouf, Algeria camel population and a certain degree of sub-division, with significant genetic differences among breeders. An important level of genetic differentiation among the different populations analyzed was found with a global FST value of 0.116.

RAPD analysis of Nectomys squamipes (Rodentia, Sigmodontinae populations

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Almeida Francisca C.

2000-01-01

Full Text Available Random amplified of polymorphic DNA (RAPD analysis was used to assess genetic distance and the genetic structure of populations of Nectomys squamipes, a semiaquatic rodent species distributed along watercourses. DNA samples of five populations were analyzed using three primers, producing 45 scorable bands, 31 of which were polymorphic. There was a significant differentiation among populations [F ST = 0.17; phiST = 0.14 (P < 0.004] but gene flow (Nm = 1.25 was sufficient to overcome genetic drift effects. No fixed specific markers were found for any population. The Mantel's test and UPGMA cluster analysis showed a lack of relationship between genetic and geographic distances. The apparent homogeneity indicated by RAPD markers coincided with morphometric data, despite the wide geographic range of N. squamipes. Alternative hypotheses for explaining our results include recurrent processes of local extinction and recolonization or a recent and sudden increase in the geographic distribution of this species.

Anthropogenic disturbances affect population size and biomass allocation of two alpine species from the headwater area of the Urumqi River, China

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Zhao, R.; Zhang, H.; An, L.

2018-01-01

The survival of alpine plants are seriously threatened by increasing anthropogenic activity. Saussurea involucrata and Rhodiola quadrifida are particularly affected because of their high medicinal value. To assess the impact of anthropogenic disturbance on the two species, their population size and biomass allocation were examined at three levels of disturbance at low and high altitudes. Anthropogenic disturbance was the most serious threat to the populations and changed the population density, biomass, and biomass allocation of both species significantly (p<0.05). The changes differed with the species and the altitude, and were also affected by the interaction between these two factors. Population density and biomass of the two species decreased with an increase in the level of anthropogenic disturbance. These results imply that the decrease in population size and in biomass allocation to reproductive organs due to anthropogenic disturbances may make the plant populations even smaller and scarce. Meanwhile, change of making their survival dependent on the extent of anthropogenic disturbance: unless such disturbance is checked and the species are protected, they will probably disappear from the headwater area of the Urumqi River. This influence of anthropogenic disturbances may be potential threats to population ability of survival and reproduction. (author)

Population genetic structure of Brazilian shrimp species (Farfantepenaeus sp., F. brasiliensis, F. paulensis and Litopenaeus schmitti: Decapoda: Penaeidae

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Jaqueline Gusmão

2005-03-01

Full Text Available Penaeid shrimps are important resources for worldwide fisheries and aquaculture. In the Southwest Atlantic, Farfantepenaeus brasiliensis, F. paulensis, F. subtilis, Farfantepenaeus sp. and Litopenaeus schmitti are among the most important commercially exploited species. Despite their high commercial value, there is little information available on the different aspects of their biology or genetics and almost no data on their stock structure. We used allozymes to estimate variability levels and population genetic structure of F. brasiliensis, F. paulensis, L. schmitti and the recently detected species Farfantepenaeus sp. along as much as 4,000 km of Brazilian coastline. No population heterogeneity was detected in F. brasiliensis or L. schmitti along the studied area. In contrast, F ST values found for Farfantepenaeus sp. and F. paulensis indicate that the populations of those two species are genetically structured, comprising different fishery stocks. The largest genetic differences in F. paulensis were found between Lagoa dos Patos (South and the two populations from Southeast Brazil. In Farfantepenaeus sp., significant differences were detected between the population from Recife and those from Fortaleza and Ilhéus.

A method to assess the population-level consequences of wind energy facilities on bird and bat species: Chapter

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Diffendorfer, James E.; Beston, Julie A.; Merrill, Matthew; Stanton, Jessica C.; Corum, Margo D.; Loss, Scott R.; Thogmartin, Wayne E.; Johnson, Douglas H.; Erickson, Richard A.; Heist, Kevin W.

2016-01-01

For this study, a methodology was developed for assessing impacts of wind energy generation on populations of birds and bats at regional to national scales. The approach combines existing methods in applied ecology for prioritizing species in terms of their potential risk from wind energy facilities and estimating impacts of fatalities on population status and trend caused by collisions with wind energy infrastructure. Methods include a qualitative prioritization approach, demographic models, and potential biological removal. The approach can be used to prioritize species in need of more thorough study as well as to identify species with minimal risk. However, the components of this methodology require simplifying assumptions and the data required may be unavailable or of poor quality for some species. These issues should be carefully considered before using the methodology. The approach will increase in value as more data become available and will broaden the understanding of anthropogenic sources of mortality on bird and bat populations.

Plant-Associated Symbiotic Burkholderia Species Lack Hallmark Strategies Required in Mammalian Pathogenesis

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Fong, Stephanie; Yerrapragada, Shailaja; Estrada-de los Santos, Paulina; Yang, Paul; Song, Nannie; Kano, Stephanie; de Faria, Sergio M.; Dakora, Felix D.; Weinstock, George; Hirsch, Ann M.

2014-01-01

Burkholderia is a diverse and dynamic genus, containing pathogenic species as well as species that form complex interactions with plants. Pathogenic strains, such as B. pseudomallei and B. mallei, can cause serious disease in mammals, while other Burkholderia strains are opportunistic pathogens, infecting humans or animals with a compromised immune system. Although some of the opportunistic Burkholderia pathogens are known to promote plant growth and even fix nitrogen, the risk of infection to infants, the elderly, and people who are immunocompromised has not only resulted in a restriction on their use, but has also limited the application of non-pathogenic, symbiotic species, several of which nodulate legume roots or have positive effects on plant growth. However, recent phylogenetic analyses have demonstrated that Burkholderia species separate into distinct lineages, suggesting the possibility for safe use of certain symbiotic species in agricultural contexts. A number of environmental strains that promote plant growth or degrade xenobiotics are also included in the symbiotic lineage. Many of these species have the potential to enhance agriculture in areas where fertilizers are not readily available and may serve in the future as inocula for crops growing in soils impacted by climate change. Here we address the pathogenic potential of several of the symbiotic Burkholderia strains using bioinformatics and functional tests. A series of infection experiments using Caenorhabditis elegans and HeLa cells, as well as genomic characterization of pathogenic loci, show that the risk of opportunistic infection by symbiotic strains such as B. tuberum is extremely low. PMID:24416172

Testing for reproductive interference in the population dynamics of two congeneric species of herbivorous mites

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Sato, Y; Alba, J M; Sabelis, M W

2014-01-01

When phylogenetically close, two competing species may reproductively interfere, and thereby affect their population dynamics. We tested for reproductive interference (RI) between two congeneric haplo-diploid spider mites, Tetranychus evansi and Tetranychus urticae, by investigating their interspecific mating and their population dynamics when they competed on the same plants. They are both pests of tomato, but differ in the host plant defences that they suppress or induce. To reduce the effect of plant-mediated interaction, we used a mutant tomato plant lacking jasmonate-mediated anti-herbivore defences in the competition experiment. In addition, to manipulate the effect of RI, we introduced founder females already mated with conspecific males in mild RI treatments or founder, virgin females in strong RI treatments (in either case together with heterospecific and conspecific males). As females show first-male sperm precedence, RI should occur especially in the founder generation under strong RI treatments. We found that T. urticae outcompeted T. evansi in mild, but not in strong RI treatments. Thus, T. evansi interfered reproductively with T. urticae. This result was supported by crossing experiments showing frequent interspecific copulations, strong postmating reproductive isolation and a preference of T. evansi males to mate with T. urticae (instead of conspecific) females, whereas T. urticae males preferred conspecific females. We conclude that interspecific mating comes at a cost due to asymmetric mate preferences of males. Because RI by T. evansi can improve its competitiveness to T. urticae, we propose that RI partly explains why T. evansi became invasive in Europe where T. urticae is endemic. PMID:24865602

Effects of harvest on the sustainability and leaf productivity of populations of two palm species in Maya homegardens.

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Martínez-Ballesté, Andrea; Martorell, Carlos

2015-01-01

Traditional management practices are usually thought to be sustainable. The Maya manage Sabal (Arecaceae) palms in homegardens, using their leaves for thatching. The sustainability of such production systems depends on the long-term persistence of palm populations, whereas resource availability also depends on the number of leaves on individual palms. We examined how leaf harvest affects Sabal yapa and S. mexicana population growth rates (λ) and leaf production, comparing traditional and alternative harvest regimes in terms of sustainability and productivity. Demographic, harvest and leaf production data were recorded for three years in two homegardens. We used general integral projection models linked to leaf-production models to describe population dynamics and productivity. Harvest had no effect on S. yapa's vital rates or on λ, but it changed the growth rate of individuals of S. mexicana, with a negligible impact on λ. Homegardens affected λ values, reflecting the species' ecological affinities. S. mexicana, introduced from mesic forests, required watering and shade; therefore, its population declined rapidly in the homegarden that lacked both water and shade. The λ of the xerophilic S. yapa was slightly larger without watering than with watering. Palms usually compensated for leaf extraction, causing the number of leaves harvested per individual to increase with harvest intensity. Nevertheless, traditional management is relatively mild, allowing standing leaves to accumulate but reducing the homegarden's yield. Apparently, the Maya do not seek to maximize annual production but to ensure the availability of large numbers of leaves in homegardens. These leaves may then be used when the entire roof of a hut needs to be replaced every few years.

High population variability and source-sink dynamics in a solitary bee species.

Science.gov (United States)

Franzén, Markus; Nilsson, Sven G

2013-06-01

Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

Population dynamics, antibiotics resistance and biofilm formation of Aeromonas and Vibrio species isolated from aquatic sources in Northern Malaysia.

Science.gov (United States)

Odeyemi, Olumide A; Ahmad, Asmat

2017-02-01

This study aimed to compare population dynamics, antibiotic resistance and biofilm formation of Aeromonas and Vibrio species from seawater and sediment collected from Northern Malaysia. Isolates with different colony morphology were characterized using both biochemical and molecular methods before testing for antibiotic resistance and biofilm formation. Results obtained from this study showed that in Kedah, the population of Aeromonas isolated from sediment was highest in Pantai Merdeka (8.22 log CFU/ml), Pulau Bunting recorded the highest population of Aeromonas from sediment (8.43 log CFU/g). It was observed that Vibrio species isolated from seawater and sediment were highest in Kuala Sanglang (9.21 log CFU/ml). In Kuala Perlis, the population of Aeromonas isolated from seawater was highest in Jeti (7.94 log CFU/ml). Highest population of Aeromonas from sediment was recorded in Kampong Tanah Baru (7.99 log CFU/g). It was observed that Vibrio species isolated from seawater was highest in Padang Benta (8.42 log CFU/g) while Jeti Kuala Perlis had highest population of Vibrio isolated from sediment. It was observed that location does not influence population of Aeromonas. The results of the independent t - test revealed that there was no significant relationship between location and population of Vibrio (df = 10, t = 1.144, p > 0.05). The occurrence of biofilm formation and prevalence of antibiotic resistant Aeromonas and Vibrio species in seawater and sediment pose danger to human and aquatic animals' health. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dorstenia luamensis (Moraceae, a new species from eastern Democratic Republic of Congo

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Miguel Leal

2014-10-01

Full Text Available A new species of Dorstenia L. (Moraceae, D. luamensis M.E.Leal, is described from the Luama Wildlife Reserve, west of Lake Tanganyika and north of the town of Kalemie in the eastern part of the Democratic Republic of Congo (DRC. This species is endemic to the region and differs from any of the other species by its fernlike lithophytic habit and lack of latex. A description and illustration of this species is presented here. Dorstenia luamensis M.E.Leal inhabits moist and shady vertical rock faces close to small waterfalls in the forest; the species is distributed in small populations within the type locality, and merits the conservation status of endangered (EN.

Combining demographic and genetic factors to assess population vulnerability in stream species

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Erin L, Landguth; Muhlfeld, Clint C.; Jones, Leslie W.; Waples, Robin S.; Whited, Diane; Lowe, Winsor H.; Lucotch, John; Neville, Helen; Luikart, Gordon

2014-01-01

Accelerating climate change and other cumulative stressors create an urgent need to understand the influence of environmental variation and landscape features on the connectivity and vulnerability of freshwater species. Here, we introduce a novel modeling framework for aquatic systems that integrates spatially explicit, individual-based, demographic and genetic (demogenetic) assessments with environmental variables. To show its potential utility, we simulated a hypothetical network of 19 migratory riverine populations (e.g., salmonids) using a riverscape connectivity and demogenetic model (CDFISH). We assessed how stream resistance to movement (a function of water temperature, fluvial distance, and physical barriers) might influence demogenetic connectivity, and hence, population vulnerability. We present demographic metrics (abundance, immigration, and change in abundance) and genetic metrics (diversity, differentiation, and change in differentiation), and combine them into a single vulnerability index for identifying populations at risk of extirpation. We considered four realistic scenarios that illustrate the relative sensitivity of these metrics for early detection of reduced connectivity: (1) maximum resistance due to high water temperatures throughout the network, (2) minimum resistance due to low water temperatures throughout the network, (3) increased resistance at a tributary junction caused by a partial barrier, and (4) complete isolation of a tributary, leaving resident individuals only. We then applied this demogenetic framework using empirical data for a bull trout (Salvelinus confluentus) metapopulation in the upper Flathead River system, Canada and USA, to assess how current and predicted future stream warming may influence population vulnerability. Results suggest that warmer water temperatures and associated barriers to movement (e.g., low flows, dewatering) are predicted to fragment suitable habitat for migratory salmonids, resulting in the loss

The epidemiology of Candida species associated with vulvovaginal candidiasis in an Iranian patient population.

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Mahmoudi Rad, M; Zafarghandi, S; Abbasabadi, B; Tavallaee, M

2011-04-01

Vulvovaginal candidiasis is a common infection among women worldwide. According to previous epidemiological studies, Candida albicans is the most common species of Candida. The prevalence of non-Candida species, however, is increasing. Identification of Candida species among the population will not only help health professionals to choose suitable antifungal treatments, but also prevent development of drug resistance. The aim of this study was to identify, using chromogenic agar medium, the Candida species associated with vulvovaginal candidiasis among a sample of the Iranian population. In a prospective cohort study during a two year period from March 2006 to March 2008, swab samples of vaginal discharge/secretion were taken from 200 patients admitted to the gynecology clinic of Mahdieh Hospital (Tehran, Iran) with a clinical presentation suggestive of vulvovaginal candidiasis. The isolates obtained were cultured on Sabouraud dextrose agar and chromogenic agar medium. Candida species were also identified by germ tube formation in serum, chlamydospore production on Corn Meal Agar and carbohydrate absorption using the API 20C-AUX kit. Participants were asked to complete a questionnaire investigating the risk factors associated with candidiasis. An assessment of the different species of recurrent and non-recurrent candidiasis was also made. Descriptive statistics, chi-square test, and t-test were used to analyze the data. A total of 191 isolates were obtained from 175 vaginal specimens. Candida albicans accounted for 67% of the strains including single and mixed infections. The other identified species were Candida glabrata (18.3%), Candida tropicalis (6.8%), Candida krusei (5.8%), Candida parapsilosis (1.6%), and Candida guilliermondii (0.5%) respectively. Mixed infection with two or more species of Candida was seen in 10.3% of patients. The most common mixed cause was the combination of Candida albicans and Candida glabrata. Participants who were sexually active

The roles of competition and habitat in the dynamics of populations and species distributions.

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Yackulic, Charles B; Reid, Janice; Nichols, James D; Hines, James E; Davis, Raymond; Forsman, Eric

2014-02-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl, Strix varia) and a resident species (Northern Spotted Owl, Strix occidentalis caurina) in a 1000-km study area over a 22-year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multi-season analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyzed survey data using models that combine the general multistate-multi-season occupancy modeling framework with autologistic modeling, allowing us to account for important aspects of our study system. We found that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale, and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern Spotted Owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species, both through its immediate effects on local extinction and by indirectly lowering colonization rates as

Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

Science.gov (United States)

Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

2011-12-01

Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

Using temporal sampling to improve attribution of source populations for invasive species.

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Sharyn J Goldstien

Full Text Available Numerous studies have applied genetic tools to the identification of source populations and transport pathways for invasive species. However, there are many gaps in the knowledge obtained from such studies because comprehensive and meaningful spatial sampling to meet these goals is difficult to achieve. Sampling populations as they arrive at the border should fill the gaps in source population identification, but such an advance has not yet been achieved with genetic data. Here we use previously acquired genetic data to assign new incursions as they invade populations within New Zealand ports and marinas. We also investigated allelelic frequency change in these recently established populations over a two-year period, and assessed the effect of temporal genetic sampling on our ability to assign new incursions to their population of source. We observed shifts in the allele frequencies among populations, as well as the complete loss of some alleles and the addition of alleles novel to New Zealand, within these recently established populations. There was no significant level of genetic differentiation observed in our samples between years, and the use of these temporal data did alter the assignment probability of new incursions. Our study further suggests that new incursions can add genetic variation to the population in a single introduction event as the founders themselves are often more genetically diverse than theory initially predicted.

Can transgenerational plasticity contribute to the invasion success of annual plant species?

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Fenesi, Annamária; Dyer, Andrew R; Geréd, Júliánna; Sándor, Dorottya; Ruprecht, Eszter

2014-09-01

Adaptive transgenerational plasticity (TGP), i.e., significantly higher fitness when maternal and offspring conditions match, might contribute to the population growth of non-native species in highly variable environments. However, comparative studies that directly test this hypothesis are lacking. Therefore, we performed a reciprocal split-brood experiment to compare TGP in response to N and water availability in single populations of two invasive (Amaranthus retroflexus, Galinsoga parviflora) and two congeneric non-invasive introduced species (Amaranthus albus, Galinsoga ciliata). We hypothesized that the transgenerational effect is adaptive: (1) in invasive species compared with non-invasive adventives, and (2) in stressful conditions compared with resource-rich environments. The phenotypic variation among offspring was generated, in large part, by our experimental treatments in the maternal generation; therefore, we demonstrated a direct TGP effect on the offspring's adult fitness. We found evidence, for the first time, that invasive and non-invasive adventive species differ regarding the expression of TGP in the adult stage, as adaptive responses were found exclusively in the invasive species. The manifestation of TGP was more explicit under resource-rich conditions; therefore, it might contribute to the population dynamics of non-native species in resource-rich sites rather than to their ecological tolerance spectra.

Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers.

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Shanmugapriya Arumugasundaram

Full Text Available Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r(2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r(2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.

Seed morphometric characteristics of European species of Elatine (Elatinaceae

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Agnieszka Popiela

2017-05-01

Full Text Available Elatine L. contains ca. 25 small, herbaceous, annual species distributed in ephemeral waters in both hemispheres. All species are amphibious and characterized by a high degree of morphological variability. The importance of seed morphology in Elatine taxonomy has been emphasized by many authors. The degree of seed curvature and seed coat reticulation have been traditionally considered very important in recognizing individual species of this genus. Seed morphometric characteristics of 10 Elatine species, including all European native taxa, are provided on the basis of material from two or three populations of each species. A total of 24–50 seeds were studied from each population, altogether 1,260 images were used for the morphometric study. In total, six parameters were measured from SEM pictures: object surface area, profile specific perimeter (object circuit, rectangle of the object (a length, rectangle of the object (b width, angle of the seed curvature, and number of pits in the seed coat counted in the middle row. Our study shows that the range of morphological variation of seeds in European species of Elatine is great, both between the species and the populations. Discrimination analysis showed that all six traits significantly differentiate the populations studied (λ = 0.001, p < 0.001, and the greatest contributions were “number of pits”, “rectangle_a”, and “the angle curvature”. Multidimensional scaling based on a correlation matrix of Mahalanobis distance of the six features studied revealed the greatest similarity between the three populations of E. alsinastrum, E. macropoda, and E. hexandra. Regarding interspecific differences, a Kruskal–Wallis tests showed that, in many cases, lack of statistically significant differences between species relative to the studied seed traits. If distinction of species is only based on seeds, especially if only a few seeds are evaluated, the following species pairs can be easily

Variation among Populations of Belonolaimus longicaudatus.

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Robbins, R T; Hirschmann, H

1974-04-01

Three North Carolina populations of Belonolairnus longicaudatus differed significantly from three Georgia populations in stylet measurements, the c ratio, the distance of the excretory pore from the anterior end for both sexes; the a ratio for females only; and the total body length, tail length, and spicule length for males only. The Georgia nematodes were stouter, and the females possessed sclerotized vaginal pieces. The distal portion of the spicules of North Carolina males had an indentation and hump lacking in those of the Georgia males. The haploid number of chromosomes was eight for males from all populations of B. longicaudatus and a North Carolina population of B. maritimus. Interpopulation matings of the Tarboro, N.C. and Tifton, Ga. populations indicated that the offspring produced were infertile. Morphological differences and reproductive isolation suggest that the North Carolina and the Georgia populations belong to different species.

Mitochondrial and nuclear markers reveal a lack of genetic structure in the entocommensal nemertean Malacobdella arrokeana in the Patagonian gulfs

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Alfaya, José E. F.; Bigatti, Gregorio; Machordom, Annie

2013-06-01

Malacobdella arrokeana is an entocommensal nemertean exclusively found in the bivalve geoduck Panopea abbreviata, and it is the only representative of the genus in the southern hemisphere. To characterize its genetic diversity, population structure and recent demographic history, we conducted the first genetic survey on this species, using sequence data for the cytochrome oxidase I gene (COI), 16S rRNA (16S) and the internal transcribed spacer (ITS2). Only four different ITS2 genotypes were found in the whole sample, and the two main haplotypes identified in the mitochondrial dataset were present among all localities with a diversity ranging from 0.583 to 0.939. Nucleotide diversity was low (π = 0.001-0.002). No significant genetic structure was detected between populations, and mismatch distribution patterns and neutrality tests results are consistent with a population in expansion or under selection. Analysis of molecular variance (AMOVA) revealed that the largest level of variance observed was due to intrapopulation variation (100, 100 and 94.39 % for 16S, COI and ITS2, respectively). F st values were also non-significant. The observed lack of population structure is likely due to high levels of genetic connectivity in combination with the lack or permeability of biogeographic barriers and episodes of habitat modification.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations.

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Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

2017-01-01

Wild tomatoes are a valuable source of disease resistance germplasm for tomato ( Solanum lycopersicum ) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense , both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense . We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens ( Alternaria solani , Phytophthora infestans and a Fusarium sp .) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense , resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

Repeatability and reproducibility of Population Viability Analysis (PVA and the implications for threatened species management

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Clare Morrison

2016-08-01

Full Text Available Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost. Population Viability Analysis (PVA is frequently used in population focused conservation prioritizations. The critical nature of many of these management decisions requires that PVA models are repeatable and reproducible to reliably rank species and/or populations quantitatively. This paper assessed the repeatability and reproducibility of a subset of previously published PVA models. We attempted to rerun baseline models from 90 publicly available PVA studies published between 2000-2012 using the two most common PVA modelling software programs, VORTEX and RAMAS-GIS. Forty percent (n = 36 failed, 50% (45 were both repeatable and reproducible, and 10% (9 had missing baseline models. Repeatability was not linked to taxa, IUCN category, PVA program version used, year published or the quality of publication outlet, suggesting that the problem is systemic within the discipline. Complete and systematic presentation of PVA parameters and results are needed to ensure that the scientific input into conservation planning is both robust and reliable, thereby increasing the chances of making decisions that are both beneficial and defensible. The implications for conservation triage may be far reaching if population viability models cannot be reproduced with confidence, thus undermining their intended value.

The roles of competition and habitat in the dynamics of populations and species distributions

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Yackulic, Charles Brandon; Reid, Janice; Nichols, James D.; Hines, James E.; Davis, Raymond; Forsman, Eric

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading (barred owl: Strix varia) and a resident species (Northern spotted owl: Strix occidentalis caurina) in a 1000 km2 study area over a 22 - year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multiseason analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyze survey data using models that combine the general multistate-multiseason occupancy modeling framework with autologistic modeling - allowing us to account for important aspects of our study system. We find that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern spotted owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species both through its immediate effects on local extinction, and by indirectly lowering colonization rates as Northern

Water-level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species.

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Nevado, B; Mautner, S; Sturmbauer, C; Verheyen, E

2013-08-01

Understanding how genetic variation is generated and maintained in natural populations, and how this process unfolds in a changing environment, remains a central issue in biological research. In this work, we analysed patterns of genetic diversity from several populations of three cichlid species from Lake Tanganyika in parallel, using the mitochondrial DNA control region. We sampled populations inhabiting the littoral rocky habitats in both very deep and very shallow areas of the lake. We hypothesized that the former would constitute relatively older, more stable and genetically more diverse populations, because they should have been less severely affected by the well-documented episodes of dramatic water-level fluctuations. In agreement with our predictions, populations of all three species sampled in very shallow shorelines showed traces of stronger population growth than populations of the same species inhabiting deep shorelines. However, contrary to our working hypothesis, we found a significant trend towards increased genetic diversity in the younger, demographically less stable populations inhabiting shallow areas, in comparison with the older and more stable populations inhabiting the deep shorelines. We interpret this finding as the result of the establishment of metapopulation dynamics in the former shorelines, by the frequent perturbation and reshuffling of individuals between populations due to the lake-level fluctuations. The repeated succession of periods of allopatric separation and secondary contact is likely to have further increased the rapid pace of speciation in lacustrine cichlids. © 2013 John Wiley & Sons Ltd.

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

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Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

A statistical assessment of population trends for data deficient Mexican amphibians.

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Quintero, Esther; Thessen, Anne E; Arias-Caballero, Paulina; Ayala-Orozco, Bárbara

2014-01-01

Background. Mexico has the world's fifth largest population of amphibians and the second country with the highest quantity of threatened amphibian species. About 10% of Mexican amphibians lack enough data to be assigned to a risk category by the IUCN, so in this paper we want to test a statistical tool that, in the absence of specific demographic data, can assess a species' risk of extinction, population trend, and to better understand which variables increase their vulnerability. Recent studies have demonstrated that the risk of species decline depends on extrinsic and intrinsic traits, thus including both of them for assessing extinction might render more accurate assessment of threats. Methods. We harvested data from the Encyclopedia of Life (EOL) and the published literature for Mexican amphibians, and used these data to assess the population trend of some of the Mexican species that have been assigned to the Data Deficient category of the IUCN using Random Forests, a Machine Learning method that gives a prediction of complex processes and identifies the most important variables that account for the predictions. Results. Our results show that most of the data deficient Mexican amphibians that we used have decreasing population trends. We found that Random Forests is a solid way to identify species with decreasing population trends when no demographic data is available. Moreover, we point to the most important variables that make species more vulnerable for extinction. This exercise is a very valuable first step in assigning conservation priorities for poorly known species.

Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

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Sáez-Laguna, Enrique; Guevara, María-Ángeles; Díaz, Luis-Manuel; Sánchez-Gómez, David; Collada, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-01-01

There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

Epigenetic variability in the genetically uniform forest tree species Pinus pinea L.

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Enrique Sáez-Laguna

Full Text Available There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments. Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.

Vitality structure of the populations of some weed species in crop sowings

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E. M. Tikhonova

2010-11-01

Full Text Available Features of development of populations of weed species (Cirsium arvense (L. Scop., Sonchus arvensis L., Melandium album (Mill. Garke, Setaria glauca (L. Beauv., Fallopia convolvulus (L. А. Lоve in most typical crops in the forest-steppe zone of the Sumy region. It was studied the crop sowings (winter wheat, rye, barley, buckwheat, pea which was not subjected to the herbicide treatment.

Variability and population genetic structure in Achyrocline flaccida (Weinm. DC., a species with high value in folk medicine in South America.

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Juliana da Rosa

Full Text Available Better knowledge of medicinal plant species and their conservation is an urgent need worldwide. Decision making for conservation strategies can be based on the knowledge of the variability and population genetic structure of the species and on the events that may influence these genetic parameters. Achyrocline flaccida (Weinm. DC. is a native plant from the grassy fields of South America with high value in folk medicine. In spite of its importance, no genetic and conservation studies are available for the species. In this work, microsatellite and ISSR (inter-simple sequence repeat markers were used to estimate the genetic variability and structure of seven populations of A. flaccida from southern Brazil. The microsatellite markers were inefficient in A. flaccida owing to a high number of null alleles. After the evaluation of 42 ISSR primers on one population, 10 were selected for further analysis of seven A. flaccida populations. The results of ISSR showed that the high number of exclusive absence of loci might contribute to the inter-population differentiation. Genetic variability of the species was high (Nei's diversity of 0.23 and Shannon diversity of 0.37. AMOVA indicated higher genetic variability within (64.7% than among (33.96% populations, and the variability was unevenly distributed (FST 0.33. Gene flow among populations ranged from 1.68 to 5.2 migrants per generation, with an average of 1.39. The results of PCoA and Bayesian analyses corroborated and indicated that the populations are structured. The observed genetic variability and population structure of A. flaccida are discussed in the context of the vegetation formation history in southern Brazil, as well as the possible anthropogenic effects. Additionally, we discuss the implications of the results in the conservation of the species.

Impacts of biogeographic history and marginal population genetics on species range limits: a case study of Liriodendron chinense.

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Yang, Aihong; Dick, Christopher W; Yao, Xiaohong; Huang, Hongwen

2016-05-10

Species ranges are influenced by past climate oscillations, geographical constraints, and adaptive potential to colonize novel habitats at range limits. This study used Liriodendron chinense, an important temperate Asian tree species, as a model system to evaluate the roles of biogeographic history and marginal population genetics in determining range limits. We examined the demographic history and genetic diversity of 29 L. chinense populations using both chloroplast and nuclear microsatellite loci. Significant phylogeographic structure was recovered with haplotype clusters coinciding with major mountain regions. Long-term demographical stability was suggested by mismatch distribution analyses, neutrality tests, and ecological niche models (ENM) and suggested the existence of LGM refuges within mountain regions. Differences in genetic diversity between central and marginal populations were not significant for either genomic region. However, asymmetrical gene flow was inferred from central populations to marginal populations, which could potentially limit range adaptation and expansion of L. chinense.

Timelines and mechanisms of wildlife population recovery following the Exxon Valdez oil spill

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Esler, Daniel N.; Ballachey, Brenda E.; Matkin, Craig O.; Cushing, Daniel; Kaler, Robert; Bodkin, James L.; Monson, Daniel; Esslinger, George G.; Kloecker, Kimberly A.

2018-01-01

Research and monitoring activities over the 28 years since the T/V Exxon Valdez ran aground and spilled oil into Prince William Sound, Alaska have led to an improved understanding of how wildlife populations were damaged, as well as the mechanisms and timelines of recovery. A key finding was that for some species, such as harlequin ducks and sea otters, chronic oil spill effects persisted for at least two decades and were a larger influence on population dynamics over the long term than acute effects of the spill. These data also offer insights into population variation resulting from factors other than the oil spill. For example, while many seabirds experienced direct and indirect effects of the spill, population trajectories of some piscivorous birds, including pigeon guillemots and marbled murrelets, were linked to long-term environmental changes independent of spill effects. Another species, killer whales, suffered population declines due to acute spill effects that have not been resolved despite lack of chronic direct effects, representing a novel pathway of long-term injury. The observed variation in mechanisms and timelines of recovery is linked to species specific life history and natural history traits, and thus may be useful for predicting population recovery for other species following other spills.

Timelines and mechanisms of wildlife population recovery following the Exxon Valdez oil spill

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Esler, Daniel; Ballachey, Brenda E.; Matkin, Craig; Cushing, Daniel; Kaler, Robert; Bodkin, James; Monson, Daniel; Esslinger, George; Kloecker, Kim

2018-01-01

Research and monitoring activities over the 28 years since the T/V Exxon Valdez ran aground and spilled oil into Prince William Sound, Alaska have led to an improved understanding of how wildlife populations were damaged, as well as the mechanisms and timelines of recovery. A key finding was that for some species, such as harlequin ducks and sea otters, chronic oil spill effects persisted for at least two decades and were a larger influence on population dynamics over the long term than acute effects of the spill. These data also offer insights into population variation resulting from factors other than the oil spill. For example, while many seabirds experienced direct and indirect effects of the spill, population trajectories of some piscivorous birds, including pigeon guillemots and marbled murrelets, were linked to long-term environmental changes independent of spill effects. Another species, killer whales, suffered population declines due to acute spill effects that have not been resolved despite lack of chronic direct effects, representing a novel pathway of long-term injury. The observed variation in mechanisms and timelines of recovery is linked to species specific life history and natural history traits, and thus may be useful for predicting population recovery for other species following other spills.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

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Remco Stam

2017-01-01

Full Text Available Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp. and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

The wild tomato species Solanum chilense shows variation in pathogen resistance between geographically distinct populations

Science.gov (United States)

Scheikl, Daniela; Tellier, Aurélien

2017-01-01

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved. PMID:28133579

Recombination-Driven Genome Evolution and Stability of Bacterial Species.

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Dixit, Purushottam D; Pang, Tin Yau; Maslov, Sergei

2017-09-01

While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well. Copyright © 2017 by the Genetics Society of America.

A statistical assessment of population trends for data deficient Mexican amphibians

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Esther Quintero

2014-12-01

Full Text Available Background. Mexico has the world’s fifth largest population of amphibians and the second country with the highest quantity of threatened amphibian species. About 10% of Mexican amphibians lack enough data to be assigned to a risk category by the IUCN, so in this paper we want to test a statistical tool that, in the absence of specific demographic data, can assess a species’ risk of extinction, population trend, and to better understand which variables increase their vulnerability. Recent studies have demonstrated that the risk of species decline depends on extrinsic and intrinsic traits, thus including both of them for assessing extinction might render more accurate assessment of threats.Methods. We harvested data from the Encyclopedia of Life (EOL and the published literature for Mexican amphibians, and used these data to assess the population trend of some of the Mexican species that have been assigned to the Data Deficient category of the IUCN using Random Forests, a Machine Learning method that gives a prediction of complex processes and identifies the most important variables that account for the predictions.Results. Our results show that most of the data deficient Mexican amphibians that we used have decreasing population trends. We found that Random Forests is a solid way to identify species with decreasing population trends when no demographic data is available. Moreover, we point to the most important variables that make species more vulnerable for extinction. This exercise is a very valuable first step in assigning conservation priorities for poorly known species.

Mitochondrial DNA in wildlife forensic science: Species identification of tissues

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Cronin, Matthew A.; Palmisciano, Daniel A.; Vyse, Ernest R.; Cameron, David G.

1991-01-01

A common problem in wildlife law enforcement is identifying the species of origin of carcasses, meat, or blood when morphological characters such as hair or bones are not available. Immunological and protein electrophoretic (allozyme or general protein) procedures have been used in species identification with considerable success (Bunch et al. 1976, McClymont et al. 1982, Wolfe 1983, Mardini 1984, Pex and Wolfe 1985, Dratch 1986), However, immunological tests often are not sensitive enough to distinguish closely related species. Furthermore, electrophoretically detectable protein polymorphisms may be lacking in certain populations or species and may not be species-specific.Analysis of DNA in human and wildlife forensics has been shown to be a potentially powerful tool for identification of individuals (Jeffreys et al. 1985, Vassartet al. 1987, Thommasen et al. 1989). Differences in copy number and nucleotide sequence of repetitive sequences in the nuclear (chromosomal) DNA result in hypervariability and individual-specific patterns which have been termed DNA "fingerprints." However, these patterns may be too variable for species identification necessitating analyses of more conservative parts of the genome.Mitochondrial DNA (mtDNA) is haploid, maternally inherited, similar in nucleotide sequence among conspecifics from the same geographic region, and more suitable for species identification, in contrast to hypervariable DNA fingerprints. MtDNA has several characteristics which make it useful as a species-specific marker. In mammals, individuals have a single mtDNA genotype shared by all tissues. Because mtDNA is haploid and reflects only maternal ancestry, the mtDNA gene number in a population is 4 times less than the nuclear gene number (Birky et al. 1983). This can result in relatively rapid loss or fixation of mtDNA genotypes so that all individuals in a population may be descended from a single ancestral female in as few as 4N (N = population size) generations

Variable Demographic Rates in an Invasive Plant Species: Differences Among Populations and Management Implications

Science.gov (United States)

Population managers are frequently faced with the challenge of selecting the most effective management strategy from a set of available strategies. In the case of classical weed biological control, this requires predicting a priori which of a group of candidate biocontrol agent species has the great...

Antigenicity of Leishmania-Activated C-Kinase Antigen (LACK in Human Peripheral Blood Mononuclear Cells, and Protective Effect of Prime-Boost Vaccination With pCI-neo-LACK Plus Attenuated LACK-Expressing Vaccinia Viruses in Hamsters

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Laura Fernández

2018-04-01

Full Text Available Leishmania-activated C-kinase antigen (LACK is a highly conserved protein among Leishmania species and is considered a viable vaccine candidate for human leishmaniasis. In animal models, prime-boost vaccination with LACK-expressing plasmids plus attenuated vaccinia viruses (modified vaccinia Ankara [MVA] and mutant M65 expressing LACK, has been shown to protect against cutaneous leishmaniasis (CL. Further, LACK demonstrated to induce the production of protective cytokines in patients with active CL or cured visceral leishmaniasis, as well as in asymptomatic individuals from endemic areas. However, whether LACK is capable to trigger cytokine release by peripheral blood mononuclear cells from patients cured of CL due to Leishmania infantum (L. infantum or induce protection in L. infantum-infected hamsters [visceral leishmaniasis (VL model], has not yet been analyzed. The present work examines the ex vivo immunogenicity of LACK in cured VL and CL patients, and asymptomatic subjects from an L. infantum area. It also evaluates the vaccine potential of LACK against L. infantum infection in hamsters, in a protocol of priming with plasmid pCI-neo-LACK (DNA-LACK followed by a booster with the poxvirus vectors MVA-LACK or M65-LACK. LACK-stimulated PBMC from both asymptomatic and cured subjects responded by producing IFN-γ, TNF-α, and granzyme B (Th1-type response. Further, 78% of PBMC samples that responded to soluble Leishmania antigen showed IFN-γ secretion following stimulation with LACK. In hamsters, the protocol of DNA-LACK prime/MVA-LACK or M65-LACK virus boost vaccination significantly reduced the amount of Leishmania DNA in the liver and bone marrow, with no differences recorded between the use of MVA or M65 virus vector options. In summary, the Th1-type and cytotoxic responses elicited by LACK in PBMC from human subjects infected with L. infantum, and the parasite protective effect of prime/boost vaccination in hamsters with DNA-LACK/MVA-LACK

Discrimination of Shark species by simple PCR of 5S rDNA repeats

OpenAIRE

Pinhal, Danillo [UNESP; Gadig, Otto Bismarck Fazzano [UNESP; Wasko, Adriane Pinto [UNESP; Oliveira, Claudio [UNESP; Ron, Ernesto; Foresti, Fausto [UNESP; Martins, Cesar [UNESP

2008-01-01

Sharks are suffering from intensive exploitation by worldwide fisheries leading to a severe decline in several populations in the last decades. The lack of biological data on a species-specific basis, associated with a k-strategist life history make it difficult to correctly manage and conserve these animals. The aim of the present study was to develop a DNA-based procedure to discriminate shark species by means of a rapid, low cost and easily applicable PCR analysis based on 5S rDNA repeat u...

Microbial Ecophysiology of Whey Biomethanation: Characterization of Bacterial Trophic Populations and Prevalent Species in Continuous Culture

OpenAIRE

Chartrain, M.; Zeikus, J. G.

1986-01-01

The organization and species composition of bacterial trophic groups associated with lactose biomethanation were investigated in a whey-processing chemostat by enumeration, isolation, and general characterization studies. The bacteria were spatially organized as free-living forms and as self-immobilized forms appearing in flocs. Three dominant bacterial trophic group populations were present (in most probable number per milliliter) whose species numbers varied with the substrate consumed: hyd...

Lead and zinc accumulation and tolerance in populations of six wetland plants

Energy Technology Data Exchange (ETDEWEB)

Deng, H. [Biology Department and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon, Hong Kong (China); Department of Environmental Science and Technology, East China Normal University, Shanghai (China); Ye, Z.H. [Biology Department and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon, Hong Kong (China); School of Life Sciences, Zhongshan (Sun Yat-sen) University, Guangzhou 510275 (China); Wong, M.H. [Biology Department and Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Kowloon, Hong Kong (China)]. E-mail: mhwong@hkbu.edu.hk

2006-05-15

Wetland plants such as Typha latifolia and Phragmites australis have been indicated to show a lack of evolution of metal tolerance in metal-contaminated populations. The aim of the present study is to verify whether other common wetland plants such as Alternanthera philoxeroides and Beckmannia syzigachne, also possess the same characteristics. Lead and zinc tolerances in populations of six species collected from contaminated and clean sites were examined by hydroponics. In general, the contaminated populations did not show higher metal tolerance and accumulation than the controls. Similar growth responses and tolerance indices in the same metal treatment solution between contaminated and control populations suggest that metal tolerance in wetland plants are generally not further evolved by contaminated environment. The reasons may be related to the special root anatomy in wetland plants, the alleviated metal toxicity by the reduced rooting conditions and the relatively high innate metal tolerance in some species. - Populations from metal contaminated sites did not have significantly higher metal tolerance indices.

Lead and zinc accumulation and tolerance in populations of six wetland plants

International Nuclear Information System (INIS)

Deng, H.; Ye, Z.H.; Wong, M.H.

2006-01-01

Wetland plants such as Typha latifolia and Phragmites australis have been indicated to show a lack of evolution of metal tolerance in metal-contaminated populations. The aim of the present study is to verify whether other common wetland plants such as Alternanthera philoxeroides and Beckmannia syzigachne, also possess the same characteristics. Lead and zinc tolerances in populations of six species collected from contaminated and clean sites were examined by hydroponics. In general, the contaminated populations did not show higher metal tolerance and accumulation than the controls. Similar growth responses and tolerance indices in the same metal treatment solution between contaminated and control populations suggest that metal tolerance in wetland plants are generally not further evolved by contaminated environment. The reasons may be related to the special root anatomy in wetland plants, the alleviated metal toxicity by the reduced rooting conditions and the relatively high innate metal tolerance in some species. - Populations from metal contaminated sites did not have significantly higher metal tolerance indices

Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

OpenAIRE

Hajirostamloo, Mahbobeh

2005-01-01

Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Sh...

Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus in China.

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Huayuan Huang

Full Text Available The Chinese crocodile lizard Shinisaurus crocodilurus is a critically endangered species, listed in Appendix II of CITES. Its populations and habitat in China have undergone significant changes in recent years. Understanding the genetic variability and phylogeography of this species is very important for successful conservation. In this study, samples were taken from 11 wild ponds and two captive populations in China. We sequenced mitochondrial CYTB, partial ND6, and partial tRNA-Glu and genotyped 10 microsatellite loci. Our analyses of these data showed low genetic variability, no strong isolation caused by distance, and a lack of a phylogeographic structure in this species. Based on our results, the basal divergence between two clades of S. crocodilurus in China may have been caused by the formation of the Pearl River system. We found a population expansion in one of these clades. Microsatellite analysis indicated the presence of three clusters, separated by significant genetic differences. We found that most individuals in the two captive populations were from the Luokeng (Guangdong and Guangxi wild source populations, respectively.

POPULATION STRUCTURES OF FOUR TREE SPECIES IN LOGGED-OVER TROPICAL FOREST IN SOUTH PAPUA, INDONESIA: AN INTEGRAL PROJECTION MODEL APPROACH

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Relawan kuswandi

2015-12-01

Full Text Available Selective logging has been taking place in Papua for several decades. In contrast, very little is known about the stand structure in post-logged forest. Hence, this paper investigates stand structures in logged-over area of tropical forest in South Papua. Four species were selected in three one-hectare permanent sample plots (PSPs: Vatica rassak, Syzygium sp, Litsea timoriana and Canarium asperum. PSPs were located in the forest concession area of PT. Tunas Sawaerma in Assiki, Boven Digul, in South Papua. Data sets comprised measurements made in 2005 and 2012 consisting of species, diameter at breast height (DBH, mortality and number of tree of each species. Integral Projection Models (IPMs were developed, taking into account mortality, growth, recruitment and fecundity. Results show the pattern of stand structures of the four species were more or less similar, i.e. more individual trees were present in the small diameter classes than in the larger diameter classes. The general pattern of the individual distribution of the four species is the typical reverse-J shape. Syzygium sp. has a greater number of individuals in the small diameter classes than the other three species. Population growth rates (λ are above one, indicating that the stand structures of the population dynamics of the four species are recuperating. Conclusively, these results suggest that species composition and population structure in these logged-over forests are recovering increasingly.

78 FR 2893 - Endangered and Threatened Species: Designation of a Nonessential Experimental Population for...

Science.gov (United States)

2013-01-15

.... mykiss exhibits perhaps the most complex suite of life history traits of any species of Pacific salmonid... functions that support the viability of populations and their primary life history strategies throughout... conservation measures in a time certain fashion versus the potential for some harm and determined that, on...

Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

Science.gov (United States)

Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

2016-09-01

Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

77 FR 20774 - Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of...

Science.gov (United States)

2012-04-06

... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration 50 CFR Part 223 RIN 0648-XZ58 Endangered and Threatened Species; Proposed Threatened Status for Distinct Population Segments of the Bearded Seal AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric...

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp. in the Nicaraguan crater lakes

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Meyer Axel

2010-10-01

Full Text Available Abstract Background Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites. We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios. Results We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s of each crater lake differs, although most of them occurred more (probably much more recently than 20,000 years ago. Conclusion The

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes.

Science.gov (United States)

Barluenga, Marta; Meyer, Axel

2010-10-26

Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios. We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old) and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s) of each crater lake differs, although most of them occurred more (probably much more) recently than 20,000 years ago. The genetic differentiation of the crater lake populations

Living in isolation - population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink).

Science.gov (United States)

Putz, Christina M; Schmid, Christoph; Reisch, Christoph

2015-09-01

The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential.

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

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Kristopher J. L. Irizarry

2016-01-01

Full Text Available Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species.

Science.gov (United States)

Irizarry, Kristopher J L; Bryant, Doug; Kalish, Jordan; Eng, Curtis; Schmidt, Peggy L; Barrett, Gini; Barr, Margaret C

2016-01-01

Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

The effect of wildfire on population dynamics for two native small mammal species in a coastal heathland in Queensland, Australia

Science.gov (United States)

Liedloff, Adam C.; Wilson, John C.; Engeman, Richard M.

2018-04-01

The influences of wildfire through population dynamics and life history for two species of small mammals in a south-east Queensland heathland on Bribie Island are presented. Trapping results provided information on breeding, immigration and movement of Melomys burtoni (Grassland melomys) and Rattus lutreolus (Swamp rat). We first investigated and optimized the design of trapping methodology for producing mark-recapture population estimates to compare two adjacent populations, one of which was subjected to an extensive wildfire during the two year study. We consider how well rodents survive wildfire and whether the immediate impacts of fire or altered habitat have the greatest impact on each species. We found the R. lutreolus population was far more influenced by the fire than the M. burtoni population both immediately after the fire and over 18 months of vegetation recovery.

Potential for adaptive evolution at species range margins: contrasting interactions between red coral populations and their environment in a changing ocean.

Science.gov (United States)

Ledoux, Jean-Baptiste; Aurelle, Didier; Bensoussan, Nathaniel; Marschal, Christian; Féral, Jean-Pierre; Garrabou, Joaquim

2015-03-01

Studying population-by-environment interactions (PEIs) at species range margins offers the opportunity to characterize the responses of populations facing an extreme regime of selection, as expected due to global change. Nevertheless, the importance of these marginal populations as putative reservoirs of adaptive genetic variation has scarcely been considered in conservation biology. This is particularly true in marine ecosystems for which the deep refugia hypothesis proposes that disturbed shallow and marginal populations of a given species can be replenished by mesophotic ones. This hypothesis therefore assumes that identical PEIs exist between populations, neglecting the potential for adaptation at species range margins. Here, we combine reciprocal transplant and common garden experiments with population genetics analyses to decipher the PEIs in the red coral, Corallium rubrum. Our analyses reveal partially contrasting PEIs between shallow and mesophotic populations separated by approximately one hundred meters, suggesting that red coral populations may potentially be locally adapted to their environment. Based on the effective population size and connectivity analyses, we posit that genetic drift may be more important than gene flow in the adaptation of the red coral. We further investigate how adaptive divergence could impact population viability in the context of warming and demonstrate differential phenotypic buffering capacities against thermal stress. Our study questions the relevance of the deep refugia hypothesis and highlights the conservation value of marginal populations as a putative reservoir of adaptive genetic polymorphism.

Temperature alters the relative abundance and population growth rates of species within the Dendroctonus frontalis (Coleoptera: Curculionidae) community.

Science.gov (United States)

L. Evans; Richard Hoffstetter; Matthew Ayres; Kier Klepzig

2011-01-01

Temperature has strong effects on metabolic processes ofindividuals and demographics of populations, but effects on ecological communities are not well known. Many economically and ecologically important pest species have obligate associations with other organisms; therefore, effects of temperature on these species might be mediated by strong interactions. The southern...

Genetic Diversity and Population Structure of a Threatened African Tree Species, Milicia excelsa, Using Nuclear Micro satellites DNA Markers

International Nuclear Information System (INIS)

Ouinsavi, Ch.; Sokpon, N.; Ouinsavi, Ch.; Khasa, D.P.

2009-01-01

To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, 212 individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific micro satellite DNA loci. All loci were variable, with the mean number of alleles per locus ranging from 5.86 to 7.69. Considerable genetic variability was detected for all populations at the seven loci (AR=4.60; HE=0.811). Moderate but statistically significant genetic differentiation was found among populations considering both FST (0.112) and RST (0.342). All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positive FIS values due to inbreeding occurring in the species. Pairwise FST values were positively and significantly correlated with geographical distances (r=0.432; P=.007, Mantel's test) indicating that populations are differentiated by isolation by distance. Bayesian analysis of population structure showed division of the genetic variation into four clusters revealing the existence of heterogeneity in population genetic structure. Altogether, these results indicate that genetic variation in Milicia excelsa is geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.

Population Size and Decadal Trends of Three Penguin Species Nesting at Signy Island, South Orkney Islands.

Science.gov (United States)

Dunn, Michael J; Jackson, Jennifer A; Adlard, Stacey; Lynnes, Amanda S; Briggs, Dirk R; Fox, Derren; Waluda, Claire M

2016-01-01

We report long-term changes in population size of three species of sympatrically breeding pygoscelid penguins: Adélie (Pygoscelis adeliae), chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua ellsworthii) over a 38 year period at Signy Island, South Orkney Islands, based on annual counts from selected colonies and decadal all-island systematic counts of occupied nests. Comparing total numbers of breeding pairs over the whole island from 1978/79 to 2015/16 revealed varying fortunes: gentoo penguin pairs increased by 255%, (3.5% per annum), chinstrap penguins declined by 68% (-3.6% per annum) and Adélie penguins declined by 42% (-1.5% per annum). The chinstrap population has declined steadily over the last four decades. In contrast, Adélie and gentoo penguins have experienced phases of population increase and decline. Annual surveys of selected chinstrap and Adélie colonies produced similar trends from those revealed by island-wide surveys, allowing total island population trends to be inferred relatively well. However, while the annual colony counts of chinstrap and Adélie penguins showed a trend consistent in direction with the results from all-island surveys, the magnitude of estimated population change was markedly different between colony wide and all island counts. Annual population patterns suggest that pair numbers in the study areas partly reflect immigration and emigration of nesting birds between different parts of the island. Breeding success for all three species remained broadly stable over time in the annually monitored colonies. Breeding success rates in gentoo and chinstrap penguins were strongly correlated, despite the differing trends in population size. This study shows the importance of effective, standardised monitoring to accurately determine long-term population trajectories. Our results indicate significant declines in the Adélie and chinstrap penguin populations at Signy Island over the last five decades, and a gradual

Assessing combined impacts of agrochemicals: Aquatic macroinvertebrate population responses in outdoor mesocosms.

Science.gov (United States)

Barmentlo, S Henrik; Schrama, Maarten; Hunting, Ellard R; Heutink, Roel; van Bodegom, Peter M; de Snoo, Geert R; Vijver, Martina G

2018-08-01

Agricultural ditches host a diverse community of species. These species often are unwarrantedly exposed to fertilizers and a wide-array of pesticides (hereafter: agrochemicals). Standardized ecotoxicological research provides valuable information to predict whether these pesticides possibly pose a threat to the organisms living within these ditches, in particular macro-invertebrates. However, knowledge on how mixtures of these agrochemicals affect macro-invertebrates under realistic abiotic conditions and with population and community complexity is mostly lacking. Therefore we examined here, using a full factorial design, the population responses of macroinvertebrate species assemblages exposed to environmentally relevant concentrations of three commonly used agrochemicals (for 35days) in an outdoor experiment. The agrochemicals selected were an insecticide (imidacloprid), herbicide (terbuthylazine) and nutrients (NPK), all having a widespread usage and often detected together in watersheds. Effects on species abundance and body length caused by binary mixture combinations could be described from single substance exposure. However, when agrochemicals were applied as tertiary mixtures, as they are commonly found in agricultural waters, species' abundance often deviated from expectations made based on the three single treatments. This indicates that pesticide-mixture induced toxicity to population relevant endpoints are difficult to extrapolate to field conditions. As in agricultural ditches often a multitude (approx. up to 7) of agrochemicals residues are detected, we call other scientist to verify the ecological complexity of non-additive induced shifts in natural aquatic invertebrate populations and aquatic species assemblages. Copyright © 2018 Elsevier B.V. All rights reserved.

Recovery of an endangered butterfly species, Shijimiaeoides divinus, population at Azumino in Nagano Prefecture, Japan

OpenAIRE

KODA, Keiko

2014-01-01

The large shijimi blue, Shijimiaeoides divinus, is a grassland lycaenid butterfly classified as an endangered species by the Ministry of Environment. In this study, I report on the life history of S. divinus barine and provide new data on the recovery of the natural population in Azumino. This butterfly is single-breeded with the adults usually appearing from late May to early June in Nagano Prefecture. Only three populations of S. divinus barine are maintained in Nagano Prefecture by several...

Species-level persistence probabilities for recovery and conservation status assessment.

Science.gov (United States)

Che-Castaldo, Judy P; Neel, Maile C

2016-12-01

Recovery planning for species listed under the U.S. Endangered Species Act has been hampered by a lack of consistency and transparency, which can be improved by implementing a standardized approach for evaluating species status and developing measurable recovery criteria. However, managers lack an assessment method that integrates threat abatement and can be used when demographic data are limited. To help meet these needs, we demonstrated an approach for evaluating species status based on habitat configuration data. We applied 3 established persistence measures (patch occupancy, metapopulation capacity, and proportion of population lost) to compare 2 conservation strategies (critical habitat designated by the U.S. Fish and Wildlife Service and the Forest Service's Carbonate Habitat Management Strategy) and 2 threat scenarios (maximum limestone mining, removal of all habitat in areas with mining claims; minimum mining, removal of habitat only in areas with existing operations and high-quality ore) against a baseline of existing habitat for 3 federally listed plant species. Protecting all area within the designated critical habitat maintained a similar level (83.9-99.9%) of species persistence as the baseline, whereas maximum mining greatly reduced persistence (0.51-38.4% maintained). The 3 persistence measures provided complementary insights reflecting different aspects of habitat availability (total area, number of patches, patch size, and connectivity). These measures can be used to link recovery criteria developed following the 3 R principles (representation, redundancy, and resilience) to the resulting improvements in species viability. By focusing on amount and distribution of habitat, our method provides a means of assessing the status of data-poor species to inform decision making under the Endangered Species Act. © 2016 Society for Conservation Biology.

Is floral divergence sufficient to maintain species boundaries upon secondary contact in Mediterranean food-deceptive orchids?

Science.gov (United States)

Zitari, A; Scopece, G; Helal, A N; Widmer, A; Cozzolino, S

2012-01-01

Analyzing the processes that determine whether species boundaries are maintained on secondary contact may shed light on the early phase of speciation. In Anacamptis morio and Anacamptis longicornu, two Mediterranean orchid sister-species, we used molecular and morphological analyses, together with estimates of pollination success and experimental crosses, to assess whether floral isolation can shelter the species' genomes from genetic admixture on secondary contact. We found substantial genetic and morphological homogenization in sympatric populations in combination with an apparent lack of postmating isolation. We further detected asymmetric introgression in the sympatric populations and an imbalance in cytotype representation, which may be due either to a difference in flowering phenology or else be a consequence of cytonuclear incompatibilities. Estimates of genetic clines for markers across sympatric zones revealed markers that significantly deviated from neutral expectations. We observed a significant correlation between spur length and reproductive success in sympatric populations, which may suggest that directional selection is the main cause of morphological differentiation in this species pair. Our results suggest that allopatric divergence has not led to the evolution of sufficient reproductive isolation to prevent genomic admixture on secondary contact in this orchid species pair. PMID:21792224

Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean.

Science.gov (United States)

Nguyen, Vy X; Detcharoen, Matsapume; Tuntiprapas, Piyalap; Soe-Htun, U; Sidik, Japar B; Harah, Muta Z; Prathep, Anchana; Papenbrock, Jutta

2014-04-30

The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphological plasticity. The relationship of genetic differentiation and geographic barriers of H. ovalis radiation was not much studied in this region. Are there misidentifications between H. ovalis and its closely related species? Does any taxonomic uncertainty among different populations of H. ovalis persist? Is there any genetic differentiation among populations in the Western Pacific and the Eastern Indian Ocean, which are separated by the Thai-Malay peninsula? Genetic markers can be used to characterize and identify individuals or species and will be used to answer these questions. Phylogenetic analyses of the nuclear ribosomal internal transcribed spacer region based on materials collected from 17 populations in the Western Pacific and the Eastern Indian Ocean showed that some specimens identified as H. ovalis belonged to the H. major clade, also supported by morphological data. Evolutionary divergence between the two clades is between 0.033 and 0.038, much higher than the evolutionary divergence among H. ovalis populations. Eight haplotypes were found; none of the haplotypes from the Western Pacific is found in India and vice versa. Analysis of genetic diversity based on microsatellite analysis revealed that the genetic diversity in the Western Pacific is higher than in the Eastern Indian Ocean. The unrooted neighbor-joining tree among 14 populations from the Western Pacific and the Eastern Indian Ocean showed six groups. The Mantel test results revealed a significant correlation between genetic and geographic distances among populations. Results from band-based and allele frequency-based approaches from Amplified Fragment Length Polymorphism showed that all

Population ecology of the sea lamprey (Petromyzon marinus) as an invasive species in the Laurentian Great Lakes and an imperiled species in Europe

Science.gov (United States)

Hansen, Michael J.; Madenjian, Charles P.; Slade, Jeffrey W.; Steeves, Todd B.; Almeida, Pedro R.; Quintella, Bernardo R.

2016-01-01

The sea lamprey Petromyzon marinus (Linnaeus) is both an invasive non-native species in the Laurentian Great Lakes of North America and an imperiled species in much of its native range in North America and Europe. To compare and contrast how understanding of population ecology is useful for control programs in the Great Lakes and restoration programs in Europe, we review current understanding of the population ecology of the sea lamprey in its native and introduced range. Some attributes of sea lamprey population ecology are particularly useful for both control programs in the Great Lakes and restoration programs in the native range. First, traps within fish ladders are beneficial for removing sea lampreys in Great Lakes streams and passing sea lampreys in the native range. Second, attractants and repellants are suitable for luring sea lampreys into traps for control in the Great Lakes and guiding sea lamprey passage for conservation in the native range. Third, assessment methods used for targeting sea lamprey control in the Great Lakes are useful for targeting habitat protection in the native range. Last, assessment methods used to quantify numbers of all life stages of sea lampreys would be appropriate for measuring success of control in the Great Lakes and success of conservation in the native range.

Comparison of species composition and fumonisin production in Aspergillus section Nigri populations in maize kernels from USA and Italy.

Science.gov (United States)

Susca, Antonia; Moretti, Antonio; Stea, Gaetano; Villani, Alessandra; Haidukowski, Miriam; Logrieco, Antonio; Munkvold, Gary

2014-10-01

Fumonisin contamination of maize is considered a serious problem in most maize-growing regions of the world, due to the widespread occurrence of these mycotoxins and their association with toxicosis in livestock and humans. Fumonisins are produced primarily by species of Fusarium that are common in maize grain, but also by some species of Aspergillus sect. Nigri, which can also occur on maize kernels as opportunistic pathogens. Understanding the origin of fumonisin contamination in maize is a key component in developing effective management strategies. Although some fungi in Aspergillus sect. Nigri are known to produce fumonisins, little is known about the species which are common in maize and whether they make a measurable contribution to fumonisin contamination of maize grain. In this work, we evaluated populations of Aspergillus sect. Nigri isolated from maize in USA and Italy, focusing on analysis of housekeeping genes, the fum8 gene and in vitro capability of producing fumonisins. DNA sequencing was used to identify Aspergillus strains belonging to sect. Nigri, in order to compare species composition between the two populations, which might influence specific mycotoxicological risks. Combined beta-tubulin/calmodulin sequences were used to genetically characterize 300 strains (199 from Italy and 101 from USA) which grouped into 4 clades: Aspergillus welwitschiae (syn. Aspergillus awamori, 14.7%), Aspergillus tubingensis (37.0%) and Aspergillus niger group 1 (6.7%) and group 2 (41.3%). Only one strain was identified as Aspergillus carbonarius. Species composition differed between the two populations; A. niger predominated among the USA isolates (69%), but comprised a smaller percentage (38%) of Italian isolates. Conversely, A. tubingensis and A. welwitschiae occurred at higher frequencies in the Italian population (42% and 20%, respectively) than in the USA population (27% and 5%). The evaluation of FB2 production on CY20S agar revealed 118 FB2 producing and 84

Winter Activity of Coastal Plain Populations of Bat Species Affected by White-Nose Syndrome and Wind Energy Facilities.

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John F Grider

Full Text Available Across the entire distribution of a species, populations may have variable responses to environmental perturbations. Many bat species experience mortality in large portions of their range during hibernation and along migratory paths to and from wintering grounds, from White-nose syndrome (WNS and wind energy development, respectively. In some areas, warm temperatures may allow bats to remain active through winter, thus decreasing their susceptibility to WNS and/or mortality associated with migration to wintering grounds. These areas could act as a refugia and be important for the persistence of local populations. To determine if warmer temperatures affect bat activity, we compared year-round activity of bat populations in the Coastal Plain and Piedmont of North Carolina, USA, two regions that differ in winter temperature. We established six recording stations, four along a 295-kilometer north-south transect in the Coastal Plain, and two in the Piedmont of North Carolina. We recorded bat activity over two years. We supplemented our recordings with mist-net data. Although bat activity was lower during winter at all sites, the odds of recording a bat during winter were higher at Coastal Plain sites when compared with Piedmont sites. Further, bats in the Piedmont had a lower level of winter activity compared to summer activity than bats in the Coastal Plain that had more similar levels of activity in the winter and summer. We found high bat species richness on the Coastal Plain in winter, with winter-active species including those known to hibernate throughout most of their range and others known to be long distance migrants. In particular, two species impacted by WNS, the northern long-eared bat (Myotis septentrionalis and tricolored bat (Perimyotis subflavus, were present year round in the Coastal Plain. The tricolored bat was also present year-round in the Piedmont. In the Coastal Plain, the long distance migratory hoary bat (Lasiurus cinereus

Winter Activity of Coastal Plain Populations of Bat Species Affected by White-Nose Syndrome and Wind Energy Facilities.

Science.gov (United States)

Grider, John F; Larsen, Angela L; Homyack, Jessica A; Kalcounis-Rueppell, Matina C

2016-01-01

Across the entire distribution of a species, populations may have variable responses to environmental perturbations. Many bat species experience mortality in large portions of their range during hibernation and along migratory paths to and from wintering grounds, from White-nose syndrome (WNS) and wind energy development, respectively. In some areas, warm temperatures may allow bats to remain active through winter, thus decreasing their susceptibility to WNS and/or mortality associated with migration to wintering grounds. These areas could act as a refugia and be important for the persistence of local populations. To determine if warmer temperatures affect bat activity, we compared year-round activity of bat populations in the Coastal Plain and Piedmont of North Carolina, USA, two regions that differ in winter temperature. We established six recording stations, four along a 295-kilometer north-south transect in the Coastal Plain, and two in the Piedmont of North Carolina. We recorded bat activity over two years. We supplemented our recordings with mist-net data. Although bat activity was lower during winter at all sites, the odds of recording a bat during winter were higher at Coastal Plain sites when compared with Piedmont sites. Further, bats in the Piedmont had a lower level of winter activity compared to summer activity than bats in the Coastal Plain that had more similar levels of activity in the winter and summer. We found high bat species richness on the Coastal Plain in winter, with winter-active species including those known to hibernate throughout most of their range and others known to be long distance migrants. In particular, two species impacted by WNS, the northern long-eared bat (Myotis septentrionalis) and tricolored bat (Perimyotis subflavus), were present year round in the Coastal Plain. The tricolored bat was also present year-round in the Piedmont. In the Coastal Plain, the long distance migratory hoary bat (Lasiurus cinereus) was active in the

Coupling Satellite Data with Species Distribution and Connectivity Models as a Tool for Environmental Management and Planning in Matrix-Sensitive Species

Science.gov (United States)

Rödder, Dennis; Nekum, Sven; Cord, Anna F.; Engler, Jan O.

2016-07-01

Climate change and anthropogenic habitat fragmentation are considered major threats for global biodiversity. As a direct consequence, connectivity is increasingly disrupted in many species, which might have serious consequences that could ultimately lead to the extinction of populations. Although a large number of reserves and conservation sites are designated and protected by law, potential habitats acting as inter-population connectivity corridors are, however, mostly ignored in the common practice of environmental planning. In most cases, this is mainly caused by a lack of quantitative measures of functional connectivity available for the planning process. In this study, we highlight the use of fine-scale potential connectivity models (PCMs) derived from multispectral satellite data for the quantification of spatially explicit habitat corridors for matrix-sensitive species of conservation concern. This framework couples a species distribution model with a connectivity model in a two-step framework, where suitability maps from step 1 are transformed into maps of landscape resistance in step 2 filtered by fragmentation thresholds. We illustrate the approach using the sand lizard ( Lacerta agilis L.) in the metropolitan area of Cologne, Germany, as a case study. Our model proved to be well suited to identify connected as well as completely isolated populations within the study area. Furthermore, due to its fine resolution, the PCM was also able to detect small linear structures known to be important for sand lizards' inter-population connectivity such as railroad embankments. We discuss the applicability and possible implementation of PCMs to overcome shortcomings in the common practice of environmental impact assessments.

Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes

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Bachtrog Doris

2008-12-01

Full Text Available Abstract Background Adaptive protein evolution is common in several Drosophila species investigated. Some studies point to very weak selection operating on amino-acid mutations, with average selection intensities on the order of Nes ~ 5 in D. melanogaster and D. simulans. Species with lower effective population sizes should undergo less adaptation since they generate fewer mutations and selection is ineffective on a greater proportion of beneficial mutations. Results Here I study patterns of polymorphism and divergence at 91 X-linked loci in D. miranda, a species with a roughly 5-fold smaller effective population size than D. melanogaster. Surprisingly, I find a similar fraction of amino-acid mutations being driven to fixation by positive selection in D. miranda and D. melanogaster. Genes with higher rates of amino-acid evolution show lower levels of neutral diversity, a pattern predicted by recurrent adaptive protein evolution. I fit a hitchhiking model to patterns of polymorphism in D. miranda and D. melanogaster and estimate an order of magnitude higher selection coefficients for beneficial mutations in D. miranda. Conclusion This analysis suggests that effective population size may not be a major determinant in rates of protein adaptation. Instead, adaptation may not be mutation-limited, or the distribution of fitness effects for beneficial mutations might differ vastly between different species or populations. Alternative explanation such as biases in estimating the fraction of beneficial mutations or slightly deleterious mutation models are also discussed.

Effectiveness of protected areas for representing species and populations of terrestrial mammals in Costa Rica.

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José F González-Maya

Full Text Available Costa Rica has one of the greatest percentages (26% of protected land in the world. The National Protected Areas System (NPAS of Costa Rica was established in 1976 and currently includes >190 protected areas within seven different protection categories. The effectiveness of the NPAS to represent species, populations, and areas with high species richness has not been properly evaluated. Such evaluations are fundamental to understand what is necessary to strengthen the NPAS and better protect biodiversity. We present a novel assessment of NPAS effectiveness in protecting mammal species. We compiled the geographical ranges of all terrestrial Costa Rican mammals then determined species lists for all protected areas and the estimated proportion of each species' geographic range protected. We also classified mammal species according to their conservation status using the IUCN Red List of Threatened Species. We found almost complete representation of mammal species (98.5% in protected areas, but low relative coverage (28.3% on average of their geographic ranges in Costa Rica and 25% of the species were classified as underprotected according to a priori representation targets. Interestingly, many species-rich areas are not protected, and at least 43% of cells covering the entire country are not included in protected areas. Though protected areas in Costa Rica represent species richness well, strategic planning for future protected areas to improve species complementarity and range protection is necessary. Our results can help to define sites where new protected areas can have a greater impact on mammal conservation, both in terms of species richness and range protection.

The West Indian manatee (Trichechus manatus) in Florida: a summary and analysis of biological, ecological, and administrative problems affecting preservation and restoration of the population. Final report

Energy Technology Data Exchange (ETDEWEB)

Wray, P.

1978-09-01

The population of the West Indian manatee (Trichechus manatus), an endangered species, is estimated at 800-1,000 individuals in peninsular Florida. Observed annual mortality between 1974 and 1977 was 6-8% of the estimated population. Human activities are implicated in much of this mortality. Direct and indirect threats include boat collisions, diver harassment, creation of artificial warm water refuges, vandalism, entanglement in fishing gear, herbicides in food resources, and possible effects of offshore oil exploration. Lack of federal commitment to manatee protection is evidenced by an absence of implementing regulations under the Marine Mammal Protection Act and the Endangered Species Act, absence of a recovery plan for the species, faulty interagency communication, and a lack of law enforcement. Problems are discussed, with recommendations for conservation. (Color illustrations reproduced in black and white)

Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae.

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Lise Roy

Full Text Available Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France, Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent

Miltefosine and antimonial drug susceptibility of Leishmania Viannia species and populations in regions of high transmission in Colombia.

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Olga Lucía Fernández

2014-05-01

Full Text Available Pentavalent antimonials have been the first line treatment for dermal leishmaniasis in Colombia for over 30 years. Miltefosine is administered as second line treatment since 2005. The susceptibility of circulating populations of Leishmania to these drugs is unknown despite clinical evidence supporting the emergence of resistance.In vitro susceptibility was determined for intracellular amastigotes of 245 clinical strains of the most prevalent Leishmania Viannia species in Colombia to miltefosine (HePC and/or meglumine antimoniate (Sb(V; 163, (80% were evaluated for both drugs. Additionally, susceptibility to Sb(V was examined in two cohorts of 85 L. V. panamensis strains isolated between 1980-1989 and 2000-2009 in the municipality of Tumaco. Susceptibility to each drug differed among strains of the same species and between species. Whereas 68% of L. V. braziliensis strains presented in vitro resistance to HePC, 69% were sensitive to Sb(V. Resistance to HePC and Sb(V occurred respectively, in 20% y 21% of L. panamensis strains. Only 3% of L. V. guyanensis were resistant to HePC, and none to Sb(V. Drug susceptibility differed between geographic regions and time periods. Subpopulations having disparate susceptibility to Sb(V were discerned among L. V. panamensis strains isolated during 1980-1990 in Tumaco where resistant strains belonged to zymodeme 2.3, and sensitive strains to zymodeme 2.2.Large scale evaluation of clinical strains of Leishmania Viannia species demonstrated species, population, geographic, and epidemiologic differences in susceptibility to meglumine antimoniate and miltefosine, and provided baseline information for monitoring susceptibility to these drugs. Sensitive and resistant clinical strains within each species, and zymodeme as a proxy marker of antimony susceptibility for L. V. panamensis, will be useful in deciphering factors involved in susceptibility and the distribution of sensitive and resistant populations.

Microsatellite analysis of the natterjack toad (Bufo calamita) in Denmark: populations are islands in a fragmented landscape

DEFF Research Database (Denmark)

Allentoft, Morten Erik; Siegismund, Hans Redlef; Briggs, Lars

2009-01-01

The European natterjack toad (Bufo calamita) has declined rapidly in recent years, primarily due to loss of habitat, and in Denmark it is estimated that 50% of the isolated populations are lost each decade. To efficiently manage and conserve this species and its genetic diversity, knowledge...... of isolation by distance within major regions supported this apparent lack of a gene flow continuum. Indications of a genetic bottleneck were found in three populations. The analyses suggest that the remaining Bufo calamita populations in Denmark are genetically isolated, and represent independent units...... in a highly fragmented gene pool. Future conservation management of this species is discussed in light of these results....

Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea.

Science.gov (United States)

Postaire, Bautisse; Gélin, Pauline; Bruggemann, J Henrich; Pratlong, Marine; Magalon, Hélène

2017-10-01

Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α ( sensu Postaire et al ., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive F IS values (from -0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (11,000 km distance), with significant pairwise F ST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.

Conservation Genetics of Threatened Dalbergia Timber Species in Indochina

DEFF Research Database (Denmark)

Hartvig, Ida

Tropical forests all over the world are disappearing at high rates primarily due to anthropogenic ecosystem changes. A high number of tropical tree species is threatened with extinction due to deforestation and unsustainable levels of logging, and the implementation of effective conservation plans...... is often hindered by the lack of basic knowledge of their biology. This study represents the first region-wide analysis of population genetic diversity for tree species in Indochina and provides valuable knowledge on how threatened tree species are affected by landscape features, ancient or recent habitat...... as several separate species and accurately identified the CITES-listed D. cochinchinensis. The results can be used to update threat assessments with correct taxonomic information and the method can be implemented as an identification tool in field studies as well as in enforcement of CITES regulations...

Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population.

Science.gov (United States)

Qi, Z; Cao, H; Jiang, H; Zhao, J; Tang, Z

2016-01-01

To use microarrays to detect 11 selected bacteria in infected root canals, revealing bacterial combinations that are associated with clinical symptoms and signs of primary endodontic infections in a Chinese population. DNA was extracted from 90 samples collected from the root canals of teeth with primary endodontic infections in a Chinese population, and the 16S rRNA gene was amplified by polymerase chain reaction (PCR). The PCR products were hybridized to microarrays containing specific oligonucleotide probes targeting 11 species, and the arrays were screened with a confocal laser scanner. Pearson's chi-squared test and cluster analysis were performed to investigate the associations between the bacterial combinations and clinical symptoms and signs using SAS 8.02. Seventy-seven samples (86%) yielded at least one of the 11 target species. Parvimonas micra (56%), Porphyromonas endodontalis (51%), Tannerella forsythia (48%), Prevotella intermedia (44%) and Porphyromonas gingivalis (37%) were the most prevalent taxa and were often concomitant. The following positive associations were found between the bacterial combinations and clinical features: P. endodontalis and T. forsythia with abscess; P. gingivalis and P. micra with sinus tract; P. gingivalis and P. endodontalis or P. micra and P. endodontalis with abscess and sinus tract; and the combination of P. endodontalis, P. micra, T. forsythia and P. gingivalis with sinus tract (P endodontalis, T. forsythia and P. gingivalis may contribute to abscesses or sinus tracts of endodontic origin with bacterial synergism in a Chinese population. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

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Julianne M O'Reilly-Wapstra

Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

Relative lack of regeneration of shade-intolerant canopy species in some South African forests

CSIR Research Space (South Africa)

Midgley, JJ

1995-01-01

Full Text Available Some species such as Celtis Africana, are experiencing relative recruitment bottlenecks, because there are usually fewer recruits [i.e. individuals <20 cm diameter at breast height, (dbh)] than canopy individuals. The species with low recruitment...

Effectiveness of Protected Areas for Representing Species and Populations of Terrestrial Mammals in Costa Rica

Science.gov (United States)

González-Maya, José F.; Víquez-R, Luis R.; Belant, Jerrold L.; Ceballos, Gerardo

2015-01-01

Costa Rica has one of the greatest percentages (26%) of protected land in the world. The National Protected Areas System (NPAS) of Costa Rica was established in 1976 and currently includes >190 protected areas within seven different protection categories. The effectiveness of the NPAS to represent species, populations, and areas with high species richness has not been properly evaluated. Such evaluations are fundamental to understand what is necessary to strengthen the NPAS and better protect biodiversity. We present a novel assessment of NPAS effectiveness in protecting mammal species. We compiled the geographical ranges of all terrestrial Costa Rican mammals then determined species lists for all protected areas and the estimated proportion of each species’ geographic range protected. We also classified mammal species according to their conservation status using the IUCN Red List of Threatened Species. We found almost complete representation of mammal species (98.5%) in protected areas, but low relative coverage (28.3% on average) of their geographic ranges in Costa Rica and 25% of the species were classified as underprotected according to a priori representation targets. Interestingly, many species-rich areas are not protected, and at least 43% of cells covering the entire country are not included in protected areas. Though protected areas in Costa Rica represent species richness well, strategic planning for future protected areas to improve species complementarity and range protection is necessary. Our results can help to define sites where new protected areas can have a greater impact on mammal conservation, both in terms of species richness and range protection. PMID:25970293

Hypernatremia in Dice snakes (Natrix tessellata) from a coastal population: implications for osmoregulation in marine snake prototypes.

Science.gov (United States)

Brischoux, François; Kornilev, Yurii V

2014-01-01

The widespread relationship between salt excreting structures (e.g., salt glands) and marine life strongly suggests that the ability to regulate salt balance has been crucial during the transition to marine life in tetrapods. Elevated natremia (plasma sodium) recorded in several marine snakes species suggests that the development of a tolerance toward hypernatremia, in addition to salt gland development, has been a critical feature in the evolution of marine snakes. However, data from intermediate stage (species lacking salt glands but occasionally using salty environments) are lacking to draw a comprehensive picture of the evolution of an euryhaline physiology in these organisms. In this study, we assessed natremia of free-ranging Dice snakes (Natrix tessellata, a predominantly fresh water natricine lacking salt glands) from a coastal population in Bulgaria. Our results show that coastal N. tessellata can display hypernatremia (up to 195.5 mmol x l(-1)) without any apparent effect on several physiological and behavioural traits (e.g., hematocrit, body condition, foraging). More generally, a review of natremia in species situated along a continuum of habitat use between fresh- and seawater shows that snake species display a concomitant tolerance toward hypernatremia, even in species lacking salt glands. Collectively, these data suggest that a physiological tolerance toward hypernatremia has been critical during the evolution of an euryhaline physiology, and may well have preceded the evolution of salt glands.

Hypernatremia in Dice snakes (Natrix tessellata from a coastal population: implications for osmoregulation in marine snake prototypes.

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François Brischoux

Full Text Available The widespread relationship between salt excreting structures (e.g., salt glands and marine life strongly suggests that the ability to regulate salt balance has been crucial during the transition to marine life in tetrapods. Elevated natremia (plasma sodium recorded in several marine snakes species suggests that the development of a tolerance toward hypernatremia, in addition to salt gland development, has been a critical feature in the evolution of marine snakes. However, data from intermediate stage (species lacking salt glands but occasionally using salty environments are lacking to draw a comprehensive picture of the evolution of an euryhaline physiology in these organisms. In this study, we assessed natremia of free-ranging Dice snakes (Natrix tessellata, a predominantly fresh water natricine lacking salt glands from a coastal population in Bulgaria. Our results show that coastal N. tessellata can display hypernatremia (up to 195.5 mmol x l(-1 without any apparent effect on several physiological and behavioural traits (e.g., hematocrit, body condition, foraging. More generally, a review of natremia in species situated along a continuum of habitat use between fresh- and seawater shows that snake species display a concomitant tolerance toward hypernatremia, even in species lacking salt glands. Collectively, these data suggest that a physiological tolerance toward hypernatremia has been critical during the evolution of an euryhaline physiology, and may well have preceded the evolution of salt glands.

ConSpeciFix: Classifying prokaryotic species based on gene flow.

Science.gov (United States)

Bobay, Louis-Marie; Ellis, Brian Shin-Hua; Ochman, Howard

2018-05-16

Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML. ljbobay@uncg.edu.

A population's of Cochranella ignota reproductive ecology (anura:centrolenidae)

International Nuclear Information System (INIS)

Restrepo, Jorge Humberto; Naranjo, Luis G. Naranjo

1999-01-01

During the first semester of 1994, we studied 30 marked males and 40 eggs clutches of Cochranella ignota in a cloud forest at 1900 m of elevation on the western Andes. The clumping of resident males at restricted sites and the regular spatial pattern of the individuals within the clumps suggest territoriality and male selection of display sites. The lack of patterns of the structural variables of the habitat used both by males and females suggest behavioral mechanisms of mate choice. The comparison of the reproductive strategy of this population with those of other species of anuran amphibians reveals the occurrence of Lek behavior in this species

75 FR 30769 - Endangered and Threatened Species; Proposed Listing of Nine Distinct Population Segments of...

Science.gov (United States)

2010-06-02

... Oceanic and Atmospheric Administration 50 CFR Parts 223 and 224 RIN 0648-AY49 Endangered and Threatened Species; Proposed Listing of Nine Distinct Population Segments of Loggerhead Sea Turtles as Endangered or... loggerhead sea turtles as endangered or threatened, which was published on March 16, 2010, until September 13...

Gene flow connects coastal populations of a habitat specialist, the Clapper Rail Rallus crepitans

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Coster, Stephanie S.; Welsh, Amy B.; Costanzo, Gary R.; Harding, Sergio R.; Anderson, James T.; Katzner, Todd

2018-01-01

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographic range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of North America, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks, and a weak pattern of genetic differentiation that increased with geographic distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the North American Atlantic coast, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioral factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.

Comparative population structure of Plasmodium malariae and Plasmodium falciparum under different transmission settings in Malawi

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Molyneux Malcolm E

2011-02-01

setting. Conclusions The extent of similarity between P. falciparum and P. malariae population structure described by the high level of multiple infection, the lack of significant population differentiation or haplotype clustering and lack of linkage disequilibrium is surprising given the differences in the biological features of these species that suggest a reduced potential for out-crossing and transmission in P. malariae. The absence of a rise in P. malariae MOI with increased transmission or a reduction in MOI with age could be explained by differences in the duration of infection or degree of immunity compared to P. falciparum.

The Use of Surrogate Data in Demographic Population Viability Analysis: A Case Study of California Sea Lions.

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Claudia J Hernández-Camacho

Full Text Available Reliable data necessary to parameterize population models are seldom available for imperiled species. As an alternative, data from populations of the same species or from ecologically similar species have been used to construct models. In this study, we evaluated the use of demographic data collected at one California sea lion colony (Los Islotes to predict the population dynamics of the same species from two other colonies (San Jorge and Granito in the Gulf of California, Mexico, for which demographic data are lacking. To do so, we developed a stochastic demographic age-structured matrix model and conducted a population viability analysis for each colony. For the Los Islotes colony we used site-specific pup, juvenile, and adult survival probabilities, as well as birth rates for older females. For the other colonies, we used site-specific pup and juvenile survival probabilities, but used surrogate data from Los Islotes for adult survival probabilities and birth rates. We assessed these models by comparing simulated retrospective population trajectories to observed population trends based on count data. The projected population trajectories approximated the observed trends when surrogate data were used for one colony but failed to match for a second colony. Our results indicate that species-specific and even region-specific surrogate data may lead to erroneous conservation decisions. These results highlight the importance of using population-specific demographic data in assessing extinction risk. When vital rates are not available and immediate management actions must be taken, in particular for imperiled species, we recommend the use of surrogate data only when the populations appear to have similar population trends.

The Use of Surrogate Data in Demographic Population Viability Analysis: A Case Study of California Sea Lions

Science.gov (United States)

2015-01-01

Reliable data necessary to parameterize population models are seldom available for imperiled species. As an alternative, data from populations of the same species or from ecologically similar species have been used to construct models. In this study, we evaluated the use of demographic data collected at one California sea lion colony (Los Islotes) to predict the population dynamics of the same species from two other colonies (San Jorge and Granito) in the Gulf of California, Mexico, for which demographic data are lacking. To do so, we developed a stochastic demographic age-structured matrix model and conducted a population viability analysis for each colony. For the Los Islotes colony we used site-specific pup, juvenile, and adult survival probabilities, as well as birth rates for older females. For the other colonies, we used site-specific pup and juvenile survival probabilities, but used surrogate data from Los Islotes for adult survival probabilities and birth rates. We assessed these models by comparing simulated retrospective population trajectories to observed population trends based on count data. The projected population trajectories approximated the observed trends when surrogate data were used for one colony but failed to match for a second colony. Our results indicate that species-specific and even region-specific surrogate data may lead to erroneous conservation decisions. These results highlight the importance of using population-specific demographic data in assessing extinction risk. When vital rates are not available and immediate management actions must be taken, in particular for imperiled species, we recommend the use of surrogate data only when the populations appear to have similar population trends. PMID:26413746

Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss.

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Sammler, Svenja; Ketmaier, Valerio; Havenstein, Katja; Krause, Ulrike; Curio, Eberhard; Tiedemann, Ralph

2012-10-12

The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow

Population Size and Decadal Trends of Three Penguin Species Nesting at Signy Island, South Orkney Islands.

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Michael J Dunn

Full Text Available We report long-term changes in population size of three species of sympatrically breeding pygoscelid penguins: Adélie (Pygoscelis adeliae, chinstrap (Pygoscelis antarctica and gentoo (Pygoscelis papua ellsworthii over a 38 year period at Signy Island, South Orkney Islands, based on annual counts from selected colonies and decadal all-island systematic counts of occupied nests. Comparing total numbers of breeding pairs over the whole island from 1978/79 to 2015/16 revealed varying fortunes: gentoo penguin pairs increased by 255%, (3.5% per annum, chinstrap penguins declined by 68% (-3.6% per annum and Adélie penguins declined by 42% (-1.5% per annum. The chinstrap population has declined steadily over the last four decades. In contrast, Adélie and gentoo penguins have experienced phases of population increase and decline. Annual surveys of selected chinstrap and Adélie colonies produced similar trends from those revealed by island-wide surveys, allowing total island population trends to be inferred relatively well. However, while the annual colony counts of chinstrap and Adélie penguins showed a trend consistent in direction with the results from all-island surveys, the magnitude of estimated population change was markedly different between colony wide and all island counts. Annual population patterns suggest that pair numbers in the study areas partly reflect immigration and emigration of nesting birds between different parts of the island. Breeding success for all three species remained broadly stable over time in the annually monitored colonies. Breeding success rates in gentoo and chinstrap penguins were strongly correlated, despite the differing trends in population size. This study shows the importance of effective, standardised monitoring to accurately determine long-term population trajectories. Our results indicate significant declines in the Adélie and chinstrap penguin populations at Signy Island over the last five decades, and a

Projected risk of population declines for native fish species in the Upper Mississippi River

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Crimmins, S.M.; Boma, P.; Thogmartin, W.E.

2015-01-01

Conservationists are in need of objective metrics for prioritizing the management of habitats. For individual species, the threat of extinction is often used to prioritize what species are in need of conservation action. Using long-term monitoring data, we applied a Bayesian diffusion approximation to estimate quasi-extinction risk for 54 native fish species within six commercial navigation reaches along a 1350-km gradient of the upper Mississippi River system. We found a strong negative linear relationship between quasi-extinction risk and distance upstream. For some species, quasi-extinction estimates ranged from nearly zero in some reaches to one in others, suggesting substantial variability in threats facing individual river reaches. We found no evidence that species traits affected quasi-extinction risk across the entire system. Our results indicate that fishes within the upper Mississippi River system face localized threats that vary across river impact gradients. This suggests that conservation actions should be focused on local habitat scales but should also consider the additive effects on downstream conditions. We also emphasize the need for identification of proximate mechanisms behind observed and predicted population declines, as conservation actions will require mitigation of such mechanisms. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Global hotspots and correlates of alien species richness across taxonomic groups

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Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

2017-01-01

Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

Interspecific introgression and changes in population structure in a flatfish species complex after the Prestige accident

International Nuclear Information System (INIS)

Crego-Prieto, V.; Danancher, D.; Campo, D.; Perez, J.; Garcia-Vazquez, E.; Roca, A.

2013-01-01

Highlights: • Impact of Prestige oil spill was studied on two sympatric megrim fish populations. • Samples before and nine years after the accident were genetically analyzed. • A large proportion of post-F1 interspecific hybrids was found in the polluted area. • Both species’ population structure was altered by introgression of foreign alleles. • The spillage likely promoted a hybrid zone for Lepidorhombus in the areas affected. -- Abstract: Oil spills cause aggressive impacts on marine ecosystems affecting immense areas and the species inhabiting them. If wastes are not cleaned up properly, the remnants may affect local populations for a long time. This work focuses on the long-term impacts of the Prestige spillage that occurred off Galician coast (Spain) in November 2002. Model species were two sympatric flatfish, the megrims Lepidorhombus whiffiagonis and Lepidorhombus boscii. Samples obtained before and nine years after the Prestige accident from affected and unaffected areas were genotyped for six hypervariable nuclear markers and for the mitochondrial D-loop sequence. The results revealed a high proportion of post-F1 interspecific hybrids in the area affected, and also increased intraspecific population differentiation likely due to such localized introgression of foreign genes. These changes suggest the appearance of a hybrid zone following the accident and emphasize the need of paying special attention to potential evolutionary impacts of oil spills

The Use of Carcasses for the Analysis of Cetacean Population Genetic Structure: A Comparative Study in Two Dolphin Species

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Bilgmann, Kerstin; Möller, Luciana M.; Harcourt, Robert G.; Kemper, Catherine M.; Beheregaray, Luciano B.

2011-01-01

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully

Demography of a reintroduced population: moving toward management models for an endangered species, the whooping crane

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Servanty, Sabrina; Converse, Sarah J.; Bailey, Larissa L.

2014-01-01

The reintroduction of threatened and endangered species is now a common method for reestablishing populations. Typically, a fundamental objective of reintroduction is to establish a self-sustaining population. Estimation of demographic parameters in reintroduced populations is critical, as these estimates serve multiple purposes. First, they support evaluation of progress toward the fundamental objective via construction of population viability analyses (PVAs) to predict metrics such as probability of persistence. Second, PVAs can be expanded to support evaluation of management actions, via management modeling. Third, the estimates themselves can support evaluation of the demographic performance of the reintroduced population, e.g., via comparison with wild populations. For each of these purposes, thorough treatment of uncertainties in the estimates is critical. Recently developed statistical methods - namely, hierarchical Bayesian implementations of state-space models - allow for effective integration of different types of uncertainty in estimation. We undertook a demographic estimation effort for a reintroduced population of endangered whooping cranes with the purpose of ultimately developing a Bayesian PVA for determining progress toward establishing a self-sustaining population, and for evaluating potential management actions via a Bayesian PVA-based management model. We evaluated individual and temporal variation in demographic parameters based upon a multi-state mark-recapture model. We found that survival was relatively high across time and varied little by sex. There was some indication that survival varied by release method. Survival was similar to that observed in the wild population. Although overall reproduction in this reintroduced population is poor, birds formed social pairs when relatively young, and once a bird was in a social pair, it had a nearly 50% chance of nesting the following breeding season. Also, once a bird had nested, it had a high

An integrated modeling approach to estimating Gunnison Sage-Grouse population dynamics: combining index and demographic data.

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Davis, Amy J.; Hooten, Mevin B.; Phillips, Michael L.; Doherty, Paul F.

2014-01-01

Evaluation of population dynamics for rare and declining species is often limited to data that are sparse and/or of poor quality. Frequently, the best data available for rare bird species are based on large-scale, population count data. These data are commonly based on sampling methods that lack consistent sampling effort, do not account for detectability, and are complicated by observer bias. For some species, short-term studies of demographic rates have been conducted as well, but the data from such studies are typically analyzed separately. To utilize the strengths and minimize the weaknesses of these two data types, we developed a novel Bayesian integrated model that links population count data and population demographic data through population growth rate (λ) for Gunnison sage-grouse (Centrocercus minimus). The long-term population index data available for Gunnison sage-grouse are annual (years 1953–2012) male lek counts. An intensive demographic study was also conducted from years 2005 to 2010. We were able to reduce the variability in expected population growth rates across time, while correcting for potential small sample size bias in the demographic data. We found the population of Gunnison sage-grouse to be variable and slightly declining over the past 16 years.

Dynamics of radioecological and genetic processes in populations of mammalian model species at contamination of ecosystems

International Nuclear Information System (INIS)

Ryabokon', N.I.; Goncharova, R.I.

2008-01-01

A short review of data on the time course of radiobiological and genetic processes in natural populations of mammalian model species inhabiting radiocontaminated ecosystems over many generations is presented here. The described time-courses of biological end-points in these populations do not reflect the time course of the whole-body dose rates, but do the outcome of multiple processes, including the direct response to individual irradiation, the transgeneration transmission and accumulation of induced damages and the development of adaptation. (authors)

Population genetics and the evolution of geographic range limits in an annual plant.

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Moeller, David A; Geber, Monica A; Tiffin, Peter

2011-10-01

Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.

Host differentiation and variability of Orobanche crenata populations from legume species in Morocco as revealed by cross-infestation and molecular analysis.

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Ennami, Mounia; Briache, Fatima Zahra; Gaboun, Fatima; Abdelwahd, Rabha; Ghaouti, Lamiae; Belqadi, Loubna; Westwood, James; Mentag, Rachid

2017-08-01

Orobanche crenata represents a major biotic constraint to production of faba bean and lentil in Morocco. While this parasitic plant attacks both of these crops, the extent to which Orobanche biotypes specialise in parasitising specific crops is unknown. To address this question, we studied O. crenata that grew on different hosts and quantified their host specificity to faba bean and lentil. The virulence of O. crenata populations on each host was investigated through field trials, pot and Petri dishes assays. Genetic diversity of the parasite populations was also assessed through molecular analyses. The two legume species showed distinct patterns of specificity. Faba bean was more susceptible to both O. crenata populations, while the specificity for lentil by lentil-grown O. crenata was evident at the final stage of the parasite life cycle as shown by correspondence factorial analyses. Considerable internal variation (81%) within O. crenata populations parasitising both legume species was observed by molecular analyses, but significant divergence (19%; Ø = 0.189; P = 0.010) among the populations was detected. These results indicate that O. crenata can adapt to specific host species, which is important knowledge when developing integrated pest management practices for parasitic weed control. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Genetic structure and gene flow among Komodo dragon populations inferred by microsatellite loci analysis.

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Ciofi, C; Bruford, M W

1999-12-01

A general concern for the conservation of endangered species is the maintenance of genetic variation within populations, particularly when they become isolated and reduced in size. Estimates of gene flow and effective population size are therefore important for any conservation initiative directed to the long-term persistence of a species in its natural habitat. In the present study, 10 microsatellite loci were used to assess the level of genetic variability among populations of the Komodo dragon Varanus komodoensis. Effective population size was calculated and gene flow estimates were compared with palaeogeographic data in order to assess the degree of vulnerability of four island populations. Rinca and Flores, currently separated by an isthmus of about 200 m, retained a high level of genetic diversity and showed a high degree of genetic similarity, with gene flow values close to one migrant per generation. The island of Komodo showed by far the highest levels of genetic divergence, and its allelic distinctiveness was considered of great importance in the maintenance of genetic variability within the species. A lack of distinct alleles and low levels of gene flow and genetic variability were found for the small population of Gili Motang island, which was identified as vulnerable to stochastic threats. Our results are potentially important for both the short- and long-term management of the Komodo dragon, and are critical in view of future re-introduction or augmentation in areas where the species is now extinct or depleted.

Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

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Vickruck, J L; Richards, M H

2017-05-01

While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

Confronting species distribution model predictions with species functional traits.

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Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

2016-02-01

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

Reactive oxygen species and transcript analysis upon excess light treatment in wild-type Arabidopsis thaliana vs a photosensitive mutant lacking zeaxanthin and lutein

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Roncaglia Enrica

2011-04-01

Full Text Available Abstract Background Reactive oxygen species (ROS are unavoidable by-products of oxygenic photosynthesis, causing progressive oxidative damage and ultimately cell death. Despite their destructive activity they are also signalling molecules, priming the acclimatory response to stress stimuli. Results To investigate this role further, we exposed wild type Arabidopsis thaliana plants and the double mutant npq1lut2 to excess light. The mutant does not produce the xanthophylls lutein and zeaxanthin, whose key roles include ROS scavenging and prevention of ROS synthesis. Biochemical analysis revealed that singlet oxygen (1O2 accumulated to higher levels in the mutant while other ROS were unaffected, allowing to define the transcriptomic signature of the acclimatory response mediated by 1O2 which is enhanced by the lack of these xanthophylls species. The group of genes differentially regulated in npq1lut2 is enriched in sequences encoding chloroplast proteins involved in cell protection against the damaging effect of ROS. Among the early fine-tuned components, are proteins involved in tetrapyrrole biosynthesis, chlorophyll catabolism, protein import, folding and turnover, synthesis and membrane insertion of photosynthetic subunits. Up to now, the flu mutant was the only biological system adopted to define the regulation of gene expression by 1O2. In this work, we propose the use of mutants accumulating 1O2 by mechanisms different from those activated in flu to better identify ROS signalling. Conclusions We propose that the lack of zeaxanthin and lutein leads to 1O2 accumulation and this represents a signalling pathway in the early stages of stress acclimation, beside the response to ADP/ATP ratio and to the redox state of both plastoquinone pool. Chloroplasts respond to 1O2 accumulation by undergoing a significant change in composition and function towards a fast acclimatory response. The physiological implications of this signalling specificity are

Reactive oxygen species and transcript analysis upon excess light treatment in wild-type Arabidopsis thaliana vs a photosensitive mutant lacking zeaxanthin and lutein

Science.gov (United States)

2011-01-01

Background Reactive oxygen species (ROS) are unavoidable by-products of oxygenic photosynthesis, causing progressive oxidative damage and ultimately cell death. Despite their destructive activity they are also signalling molecules, priming the acclimatory response to stress stimuli. Results To investigate this role further, we exposed wild type Arabidopsis thaliana plants and the double mutant npq1lut2 to excess light. The mutant does not produce the xanthophylls lutein and zeaxanthin, whose key roles include ROS scavenging and prevention of ROS synthesis. Biochemical analysis revealed that singlet oxygen (1O2) accumulated to higher levels in the mutant while other ROS were unaffected, allowing to define the transcriptomic signature of the acclimatory response mediated by 1O2 which is enhanced by the lack of these xanthophylls species. The group of genes differentially regulated in npq1lut2 is enriched in sequences encoding chloroplast proteins involved in cell protection against the damaging effect of ROS. Among the early fine-tuned components, are proteins involved in tetrapyrrole biosynthesis, chlorophyll catabolism, protein import, folding and turnover, synthesis and membrane insertion of photosynthetic subunits. Up to now, the flu mutant was the only biological system adopted to define the regulation of gene expression by 1O2. In this work, we propose the use of mutants accumulating 1O2 by mechanisms different from those activated in flu to better identify ROS signalling. Conclusions We propose that the lack of zeaxanthin and lutein leads to 1O2 accumulation and this represents a signalling pathway in the early stages of stress acclimation, beside the response to ADP/ATP ratio and to the redox state of both plastoquinone pool. Chloroplasts respond to 1O2 accumulation by undergoing a significant change in composition and function towards a fast acclimatory response. The physiological implications of this signalling specificity are discussed. PMID:21481232

Change Points in the Population Trends of Aerial-Insectivorous Birds in North America: Synchronized in Time across Species and Regions.

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Adam C Smith

Full Text Available North American populations of aerial insectivorous birds are in steep decline. Aerial insectivores (AI are a group of bird species that feed almost exclusively on insects in flight, and include swallows, swifts, nightjars, and flycatchers. The causes of the declines are not well understood. Indeed, it is not clear when the declines began, or whether the declines are shared across all species in the group (e.g., caused by changes in flying insect populations or specific to each species (e.g., caused by changes in species' breeding habitat. A recent study suggested that population trends of aerial insectivores changed for the worse in the 1980s. If there was such a change point in trends of the group, understanding its timing and geographic pattern could help identify potential causes of the decline. We used a hierarchical Bayesian, penalized regression spline, change point model to estimate group-level change points in the trends of 22 species of AI, across 153 geographic strata of North America. We found evidence for group-level change points in 85% of the strata. Change points for flycatchers (FC were distinct from those for swallows, swifts and nightjars (SSN across North America, except in the Northeast, where all AI shared the same group-level change points. During the 1980s, there was a negative change point across most of North America, in the trends of SSN. For FC, the group-level change points were more geographically variable, and in many regions there were two: a positive change point followed by a negative change point. This group-level synchrony in AI population trends is likely evidence of a response to a common environmental factor(s with similar effects on many species across broad spatial extents. The timing and geographic patterns of the change points that we identify here should provide a spring-board for research into the causes behind aerial insectivore declines.

78 FR 66139 - Endangered and Threatened Species; Delisting of the Eastern Distinct Population Segment of...

Science.gov (United States)

2013-11-04

... likely to cause the eastern DPS of Steller sea lion to become in danger of extinction throughout all or a... low and not likely to cause this population to become in danger of extinction within the foreseeable... threatened species under the ESA: It is not in danger of extinction or likely to become so within the...

Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.

Science.gov (United States)

Kim, HyunJung; Jung, Janelle; Singh, Namrata; Greenberg, Anthony; Doyle, Jeff J; Tyagi, Wricha; Chung, Jong-Wook; Kimball, Jennifer; Hamilton, Ruaraidh Sackville; McCouch, Susan R

2016-12-01

Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2  = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.

Dispersal, dormancy and life-history tradeoffs at the individual, population and species levels in southern African Asteraceae.

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de Waal, Caroli; Anderson, Bruce; Ellis, Allan G

2016-04-01

Dispersal and dormancy are important risk-reducing strategies in unpredictable environments. Negative covariation between these strategies is theoretically expected, but empirical evidence is limited and inconsistent. Moreover, covariation may be affected by other life-history traits and may vary across levels of biological organization. We assessed dispersal (vertical fall time of fruits, a proxy for wind dispersal ability) and dormancy (germination fractions measured during germination trials) in populations of 15 annual and 12 perennial wind-dispersed species in six Asteraceae genera from South Africa. Dormancy was higher in annuals than in perennials, whereas fall time was largely determined by evolutionary history. Controlling for phylogeny, dispersal and dormancy was negatively associated across species and life-history categories. Negative covariation between dispersal and dormancy was not evident at either the individual level (except for seed heteromorphic species) or the population level. Our study provides rare empirical support for the theoretical expectation of tradeoffs between dormancy and the alternative risk-reducing strategies, perenniality and dispersal, but refutes the expectation of increased dispersability in perennials. Although negative covariation between dispersal and dormancy at the species level appears not to be a simple consequence of upscaling individual-level mechanistic tradeoffs, our findings suggest that selection for one strategy may constrain evolution of the other. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Gene flow and population subdivision in a pantropical plant with sea-drifted seeds Hibiscus tiliaceus and its allied species: evidence from microsatellite analyses.

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Takayama, Koji; Tateishi, Yoichi; Murata, Jin; Kajita, Tadashi

2008-06-01

The genetic differentiation and structure of Hibiscus tiliaceus, a pantropical plant with sea-drifted seeds, and four allied species were studied using six microsatellite markers. A low level of genetic differentiation was observed among H. tiliaceus populations in the Pacific and Indian Ocean regions, similar to the results of a previous chloroplast DNA (cpDNA) study. Frequent gene flow by long-distance seed dispersal is responsible for species integration of H. tiliaceus in the wide distribution range. On the other hand, highly differentiated populations of H. tiliaceus were detected in West Africa, as well as of Hibiscus pernambucensis in southern Brazil. In the former populations, the African continent may be a geographical barrier that prevents gene flow by sea-drifted seeds. In the latter populations, although there are no known land barriers, the bifurcating South Equatorial Current at the north-eastern horn of Brazil can be a potential barrier to gene flow and may promote the genetic differentiation of these populations. Our results also suggest clear species segregation between H. tiliaceus and H. pernambucensis, which confirms the introgression scenario between these two species that was suggested by a previous cpDNA study. Our results also provide good evidence for recent transatlantic long-distance seed dispersal by sea current. Despite the distinct geographical structure observed in the cpDNA haplotypes, a low level of genetic differentiation was found between Pacific and Atlantic populations of H. pernambucensis, which could be caused by transisthmian gene flow.

Avian malaria in Hawaiian forest birds: Infection and population impacts across species and elevations

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Samuel, Michael D.; Woodworth, Bethany L.; Atkinson, Carter T.; Hart, P. J.; LaPointe, Dennis

2015-01-01

Wildlife diseases can present significant threats to ecological systems and biological diversity, as well as domestic animal and human health. However, determining the dynamics of wildlife diseases and understanding the impact on host populations is a significant challenge. In Hawai‘i, there is ample circumstantial evidence that introduced avian malaria (Plasmodium relictum) has played an important role in the decline and extinction of many native forest birds. However, few studies have attempted to estimate disease transmission and mortality, survival, and individual species impacts in this distinctive ecosystem. We combined multi-state capture-recapture (longitudinal) models with cumulative age-prevalence (cross-sectional) models to evaluate these patterns in Apapane, Hawai‘i Amakihi, and Iiwi in low-, mid-, and high-elevation forests on the island of Hawai‘i based on four longitudinal studies of 3–7 years in length. We found species-specific patterns of malaria prevalence, transmission, and mortality rates that varied among elevations, likely in response to ecological factors that drive mosquito abundance. Malaria infection was highest at low elevations, moderate at mid elevations, and limited in high-elevation forests. Infection rates were highest for Iiwi and Apapane, likely contributing to the absence of these species in low-elevation forests. Adult malaria fatality rates were highest for Iiwi, intermediate for Amakihi at mid and high elevations, and lower for Apapane; low-elevation Amakihi had the lowest malaria fatality, providing strong evidence of malaria tolerance in this low-elevation population. Our study indicates that hatch-year birds may have greater malaria infection and/or fatality rates than adults. Our study also found that mosquitoes prefer feeding on Amakihi rather than Apapane, but Apapane are likely a more important reservoir for malaria transmission to mosquitoes. Our approach, based on host abundance and infection rates, may be an

Influence of demography and environment on persistence in toad populations

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Lambert, Brad A.; Schorr, Robert A.; Schneider, Scott C.; Muths, Erin L.

2016-01-01

Effective conservation of rare species requires an understanding of how potential threats affect population dynamics. Unfortunately, information about population demographics prior to threats (i.e., baseline data) is lacking for many species. Perturbations, caused by climate change, disease, or other stressors can lead to population declines and heightened conservation concerns. Boreal toads (Anaxyrus boreas boreas) have undergone rangewide declines due mostly to the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), with only a few sizable populations remaining in the southern Rocky Mountains, USA, that are disease-free. Despite the apparent region-wide occurrence of Bd, our focal populations in central Colorado were disease free over a 14-year capture-mark-recapture study until the recent discovery of Bd at one of the sites. We used recapture data and the Pradel reverse-time model to assess the influence of environmental and site-specific conditions on survival and recruitment. We then forecast changes in the toad populations with 2 growth models; one using an average lambda value to initiate the projection, and one using the most recent value to capture potential effects of the incursion of disease into the system. Adult survival was consistently high at the 3 sites, whereas recruitment was more variable and markedly low at 1 site. We found that active season moisture, active season length, and breeding shallows were important factors in estimating recruitment. Population growth models indicated a slight increase at 1 site but decreasing trends at the 2 other sites, possibly influenced by low recruitment. Insight into declining species management can be gained from information on survival and recruitment and how site-specific environmental factors influence these demographic parameters. Our data are particularly useful because they provide baseline data on demographics in populations before a disease outbreak and enhance our ability to detect changes

When is a species declining? Optimizing survey effort to detect population changes in reptiles.

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David Sewell

Full Text Available Biodiversity monitoring programs need to be designed so that population changes can be detected reliably. This can be problematical for species that are cryptic and have imperfect detection. We used occupancy modeling and power analysis to optimize the survey design for reptile monitoring programs in the UK. Surveys were carried out six times a year in 2009-2010 at multiple sites. Four out of the six species--grass snake, adder, common lizard, slow-worm -were encountered during every survey from March-September. The exceptions were the two rarest species--sand lizard and smooth snake--which were not encountered in July 2009 and March 2010 respectively. The most frequently encountered and most easily detected species was the slow-worm. For the four widespread reptile species in the UK, three to four survey visits that used a combination of directed transect walks and artificial cover objects resulted in 95% certainty that a species would be detected if present. Using artificial cover objects was an effective detection method for most species, considerably increased the detection rate of some, and reduced misidentifications. To achieve an 85% power to detect a decline in any of the four widespread species when the true decline is 15%, three surveys at a total of 886 sampling sites, or four surveys at a total of 688 sites would be required. The sampling effort needed reduces to 212 sites surveyed three times, or 167 sites surveyed four times, if the target is to detect a true decline of 30% with the same power. The results obtained can be used to refine reptile survey protocols in the UK and elsewhere. On a wider scale, the occupancy study design approach can be used to optimize survey effort and help set targets for conservation outcomes for regional or national biodiversity assessments.

Molecular assessment of Podarcis sicula populations in Britain, Greece and Turkey reinforces a multiple-origin invasion pattern in this species

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Iolanda Silva-Rocha

2014-12-01

Full Text Available Biological invasions are a challenge to conservation and constitute a threat to biodiversity worldwide. The Italian wall lizard Podarcis sicula has been widely introduced, and seems capable of adapting to most of the regions where it is established and to impact on native biota. Here we construct a phylogenetic framework to assess the origin of the introduced populations in the United Kingdom, Greece and Turkey comparing cytochrome-b gene sequences of lizards from five locations to published sequences from the native range and other non-native locations. The results support an origin from central Italy for the United Kingdom population, from the Adriatic region for the Greek population and from Calabria for the population from Turkey. These results emphasise the multiple-source pattern of introduction of this species identified in previous studies. The improvement in the knowledge of the origin and pathways by which invaders arrive in new areas, as well as the monitoring of their populations, are crucial for successful strategies to deal with exotic species.

Persistence and extinction of a stochastic single-species population model in a polluted environment with impulsive toxicant input

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Meng Liu

2013-10-01

Full Text Available A stochastic single-species population system in a polluted environment with impulsive toxicant input is proposed and studied. Sufficient conditions for extinction, non-persistence in the mean, strong persistence in the mean and stochastic permanence of the population are established. The threshold between strong persistence in the mean and extinction is obtained. Some simulation figures are introduced to illustrate the main results.

Effects of climate change on a mutualistic coastal species: Recovery from typhoon damages and risks of population erosion.

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Chiu, Yu-Ting; Bain, Anthony; Deng, Shu-Lin; Ho, Yi-Chiao; Chen, Wen-Hsuan; Tzeng, Hsy-Yu

2017-01-01

Presently, climate change has increased the frequency of extreme meteorological events such as tropical cyclones. In the western Pacific basin, these cyclones are called typhoons, and in this area, around Taiwan Island, their frequency has almost doubled since 2000. When approaching landmasses, typhoons have devastating effects on coastal vegetation. The increased frequency of these events has challenged the survival of coastal plant species and their posttyphoon recovery. In this study, a population of coastal gynodioecious Ficus pedunculosa var. mearnsii (Mearns fig) was surveyed for two years to investigate its recovery after Typhoon Morakot, which occurred in August 2009. Similar to all the Ficus species, the Mearns fig has an obligate mutualistic association with pollinating fig wasp species, which requires syconia (the closed Ficus inflorescence) to complete its life cycle. Moreover, male gynodioecious fig species produces both pollen and pollen vectors, whereas the female counterpart produces only seeds. The recovery of the Mearns fig was observed to be rapid, with the production of both leaves and syconia. The syconium:leaf ratio was greater for male trees than for female trees, indicating the importance of syconium production for the wasp survival. Pollinating wasps live for approximately 1 day; therefore, receptive syconia are crucial. Every typhoon season, few typhoons pass by the coasts where the Mearns fig grows, destroying all the leaves and syconia. In this paper, we highlight the potential diminution of the fig population that can lead to the extinction of the mutualistic pair of species. The effects of climate change on coastal species warrant wider surveys.

Effects of climate change on a mutualistic coastal species: Recovery from typhoon damages and risks of population erosion.

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Yu-Ting Chiu

Full Text Available Presently, climate change has increased the frequency of extreme meteorological events such as tropical cyclones. In the western Pacific basin, these cyclones are called typhoons, and in this area, around Taiwan Island, their frequency has almost doubled since 2000. When approaching landmasses, typhoons have devastating effects on coastal vegetation. The increased frequency of these events has challenged the survival of coastal plant species and their posttyphoon recovery. In this study, a population of coastal gynodioecious Ficus pedunculosa var. mearnsii (Mearns fig was surveyed for two years to investigate its recovery after Typhoon Morakot, which occurred in August 2009. Similar to all the Ficus species, the Mearns fig has an obligate mutualistic association with pollinating fig wasp species, which requires syconia (the closed Ficus inflorescence to complete its life cycle. Moreover, male gynodioecious fig species produces both pollen and pollen vectors, whereas the female counterpart produces only seeds. The recovery of the Mearns fig was observed to be rapid, with the production of both leaves and syconia. The syconium:leaf ratio was greater for male trees than for female trees, indicating the importance of syconium production for the wasp survival. Pollinating wasps live for approximately 1 day; therefore, receptive syconia are crucial. Every typhoon season, few typhoons pass by the coasts where the Mearns fig grows, destroying all the leaves and syconia. In this paper, we highlight the potential diminution of the fig population that can lead to the extinction of the mutualistic pair of species. The effects of climate change on coastal species warrant wider surveys.

Estimation of Potential Population Level Effects of Contaminants on Wildlife; FINAL

International Nuclear Information System (INIS)

Loar, J.M.

2001-01-01

The objective of this project is to provide DOE with improved methods to assess risks from contaminants to wildlife populations. The current approach for wildlife risk assessment consists of comparison of contaminant exposure estimates for individual animals to literature-derived toxicity test endpoints. These test endpoints are assumed to estimate thresholds for population-level effects. Moreover, species sensitivities to contaminants is one of several criteria to be considered when selecting assessment endpoints (EPA 1997 and 1998), yet data on the sensitivities of many birds and mammals are lacking. The uncertainties associated with this approach are considerable. First, because toxicity data are not available for most potential wildlife endpoint species, extrapolation of toxicity data from test species to the species of interest is required. There is no consensus on the most appropriate extrapolation method. Second, toxicity data are represented as statistical measures (e.g., NOAEL s or LOAELs) that provide no information on the nature or magnitude of effects. The level of effect is an artifact of the replication and dosing regime employed, and does not indicate how effects might increase with increasing exposure. Consequently, slight exceedance of a LOAEL is not distinguished from greatly exceeding it. Third, the relationship of toxic effects on individuals to effects on populations is poorly estimated by existing methods. It is assumed that if the exposure of individuals exceeds levels associated with impaired reproduction, then population level effects are likely. Uncertainty associated with this assumption is large because depending on the reproductive strategy of a given species, comparable levels of reproductive impairment may result in dramatically different population-level responses. This project included several tasks to address these problems: (1) investigation of the validity of the current allometric scaling approach for interspecies extrapolation

Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae detect gene flow between island populations and genetic diversity loss

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Sammler Svenja

2012-10-01

Full Text Available Abstract Background The Visayan Tarictic Hornbill (Penelopides panini and the Walden’s Hornbill (Aceros waldeni are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp of the mitochondrial control region I and at 12–19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay, and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant sister taxa, the Luzon Tarictic Hornbill (P. manillae from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A

A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

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Robert J Elshire

Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

Assessing three fish species ecological status in Colorado River, Grand Canyon based on physical habitat and population models.

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Yao, Weiwei; Chen, Yuansheng

2018-04-01

Colorado River is a unique ecosystem and provides important ecological services such as habitat for fish species as well as water power energy supplies. River management for this ecosystem requires assessment and decision support tools for fish which involves protecting, restoring as well as forecasting of future conditions. In this paper, a habitat and population model was developed and used to determine the levels of fish habitat suitability and population density in Colorado River between Lees Ferry and Lake Mead. The short term target fish populations are also predicted based on native fish recovery strategy. This model has been developed by combining hydrodynamics, heat transfer and sediment transport models with a habitat suitability index model and then coupling with habitat model into life stage population model. The fish were divided into four life stages according to the fish length. Three most abundant and typical native and non-native fish were selected as target species, which are rainbow trout (Oncorhynchus mykiss), brown trout (Salmo trutta) and flannelmouth sucker (Catostomus latipinnis). Flow velocity, water depth, water temperature and substrates were used as the suitability indicators in habitat model and overall suitability index (OSI) as well as weight usable area (WUA) was used as an indicator in population model. A comparison was made between simulated fish population alteration and surveyed fish number fluctuation during 2000 to 2009. The application of this habitat and population model indicates that this model can be accurate present habitat situation and targets fish population dynamics of in the study areas. The analysis also indicates the flannelmouth sucker population will steadily increase while the rainbow trout will decrease based on the native fish recovery scheme. Copyright © 2018. Published by Elsevier Inc.

Live Fast, Die Young: Experimental Evidence of Population Extinction Risk due to Climate Change

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Bestion, Elvire; Teyssier, Aimeric; Richard, Murielle; Clobert, Jean; Cote, Julien

2015-01-01

Evidence has accumulated in recent decades on the drastic impact of climate change on biodiversity. Warming temperatures have induced changes in species physiology, phenology, and have decreased body size. Such modifications can impact population dynamics and could lead to changes in life cycle and demography. More specifically, conceptual frameworks predict that global warming will severely threaten tropical ectotherms while temperate ectotherms should resist or even benefit from higher temperatures. However, experimental studies measuring the impacts of future warming trends on temperate ectotherms' life cycle and population persistence are lacking. Here we investigate the impacts of future climates on a model vertebrate ectotherm species using a large-scale warming experiment. We manipulated climatic conditions in 18 seminatural populations over two years to obtain a present climate treatment and a warm climate treatment matching IPCC predictions for future climate. Warmer temperatures caused a faster body growth, an earlier reproductive onset, and an increased voltinism, leading to a highly accelerated life cycle but also to a decrease in adult survival. A matrix population model predicts that warm climate populations in our experiment should go extinct in around 20 y. Comparing our experimental climatic conditions to conditions encountered by populations across Europe, we suggest that warming climates should threaten a significant number of populations at the southern range of the distribution. Our findings stress the importance of experimental approaches on the entire life cycle to more accurately predict population and species persistence in future climates. PMID:26501958

Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove.

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Calderón, Luciano; Campagna, Leonardo; Wilke, Thomas; Lormee, Hervé; Eraud, Cyril; Dunn, Jenny C; Rocha, Gregorio; Zehtindjiev, Pavel; Bakaloudis, Dimitrios E; Metzger, Benjamin; Cecere, Jacopo G; Marx, Melanie; Quillfeldt, Petra

2016-11-07

Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.

Invasive species and biodiversity crises: testing the link in the late devonian.

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Alycia L Stigall

Full Text Available During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the

Invasive species and biodiversity crises: testing the link in the late devonian.

Science.gov (United States)

Stigall, Alycia L

2010-12-29

During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity

Phylogeographical patterns among Mediterranean sepiolid squids and their Vibrio symbionts: environment drives specificity among sympatric species.

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Zamborsky, D J; Nishiguchi, M K

2011-01-01

Bobtail squid from the genera Sepiola and Rondeletiola (Cephalopoda: Sepiolidae) form mutualistic associations with luminous Gram-negative bacteria (Gammaproteobacteria: Vibrionaceae) from the genera Vibrio and Photobacterium. Symbiotic bacteria proliferate inside a bilobed light organ until they are actively expelled by the host into the surrounding environment on a diel basis. This event results in a dynamic symbiont population with the potential to establish the symbiosis with newly hatched sterile (axenic) juvenile sepiolids. In this study, we examined the genetic diversity found in populations of sympatric sepiolid squid species and their symbionts by the use of nested clade analysis with multiple gene analyses. Variation found in the distribution of different species of symbiotic bacteria suggests a strong influence of abiotic factors in the local environment, affecting bacterial distribution among sympatric populations of hosts. These abiotic factors include temperature differences incurred by a shallow thermocline, as well as a lack of strong coastal water movement accompanied by seasonal temperature changes in overlapping niches. Host populations are stable and do not appear to have a significant role in the formation of symbiont populations relative to their distribution across the Mediterranean Sea. Additionally, all squid species examined (Sepiola affinis, S. robusta, S. ligulata, S. intermedia, and Rondeletiola minor) are genetically distinct from one another regardless of location and demonstrate very little intraspecific variation within species. These findings suggest that physical boundaries and distance in relation to population size, and not host specificity, are important factors in limiting or defining gene flow within sympatric marine squids and their associated bacterial symbionts in the Mediterranean Sea.

Genetic evidence of population structuring in the neotropical freshwater fish Brycon hilarii (Valenciennes, 1850

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A Sanches

Full Text Available Brycon hilarii is a migratory fish widely distributed throughout the Paraguay River Basin. It is appreciated in sport fishing and for its superior meat quality. It is also the main species for tourist attraction in the Bonito region (State of Mato Grosso do Sul, Brazil. Considering the lack of information on the genetic structure of the fish of this species, the aim of the present study was to detect the genetic variability of Brycon hilarii through RAPD markers. A total of eighty specimens collected in different seasons at four sites of the Miranda River sub-basin (Paraguay River Basin, Brazil were used for analysis. The results of genetic similarity, Shannon diversity, and AMOVA revealed differences between the sampling sites. Through AMOVA, differences between populations were more evident among the animals collected during the non-reproductive season, corresponding to a time of less movement of these fish. A population structuring model in which B. hilarii appears organized into genetically differentiated reproductive units that coexist and co-migrate through the studied system was suggested, contrasting the currently accepted idea that freshwater migratory fish form large panmictic populations in a determined hydrographic system. Despite the lack of a complete picture regarding the distribution of B. hilarii in the studied region, this initial idea on its population genetic structure could be an important contribution to providing aid for management and conservation programs of these fish.

Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions.

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Garnica, Sigisfredo; Spahn, Philipp; Oertel, Bernhard; Ammirati, Joseph; Oberwinkler, Franz

2011-07-19

Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred evolutionary histories of four species, 1) C. arcuatorum, 2) C. aureofulvus, 3) C. elegantior and 4) C. napus, from populations distributed throughout the Old World, and portions of the New World (Central- and North America) based on genetic variation of 154 haplotype internal transcribed spacer (ITS) sequences from 83 population samples. By describing the population structure of these species across their geographical distribution, we attempt to identify their historical migration and patterns of diversification. Models of population structure from nested clade, demographic and coalescent-based analyses revealed genetically differentiated and geographically structured haplotypes in C. arcuatorum and C. elegantior, while C. aureofulvus showed considerably less population structure and C. napus lacked sufficient genetic differentiation to resolve any population structure. Disjunct populations within C. arcuatorum, C. aureofulvus and C. elegantior show little or no morphological differentiation, whereas in C. napus there is a high level of homoplasy and phenotypic plasticity for veil and lamellae colour. The ITS sequences of the type specimens of C. albobrunnoides and C. albobrunnoides var. violaceovelatus were identical to one another and are treated as one species with a wider range of geographic distribution under C. napus. Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1) a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric populations in the New World; 2) two divergent lineages in C

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama.

Science.gov (United States)

Crawford, Andrew J; Lips, Karen R; Bermingham, Eldredge

2010-08-03

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis. Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

Invader Relative Impact Potential: a new metric to understand and predict the ecological impacts of existing, emerging and future invasive alien species

OpenAIRE

Dick, JTA; Laverty, C; Lennon, JJ; Barrios-O'Neill, D; Mensink, PJ; Britton, JR; Medoc, V; Boets, P; Alexander, ME; Taylor, NG; Dunn, AM; Hatcher, MJ; Rosewarne, PJ; Crookes, S; MacIsaac, HJ

2017-01-01

1. Predictions of the identities and ecological impacts of invasive alien species are critical for risk assessment, but presently we lack universal and standardized metrics that reliably predict the likelihood and degree of impact of such invaders (i.e. measurable changes in populations of affected species). This need is especially pressing for emerging and potential future invaders that have no invasion history. Such a metric would also ideally apply across diverse taxonomic and trophic gro...

Setting population targets for mammals using body mass as a predictor of population persistence.

Science.gov (United States)

Hilbers, Jelle P; Santini, Luca; Visconti, Piero; Schipper, Aafke M; Pinto, Cecilia; Rondinini, Carlo; Huijbregts, Mark A J

2017-04-01

Conservation planning and biodiversity assessments need quantitative targets to optimize planning options and assess the adequacy of current species protection. However, targets aiming at persistence require population-specific data, which limit their use in favor of fixed and nonspecific targets, likely leading to unequal distribution of conservation efforts among species. We devised a method to derive equitable population targets; that is, quantitative targets of population size that ensure equal probabilities of persistence across a set of species and that can be easily inferred from species-specific traits. In our method, we used models of population dynamics across a range of life-history traits related to species' body mass to estimate minimum viable population targets. We applied our method to a range of body masses of mammals, from 2 g to 3825 kg. The minimum viable population targets decreased asymptotically with increasing body mass and were on the same order of magnitude as minimum viable population estimates from species- and context-specific studies. Our approach provides a compromise between pragmatic, nonspecific population targets and detailed context-specific estimates of population viability for which only limited data are available. It enables a first estimation of species-specific population targets based on a readily available trait and thus allows setting equitable targets for population persistence in large-scale and multispecies conservation assessments and planning. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

Science.gov (United States)

Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

Blinded by the bright: a lack of congruence between colour morphs, phylogeography and taxonomy for a cosmopolitan Indo-Pacific butterflyfish, Chaetodon auriga

KAUST Repository

DiBattista, Joseph

2015-07-01

Aim: We assess genetic differentiation among biogeographical provinces and colour morphs of the threadfin butterflyfish, Chaetodon auriga. This species is among the most broadly distributed butterflyfishes in the world, occurring on reefs from the Red Sea and western Indian Ocean to French Polynesia and Hawai\\'i. The Red Sea form lacks a conspicuous \\'eye-spot\\' on the dorsal fin, which may indicate an evolutionary distinction. Location: Red Sea, Indian Ocean and Pacific Ocean. Methods: Specimens were obtained at 17 locations (n = 358) spanning the entire range of this species. The genetic data included 669 base pairs of mitochondrial DNA (mtDNA) cytochrome b and allele frequencies at six microsatellite loci. Analysis of molecular variance, structure plots, haplotype networks and estimates of population expansion time were used to assess phylogeographical patterns. Results: Population structure was low overall, but significant and concordant between molecular markers (mtDNA: ΦST = 0.027, P < 0.001; microsatellites: FST = 0.023, P < 0.001). Significant population-level partitions were only detected at peripheral locations including the Red Sea and Hawai\\'i. Population expansion events in the Red Sea and Socotra are older (111,940-223,881 years) relative to all other sites (16,343-87,910 years). Main conclusions: We find little genetic evidence to support an evolutionary partition of a previously proposed Red Sea subspecies. The oldest estimate of population expansion in the Red Sea and adjacent Gulf of Aden indicates a putative refuge in this region during Pleistocene glacial cycles. The finding of population separations at the limits of the range, in the Red Sea and Hawai\\'i, is consistent with peripheral speciation. © 2015 John Wiley & Sons Ltd.

Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa in Brazil

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Camila L. Clozato

Full Text Available Abstract The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758 belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b and two nuclear markers (AMELY and RAG2. We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil.

Science.gov (United States)

Clozato, Camila L; Miranda, Flávia R; Lara-Ruiz, Paula; Collevatti, Rosane G; Santos, Fabrício R

2017-01-01

The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b) and two nuclear markers (AMELY and RAG2). We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

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Guo Yufang

2012-11-01

Full Text Available Abstract Background Cultivated peanut or groundnut (Arachis hypogaea L. is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40. Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20, which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons derived from 70,771 long-read (Sanger and 270,957 short-read (454 sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639 and GKBSPSc 30081 (PI 468327 in the B-genome species A. batizocoi. A high degree of macrosynteny was observed

Population Development of Baltic Bird Species: Great Cormorant (Phalacrocorax carbo sinensis) - Update with results from 2011

DEFF Research Database (Denmark)

Herrmann, Christof; Bregnballe, Thomas; Larsson, Kjell

2011-01-01

pair numbers started to increase during the second half of the 1970s. During the 1980s, the Cormorant started to expand its range towards the northern and eastern parts of the Baltic. Currently, the species is present in the whole Baltic Sea area, including the northern parts of the Gulf of Bothnia....... After a decade of exponential growth, the breeding population of the Cormorant has stabilized in the south-western Baltic (Denmark and the northern Federal States of Germany - Schleswig-Holstein and Mecklenburg-Western Pomerania) in the 1990s, but breeding populations are still growing in the central...

Geographic variation in floral traits and the capacity of autonomous selfing across allopatric and sympatric populations of two closely related Centaurium species.

Science.gov (United States)

Schouppe, Dorien; Brys, Rein; Vallejo-Marin, Mario; Jacquemyn, Hans

2017-04-21

Floral traits and the relative contribution of autonomous selfing to total seed set varies geographically and is often driven by the availability and abundance of suitable pollinators and/or the presence of co-flowering relatives. In the latter case, competition for pollinator services and costs of hybridization can select for floral traits that reduce interspecific gene flow and contribute to prezygotic isolation, potentially leading to geographic variation in floral divergence between allopatric and sympatric populations. In this study, we investigated variation in floral traits and its implications on the capacity of autonomous selfing in both allopatric and sympatric populations of two closely related Centaurium species(Gentianaceae) across two distinct geographic regions(UK and mainland Europe). Although the magnitude and direction of floral differentiation varied between regions, sympatric populations were always significantly more divergent in floral traits and the capacity to self autonomously than allopatric populations. These results indicate that mating systems can vary substantially within a species and that the joint occurrence of plant species can have a major impact on floral morphology and capacity of autonomous selfing, most likely as a way to reduce the probability of interspecific interference.

Population structure and genetic variability of mainland and insular populations of the Neotropical water rat, Nectomys squamipes (Rodentia, Sigmodontinae

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Francisca C. Almeida

2005-12-01

Full Text Available Seven microsatellite loci were used to investigate the genetic variability and structure of six mainland and two island populations of the Neotropical water rat Nectomys squamipes, a South American semi-aquatic rodent species with a wide distribution. High levels of variability were found within mainland populations while island populations were less variable but the more differentiated in respect to allele number and frequency. The time of biological divergence between mainland and island populations coincided with geological data. A significant geographic structure was found in mainland populations (theta = 0.099; rho = 0.086 although the degree of differentiation was relatively low in respect to the distance between surveyed localities (24 to 740 km. Genetic and geographic distances were not positively correlated as previously found with random amplified polymorphic DNA (RAPD markers. Significant but low genetic differentiation in the mainland and lack of isolation by distance can be explained by large population size and/or recent population expansion. Additionally, the agreement between the age of geologic events (sea level fluctuations and divergence times for insular populations points to a good reference for molecular clock calibration to associate recent environmental changes and the distribution pattern of small mammals in the Brazilian Atlantic Forest.

Population genetic structure of a centipede species with high levels of developmental instability.

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Giuseppe Fusco

Full Text Available European populations of the geophilomorph centipede Haplophilus subterraneus show a high proportion of individuals with morphological anomalies, suggesting high levels of developmental instability. The broad geographic distribution of this phenomenon seems to exclude local environmental causes, but the source of instability is still to be identified. The goal of the present study was to collect quantitative data on the occurrence of phenodeviants in different populations, along with data on the patterns of genetic variation within and between populations, in order to investigate possible association between developmental instability and genetic features. In a sample of 11 populations of H. subterraneus, distributed in western and central Europe, we looked for phenodeviants, in particular with respect to trunk morphology, and studied genetic variation through the genotyping of microsatellite loci. Overall, no support was found to the idea that developmental instability in H. subterraneus is related to a specific patterns of genetic variation, including inbreeding estimates. We identified a major genetic partition that subdivides French populations from the others, and a low divergence among northwestern areas, which are possibly related to the post-glacial recolonization from southern refugia and/or to recent anthropogenic soil displacements. A weak correlation between individual number of leg bearing segments and the occurrence of trunk anomalies seems to support a trade-off between these two developmental traits. These results, complemented by preliminary data on developmental stability in two related species, suggest that the phenomenon has not a simple taxonomic distribution, while it exhibits an apparent localization in central and eastern Europe.

The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

Science.gov (United States)

Pomilla, Cristina; Amaral, Ana R; Collins, Tim; Minton, Gianna; Findlay, Ken; Leslie, Matthew S; Ponnampalam, Louisa; Baldwin, Robert; Rosenbaum, Howard

2014-01-01

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

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Cristina Pomilla

Full Text Available A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

Integrated analysis for population estimation, management impact evaluation, and decision-making for a declining species

Science.gov (United States)

Crawford, Brian A.; Moore, Clinton; Norton, Terry M.; Maerz, John C.

2018-01-01

A challenge for making conservation decisions is predicting how wildlife populations respond to multiple, concurrent threats and potential management strategies, usually under substantial uncertainty. Integrated modeling approaches can improve estimation of demographic rates necessary for making predictions, even for rare or cryptic species with sparse data, but their use in management applications is limited. We developed integrated models for a population of diamondback terrapins (Malaclemys terrapin) impacted by road-associated threats to (i) jointly estimate demographic rates from two mark-recapture datasets, while directly estimating road mortality and the impact of management actions deployed during the study; and (ii) project the population using population viability analysis under simulated management strategies to inform decision-making. Without management, population extirpation was nearly certain due to demographic impacts of road mortality, predators, and vegetation. Installation of novel flashing signage increased survival of terrapins that crossed roads by 30%. Signage, along with small roadside barriers installed during the study, increased population persistence probability, but the population was still predicted to decline. Management strategies that included actions targeting multiple threats and demographic rates resulted in the highest persistence probability, and roadside barriers, which increased adult survival, were predicted to increase persistence more than other actions. Our results support earlier findings showing mitigation of multiple threats is likely required to increase the viability of declining populations. Our approach illustrates how integrated models may be adapted to use limited data efficiently, represent system complexity, evaluate impacts of threats and management actions, and provide decision-relevant information for conservation of at-risk populations.

An emperor penguin population estimate: the first global, synoptic survey of a species from space.

Science.gov (United States)

Fretwell, Peter T; Larue, Michelle A; Morin, Paul; Kooyman, Gerald L; Wienecke, Barbara; Ratcliffe, Norman; Fox, Adrian J; Fleming, Andrew H; Porter, Claire; Trathan, Phil N

2012-01-01

Our aim was to estimate the population of emperor penguins (Aptenodytes fosteri) using a single synoptic survey. We examined the whole continental coastline of Antarctica using a combination of medium resolution and Very High Resolution (VHR) satellite imagery to identify emperor penguin colony locations. Where colonies were identified, VHR imagery was obtained in the 2009 breeding season. The remotely-sensed images were then analysed using a supervised classification method to separate penguins from snow, shadow and guano. Actual counts of penguins from eleven ground truthing sites were used to convert these classified areas into numbers of penguins using a robust regression algorithm.We found four new colonies and confirmed the location of three previously suspected sites giving a total number of emperor penguin breeding colonies of 46. We estimated the breeding population of emperor penguins at each colony during 2009 and provide a population estimate of ~238,000 breeding pairs (compared with the last previously published count of 135,000-175,000 pairs). Based on published values of the relationship between breeders and non-breeders, this translates to a total population of ~595,000 adult birds.There is a growing consensus in the literature that global and regional emperor penguin populations will be affected by changing climate, a driver thought to be critical to their future survival. However, a complete understanding is severely limited by the lack of detailed knowledge about much of their ecology, and importantly a poor understanding of their total breeding population. To address the second of these issues, our work now provides a comprehensive estimate of the total breeding population that can be used in future population models and will provide a baseline for long-term research.

Population Connectivity Measures of Fishery-Targeted Coral Reef Species to Inform Marine Reserve Network Design in Fiji.

Science.gov (United States)

Eastwood, Erin K; López, Elora H; Drew, Joshua A

2016-01-25

Coral reef fish serve as food sources to coastal communities worldwide, yet are vulnerable to mounting anthropogenic pressures like overfishing and climate change. Marine reserve networks have become important tools for mitigating these pressures, and one of the most critical factors in determining their spatial design is the degree of connectivity among different populations of species prioritized for protection. To help inform the spatial design of an expanded reserve network in Fiji, we used rapidly evolving mitochondrial genes to investigate connectivity patterns of three coral reef species targeted by fisheries in Fiji: Epinephelus merra (Serranidae), Halichoeres trimaculatus (Labridae), and Holothuria atra (Holothuriidae). The two fish species, E. merra and Ha. trimaculatus, exhibited low genetic structuring and high amounts of gene flow, whereas the sea cucumber Ho. atra displayed high genetic partitioning and predominantly westward gene flow. The idiosyncratic patterns observed among these species indicate that patterns of connectivity in Fiji are likely determined by a combination of oceanographic and ecological characteristics. Our data indicate that in the cases of species with high connectivity, other factors such as representation or political availability may dictate where reserves are placed. In low connectivity species, ensuring upstream and downstream connections is critical.

Chronic lack of breeding by Galápagos Blue-footed Boobies and associated population decline

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David Anchundia

2014-06-01

Full Text Available A survey of Blue-footed Boobies (Sula nebouxii excisa throughout the taxon's range in Galápagos, Ecuador found ~6400 adults, compared to a rough estimate of 20,000 in the 1960s. Few pairs bred in 2011-2013 and almost no birds in juvenile plumage were seen. Long-term data suggest that poor breeding began in 1998. Lack of recruitment over this period would mean that the current population is mostly elderly and experiencing senescent decline in performance. Anthropogenic effects such as introduced predators are unlikely to explain this decline because islands with and without such factors exhibited the same low breeding. The poor reproduction seems to be linked to diet. Previous work indicated that sardine and herring (Clupeidae supported successful breeding, but these fish were mostly absent from the diet during this study, except in the central part of Galápagos, where most breeding attempts during this study occurred. Elsewhere in the eastern Pacific sardine abundance has decreased dramatically by natural processes in the last 15 years, as part of a well-documented and apparently natural cycle. This cyclic change in abundance provides a possible explanation for the recent demographic changes in Blue-footed Boobies in Galápagos. Whether natural or anthropogenic in origin, the implications of senescent decline in breeding ability and survival are dramatic for this genetically distinct icon of biodiversity and ecotourism.

DNA barcoding of recently diverged species: relative performance of matching methods.

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Robin van Velzen

Full Text Available Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based, nearest neighbor and BLAST (similarity-based, and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75% than for older species (∼97% (P<0.00001. Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001. The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2% as well as empirical data (93.1%, indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

Broad-scale Population Genetics of the Host Sea Anemone, Heteractis magnifica

KAUST Repository

Emms, Madeleine

2015-12-01

Broad-scale population genetics can reveal population structure across an organism’s entire range, which can enable us to determine the most efficient population-wide management strategy depending on levels of connectivity. Genetic variation and differences in genetic diversity on small-scales have been reported in anemones, but nothing is known about their broad-scale population structure, including that of “host” anemone species, which are increasingly being targeted in the aquarium trade. In this study, microsatellite markers were used as a tool to determine the population structure of a sessile, host anemone species, Heteractis magnifica, across the Indo-Pacific region. In addition, two rDNA markers were used to identify Symbiodinium from the samples, and phylogenetic analyses were used to measure diversity and geographic distribution of Symbiodinium across the region. Significant population structure was identified in H. magnifica across the Indo-Pacific, with at least three genetic breaks, possibly the result of factors such as geographic distance, geographic isolation and environmental variation. Symbiodinium associations were also affected by environmental variation and supported the geographic isolation of some regions. These results suggests that management of H. magnifica must be implemented on a local scale, due to the lack of connectivity between clusters. This study also provides further evidence for the combined effects of geographic distance and environmental distance in explaining genetic variance.

Integration of genetic and demographic data to assess population risk in a continuously distributed species

Science.gov (United States)

Fedy, Bradley C.; Row, Jeffery R.; Oyler-McCance, Sara J.

2017-01-01

The identification and demographic assessment of biologically meaningful populations is fundamental to species’ ecology and management. Although genetic tools are used frequently to identify populations, studies often do not incorporate demographic data to understand their respective population trends. We used genetic data to define subpopulations in a continuously distributed species. We assessed demographic independence and variation in population trends across the distribution. Additionally, we identified potential barriers to gene flow among subpopulations. We sampled greater sage-grouse (Centrocercus urophasianus) leks from across their range (≈175,000 Km2) in Wyoming and amplified DNA at 14 microsatellite loci for 1761 samples. Subsequently, we assessed population structure in unrelated individuals (n = 872) by integrating results from multiple Bayesian clustering approaches and used the boundaries to inform our assessment of long-term population trends and lek activity over the period of 1995–2013. We identified four genetic clusters of which two northern ones showed demographic independence from the others. Trends in population size for the northwest subpopulation were statistically different from the other three genetic clusters and the northeast and southwest subpopulations demonstrated a general trend of increasing proportion of inactive leks over time. Population change from 1996 to 2012 suggested population growth in the southern subpopulations and decline, or neutral, change in the northern subpopulations. We suggest that sage-grouse subpopulations in northern Wyoming are at greater risk of extirpation than the southern subpopulations due to smaller census and effective population sizes and higher variability within subpopulations. Our research is an example of incorporating genetic and demographic data and provides guidance on the identification of subpopulations of conservation concern.

Do species conservation assessments capture genetic diversity?

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Malin C. Rivers

2014-12-01

Full Text Available The best known system for classifying threat status of species, the IUCN Red List, currently lacks explicit considerations of genetic diversity, and consequently may not account for potential adaptation of species to future environmental change. To address this gap, we integrate range-wide genetic analysis with IUCN Red List assessments.We calculated the loss of genetic diversity under simulated range loss for species of Delonix (Leguminosae. Simulated range loss involved random loss of populations and was intended to model ongoing habitat destruction. We found a strong relationship between loss of genetic diversity and range. Moreover, we found correspondence between levels of genetic diversity and thresholds for ‘non-threatened’ versus ‘threatened’ IUCN Red List categories.Our results support the view that current threat thresholds of the IUCN Red List criteria reflect genetic diversity, and hence evolutionary potential; although the genetic diversity distinction between threatened categories was less evident. Thus, by supplementing conventional conservation assessments with genetic data, new insights into the biological robustness of IUCN Red List assessments for targeted conservation initiatives can be achieved. Keywords: Conservation assessment, Conservation genetics, Extinction risk, Genetic diversity, IUCN Red List, Range

Invertebrate population genetics across Earth's largest habitat: The deep-sea floor.

Science.gov (United States)

Taylor, M L; Roterman, C N

2017-10-01

Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Genetic population structure of the desert shrub species lycium ruthenicum inferred from chloroplast dna

International Nuclear Information System (INIS)

Chen, H.; Yonezawa, T.

2014-01-01

Lycium ruthenicum (Solananeae), a spiny shrub mostly distributed in the desert regions of north and northwest China, has been shown to exhibit high tolerance to the extreme environment. In this study, the phylogeography and evolutionary history of L. ruthenicum were examined, on the basis of 80 individuals from eight populations. Using the sequence variations of two spacer regions of chloroplast DNA (trnH-psbA and rps16-trnK) , the absence of a geographic component in the chloroplast DNA genetic structure was identified (GST = 0.351, NST = 0.304, NST< GST), which was consisted with the result of SAMOVA, suggesting weak phylogeographic structure of this species. Phylogenetic and network analyses showed that a total of 10 haplotypes identified in the present study clustered into two clades, in which clade I harbored the ancestral haplotypes that inferred two independent glacial refugia in the middle of Qaidam Basin and the western Inner Mongolia. The existence of regional evolutionary differences was supported by GENETREE, which revealed that one of the population in Qaidam Basin and the two populations in Tarim Basin had experienced rapid expansion, and the other populations retained relatively stable population size during the Pleistocene . Given the results of long-term gene flow and pairwise differences, strong gene flow was insufficient to reduce the genetic differentiation among populations or within populations, probably due to the genetic composition containing a common haplotype and the high number of private haplotypes fixed for most of the population. The divergence times of different lineages were consistent with the rapid uplift phases of the Qinghai-Tibetan Plateau and the initiation and expansion of deserts in northern China, suggesting that the origin and evolution of L. ruthenicum were strongly influenced by Quaternary environment changes. (author)

Wolbachia infections in native and introduced populations of fire ants (Solenopsis spp.).

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Shoemaker, D D; Ross, K G; Keller, L; Vargo, E L; Werren, J H

2000-12-01

Wolbachia are cytoplasmically inherited bacteria that induce a variety of effects with fitness consequences on host arthropods, including cytoplasmic incompatibility, parthenogenesis, male-killing and feminization. We report here the presence of Wolbachia in native South American populations of the fire ant Solenopsis invicta, but the apparent absence of the bacteria in introduced populations of this pest species in the USA. The Wolbachia strains in native S. invicta are of two divergent types (A and B), and the frequency of infection varies dramatically between geographical regions and social forms of this host. Survey data reveal that Wolbachia also are found in other native fire ant species within the Solenopsis saevissima species complex from South America, including S. richteri. This latter species also has been introduced in the USA, where it lacks Wolbachia. Sequence data reveal complete phylogenetic concordance between mtDNA haplotype in S. invicta and Wolbachia infection type (A or B). In addition, the mtDNA and associated group A Wolbachia strain in S. invicta are more closely related to the mtDNA and Wolbachia strain found in S. richteri than they are to the mtDNA and associated group B Wolbachia in S. invicta. These data are consistent with historical introgression of S. richteri cytoplasmic elements into S. invicta populations, resulting in enhanced infection and mtDNA polymorphisms in S. invicta. Wolbachia may have significant fitness effects on these hosts (either directly or by cytoplasmic incompatibility) and therefore these microbes potentially could be used in biological control programmes to suppress introduced fire ant populations.

Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species

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Brusentsov, Ilja I.; Katokhin, Alexey V.; Brusentsova, Irina V.; Shekhovtsov, Sergei V.; Borovikov, Sergei N.; Goncharenko, Grigoriy G.; Lider, Lyudmila A.; Romashov, Boris V.; Rusinek, Olga T.; Shibitov, Samat K.; Suleymanov, Marat M.; Yevtushenko, Andrey V.; Mordvinov, Viatcheslav A.

2013-01-01

Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species. PMID:23634228

Using species distribution model to estimate the wintering population size of the endangered scaly-sided merganser in China.

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Qing Zeng

Full Text Available Scaly-sided Merganser is a globally endangered species restricted to eastern Asia. Estimating its population is difficult and considerable gap exists between populations at its breeding grounds and wintering sites. In this study, we built a species distribution model (SDM using Maxent with presence-only data to predict the potential wintering habitat for Scaly-sided Merganser in China. Area under the receiver operating characteristic curve (AUC method suggests high predictive power of the model (training and testing AUC were 0.97 and 0.96 respectively. The most significant environmental variables included annual mean temperature, mean temperature of coldest quarter, minimum temperature of coldest month and precipitation of driest quarter. Suitable conditions for Scaly-sided Merganser are predicted in the middle and lower reaches of the Yangtze River, especially in Jiangxi, Hunan and Hubei Provinces. The predicted suitable habitat embraces 6,984 km of river. Based on survey results from three consecutive winters (2010-2012 and previous studies, we estimated that the entire wintering population of Scaly-sided Merganser in China to be 3,561 ± 478 individuals, which is consistent with estimate in its breeding ground.

Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species.

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Prunier, Rachel; Akman, Melis; Kremer, Colin T; Aitken, Nicola; Chuah, Aaron; Borevitz, Justin; Holsinger, Kent E

2017-05-01

The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian F ST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species. © 2017 Prunier et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY-NC).

Determining the numbers of a landscape architect species (Tapirus terrestris), using footprints.

Science.gov (United States)

Moreira, Danielle O; Alibhai, Sky K; Jewell, Zoe C; da Cunha, Cristina J; Seibert, Jardel B; Gatti, Andressa

2018-01-01

As a landscape architect and a major seed disperser, the lowland tapir ( Tapirus terrestris ) is an important indicator of the ecological health of certain habitats. Therefore, reliable data regarding tapir populations are fundamental in understanding ecosystem dynamics, including those associated with the Atlantic Forest in Brazil. Currently, many population monitoring studies use invasive tagging with radio or satellite/Global Positioning System (GPS) collars. These techniques can be costly and unreliable, and the immobilization required carries physiological risks that are undesirable particularly for threatened and elusive species such as the lowland tapir. We collected data from one of the last regions with a viable population of lowland tapir in the south-eastern Atlantic Forest, Brazil, using a new non-invasive method for identifying species, the footprint identification technique (FIT). We identified the minimum number of tapirs in the study area and, in addition, we observed that they have overlapping ranges. Four hundred and forty footprints from 46 trails collected from six locations in the study area in a landscape known to contain tapir were analyzed, and 29 individuals were identified from these footprints. We demonstrate a practical application of FIT for lowland tapir censusing. Our study shows that FIT is an effective method for the identification of individuals of a threatened species, even when they lack visible natural markings on their bodies. FIT offers several benefits over other methods, especially for tapir management. As a non-invasive method, it can be used to census or monitor species, giving rapid feedback to managers of protected areas.

Determining the numbers of a landscape architect species (Tapirus terrestris, using footprints

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Danielle O. Moreira

2018-03-01

Full Text Available Background As a landscape architect and a major seed disperser, the lowland tapir (Tapirus terrestris is an important indicator of the ecological health of certain habitats. Therefore, reliable data regarding tapir populations are fundamental in understanding ecosystem dynamics, including those associated with the Atlantic Forest in Brazil. Currently, many population monitoring studies use invasive tagging with radio or satellite/Global Positioning System (GPS collars. These techniques can be costly and unreliable, and the immobilization required carries physiological risks that are undesirable particularly for threatened and elusive species such as the lowland tapir. Methods We collected data from one of the last regions with a viable population of lowland tapir in the south-eastern Atlantic Forest, Brazil, using a new non-invasive method for identifying species, the footprint identification technique (FIT. Results We identified the minimum number of tapirs in the study area and, in addition, we observed that they have overlapping ranges. Four hundred and forty footprints from 46 trails collected from six locations in the study area in a landscape known to contain tapir were analyzed, and 29 individuals were identified from these footprints. Discussion We demonstrate a practical application of FIT for lowland tapir censusing. Our study shows that FIT is an effective method for the identification of individuals of a threatened species, even when they lack visible natural markings on their bodies. FIT offers several benefits over other methods, especially for tapir management. As a non-invasive method, it can be used to census or monitor species, giving rapid feedback to managers of protected areas.

Contrasting modes and tempos of venom expression evolution in two snake species.

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Margres, Mark J; McGivern, James J; Seavy, Margaret; Wray, Kenneth P; Facente, Jack; Rokyta, Darin R

2015-01-01

Selection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process and thus the genetic basis of adaptive evolution requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom gland toward toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype. To determine the extent of expression variation and identify the processes driving patterns of phenotypic diversity, we constructed genotype-phenotype maps and compared range-wide toxin-protein expression variation for two species of snake with nearly identical ranges: the eastern diamondback rattlesnake (Crotalus adamanteus) and the eastern coral snake (Micrurus fulvius). We detected significant expression variation in C. adamanteus, identified the specific loci associated with population differentiation, and found that loci expressed at all levels contributed to this divergence. Contrary to expectations, we found no expression variation in M. fulvius, suggesting that M. fulvius populations are not locally adapted. Our results not only linked expression variation at specific loci to divergence in a polygenic, complex trait but also have extensive conservation and biomedical implications. C. adamanteus is currently a candidate for federal listing under the Endangered Species Act, and the loss of any major population would result in the irrevocable loss of a unique venom phenotype. The lack of variation in M. fulvius has significant biomedical application because our data will assist in the development of effective antivenom for this species. Copyright © 2015 by the Genetics Society of America.

Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

Science.gov (United States)

Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

2016-08-01

Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species. © 2016 Society for Conservation Biology.

Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions

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Ammirati Joseph

2011-07-01

Full Text Available Abstract Background Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred evolutionary histories of four species, 1 C. arcuatorum, 2 C. aureofulvus, 3 C. elegantior and 4 C. napus, from populations distributed throughout the Old World, and portions of the New World (Central- and North America based on genetic variation of 154 haplotype internal transcribed spacer (ITS sequences from 83 population samples. By describing the population structure of these species across their geographical distribution, we attempt to identify their historical migration and patterns of diversification. Results Models of population structure from nested clade, demographic and coalescent-based analyses revealed genetically differentiated and geographically structured haplotypes in C. arcuatorum and C. elegantior, while C. aureofulvus showed considerably less population structure and C. napus lacked sufficient genetic differentiation to resolve any population structure. Disjunct populations within C. arcuatorum, C. aureofulvus and C. elegantior show little or no morphological differentiation, whereas in C. napus there is a high level of homoplasy and phenotypic plasticity for veil and lamellae colour. The ITS sequences of the type specimens of C. albobrunnoides and C. albobrunnoides var. violaceovelatus were identical to one another and are treated as one species with a wider range of geographic distribution under C. napus. Conclusions Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1 a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric

Evaluation of multi-species weed competition and weeds population dynamic in corn Zea mays L. field

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S Mijani

2016-05-01

Full Text Available In order to examine the multi-species weed competition in corn field an experiment as an interval mapping was carried out at the Agricultural Research field of Ferdowsi University of Mashhad during growing season 2009-2010. At 3-4 leafy stages of corn, 20 non-destructive quadrates determine and the density of weeds was counted separately. At the same time, 20 destructive quadrates determine and in addition of counting number of plants, leaf area index and dry weight of each species were recorded separately. By using data from previous section, hyperbolic functions were fitted. In these functions number of species serve as the independent variable, weight or leaf area was considered as the dependent variable. With the help of these functions and leaf dry weight of each species was determined for non-destructive quadrates at this stage. Relative leaf area at early season as independent variables and natural logarithm of individual plant weight at later season as dependent variable in a multiple linear regression was fitted to obtain the interspecies competition coefficients. Based on ln of weight of single plant equation the weed interference effects on the corn yield can be divided into two groups: inhibition (negative sign and stimulation (positive sign. Among all weeds, night shade (Solanum nigrum L., redroot pigweed (Amaranthus retroflexus L. and lambsquarter (Chenopodium album L. had positive effects on corn yield, respectively. In fact, these weeds had competition and negative impacts on other weeds and reduced their competition power with corn and caused facilitation role on corn yield. At the end of growing season of corn, population of lambsquarter and Common purslane (Portulaca oleracea L. decreased while population of barnyard grass(Echinochloa crus-galli L., redroot pigweed and night shade increased.

Holocene re-colonisation, central-marginal distribution and habitat specialisation shape population genetic patterns within an Atlantic European grass species.

Science.gov (United States)

Harter, D E V; Jentsch, A; Durka, W

2015-05-01

Corynephorus canescens (L.) P.Beauv. is an outbreeding, short-lived and wind-dispersed grass species, highly specialised on scattered and disturbance-dependent habitats of open sandy sites. Its distribution ranges from the Iberian Peninsula over Atlantic regions of Western and Central Europe, but excludes the two other classical European glacial refuge regions on the Apennine and Balkan Peninsulas. To investigate genetic patterns of this uncommon combination of ecological and biogeographic species characteristics, we analysed AFLP variation among 49 populations throughout the European distribution range, expecting (i) patterns of SW European glacial refugia and post-glacial expansion to the NE; (ii) decreasing genetic diversity from central to marginal populations; and (iii) interacting effects of high gene flow and disturbance-driven genetic drift. Decreasing genetic diversity from SW to NE and distinct gene pool clustering imply refugia on the Iberian Peninsula and in western France, from where range expansion originated towards the NE. High genetic diversity within and moderate genetic differentiation among populations, and a significant pattern of isolation-by-distance indicate a gene flow drift equilibrium within C. canescens, probably due to its restriction to scattered and dynamic habitats and limited dispersal distances. These features, as well as the re-colonisation history, were found to affect genetic diversity gradients from central to marginal populations. Our study emphasises the need for including the specific ecology into analyses of species (re-)colonisation histories and range centre-margin analyses. To account for discontinuous distributions, new indices of marginality were tested for their suitability in studies of centre-periphery gradients. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Ghosts of yellowstone: multi-decadal histories of wildlife populations captured by bones on a modern landscape.

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Joshua H Miller

Full Text Available Natural accumulations of skeletal material (death assemblages have the potential to provide historical data on species diversity and population structure for regions lacking decades of wildlife monitoring, thereby contributing valuable baseline data for conservation and management strategies. Previous studies of the ecological and temporal resolutions of death assemblages from terrestrial large-mammal communities, however, have largely focused on broad patterns of community composition in tropical settings. Here, I expand the environmental sampling of large-mammal death assemblages into a temperate biome and explore more demanding assessments of ecological fidelity by testing their capacity to record past population fluctuations of individual species in the well-studied ungulate community of Yellowstone National Park (Yellowstone. Despite dramatic ecological changes following the 1988 wildfires and 1995 wolf re-introduction, the Yellowstone death assemblage is highly faithful to the living community in species richness and community structure. These results agree with studies of tropical death assemblages and establish the broad capability of vertebrate remains to provide high-quality ecological data from disparate ecosystems and biomes. Importantly, the Yellowstone death assemblage also correctly identifies species that changed significantly in abundance over the last 20 to ∼80 years and the directions of those shifts (including local invasions and extinctions. The relative frequency of fresh versus weathered bones for individual species is also consistent with documented trends in living population sizes. Radiocarbon dating verifies the historical source of bones from Equus caballus (horse: a functionally extinct species. Bone surveys are a broadly valuable tool for obtaining population trends and baseline shifts over decadal-to-centennial timescales.

Extinction risk assessment for the species survival plan (SSP) population of the Bali mynah (Leucopsar rothschildi).

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Earnhardt, Joanne M; Thompson, Steven D; Faust, Lisa J

2009-05-01

The Bali mynah Species Survival Plan (SSP), an Association of Zoos and Aquariums program, strives to maintain the genetic and demographic health of its population, avoid unplanned changes in size, and minimize the risk of population extinction. The SSP population meets current demographic and genetic objectives with a population size of 209 birds at 61 institutions and 96% genetic diversity (GD) retained from the source population. However, participating institutions have expressed concerns regarding space allocation, target population size (TPS), breeding restrictions, inbreeding depression, and harvest in relation to future population availability and viability. Based on these factors, we assess five questions with a quantitative risk assessment, specifically a population viability analysis (PVA) using ZooRisk software. Using an individual-based stochastic model, we project potential population changes under different conditions (e.g. changes in TPS and genetic management) to identify the most effective management actions. Our projections indicate that under current management conditions, population decline and extinction are unlikely and that although GD will decline over 100 years the projected loss does not exceed levels acceptable to population managers (less than 90% GD retained). Model simulations indicate that the combination of two genetic management strategies (i.e. priority breeding based on mean kinship and inbreeding avoidance) benefits the retention of GD and reduces the accumulation of inbreeding. The current TPS (250) is greater than necessary to minimize the risk of extinction for the SSP population but any reduction in TPS must be accompanied by continued application of genetic management. If carefully planned, birds can be harvested for transfer to Bali for a reintroduction program without jeopardizing the SSP population.

Phenotypic covariance at species' borders.

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Caley, M Julian; Cripps, Edward; Game, Edward T

2013-05-28

Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

DEFF Research Database (Denmark)

André, C.; Larsson, L. C.; Laikre, L.

2010-01-01

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers t...

Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

KAUST Repository

Horne, J. B.

2013-01-11

Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged. © 2013 The Authors. Journal

Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

KAUST Repository

Horne, J. B.; van Herwerden, L.

2013-01-01

Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged. © 2013 The Authors. Journal

Model-based analyses reveal insular population diversification and cryptic frog species in the Ischnocnema parva complex in the Atlantic forest of Brazil.

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Gehara, Marcelo; Barth, Adriane; Oliveira, Eliana Faria de; Costa, Marco Antonio; Haddad, Célio Fernando Baptista; Vences, Miguel

2017-07-01

The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands. However, the timing and mode of diversification of insular populations in the AF region were rarely investigated. Here, we analyze the phylogeography and species diversity of the small-sized direct-developing frog Ischnocnema parva. These frogs are independent from water bodies but dependent on forest cover and high humidity, and provide good models to understand forest dynamics and insular diversification. Our analysis was based on DNA sequences for one mitochondrial and four nuclear genes of 71 samples from 18 localities including two islands, São Sebastião, municipality of Ilhabela, and Mar Virado, municipality of Ubatuba, both in the state of São Paulo. We use molecular taxonomic methods to show that I. parva is composed of six independently evolving lineages, with the nominal I. parva likely endemic to the type locality. The time-calibrated species tree shows that these lineages have diverged in the Pliocene and Pleistocene, suggesting the persistence of micro-refuges of forest in the AF. For the two insular populations we used approximate Bayesian computation to test different diversification hypotheses. Our findings support isolation with migration for São Sebastião population, with ∼1Mya divergence time, and isolation without migration for Mar Virado population, with ∼13Kya divergence time, suggesting a combination of different processes for diversification on AF islands. Copyright © 2017. Published

A positive relationship between spring temperature and productivity in 20 songbird species in the boreal zone.

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Meller, Kalle; Piha, Markus; Vähätalo, Anssi V; Lehikoinen, Aleksi

2018-03-01

Anthropogenic climate warming has already affected the population dynamics of numerous species and is predicted to do so also in the future. To predict the effects of climate change, it is important to know whether productivity is linked to temperature, and whether species' traits affect responses to climate change. To address these objectives, we analysed monitoring data from the Finnish constant effort site ringing scheme collected in 1987-2013 for 20 common songbird species together with climatic data. Warm spring temperature had a positive linear relationship with productivity across the community of 20 species independent of species' traits (realized thermal niche or migration behaviour), suggesting that even the warmest spring temperatures remained below the thermal optimum for reproduction, possibly due to our boreal study area being closer to the cold edge of all study species' distributions. The result also suggests a lack of mismatch between the timing of breeding and peak availability of invertebrate food of the study species. Productivity was positively related to annual growth rates in long-distance migrants, but not in short-distance migrants. Across the 27-year study period, temporal trends in productivity were mostly absent. The population sizes of species with colder thermal niches had decreasing trends, which were not related to temperature responses or temporal trends in productivity. The positive connection between spring temperature and productivity suggests that climate warming has potential to increase the productivity in bird species in the boreal zone, at least in the short term.

Detection of sister-species in invasive populations of the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Uganda

Science.gov (United States)

Tay, Wee Tek; Walsh, Thomas K.; Kanyesigye, Dalton; Adumo, Stella; Abongosi, Joseph; Ochen, Stephen; Sserumaga, Julius; Alibu, Simon; Abalo, Grace; Asea, Godfrey; Agona, Ambrose

2018-01-01

The fall armyworm (FAW) Spodoptera frugiperda (J. E. Smith) is a species native to the Americas. This polyphagous lepidopteran pest was first reported in Nigeria and the Democratic Republic of São Tomé and Principe in 2016, but its presence in eastern Africa has not been confirmed via molecular characterisation. In this study, FAW specimens from western and central Uganda were identified based on the partial mtDNA COI gene sequences, with mtDNA COI haplotypes matching those identified in Nigeria and São Tomé. In this study, we sequence an additional partial mtDNA Cyt b gene and also the partial mtDNA COIII gene in Ugandan FAW samples. We detected identical mitochondrial DNA haplotypes for both the mtDNA Cyt b and COI partial genes, while combining the mtDNA COI/Cyt b haplotypes and mtDNA COIII haplotypes enabled a new maternal lineage in the Ugandan corn-preferred FAW samples to be identified. Our results suggested that the African incursions of S. frugiperda involved at least three maternal lineages. Recent full genome, phylogenetic and microsatellite analyses provided evidence to support S. frugiperda as likely consisted of two sympatric sister species known as the corn-preferred and rice-preferred strains. In our Ugandan FAW populations, we identified the presence of mtDNA haplotypes representative of both sister species. It is not known if both FAW sister species were originally introduced together or separately, and whether they have since spread as a single population. Further analyses of additional specimens originally collected from São Tomé, Nigeria and throughout Africa would be required to clarify this issue. Importantly, our finding showed that the genetic diversity of the African corn-preferred FAW species is higher than previously reported. This potentially contributed to the success of FAW establishment in Africa. Furthermore, with the additional maternal lineages detected, there is likely an increase in paternal lineages, thereby increasing

Developing population models with data from marked individuals

Science.gov (United States)

Hae Yeong Ryu,; Kevin T. Shoemaker,; Eva Kneip,; Anna Pidgeon,; Patricia Heglund,; Brooke Bateman,; Thogmartin, Wayne E.; Reşit Akçakaya,

2016-01-01

Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method

Description of new andean species of the genus Phymaturus (Iguania: Liolaemidae) from Northwestern Argentina.

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Lobo, Fernando; Laspiur, Alejandro; Acosta, Juan Carlos

2013-01-01

As a result of several field trips and studies of collections of Phymaturus samples from Andean areas of central western Argentina (San Juan province), we discovered two populations that exhibit a particular character combination not seen in other species formally recognized in the literature. Based on a detailed analysis of an extended list of morphological characters (93), including scalation, color pattern, gular and nuchal folds, precloacal pores, and morphometric data, we conclude that these populations represent independent lineages that deserve to be considered as new species. According to the most recent revision of the genus and considering the descriptions made in another recent contribution, the taxonomic composition of the genus was increased to 38 species. In this study we provide the formal description of two additional new taxa, including their diagnosis and detailed comparisons with other members of their species group. The two new species belong to the palluma group, and can be assigned to the Puna subclade because they present the typical dorsal "spray" pattern. Other characters described in this study suggest their close phylogenetic relationship with other species of this subclade inhabiting the southern Puna region of Argentina, such as Phymaturus punae. Within the Puna subclade, Phymaturus aguanegra sp. nov. differs from all other members (P. antofagastensis, P. denotatus, P. laurenti, P punae, P extrilidus, P mallimaccii and P paihuanense) exhibiting the following combination of diagnostic characters: a complete melanism over the dorsum of neck, the presence of enlarged scales at the base of tail in males, having strongly keeled tarsal scales, lacking enlarged scales on the anterior margin of the antehumeral fold and centre of chest, females without flank coloration, a vertebral dark gray stripe usually present on the dorsum, females exhibiting a tricolor dorsal pattern, with two types of brown and scattered ferriferous oxide spots, and the

Population genetic structure of the major malaria vector Anopheles funestus s.s. and allied species in southern Africa

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Choi Kwang Shik

2012-12-01

Full Text Available Abstract Background Anopheles funestus s.s., one of the major malaria vectors in sub-Saharan Africa, belongs to a group of eleven African species that are morphologically similar at the adult stage, most of which do not transmit malaria. The population structure of An. funestus based on mitochondrial DNA data led to the description of two cryptic subdivisions, clade I widespread throughout Africa and clade II known only from Mozambique and Madagascar. In this study, we investigated five common members of the Anopheles funestus group in southern Africa in order to determine relationships within and between species. Methods A total of 155 specimens of An. funestus, An. parensis, An. vaneedeni, An. funestus-like and An. rivulorum from South Africa, Mozambique and Malawi were used for the study. The population genetic structure was assessed within and between populations using mitochondrial DNA. Results The phylogenetic trees revealed three main lineages: 1 An. rivulorum; 2 An. funestus-like clade I and An. parensis clade II; and 3 An. funestus clades I and II, An. funestus-like clade II, An. parensis clade I and An. vaneedeni clades I and II. Within An. funestus, 32 specimens from Mozambique consisted of 40.6% clade I and 59.4% clade II while all 21 individuals from Malawi were clade I. In the analysis of mitochondrial DNA sequences, there were 37 polymorphic sites and 9 fixed different nucleotides for ND5 and 21 polymorphic sites and 6 fixed different nucleotides for COI between the two An. funestus clades. The results for COI supported the ND5 analysis. Conclusion This is the first report comparing An. funestus group species including An. funestus clades I and II and the new species An. funestus-like. Anopheles funestus clade I is separated from the rest of the members of the An. funestus subgroup and An. funestus-like is distinctly distributed from the other species in this study. However, there were two clades for An. funestus-like, An

Assessment of ecological risks to wide-ranging wildlife species on the Oak Ridge Reservation

International Nuclear Information System (INIS)

Sample, B.

1995-01-01

Ecological risk assessment at CERCLA sites generally focuses on species that may be definitively associated with a contaminated area. While appropriate for sites with single, discrete areas of contamination, this approach is not adequate for sites with multiple, spatially separated contaminated areas such as the Oak Ridge Reservation (ORR). Wide-ranging wildlife species may travel between and use multiple contaminated sites. These species may therefore be exposed to and be at risk from contaminants from multiple locations. Use of a site (and therefore exposure and risk) by wildlife is dependent upon the availability of habitat. Availability and distribution of habitat on the ORR was determined using satellite imagery. The proportion of habitat within contaminated areas was then determined by overlaying boundaries of contaminated areas (Operable Units or OUs) on the ORR habitat map. The likelihood of contaminant exposure was estimated by comparing the habitat requirements for wildlife species to the proportion of suitable habitat within OUs. OU-specific contaminant concentrations in surface water, soil, or biota were used to estimate the magnitude of risk presented by each DU. The proportion of ORR-wide population likely to be exposed was estimated using literature-derived population density data for each endpoint. At present, due to major data gaps (i.e., lack of data for all OUs, site-specific population density or habitat use data, etc.) uncertainty associated with conclusions is high. Results of this assessment must therefore be considered to be preliminary

Rapid changes in transcription profiles of the Plasmodium yoelii yir multigene family in clonal populations: lack of epigenetic memory?

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Deirdre Cunningham

Full Text Available The pir multigene family, found in the genomes of Plasmodium vivax, P. knowlesi and the rodent malaria species, encode variant antigens that could be targets of the immune response. Individual parasites of the rodent malaria Plasmodium yoelii, selected by micromanipulation, transcribe only 1 to 3 different pir (yir suggesting tight transcriptional control at the level of individual cells. Using microarray and quantitative RT-PCR, we show that despite this very restricted transcription in a single cell, many yir genes are transcribed throughout the intra-erythrocytic asexual cycle. The timing and level of transcription differs between genes, with some being more highly transcribed in ring and trophozoite stages, whereas others are more highly transcribed in schizonts. Infection of immunodeficient mice with single infected erythrocytes results in populations of parasites each with transcriptional profiles different from that of the parent parasite population and from each other. This drift away from the original 'set' of transcribed genes does not appear to follow a preset pattern and "epigenetic memory" of the yir transcribed in the parent parasite can be rapidly lost. Thus, regulation of pir gene transcription may be different from that of the well-characterised multigene family, var, of Plasmodium falciparum.

Spatial and temporal variation in population dynamics of Andean frogs: Effects of forest disturbance and evidence for declines

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Esther M. Cole

2014-08-01

Full Text Available Biodiversity loss is a global phenomenon that can result in the collapse of food webs and critical ecosystem services. Amphibian population decline over the last century is a notable case of species loss because amphibians survived the last four major extinction events in global history, their current rate of extinction is unprecedented, and their rate of extinction is greater than that for most other taxonomic groups. Despite the severity of this conservation problem and its relevance to the study of global biodiversity loss, major knowledge gaps remain for many of the most threatened species and regions in the world. Rigorous estimates of population parameters are lacking for many amphibian species in the Neotropics. The goal of our study was to determine how the demography of seven species of the genus Pristimantis varied over time and space in two cloud forests in the Ecuadorian Andes. We completed a long term capture–mark–recapture study to estimate abundance, survival, and population growth rates in two cloud forests in the Ecuadorian Andes; from 2002 to 2009 at Yanayacu in the Eastern Cordillera and from 2002 to 2003 at Cashca Totoras in the Western Cordillera. Our results showed seasonal and annual variation in population parameters by species and sex. P. bicantus experienced significant reductions in abundance over the course of our study. Abundance, apparent survival, and population growth rates were lower in disturbed than in primary or mature secondary forest. The results of our study raise concerns for the population status of understudied amphibian groups and provide insights into the population dynamics of Neotropical amphibians.

Vegetation development following stream/river restoration: more natural fluvial dynamics and morphology, return of aquatic and riparian plant species?

Science.gov (United States)

Soons, M. B.

2012-04-01

After centuries of human interventions in stream/river dynamics and morphology aimed at optimizing landscapes for agricultural and industrial purposes, new insights have inspired water managers to try and combine stream and river ecosystem functions with the conservation of biodiversity. Around the world, aquatic and riparian species have declined strongly due to pollution, destruction and fragmentation of their habitat, so that biodiversity conservation initiatives primarily focus on habitat restoration. In the past decades many stream and river restoration projects have been carried out and often hydrological dynamics and morphology have been restored to a more natural state. However, the successful restoration of aquatic and riparian habitats very often failed to result in restoration of their biodiversity. This lack of success from a biodiversity conservation perspective is usually attributed to 'dispersal limitation', meaning that the habitat may be restored, but species fail to reach the site and re-colonize it. Especially re-colonization by aquatic and riparian plant species is important, as such species function as ecosystem engineers: their presence alters fluvial dynamics and morphology, generates additional habitat heterogeneity and provides habitat and food for animal species. Following minor disturbances, re-colonization is often possible through locally remaining populations, by seeds in the seed bank or by surviving plant fragments. However, following major disturbances, colonization and establishment from other source populations are necessary. This usually occurs through dispersal of seeds (and in more aquatic species also by dispersal of vegetative fragments) into the restored wetland area. As dispersal occurs predominantly over short distances and source populations of aquatic and riparian species may be lacking in the surroundings, dispersal may be a limiting factor in the development of aquatic and riparian vegetation at a restored site. But

Defining population structure and genetic signatures of decline in the giant garter snake (Thamnophis gigas): implications for conserving threatened species within highly altered landscapes

Science.gov (United States)

Wood, Dustin A.; Halstead, Brian J.; Casazza, Michael L.; Hansen, Eric C.; Wylie, Glenn D.; Vandergast, Amy

2015-01-01

Anthropogenic habitat fragmentation can disrupt the ability of species to disperse across landscapes, which can alter the levels and distribution of genetic diversity within populations and negatively impact long-term viability. The giant gartersnake (Thamnophis gigas) is a state and federally threatened species that historically occurred in the wetland habitats of California’s Great Central Valley. Despite the loss of 93 % of historic wetlands throughout the Central Valley, giant gartersnakes continue to persist in relatively small, isolated patches of highly modified agricultural wetlands. Gathering information regarding genetic diversity and effective population size represents an essential component for conservation management programs aimed at this species. Previous mitochondrial sequence studies have revealed historical patterns of differentiation, yet little is known about contemporary population structure and diversity. On the basis of 15 microsatellite loci, we estimate population structure and compare indices of genetic diversity among populations spanning seven drainage basins within the Central Valley. We sought to understand how habitat loss may have affected genetic differentiation, genetic diversity and effective population size, and what these patterns suggest in terms of management and restoration actions. We recovered five genetic clusters that were consistent with regional drainage basins, although three northern basins within the Sacramento Valley formed a single genetic cluster. Our results show that northern drainage basin populations have higher connectivity than among central and southern basins populations, and that greater differentiation exists among the more geographically isolated populations in the central and southern portion of the species’ range. Genetic diversity measures among basins were significantly different, and were generally lower in southern basin populations. Levels of inbreeding and evidence of population

Manipulation of the fertility of marsupials for conservation of endangered species and control of over-abundant populations.

Science.gov (United States)

Mate, K E; Molinia, F C; Rodger, J C

1998-10-01

Marsupials present a dichotomy in population management; the numbers of many Australian marsupial species have declined due to loss of habitat, competition from introduced herbivores and predation by introduced carnivores, but other species have become locally overabundant in Australia or are introduced pests in New Zealand. The manipulation of reproduction offers the means to increase or decrease productivity; however, considerable fundamental research is required before reproductive technologies can be applied to marsupials. Marsupials differ from eutherian mammals in several aspects of their reproduction including sex differentiation, gamete function and endocrinology, as well as in the relative lengths of gestation and lactation. Although these differences present unique problems in the application of reproductive technologies to marsupials, they also present unique opportunities for marsupial-specific fertility control. This paper summarises the assisted breeding technologies currently being applied to marsupials including superovulation, artificial insemination, in vitro fertilization and gene banking; unique marsupial targets for contraceptive intervention including gamete production, sperm capacitation, gamete surface antigens and embryonic development; and some options for the delivery of contraceptive vaccines to marsupial populations.

Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

Science.gov (United States)

Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

2015-01-01

Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

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Riccardo Baroncelli

Full Text Available Fragaria × ananassa (common name: strawberry is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l. is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

Population Fluctuations of Insect Predators Species Found on Almond and WildAlmond Tree Adjacent to Pistachio Orchard in Şanlıurfa

OpenAIRE

YANIK, Ertan

2013-01-01

Almond (Prunus amygdalus Batsch) and wild almond (Amygdalus orientalis) trees are the most abundant species adjacent to pistachio orchards of Sanliurfa province. This study focused on trees that located in the vicinity of the pistachio orchards, to determine whether these alternative habitats are a source of pistachio psilla’s (Agonoscena pistaciae Burck. and Laut.) insect predators species. For this purpose surveys were conducted to population fluctuations of insect predatory species of pist...

Hitting an Unintended Target: Phylogeography of Bombus brasiliensis Lepeletier, 1836 and the First New Brazilian Bumblebee Species in a Century (Hymenoptera: Apidae.

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José Eustáquio Santos Júnior

Full Text Available This work tested whether or not populations of Bombus brasiliensis isolated on mountain tops of southeastern Brazil belonged to the same species as populations widespread in lowland areas in the Atlantic coast and westward along the Paraná-river valley. Phylogeographic and population genetic analyses showed that those populations were all conspecific. However, they revealed a previously unrecognized, apparently rare, and potentially endangered species in one of the most threatened biodiversity hotspots of the World, the Brazilian Atlantic Forest. This species is described here as Bombus bahiensis sp. n., and included in a revised key for the identification of the bumblebee species known to occur in Brazil. Phylogenetic analyses based on two mtDNA markers suggest this new species to be sister to B. brasiliensis, from which its workers and queens can be easily distinguished by the lack of a yellow hair-band on the first metasomal tergum. The results presented here are consistent with the hypothesis that B. bahiensis sp. n. may have originated from an ancestral population isolated in an evergreen-forest refuge (the so-called Bahia refuge during cold, dry periods of the Pleistocene. This refuge is also known as an important area of endemism for several animal taxa, including other bees. Secondary contact between B. bahiensis and B. brasiliensis may be presently prevented by a strip of semi-deciduous forest in a climate zone characterized by relatively long dry seasons. Considering the relatively limited range of this new species and the current anthropic pressure on its environment, attention should be given to its conservation status.

Tripartite Governance: Enabling Successful Implementations with Vulnerable Populations.

Science.gov (United States)

Kennedy, Margaret Ann

2016-01-01

Vulnerable populations are often at a distinct disadvantage when it comes to the implementation of health information systems in an equitable, appropriate, and timely manner. The disadvantages experienced by vulnerable populations are innumerable and include lack of representation, lack of appropriate levels of funding, lack of resources and capacity, and lack of representation. Increasingly, models of representation for complex implementations involve a tripartite project governance model. This tripartite partnership distributes accountability across all partners, and ensures that vulnerable populations have an equitable contribution to the direction of implementation according to their needs. This article shares lessons learned and best practices from complex tripartite partnerships supporting implementations with vulnerable populations in Canada.

Lack of genetic differentiation between contrasted overwintering strategies of a major pest predator Episyrphus balteatus (Diptera: Syrphidae: implications for biocontrol.

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Lucie Raymond

Full Text Available Winter ecology of natural enemies has a great influence on the level and efficiency of biological control at spring. The hoverfly Episyrphus balteatus (DeGeer (Diptera: Syrphidae is one of the most important natural predators of crop aphids in Europe. Three different overwintering strategies coexist in this species which makes it a good model in order to study ecologically-based speciation processes. The purpose of this study was to determine whether E. balteatus populations with alternative overwintering strategies are genetically differentiated. To that aim, we developed 12 specific microsatellite markers and evaluated the level of neutral genetic differentiation between E. balteatus field populations that overwinter in the three different ways described in this species (i.e. migration, local overwintering at a pre-imaginal stage, and local overwintering at adult stage. Results showed a lack of neutral genetic differentiation between individuals with different overwintering strategies although there are strong ecological differences between them. All pair-wise FST values are below 0.025 and non-significant, and Bayesian clustering showed K=1 was the most likely number of genetic clusters throughout our sample. The three overwintering strategies form one unique panmictic population. This suggests that all the individuals may have genetic material for the expression of different overwintering phenotypes, and that their commitment in one particular overwintering strategy may depend on environmental and individual factors. Consequently, the prevalence of the different overwintering strategies would be potentially modified by landscape engineering and habitat management which could have major implications for biological control.

Multi-gene analysis reveals a lack of genetic divergence between Calanus agulhensis and C. sinicus (Copepoda; Calanoida.

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Robert Kozol

Full Text Available The discrimination and taxonomic identification of marine species continues to pose a challenge despite the growing number of diagnostic metrics and approaches. This study examined the genetic relationship between two sibling species of the genus Calanus (Crustacea; Copepoda; Calanidae, C. agulhensis and C. sinicus, using a multi-gene analysis. DNA sequences were determined for portions of the mitochondrial cytochrome c oxidase I (mtCOI; nuclear citrate synthase (CS, and large subunit (28S rRNA genes for specimens collected from the Sea of Japan and North East (NE Pacific Ocean for C. sinicus and from the Benguela Current and Agulhas Bank, off South Africa, for C. agulhensis. For mtCOI, C. sinicus and C. agulhensis showed similar levels of haplotype diversity (H(d = 0.695 and 0.660, respectively and nucleotide diversity (π = 0.003 and 0.002, respectively. Pairwise F(ST distances for mtCOI were significant only between C. agulhensis collected from the Agulhas and two C. sinicus populations: the Sea of Japan (F(ST = 0.152, p<0.01 and NE Pacific (F(ST = 0.228, p<0.005. Between the species, F(ST distances were low for both mtCOI (F(ST = 0.083, p = 0.003 and CS (F(ST = 0.050, p = 0.021. Large subunit (28S rRNA showed no variation between the species. Our results provide evidence of the lack of genetic distinction of C. sinicus and C. agulhensis, raise questions of whether C. agulhensis warrants status as a distinct species, and indicate the clear need for more intensive and extensive ecological and genetic analysis.

Genetic isolation between coastal and fishery-impacted, offshore bottlenose dolphin (Tursiops spp.) populations.

Science.gov (United States)

Allen, Simon J; Bryant, Kate A; Kraus, Robert H S; Loneragan, Neil R; Kopps, Anna M; Brown, Alexander M; Gerber, Livia; Krützen, Michael

2016-06-01

The identification of species and population boundaries is important in both evolutionary and conservation biology. In recent years, new population genetic and computational methods for estimating population parameters and testing hypotheses in a quantitative manner have emerged. Using a Bayesian framework and a quantitative model-testing approach, we evaluated the species status and genetic connectedness of bottlenose dolphin (Tursiops spp.) populations off remote northwestern Australia, with a focus on pelagic 'offshore' dolphins subject to incidental capture in a trawl fishery. We analysed 71 dolphin samples from three sites beyond the 50 m depth contour (the inshore boundary of the fishery) and up to 170 km offshore, including incidentally caught and free-ranging individuals associating with trawl vessels, and 273 dolphins sampled at 12 coastal sites inshore of the 50 m depth contour and within 10 km of the coast. Results from 19 nuclear microsatellite markers showed significant population structure between dolphins from within the fishery and coastal sites, but also among dolphins from coastal sites, identifying three coastal populations. Moreover, we found no current or historic gene flow into the offshore population in the region of the fishery, indicating a complete lack of recruitment from coastal sites. Mitochondrial DNA corroborated our findings of genetic isolation between dolphins from the offshore population and coastal sites. Most offshore individuals formed a monophyletic clade with common bottlenose dolphins (T. truncatus), while all 273 individuals sampled coastally formed a well-supported clade of Indo-Pacific bottlenose dolphins (T. aduncus). By including a quantitative modelling approach, our study explicitly took evolutionary processes into account for informing the conservation and management of protected species. As such, it may serve as a template for other, similarly inaccessible study populations. © 2016 John Wiley & Sons Ltd.

Historical Population Estimates For Several Fish Species At Offshore Oil and Gas Structures in the US Gulf of Mexico

Science.gov (United States)

Gitschlag, G.

2016-02-01

Population estimates were calculated for four fish species occurring at offshore oil and gas structures in water depths of 14-32 m off the Louisiana and upper Texas coasts in the US Gulf of Mexico. From 1993-1999 sampling was conducted at eight offshore platforms in conjunction with explosive salvage of the structures. To estimate fish population size prior to detonation of explosives, a fish mark-recapture study was conducted. Fish were captured on rod and reel using assorted hook sizes. Traps were occasionally used to supplement catches. Fish were tagged below the dorsal fin with plastic t-bar tags using tagging guns. Only fish that were alive and in good condition were released. Recapture sampling was conducted after explosives were detonated during salvage operations. Personnel operating from inflatable boats used dip nets to collect all dead fish that floated to the surface. Divers collected representative samples of dead fish that sank to the sea floor. Data provided estimates for red snapper (Lutjanus campechanus), Atlantic spadefish (Chaetodipterus faber), gray triggerfish (Balistes capriscus), and blue runner (Caranx crysos) at one or more of the eight platforms studied. At seven platforms, population size for red snapper was calculated at 503-1,943 with a 95% CI of 478. Abundance estimates for Atlantic spadefish at three platforms ranged from 1,432-1,782 with a 95% CI of 473. At three platforms, population size of gray triggerfish was 63-129 with a 95% CI of 82. Blue runner abundance at one platform was 558. Unlike the other three species which occur close to the platforms, blue runner range widely and recapture of this species was dependent on fish schools being in close proximity to the platform at the time explosives were detonated. Tag recapture was as high as 73% for red snapper at one structure studied.

Respiratory adaptations to oxygen lack in three species of Glossiphoniidae (Hirudinea) in Lake Esrom, Denmark

DEFF Research Database (Denmark)

Pohle, B. D.; Hamburger, K.

2005-01-01

The weight-specific respiration rate (µl O2 mg-1 AFDW h-1) of three species of leech from Lake Esrom, Denmark, Glossiphonia concolor, G. complanata and Helobdella stagnalis was measured in a closed stirred chamber with a micro electrode. At declining oxygen concentration (mg O2 l-1) all three spe...... at 10 and 20 °C, respectively. The results were discussed in relation to habitat and spatial distribution of the three species in the lake....

Population resources of an endangered species Salix lapponum L. in Polesie Lubelskie Region (eastern Poland

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Magdalena Pogorzelec

2014-12-01

Full Text Available This research, carried out in the years 2011–2013, aimed to evaluate Salix lapponum stands in the peat bogs of Polesie Lubelskie Region as well as to determine the condition of the population and the changes that have taken place since the 1950’s. An inventory carried out in 25 stands of S. lapponum known from the literature shows that the number of its stands has decreased by 80% in Polesie Lubelskie Region. In all the confirmed locations, a decrease in population numbers was also found in relation to the data known from the literature since the 1950’s. In the majority of the population locations that were considered to be extinct, there were no significant changes in habitat conditions, and ecological succession and changes in hydrological conditions could have been the cause of habitat changes only at a few sites. In the light of the study, the preservation of the S. lapponum population in Polesie Lubelskie seems to be impossible if appropriate active conservation measures are not taken immediately. Because area-based conservation, which covers most of the habitats of the studied species, does not bring the expected results, the possibility of ex situ conservation and enlargement of the populations existing in the natural environment in peat bog ecosystems in Polesie should be explored.

Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide.

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Baeza, J Antonio; Behringer, Donald C

2017-01-01

The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi , an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni . Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across  550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.

Estimating trends of population decline in long-lived marine species in the Mediterranean Sea based on fishers' perceptions.

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Francesc Maynou

Full Text Available We conducted interviews of a representative sample of 106 retired fishers in Italy, Spain and Greece, asking specific questions about the trends they perceived in dolphin and shark abundances between 1940 and 1999 (in three 20 year periods compared to the present abundance. The large marine fauna studied were not target species of the commercial fleet segment interviewed (trawl fishery. The fishers were asked to rank the perceived abundance in each period into qualitative ordinal classes based on two indicators: frequency of sightings and frequency of catches (incidental or intentional of each taxonomic group. The statistical analysis of the survey results showed that both incidental catches and the sighting frequency of dolphins have decreased significantly over the 60+ years of the study period (except for in Greece due to the recent population increase. This shows that fishers' perceptions are in agreement with the declining population trends detected by scientists. Shark catches were also perceived to have diminished since the early 1940s for all species. Other long-lived Mediterranean marine fauna (monk seals, whales were at very low levels in the second half of the 20(th century and no quantitative data could be obtained. Our study supports the results obtained in the Mediterranean and other seas that show the rapid disappearance (over a few decades of marine fauna. We show that appropriately designed questionnaires help provide a picture of animal abundance in the past through the valuable perceptions of fishers. This information can be used to complement scientific sources or in some cases be taken as the only information source for establishing population trends in the abundance of sensitive species.

Ecology and Conservation of the Critically Endangered Tree Species Gymnocladus assamicus in Arunachal Pradesh, India

International Nuclear Information System (INIS)

Choudhury, B.I.; Khan, M.L.; Arunachalam, A.; Das, A.K.

2007-01-01

Gymnocladus assamicus is a critically endangered leguminous tree species endemic to Northeast India. Mature pods of the trees yield soap material and are collected by local people for domestic purposes and religious activities. G. assamicus grows on hill slopes and along banks of streams. Male and hermaphrodite flowers are borne by separate individual trees. Altogether 28 mature trees were documented from nine populations. Of these, very few regenerating trees were found. This species regenerates only through seeds. The major constraints to natural regeneration are over harvesting of mature fruits, habitat destruction, grazing, predation of seeds by scatter-hoarding animals, poor percentage of seed germination due to their hard-waxy seed coats, and the lack of seed dispersal. Effective conservation initiatives should emphasize sustainable harvesting of mature pods, awareness among local people, and preservation of surviving individuals of the species. Nonetheless, reintroduction of the species to suitable ecological habitats is also recommended.

Population genetics at three spatial scales of a rare sponge living in fragmented habitats

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Uriz Maria J

2010-01-01

population makeup was minor (only ca. 4%. Conclusions The structure of the S. lophyropoda populations at all spatial scales examined confirms the philopatric larval dispersal that has been reported. Asexual reproduction does not seem to play a relevant role in the populations. The heterozygote excess and the lack of inbreeding could be interpreted as a hitherto unknown outcrossing strategy of the species. The envisaged causes for this strategy are sperm dispersal, a strong selection against the mating of genetically related individuals to avoid inbreeding depression or high longevity of genets combined with stochastic recruitment events by larvae from other populations. It should be investigated whether this strategy could also explain the genetic diversity of many other patchy marine invertebrates whose populations remain healthy over time, despite their apparent rarity.

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus.

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Jordan D Satler

Full Text Available The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley, and the genus as a whole occupies an impressive variety of habitats.We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches recovered a general "3 clade" structure for the genus (A. gulosus, californicus group, erebus group, with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations. Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism.This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to

Population dynamics of the species Plantago major L. and Poa annua L. in a replacement series experiment

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Mijović A.

2009-01-01

Full Text Available Population dynamics of the species Plantago major L. and Poa annua L., typical representatives of ruderal vegetation, was analyzed in a replacement series experiment. The analyzed species were sown in an area with meadow vegetation, where the vegetation present had been previously removed by a total herbicide and additionally by hoeing. The objective of the experiment was to monitor growth dynamics and the effect of intra- and inter-specific interaction of the species Plantago major and Poa annua in conditions of different sowing densities and proportions. The effects of intra- and inter-specific interference and the density-dependent responses were assessed on the basis of several parameters (natality, mortality, age structure, and measures of ontogenetic changes. Based on the study results, it can be concluded that the responses of the species in the experiment were different, which is explained by different adaptive mechanisms, i.e., strategies, in the specific environmental conditions. An effect of the density dependent response was present in both species in the replacement series experiment. The response was amplified by water deficit caused by intensive evapora­tion of the bare soil. No effect of inter-specific interference was observed at the given densities of the study species on the sample plots. An effect of intra-specific interference of the species Plantago major and Poa annua was observed in the guise of a density-negative response of the rate of ontogenetic changes and fecundity.

Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

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Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

2016-06-17

In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

Population Diversity and Dispersal of Two Species of Stoneflies (Order Plecoptera) Within Four Watersheds of Northeastern Ohio.

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Yasick, A. L.; Wolin, J. A.; Krebs, R. A.

2005-05-01

This study investigates two species of stoneflies with potentially opposing dispersal capabilities and genetic structure within four watersheds in the Lake Erie drainage system of Northeast Ohio. This research is two fold; it provides information on genetic variation of two understudied aquatic invertebrate species and the impact of human land-use practices on this variation. Populations of Allocapnia recta, a winter emerging stonefly are predicted to have the least genetic variation within the four watersheds and most differences among sites due to its rudimentary wing structure and winter emergence. Leuctra tenuis is predicted to have greater genetic variability within sites and fewer differences among sites because of its higher migration potential. In both species, models of isolation by distance will be tested. Distinct polymorphisms exist within the 16s rRNA region of A. recta suggesting that this fragment has sufficient variation to address these questions.

Phylogenetic patterns in populations of Chilean species of the genus Orestias (Teleostei: Cyprinodontidae): results of mitochondrial DNA analysis.

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Lüssen, Arne; Falk, Thomas M; Villwock, Wolfgang

2003-10-01

Patterns of molecular genetic differentiation among taxa of the "agassii species complex" (Parenti, 1984) were analysed based on partial mtDNA control region sequences. Special attention has been paid to Chilean populations of Orestias agassii and species from isolated lakes of northern Chile, e.g., O. agassii, Orestias chungarensis, Orestias parinacotensis, Orestias laucaensis, and Orestias ascotanensis. Orestias tschudii, Orestias luteus, and Orestias ispi were analysed comparatively. Our findings support the utility of mtDNA control region sequences for phylogenetic studies within the "agassii species complex" and confirmed the monophyly of this particular lineage, excluding O. luteus. However, the monophyly of further morphologically defined lineages within the "agassii complex" appears doubtful. No support was found for the utility of these data sets for inferring phylogenetic relationships between more distantly related taxa originating from Lake Titicaca.

REPROBATION AND LACK OF INTEREST IN MECHATRONICS ENGINEERING STUDENTS

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César Humberto Guzmán Valdivia

2013-07-01

Full Text Available Engineering education in mechatronics is an attractive field of research because it is a new multidisciplinary career. However, a potential problem is the reprobation rate. In the period from January to April 2012 at the Universidad Politécnica de Zacatecas a 53% regular students of a total of 197 were registered. To find the causes of this problem, a survey was conducted to determine the causes of reprobation, lack of motivation and interest to a population of 96 students, of which 40 were the first training cycle, 32 the second and 24 the third. The surveys yielded three main results. The first indicates that the lack of interest is proportional to the time spent in college. The second shows that the reprobation rate is linked to the laziness and the excess of courses. And the last shows a lack of motivation and low expectations of student due to the monotony of the theoretical courses. In conclusion, more research is needed to have a motivated student in an engineering career in mechatronics.

Genetic connectivity and self-replenishment of inshore and offshore populations of the endemic anemonefish, Amphiprion latezonatus

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Steinberg, Rosemary

2016-02-19

Globally, marine species are under increasing pressure from human activities, including ocean warming, acidification, pollution, and overfishing. Species most vulnerable to these pressures tend to be ecological specialists that have low abundance and small distribution ranges (endemics). Marine endemics often exist as meta-populations distributed among few isolated locations. Determining genetic connectivity among these locations is essential to understanding the recovery potential of endemics after local extinction events. This study examined connectivity in the endemic anemonefish, Amphiprion latezonatus, a habitat specialist with low abundance at most locations. Evolutionary and contemporary migration, genetic diversity, and self-replenishment among the four main locations (Sunshine Coast, North Solitary Island, Lord Howe Island, and Norfolk Island) that comprise the entire A. latezonatus geographic range were assessed using mtDNA and microsatellite markers. Though historical gene flow inferred from mtDNA appeared high, population genetic differentiation was evident and contemporary gene flow inferred from microsatellites was limited, alongside very high (≥89 %) self-replenishment at all locations. Together, these data suggest prolonged recovery times following severe population decline (or extirpation) and indicate a need to protect this species at all locations, particularly Norfolk Island and Sunshine Coast where marine protected areas are lacking.

Design and construction of "synthetic species".

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Eduardo Moreno

Full Text Available Synthetic biology is an area of biological research that combines science and engineering. Here, I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr's Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term "synthetic species" to distinguish it from "natural species", not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment. The use of genetic engineering to design artificial species barriers could help us understand natural speciation and may have practical applications. For instance, the transition from transgenic organisms towards synthetic species could constitute a safety mechanism to avoid the hybridization of genetically modified animals with wild type populations, preserving biodiversity.

Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers.

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Sethi, Khushboo; Siwach, Priyanka; Verma, Surender Kumar

2015-10-01

Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it  has not been explored fully. During the present study, 100 polymorphic SSR loci were  used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.

Assessing local population vulnerability to wind energy development with branching process models: an application to wind energy development

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Erickson, Richard A.; Eager, Eric A.; Stanton, Jessica C.; Beston, Julie A.; Diffendorfer, James E.; Thogmartin, Wayne E.

2015-01-01

Quantifying the impact of anthropogenic development on local populations is important for conservation biology and wildlife management. However, these local populations are often subject to demographic stochasticity because of their small population size. Traditional modeling efforts such as population projection matrices do not consider this source of variation whereas individual-based models, which include demographic stochasticity, are computationally intense and lack analytical tractability. One compromise between approaches is branching process models because they accommodate demographic stochasticity and are easily calculated. These models are known within some sub-fields of probability and mathematical ecology but are not often applied in conservation biology and applied ecology. We applied branching process models to quantitatively compare and prioritize species locally vulnerable to the development of wind energy facilities. Specifically, we examined species vulnerability using branching process models for four representative species: A cave bat (a long-lived, low fecundity species), a tree bat (short-lived, moderate fecundity species), a grassland songbird (a short-lived, high fecundity species), and an eagle (a long-lived, slow maturation species). Wind turbine-induced mortality has been observed for all of these species types, raising conservation concerns. We simulated different mortality rates from wind farms while calculating local extinction probabilities. The longer-lived species types (e.g., cave bats and eagles) had much more pronounced transitions from low extinction risk to high extinction risk than short-lived species types (e.g., tree bats and grassland songbirds). High-offspring-producing species types had a much greater variability in baseline risk of extinction than the lower-offspring-producing species types. Long-lived species types may appear stable until a critical level of incidental mortality occurs. After this threshold, the risk of

Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment.

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Gouskov, Alexandre; Reyes, Marta; Wirthner-Bitterlin, Lisa; Vorburger, Christoph

2016-02-01

The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power stations, two weirs and the Rhine Falls. The shallow genetic population structure reflected drainage topology and was affected significantly by barriers to migration. The effect of power stations equipped with fishpasses on genetic differentiation was detectable, albeit weaker than that of man-made barriers without fishpasses. The Rhine Falls as the only long-standing natural obstacle (formed 14 000 to 17 000 years ago) also had a strong effect. Man-made barriers also exacerbated the upstream decrease in allelic diversity in the catchment, particularly when lacking fishpasses. Thus, existing fishpasses do have the desired effect of mitigating fragmentation, but barriers still reduce population connectivity in a fish that traverses fishpasses better than many other species. Less mobile species are likely to be affected more severely.

Site-specific assessments of the abundance of three inshore dolphin species to inform conservation and management

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Alexander Mark Brown

2016-02-01

Full Text Available Assessing the abundance of wildlife populations is essential to their effective conservation and management. Concerns have been raised over the vulnerability of tropical inshore dolphins in waters off northern Australia to anthropogenic impacts on local populations, yet a lack of abundance data precludes assessment of their conservation status and the management of threats. Using small vessels as cost-effective research platforms, photo-identification surveys and capture-recapture models were applied to provide the first quantitative abundance data for Australian snubfin (Orcaella heinsohni, Australian humpback (Sousa sahulensis, and Indo-Pacific bottlenose dolphins (Tursiops aduncus at five sites in the Kimberley region of north-western Australia. The abundance of each species was highly variable between different sites, likely reflecting species-specific habitat preferences. Within the c. 130 km2 study sites, the estimated abundance of most species was ≤ 60 individuals (excluding calves, and fewer than 20 humpback dolphins were identified at each site in any one 3-5 week sampling period. However, larger estimates of c. 130 snubfin and c. 160 bottlenose dolphins were obtained at two different sites. Several local populations showed evidence of site fidelity, particularly snubfin dolphins. By implementing a standardized, multi-site approach, data on local populations were provided within a broader, regional context, and indicated that each species is patchily distributed in the region. This highlights the need for site-specific baseline data collection using appropriate survey techniques to quantitatively assess the potential impacts of threatening activities to local populations. These findings further illustrate the need to gain a greater understanding of known and potential threats to inshore dolphin populations, their relative impacts, and to mitigate where necessary. In particular, the level of interactions with inshore gillnet fisheries

Host-related genetic differentiation in the anther smut fungus Microbotryum violaceum in sympatric, parapatric and allopatric populations of two host species Silene latifolia and S. dioica

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Van Putten, W.F.; Biere, A.; Van Damme, J.M.M.

2005-01-01

We investigated genetic diversity in West European populations of the fungal pathogen Microbotryum violaceum in sympatric, parapatric and allopatric populations of the host species Silene latifolia and S. dioica, using four polymorphic microsatellite loci. In allopatric host populations, the fungus

Host-related genetic differentiation in the anther smut fungus Microbotryum violaceum in sympatric, parapatric and allopatric populations of two host species Silene latifolia and S-dioica

NARCIS (Netherlands)

Van Putten, WF; Biere, A; Van Damme, JMM

We investigated genetic diversity in West European populations of the fungal pathogen Microbotryum violaceum in sympatric, parapatric and allopatric populations of the host species Silene latifolia and S. dioica, using four polymorphic microsatellite loci. In allopatric host populations, the fungus

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

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Dale, Julia; Price, Erin P; Hornstra, Heidie; Busch, Joseph D; Mayo, Mark; Godoy, Daniel; Wuthiekanun, Vanaporn; Baker, Anthony; Foster, Jeffrey T; Wagner, David M; Tuanyok, Apichai; Warner, Jeffrey; Spratt, Brian G; Peacock, Sharon J; Currie, Bart J; Keim, Paul; Pearson, Talima

2011-12-01

Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics

Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

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Julia Dale

2011-12-01

Full Text Available Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST. These populations correlate with the major foci of endemicity (Australia and Southeast Asia. Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs. Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

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Lu Hou

2018-04-01

Full Text Available Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548 and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958 were found in this species. Molecular variance analysis suggested that most of the variation (83% existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.

Babesia behnkei sp. nov., a novel Babesia species infecting isolated populations of Wagner's gerbil, Dipodillus dasyurus, from the Sinai Mountains, Egypt.

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Bajer, Anna; Alsarraf, Mohammed; Bednarska, Małgorzata; Mohallal, Eman M E; Mierzejewska, Ewa J; Behnke-Borowczyk, Jolanta; Zalat, Sammy; Gilbert, Francis; Welc-Falęciak, Renata

2014-12-09

Although a number of new species of Babesia/Theileria have been described recently, there are still relatively few reports of species from Africa. In this study based on the evaluation of morphology and phylogenetic relationships, we describe a novel species from Wagner's gerbil, Babesia behnkei n. sp. Rodents (n = 1021) were sampled in four montane valleys (wadies) in 2000, 2004, 2008 and 2012 in the Sinai Mountains, Egypt. The overall prevalence of Babesia spp. was highest in the Wagner's gerbil (Dipodillus dasyurus; 38.7%) in comparison to the prevalence in the spiny mice species, Acomys dimidiatus and A. russatus. Morphological investigations were conducted for the comparison of trophozoites of the novel species of Babesia with the B. microti King's 67 reference strain. Thirty-two isolates derived from D. dasyurus over a 9 year period (2004-2012) from two wadies (29 isolates from Wadi Gebel and 3 from Wadi El-Arbaein) were investigated by microscopic, molecular and phylogenetic analysis. A near-full-length sequence of the 18S rRNA gene and the second internal transcribed spacer (ITS2) region were amplified, sequenced and used for the construction of phylogenetic trees. A novel species of Babesia was identified in two isolated populations of D. dasyurus. Phylogenetic analysis of 18S rDNA and ITS2 sequences revealed that B. behnkei n. sp. is most closely related to B. lengau from cheetahs from South Africa and to Nearctic species found only in North America (the pathogenic B. duncani and B. conradae) and that it is more distant to the cosmopolitan rodent parasite B. microti. Trophozoites of B. behnkei were smaller and less polymorphic than trophozoites of B. microti. Babesia behnkei n. sp. is a novel species of the 'Duncani group' maintained in isolated populations of Dipodillus dasyurus occurring in the Sinai Mountains of Egypt.

Dynamics of Woodpecker – Common Starling interactions: a comparison of Old World and New World species and populations

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Jackson Jerome A.

2016-06-01

Full Text Available Woodpecker species whose cavities are most usurped by Common Starlings (Sturnus vulgaris are widespread and generalists in their use of habitats. These include primarily woodpeckers that are similar in size to or slightly larger than the starling - such as the Great-spotted Woodpecker (Dendrocopos major of Eurasia and the Northern Flicker (Colaptes auratus and Red-bellied (Melanerpes carolinus and Red-headed (M. erythrocephalus Woodpeckers of North America. Usurpation occurs primarily in human-dominated urban, suburban and exurban habitats with pastures, sports fields and other open areas that serve as prime feeding habitats for starlings. Starlings prefer high, more exposed cavities with a minimal entrance diameter relative to their body size. Usurpation success depends on timing - optimally just as a cavity is completed and before egg-laying by the woodpeckers. Starlings likely reduce woodpecker populations in more open, human-dominated habitats. Woodpecker habitat losses and fragmentation are more serious problems that enhance habitat quality for starlings and reduce habitat quality for most woodpeckers. The only woodpeckers that might become in danger of extinction as a primary result of starling cavity usurpation are likely island species with small populations. Conservation of rare species limited to islands, such as Fernandina’s Flicker (Colaptes fernandinae of Cuba, may depend on our ability to prevent the establishment of the Common Starling or other aggressive cavity competitors on their island.

Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

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Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

2011-02-01

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

Uniform Selection as a Primary Force Reducing Population Genetic Differentiation of Cavitation Resistance across a Species Range

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Lamy, Jean-Baptiste; Bouffier, Laurent; Burlett, Régis; Plomion, Christophe; Cochard, Hervé; Delzon, Sylvain

2011-01-01

Background Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. Methodology We assessed cavitation resistance (P 50), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F ST) and quantitative genetic differentiation (Q ST), for retrospective identification of the evolutionary forces acting on these traits. Results/Discussion In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h2 ns = 0.43±0.18, CVA = 4.4%). Q ST was significantly lower than F ST, indicating uniform selection for P 50, rather than genetic drift. Putative mechanisms underlying QST

Evaluating within-population variability in behavior and demography for the adaptive potential of a dispersal-limited species to climate change

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Muñoz, David J.; Miller Hesed, Kyle; Grant, Evan H. Campbell; Miller, David A.W.

2016-01-01

Multiple pathways exist for species to respond to changing climates. However, responses of dispersal-limited species will be more strongly tied to ability to adapt within existing populations as rates of environmental change will likely exceed movement rates. Here, we assess adaptive capacity in Plethodon cinereus, a dispersal-limited woodland salamander. We quantify plasticity in behavior and variation in demography to observed variation in environmental variables over a 5-year period. We found strong evidence that temperature and rainfall influence P. cinereus surface presence, indicating changes in climate are likely to affect seasonal activity patterns. We also found that warmer summer temperatures reduced individual growth rates into the autumn, which is likely to have negative demographic consequences. Reduced growth rates may delay reproductive maturity and lead to reductions in size-specific fecundity, potentially reducing population-level persistence. To better understand within-population variability in responses, we examined differences between two common color morphs. Previous evidence suggests that the color polymorphism may be linked to physiological differences in heat and moisture tolerance. We found only moderate support for morph-specific differences for the relationship between individual growth and temperature. Measuring environmental sensitivity to climatic variability is the first step in predicting species' responses to climate change. Our results suggest phenological shifts and changes in growth rates are likely responses under scenarios where further warming occurs, and we discuss possible adaptive strategies for resulting selective pressures.