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The article examines the population genetics of the Pteropus niger or the Mauritius flying fox. Topics discussed include the mitochondrial DNA sequence showing a moderate level of genetic variation among P. niger's population, the implications of the results for fox conservation and disease surveillance and the factors that pose risks to the population of the animals.

Although many classic radiations on islands are thought to be the result of repeated lineage splitting, the role of past fusion is rarely known because during these events, purebreds are rapidly replaced by a swarm of admixed individuals. Here, we capture lineage fusion in action in a Galápagos giant tortoise species, Chelonoidis becki, from Wolf Volcano (Isabela Island). The long generation time of Galápagos tortoises and dense sampling (841 individuals) of genetic and demographic data were integral in detecting and characterizing this phenomenon. In C. becki, we identified two genetically distinct, morphologically cryptic lineages. Historical reconstructions show that they colonized Wolf Volcano from Santiago Island in two temporally separated events, the first estimated to have occurred ~199 000 years ago. Following arrival of the second wave of colonists, both lineages coexisted for approximately ~53 000 years. Within that time, they began fusing back together, as microsatellite data reveal widespread introgressive hybridization. Interestingly, greater mate selectivity seems to be exhibited by purebred females of one of the lineages. Forward-in-time simulations predict rapid extinction of the early arriving lineage. This study provides a rare example of reticulate evolution in action and underscores the power of population genetics for understanding the past, present and future consequences of evolutionary phenomena associated with lineage fusion. [ABSTRACT FROM AUTHOR]

Background The margins of a species' range might be located at the margins of a species' niche, and in such cases, can be highly vulnerable to climate changes. They, however, may also undergo significant evolutionary change due to drastic population dynamics; e.g., changes in population size and distribution, which may increase the chance of contact among species. Such species interactions induced by climate changes could then regulate or facilitate further responses to climatic changes. We hypothesized that climate change-induced species contacts and subsequent genetic exchanges due to differences in population dynamics take place at the species boundaries. We sampled two closely related Rubus species, one temperate (Rubus palmatus) and the other subtropical (R. grayanus) near their joint species boundaries in southern Japan. Coalescent analysis, based on molecular data and ecological niche modelling during the Last Glacial Maximum (LGM), were used to infer past population dynamics. At the contact zones on Yakushima (Yaku Island), where the two species are parapatrically distributed, we tested hybridization along altitudinal gradients. Results Coalescent analysis suggested that the southernmost populations of R. palmatus predated the LGM (~20,000 ya). Conversely, populations at the current northern limit of R. grayanus diverged relatively recently and likely represent young outposts of a northbound range shift. These population dynamics were partly supported by the ensemble forecasting of six different species distribution models. Both past and ongoing hybridizations were detected near and on Yakushima. Backcrosses and advanced-generation hybrids likely generated the clinal hybrid zones along altitudinal gradients on the island where the two species are currently parapatrically distributed. Conclusions Climate oscillations during the Quaternary Period and the response of a species in range shifts likely led to repeated contacts with the gene pools of ecologically distinct relatives. Such species interactions, induced by climate changes, may bring new genetic material to the marginal populations where species tend to experience more extreme climatic conditions at the margins of the species distribution. [ABSTRACT FROM AUTHOR]

The population dynamics of snowshoe hares ( Lepus americanus) are fundamental to the ecosystem dynamics of Canada's boreal forest. During the 8- to 11-year population cycle, hare densities can fluctuate up to 40-fold. Predators in this system (lynx, coyotes, great-horned owls) affect population numbers not only through direct mortality but also through sublethal effects. The chronic stress hypothesis posits that high predation risk during the decline severely stresses hares, leading to greater stress responses, heightened ability to mobilize cortisol and energy, and a poorer body condition. These effects may result in, or be mediated by, differential gene expression. We used an oligonucleotide microarray designed for a closely-related species, the European rabbit ( Oryctolagus cuniculus), to characterize differences in genome-wide hippocampal RNA transcript abundance in wild hares from the Yukon during peak and decline phases of a single cycle. A total of 106 genes were differentially regulated between phases. Array results were validated with quantitative real-time PCR, and mammalian protein sequence similarity was used to infer gene function. In comparison to hares from the peak, decline phase hares showed increased expression of genes involved in metabolic processes and hormone response, and decreased expression of immune response and blood cell formation genes. We found evidence for predation risk effects on the expression of genes whose putative functions correspond with physiological impacts known to be induced by predation risk in snowshoe hares. This study shows, for the first time, a link between changes in demography and alterations in neural RNA transcript abundance in a natural population. [ABSTRACT FROM AUTHOR]

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of FST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global FST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation. [ABSTRACT FROM AUTHOR]

Natural infections of ectothermic vertebrates by ranaviruses (RV, family Iridoviridae) are rapidly increasing, with an alarming expansion of RV tropism and resulting die-offs of numerous animal populations. Notably, infection studies of the amphibian Xenopus laevis with the ranavirus Frog Virus 3 (FV3) have revealed that although the adult frog immune system is efficient at controlling RV infections, residual quiescent virus can be detected in mononuclear phagocytes of otherwise asymptomatic animals following the resolution of RV infections. It is noteworthy that macrophage-lineage cells are now believed to be a critical element in the RV infection strategy. In the present work, we report that inflammation induced by peritoneal injection of heat-killed bacteria in asymptomatic frogs one month after infection with FV3 resulted in viral reactivation including detectable viral DNA and viral gene expression in otherwise asymptomatic frogs. FV3 reactivation was most prominently detected in kidneys and in peritoneal HAM56+ mononuclear phagocytes. Notably, unlike adult frogs that typically clear primary FV3 infections, a proportion of the animals succumbed to the reactivated FV3 infection, indicating that previous exposure does not provide protection against subsequent reactivation in these animals. [ABSTRACT FROM AUTHOR]

Aposematic organisms have warning signals advertising their unpalatability to predators, and because signal efficiency is better in higher densities, positive frequency-dependent selection is expected to select against less common signals. The wood tiger moth ( Parasemia plantaginis) occurs across the Holarctic and its conspicuous hindwings serve as warning signals to predators. It also has conspicuous black and white forewing patterns that could act as warning signals, or help to hide the moth by preventing predators from seeing the outline of the moth's body (a strategy known as disruptive coloration). In Alaska, the predominant forewing pattern changes distinctly between the regions around Fairbanks and Anchorage, suggesting local predators may maintain differences if the pattern functions as a warning signal. Alternatively, restricted gene flow along with drift could be responsible. We placed artificial moths with both local dominant and foreign forewing patterns in each of the two regions to test if predators select against the foreign forewing types, which would suggest the warning signal function of forewing patters. We also manipulated the level of disruptiveness in the forewing patterns to see if disruptiveness works in concert with the warning signal. The locally dominant forewing type was better protected in Fairbanks, but not in Anchorage where morphs were attacked equally. Manipulating the level of disruptiveness in the forewing pattern did not influence predation. Population genetic analyses from specimens caught during fieldwork showed the existence of two populations and restricted gene flow. Our results suggest that positive frequency dependent selection may be partially responsible for maintaining local signal differences, although predators seem to avoid both forewing patterns in Anchorage. Restricted gene flow between the two populations could be attributed to a combination of selection against foreign morphs in Fairbanks and physical barriers, which both likely contribute to warning signal differences in Alaska. [ABSTRACT FROM AUTHOR]

Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population of large effective size using a GS approach. A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) mined in 2660 gene sequences. GS models were built to predict estimated breeding values using all the available SNPs or SNP subsets of the largest absolute effects, and they were validated using various cross-validation schemes. The accuracy of genomic estimated breeding values (GEBVs) varied from 0.327 to 0.435 when the training and the validation data sets shared half-sibs that were on average 90% of the accuracies achieved through traditionally estimated breeding values. The trend was also the same for validation across sites. As expected, the accuracy of GEBVs obtained after cross-validation with individuals of unknown relatedness was lower with about half of the accuracy achieved when half-sibs were present. We showed that with the marker densities used in the current study, predictions with low to moderate accuracy could be obtained within a large undomesticated population of related individuals, potentially resulting in larger gains per unit of time with GS than with the traditional approach. [ABSTRACT FROM AUTHOR]

More than two decades have passed since the first studies documenting genetic population structure of green turtles (Chelonia mydas) were published. Since then many more have followed and characterization of the genetic structure of green turtle rookeries now covers most of the global distribution of the species, benefitting conservation of this threatened species worldwide. However, important data gaps still exist across a large part of the western and central Pacific Ocean ( WCPO). This large area is made up of hundreds of scattered islands and atolls of Micronesia, Melanesia, and Polynesia, most of which are remote and difficult to access. In this study, we assessed stock structure of green turtles throughout the WCPO using mitochondrial (mt) DNA from 805 turtles sampled across 25 nesting locations. We examined whether sequencing longer fragments (770 bp) of the control region increases resolution of stock structure and used genetic analysis to evaluate level of demographic connectivity among island nesting populations in the WCPO. We identified a total of 25 haplotypes characterized by polymorphism within the 770 bp sequences, including five new variants of haplotypes that were indistinguishable with shorter 384 bp reads from previous studies. Stock structure analysis indicated that rookeries separated by more than 1,000 km were significantly differentiated from each other, but neighboring rookeries within 500 km showed no genetic differentiation. Results presented in this paper establish that sequencing of longer fragments (770 bp) of the control region does in some cases increase resolution and that there are at least seven independent stocks in the region. [ABSTRACT FROM AUTHOR]

As one of the few known species in an active phase of intron proliferation, the microcrustacean Daphnia pulex is an especially attractive system for interrogating the gain and loss of introns in natural populations. In this study, we used a comparative population-genomic approach to identify and characterize 90 recently gained introns in this species. Molecular clock analyses indicate that these introns arose between 3.9 × 105 and 1.45 × 104 years ago, with a spike in intron proliferation approximately 5.2 × 104 to 1.22 × 105 years ago. Parallel gains at homologous positions contribute to 47.8% (43/90) of discovered new introns. A disproportionally large number of new introns were found in historically isolated populations in Oregon. Nonetheless, derived, intron-bearing alleles were also identified in a wide range of geographic locations, suggesting intron gain and, to a lesser degree, intron loss are important sources of genetic variation in natural populations of Daphnia. A majority (55/90 or 61.1%) of the identified neointrons have associated internal direct repeats with lengths and compositions that are unlikely to occur by chance, suggesting repeated bouts of staggered double-strand breaks (DSBs) during their evolution. Accordingly, internal, staggered DSBs may contribute to a passive trend toward increased length and sequence diversity in nascent introns. [ABSTRACT FROM AUTHOR]

Linear mixed models, for which the prior multivariate normal distributions of random effects are assumed to have a mean equal to 0, are commonly used in animal breeding. However, some statistical analyses (e.g., the consideration of a population under selection into a genomic scheme breeding, multiple-trait predictions of lactation yields, and Bayesian approaches integrating external information into genetic evaluations) need to alter both the mean and (co)variance of the prior distributions and, to our knowledge, most software packages available in the animal breeding community do not permit such alterations. Therefore, the aim of this study was to propose a method to alter both the mean and (co)variance of the prior multivariate normal distributions of random effects of linear mixed models while using currently available software packages. The proposed method was tested on simulated examples with 3 different software packages available in animal breeding. The examples showed the possibility of the proposed method to alter both the mean and (co)variance of the prior distributions with currently available software packages through the use of an extended data file and a user-supplied (co)variance matrix. [ABSTRACT FROM AUTHOR]

The effects of ontogenetic niche shifts on community structure and dynamics are underexplored, despite the occurrence of such shifts in the majority of animal species. We studied the form of niche shifts in a predator that exhibits multiple ontogenetic niche shifts, and analyzed how this life history complexity affects the size-structured predator-prey dynamics in the system. The predator represents either an ontogenetic generalist, exhibiting a partial shift to prédation (in which case an alternative resource is also available) or an ontogenetic specialist, exhibiting a complete shift (in which case the predator depends entirely on prédation). We showed two effects on community dynamics from accounting for a complete niche shift to prédation: (1) occurrence of alternative stable community states (coexistence and a prey-oniy community state) and (2) occurrence of deterministic extinction following initially successful invasion (predators can invade an equilibrium with only prey, but are bound to go extinct after a few generations). Both phenomena are due to the match or mismatch in the timing of predators and suitably sized prey and the growth trajectory of the predator, which is plastic, due to the population feedback on available resources. In the case of persistence without invasion (alternative stable community states), slow growth during the pre-piscivorous life stage is necessary to stay in tune with the prey cycle; in the case of extinction following invasion, slow growth through the pre-piscivorous life stage causes the predator to reach the completely piscivorous stage when there is no prey available to feed upon. Somatic growth rates are directly coupled to food availability, which, in turn, is the result of density-dependent feedbacks in the system. Since they primarily determine these density-dependent feedbacks, the ontogenetic niche shifts in predator life history structure the community to a major extent. [ABSTRACT FROM AUTHOR]

Relatively little work has been done on the population genetics and phylogenetic patterns in Notophthalmus viridescens (Eastern Newt). The most recent study by Gabor and Nice (2004) divided the sampled populations into northern and southern groups rather than along taxonomic lines, and patterns of genetic variation indicated the southern populations were isolated and undergoing genetic drift. To re-evaluate these patterns, we collected sequence data on the mitochondrial ND2 and the flanking tRNAMet genes in fifteen South Carolina populations in the piedmont, sandhills, and lower coastal plain where three of the four subspecies were located (we found no Eastern Newts in the upper coastal plain). Haplotypes did not group by taxonomic designation in phylogenetic analyses, suggesting introgressive hybridization has occurred. Statistical parsimony analysis resolved the haplotype groups into two geographic groups, and partitioning of genetic variation between these groups was significant. We suggest these groups represent populations established during the last glacial maximum, a pattern that has been observed in other pond-breeding salamanders. [ABSTRACT FROM AUTHOR]

Although male and female lizards have different dispersal behaviors that are subject to selection, these differences do not impact genetic structure on islands. This is important because we currently understand little about the consequences of dispersal in terms of natural selection and our study aimed to address that shortcoming. Our study measured natural selection on dispersal behavior using island lizards from The Bahamas. We discuss the importance of spatial and temporal scales to this result.Dispersal is a potentially risky behavior that has several important implications for demography. Dispersal may be measured directly through behavioral observations or indirectly using genetic analyses. The direct approach is accurate but labor-intensive, whereas the indirect approach depends on population subdivision to infer dispersal events. Here, we combine field studies of behavior and natural selection in an island lizard (Anolis sagrei) to provide direct estimates of sex-specific dispersal and then compare these estimates to measures of population subdivision at both nuclear (biparental inheritance) and mitochondrial (uniparental inheritance) genetic markers. Juvenile males dispersed 4 times further than juvenile females. Natural selection acted against long-distance dispersal in females, but we measured no such selection on dispersal distance in males. Despite strong evidence for sex-biased dispersal accompanied by selection, we detected no population genetic signature of dispersal at either nuclear or mitochondrial loci. In closed populations, such as those occurring on small islands, repeated dispersal events may have important demographic consequences and yet produce no population genetic signature owing to continuous admixture of genotypes. [ABSTRACT FROM PUBLISHER]

Northern small rodents are well known for their population cycles which represent a key process for the functioning of arctic and boreal ecosystems. Habitat use often changes in the course of the cycle. Higher densities can either lead to spill-over into secondary habitats or to increased habitat specificity because of interspecific competition. Here we investigate whether voles in the shrub tundra of southern Yamal exhibit density dependent habitat use. Voles were trapped at the Erkuta Tundra Monitoring Site (N 68.2°, E 69.2°) in three characteristic habitats over five years covering all phases of the population cycle. Our analyses focused on the two most numerous species Microtus gregalis (52% of individuals caught) and M. middendorffii (36%). A small-scale spill-over effect was observed for M. gregalis, which increasingly used the open habitat adjacent to their preferred willow thickets at high abundance. At a larger scale no such effect was observed for the two Microtus species - a result which is explained by the overall moderate densities of voles and the large spatial extent of the primary habitat of M. middendorffii: moist moss dwarf shrub tundra. [ABSTRACT FROM AUTHOR]

The snow leopard ( Panthera uncia) is an endangered carnivore of southern and central Asia. Approximate 10% of the global population occurs in the Himalayan region of Nepal. The snow leopard is thought to be in decline because of human-snow leopard conflicts, poaching, habitat loss and fragmentation, decreasing prey populations, and a lack of awareness and enforcement of conservation legislation. In this study, we used habitat surveys and genetic analyses of putative snow leopard scats to estimate the abundance, habitat preferences, and diet profile of the snow leopard in the Annapurna Conservation Area, Nepal. Cliffs, grassland, and shrubland at high elevation (3,000-5,000 m) were the preferred habitats of snow leopards. Eighty-three percent of collected scats collected were verified to be from snow leopards using mitochondrial DNA cytochrome- b species-specific polymerase chain reaction assays. Sixty-two percent of the scats were successfully genotyped using 6 microsatellite markers, and identified as having originated from 5 different individuals. The dispersion of multiple scats from the same individual suggested minimum movement ranges of 89.4 km2 for males and 59.3 km2 for females. Estimated population density was 1.9 individuals/100 km2 and 22 snow leopards were estimated to inhabit the upper Mustang region. Microhistological analysis of scats ( n = 248) revealed that blue sheep ( Pseudois nayaur) was the primary wild prey (63%), and livestock also contributed significantly (18%) to snow leopard diet. We used a multipronged strategy for assessing conservation options for this rare carnivore and compared our findings with those pertaining to other predators of the region that share similar habitats and resources. The findings from this study will be helpful in managing snow leopards and similar carnivore populations across the snow leopard's entire geographic range. [ABSTRACT FROM AUTHOR]

The Eurasian otter ( Lutra lutra) is recovering from well-documented population declines that occurred during the 20th century. Little is known about the genetic impact of these declines in northern Britain and the current understanding of otter genetic structure in Britain is incomplete. This study reexamines genetic structure in Scotland, one of the otter's major strongholds in the United Kingdom, and combines data with a published microsatellite data set from the remainder of the United Kingdom to produce the 1st comprehensive assessment of genetic structure across the entirety of mainland Britain. We show that there is a remarkable contrast in genetic structure of otters in northern Britain compared to the south. Population fragmentation and high levels of genetic structure were typical of southern Britain, whereas in the north we observed a virtually panmictic population. These results imply very different demographic histories of otters in these 2 regions. Our findings also suggest a more favorable environment for the Eurasian otter in recent times in the north of the United Kingdom, possibly linked to human population density and anthropogenic habitat impacts. This study therefore provides a complete description of population genetics of the Eurasian otter in the United Kingdom, and allows inferences to be made regarding the relative importance of landscape characteristics on the recovery of otter populations. [ABSTRACT FROM AUTHOR]

Of the three mouse species inhabiting Western Siberia, the striped field mouse is characterized by the highest level of genetic variation, a uniform distribution of polymorphism indicators, lower values of genetic differentiation, and higher values of gene flow, as compared to the house mouse and pygmy wood mouse. The house mouse populations have abrupt changes in the parameters of protein polymorphism in different localities. This is due to the considerable spatial dissociation of the cities of Siberia and the differing histories of their settlement. Inhabitation of an urban area leads to the partitioning of striped wood mouse populations into groups that considerably differ in allele frequencies and genetic variation indices. These changes are not related to the degree of urbanization and are determined by genetic drift. Some characteristics of these groups, like reduced variability, heterozygote deficit, and deviation from the Hardy-Weinberg equilibrium, limit their adaptive potential and make them dependent on the populations of inter-settlement territories. [ABSTRACT FROM AUTHOR]

Two Norway rat ( Rattus norvegicus) populations contrasting in behavior have been raised at the Institute of Cytology and Genetics, Novosibirsk, Russia with long-term selection for the absence or enhancement of an aggressive response towards humans. They are designated as tame and aggressive, respectively. In this work we investigated the effects of the selection on behavior, stress responsiveness, and function of testes in males of the 78th generation. It is shown that the difference between the strains in their response to humans remains the same as in previous generations. However, the differences in stress response and rate of maturation contradict earlier data. For the first time, we note a higher glucocorticoid-mediated response to restriction stress and retarded sexual maturation in tame rats compared to aggressive ones, according to morphometric indices of gonads and testosterone levels. It is conceivable that the change in selection effects is determined by the disjunction of the directions of selection for behavior and the modification of the stress response. This study is the first to characterize males recently (six or seven generations of propagation in captivity) caught in the wild with regard to the indices under consideration and used as a control group. Wild rats have the highest stress response and rate of sexual maturation as compared to those selected. [ABSTRACT FROM AUTHOR]

Emerging diseases are impacting animals under high-density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations. [ABSTRACT FROM AUTHOR]

Red deer ( Cervus elaphus) did not recolonise Ireland after the last glaciation, but the population in Co. Kerry is descended from an ancient (c. 5000 BP) introduction and merits conservation. During the mid-19th century exotic species including North American wapiti ( C. canadensis) and Japanese sika deer ( C. nippon nippon) were introduced to Ireland, mainly via Powerscourt Park, Co. Wicklow. While wapiti failed to establish, sika thrived, dispersed within Co. Wicklow and were translocated to other sites throughout Ireland. Red deer and sika are known to have hybridised in Ireland, particularly in Co. Wicklow, but an extensive survey with a large, highly diagnostic marker panel is required to assess the threat hybridisation potentially poses to the Co. Kerry red deer population. Here, 374 individuals were genotyped at a panel of 22 microsatellites and at a single mtDNA marker that are highly diagnostic for red deer and Japanese sika. The microsatellites are also moderately diagnostic for red deer and wapiti. Wapiti introgression was very low [trace evidence in 2 (0.53 %) individuals]. Despite long-standing sympatry of red deer and sika in the area, no red deer-sika hybrids were detected in Co. Kerry suggesting strong assortative mating by both species in this area. However, 80/197 (41 %) of deer sampled in Co. Wicklow and 7/15 (47 %) of deer sampled in Co. Cork were red-sika hybrids. Given their proximity and that hybrids are less likely to mate assortatively than pure individuals, the Co. Cork hybrids pose a threat to the Co. Kerry red deer. [ABSTRACT FROM AUTHOR]

Chondrostoma nasus is a cyprinid fish with highly specialized, ecologically and geographically distinct, ontogenetic trophic niches. Nase population numbers across their Swiss range have shown massive declines and many localized extinctions. In this study, we integrate genetic data (AFLP, microsatellite, mtDNA sequence) with phenotypic and demographic analyses to survey patterns of neutral and adaptive genetic diversity in all extant (and one extinct) Swiss nase populations, with the aim to delineate intraspecific conservation units (CUs) and to inform future population management strategies. We discovered two major genetically and geographically distinct population groupings. The first population grouping comprises nase inhabiting rivers flowing into Lake Constance; the second comprises nase populations from Rhine drainages below Lake Constance. Within these clusters there is generally limited genetic differentiation among populations. Genomic outlier scans based on 256 to 377 polymorphic AFLP loci revealed little evidence of local adaptation both within and among population clusters, with the exception of one candidate locus identified in scans involving the low genetic diversity Schanzengraben population. However, significant phenotypic differentiation in body shape between certain populations suggests a need for more intensive future studies of local adaptation. Our data strongly suggests that the two major population groups should be treated as distinct CUs, with any supplemental stocking and reintroductions sourced only from within the range of the CU concerned. [ABSTRACT FROM AUTHOR]

The Asian elephant is a flagship species for conservation in tropical Asia, but reliable population estimates are available only from a few populations. This is because the species can be elusive and occurs at low densities in dense habitat over a large part of its range. Phnom Prich Wildlife Sanctuary in the Eastern Plains, Cambodia, which is part of one of the largest protected area complexes in South-East Asia, is one such habitat that had not been systematically censused for elephants. We, therefore, used fecal-DNA based capture-mark-recapture sampling to estimate the population size for establishing a monitoring baseline. Five sampling sessions targeted all areas in and adjacent to Phnom Prich Wildlife Sanctuary believed to be used by elephants. Fresh dung was collected as the source of DNA and genotyping was carried out based on nine microsatellite loci. The 224 samples collected yielded 78 unique genotypes. Using model averaging of closed population capture-mark-recapture models, the elephant population in Phnom Prich Wildlife Sanctuary was estimated to number 136 ± 18 (SE) individuals. Our results suggest that eastern Cambodia supports a regionally important Asian elephant population. [ABSTRACT FROM AUTHOR]

Knowledge about the ecology of bottlenose dolphins in the Southwestern Atlantic Ocean is scarce. Increased by-catch rates over the last decade in coastal waters of southern Brazil have raised concerns about the decline in abundance of local dolphin communities. Lack of relevant data, including information on population structure and connectivity, have hampered an assessment of the conservation status of bottlenose dolphin communities in this region. Here we combined analyses of 16 microsatellite loci and mitochondrial DNA (mtDNA) control region sequences to investigate genetic diversity, structure and connectivity in 124 biopsy samples collected over six communities of photographically identified coastal bottlenose dolphins in southern Brazil, Uruguay and central Argentina. Levels of nuclear genetic diversity were remarkably low (mean values of allelic diversity and heterozygosity across all loci were 3.6 and 0.21, respectively), a result that possibly reflects the small size of local dolphin communities. On a broad geographical scale, strong and significant genetic differentiation was found between bottlenose dolphins from southern Brazil-Uruguay (SB-U) and Bahía San Antonio (BSA), Argentina (AMOVA mtDNA Φ = 0.43; nuclear F = 0.46), with negligible contemporary gene flow detected based on Bayesian estimates. On a finer scale, moderate but significant differentiation (AMOVA mtDNA Φ = 0.29; nuclear F = 0.13) and asymmetric gene flow was detected between five neighbouring communities in SB-U. Based on the results we propose that BSA and SB-U represent two distinct evolutionarily significant units, and that communities from SB-U comprise five distinct Management Units (MUs). Under this scenario, conservation efforts should prioritize the areas in southern Brazil where dolphins from three MUs overlap in their home ranges and where by-catch rates are reportedly higher. [ABSTRACT FROM AUTHOR]

Although there have been several studies based on the molecular data of green toads, some ambiguities related to the systematics of these toads in Turkey still remain. Thus, we used combined mitochondrial genes (D-loop and 12S ribosomal RNA) to resolve these taxonomic problems. We also applied demographic analysis to elucidate the evolutionary history using these genes. We found 3 haplotype groups: 1 for Bufo viridis and 2 lineages for Bufotes variabilis, with only the latter represented in Turkey. This study showed a genetic diversity within Anatolian B. variabilis. Population genetic analysis of mismatch distributions, Tajima's D-statistic, and Fu's Fs test are consistent with a range expansion of the Bufotes variabilis group covering western Turkey. B. variabilis populations of lineage 1 and lineage 2, from western and eastern Anatolia respectively, are genetically identical. Mitochondrial DNA haplotype groups may reflect historical separation within B. variabilis. Our study indicated that allopatric distribution of B. variabilis within Anatolia occurred due to climatic shifts during the Pliocene. This study shows that Anatolia likely has served as a factor in vicariant species formation. [ABSTRACT FROM AUTHOR]

Objective of this study was to evaluate microsatellite markers in paternity testing of native cattle breeds in Turkey. Blood samples were collected from Anatolian Black (n=51), Anatolian Grey (n=54), South Anatolian Red (n=51), Native Southern Anatolian Yellow (n=51), East Anatolian Red (n=45) and Zavot (n = 19) cattle. From the blood samples DNA was isolated by using a standard phenol/ chloroform method. A total of 20 microsatellite loci were selected from a FAO/ISAG-suggested list. Polymerase chain reaction products were separated by capillary electrophoresis and marker genotypes were determined by fragment analysis. In statistical analyses, allel numbers, observed (Ho) and expected (He) heterozygosities, deviation from Hardy-Weinberg Equilibrium and probability of exclusion (PE) at each microsatellite locus were calculated. A total of 269 different alleles were observed and the mean allele was identified as 13.45. Mean Ho and He values were observed as 0.619-0.852 and 0.669-0.877, respectively. The results indicated that the microsatellite test panel including the most informative 7 loci had total PE value of >0.9999 in each populations and can thereby be used for parentage testing studies of native cattle breeds in Turkey. [ABSTRACT FROM AUTHOR]

Background Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers. Results 23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed betweenthe two species. Conclusions Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc- DQB1 genes in these macaques. Balancing selection plays an important role in sharing allelic lineages between species, but genetic drift may share balancing selection dominance to maintain MHC diversity. Great divergence at neutral or adaptive markers showed that moderate genetic differentiation had occurred in rhesus macaque populations in western Sichuan, China, due to the habitat fragmentation caused by long-term geographic barriers and human activity. The Heishui population should be paid more attention for its lowest level of genetic diversity and relatively great divergence from others. [ABSTRACT FROM AUTHOR]

Crossing between the local Black Baladi (BB) and a commercial White Nicholas (WW) was carried out to estimate heterosis, direct additive and maternal effects for fitness traits, in addition to season effect. The breeding plan permitted the simultaneous production of the two pure varieties (BB and WW) and their reciprocal crosses (BWand WB) throughout two successive years from 2006 to 2007. Crossing and season had significant effect on most fitness traits studied (fertility, hatchability, late embryonic mortality, total egg loss, mortality rate, survival rate, and fitness index). The interactions between Genotypes and seasons were significant for all fitness traits studied. Eggs of BB hens and those produced from WW hens mated with BB toms had significantly the highest means for most fitness traits. The estimates of heterosis percentages for fitness traits indicated that the BW crosses had superior heterotic effect than the WB cross. The values of maternal additive and direct additive effects showed superiority of BB as sires which suggest that using of this variety as a terminal sire breed in crossbreeding programs including WW dams would be beneficial for improving the fitness traits. It could be concluded that crossing between BB variety and WW strain of turkey can improve fertility, hatchability and late embryonic mortality percentages, total egg loss, morality rate, survival rate and fitness index. [ABSTRACT FROM AUTHOR]

A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs ( Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation. [ABSTRACT FROM AUTHOR]

The yak is one of the few animals that can thrive in the harsh environment of the Qinghai-Tibetan Plateau and adjacent Alpine regions. Yak provides essential resources allowing Tibetans to live at high altitudes. However, genetic variation within and between wild and domestic yak remain unknown. Here, we present a genome-wide study of the genetic variation within and between wild and domestic yak. Using next-generation sequencing technology, we resequenced three wild and three domestic yak with a mean of fivefold coverage using our published domestic yak genome as a reference. We identified a total of 8.38 million SNPs (7.14 million novel), 383 241 InDels and 126 352 structural variants between the six yak. We observed higher linkage disequilibrium in domestic yak than in wild yak and a modest but distinct genetic divergence between these two groups. We further identified more than a thousand of potential selected regions ( PSRs) for the three domestic yak by scanning the whole genome. These genomic resources can be further used to study genetic diversity and select superior breeds of yak and other bovid species. [ABSTRACT FROM AUTHOR]

Geographic variation in life-history traits among populations of wide-ranging species is influenced by both spatial and temporal aspects of the environment. Rarely, however, are the effects of both aspects examined concurrently. We collected gravid female lizards ( Sceloporus undulatus) from northern (Indiana), central (Mississippi) and southern (Florida) populations, spanning nearly the full latitudinal range of the species, to examine amongpopulation differences in strategies of reproductive energy allocation. Adult females from the southern population were smaller, and produced fewer and smaller eggs in their first clutches than did females from the more northern populations. Southern females were more likely to produce a second clutch, and second clutches were smaller than first clutches for females from the 2 northern populations. Together these trends eliminated population differences in overall reproductive output after accounting for body size. The trend for greater reproductive energy to be allocated to first clutches at higher latitudes, and to later clutches at lower latitudes is corroborated by published data from field studies on multiple populations. Distributing reproductive effort by producing more clutches of smaller eggs may be an adaptive response to the long season available for egg incubation and lizard activity in sub-tropical southern environments. In contrast, allocating greater resources to early reproduction may enhance maternal fitness in the relatively short activity seasons that characterize more northern sites. [ABSTRACT FROM AUTHOR]

Abstract: Secreted frizzled-related protein 3 (sFRP3), encoded by the gene FRZB, is a member of the sFRP family with important roles in inhibition of the Wnt signalling pathway through competitive binding of the Wnt receptor. Here, we investigated pig FRZB as a candidate gene for growth traits and identified three polymorphic sites, an insertion (A-532B) and two SNPs (G636A and C650T) in its 5′-UTR. The genotype distributions of G636A and C650T were significantly different among mini-type indigenous (Diannan Small-ear and Tibetan), normal indigenous (Laiwu and Huai), and introduced (Large Yorkshire and Landrace) breeds. In semi-quantitative PCR expression analysis, expression of FRZB mRNA was abundant in tissues of hypophysis, longissimus dorsi muscle, and adipose tissues, and low in the heart, hypothalamus, and brain. Quantitative determination of mRNA level and protein expression analysis were corresponding. The results demonstrated that FRZB gene expression in longissimus dorsi muscle and liver tissue was significantly higher in Diannan Small-ear and Tibetan pigs than in the Large Yorkshire breed (P<0.05); however, in back fat tissue, the expression was significantly higher in Diannan Small-ear pig than in Tibetan or Large Yorkshire breeds (P<0.05). Given the known growth and fat characteristics of the breeds, these results indicate that FRZB expression has a negative association with muscle growth and a positive association with fat deposition. In conclusion, FRZB may be a major candidate gene for growth traits in pigs. [Copyright &y& Elsevier]

We investigate the population genetic structure of the declining western subspecies of the purple-crowned fairy-wren (Malurus coronatus coronatus) in order to guide conservation management recommendations for this riparian habitat specialist. Our analysis of multilocus microsatellite data, from 79 individuals sampled from across the species' range, indicates that M. c. coronatus occurs as genetically differentiated subpopulations that correspond to catchment boundaries or expansive gaps in habitat along waterways. The genetic similarity of large populations of fairy-wrens on four catchments (Fitzroy, Durack, Drysdale and Victoria) indicates widespread recent gene flow, whereas the high genetic distinctiveness of the Bindoola and Isdell catchments may reflect the current geographic isolation of these smaller populations. Genetic differentiation of these smaller geographically isolated populations affirms the negative effect that habitat degradation and fragmentation can have on population connectivity. A regional-scale approach to conservation with a focus on preventing degradation and enhancing connectivity may be critical to safeguard the persistence of M. c. coronatus subpopulations. Population genetic analysis indicates that the declining western subspecies of the purple-crowned fairy-wren (Malurus coronatus coronatus) occurs as five genetically distinct populations within the Fitzroy, Durack, Drysdale, Victoria and Pentecost catchments. A regional approach to conservation, focusing on prevention of degradation, is needed to safeguard the persistence of these populations. [ABSTRACT FROM AUTHOR]

The endangered northern hairy-nosed wombat (Lasiorhinus krefftii) has been monitored via remote sampling and genetic techniques since 2000, thus avoiding the detrimental effects on the animals of trapping and increasing the precision of abundance estimates. The currently available dinucleotide microsatellite markers used for this task are prone to stutter and other polymerase chain reaction artefacts, making allele calling difficult, and requiring costly duplication to ensure accuracy. To remedy this we have developed eight new tri- and tetranucleotide microsatellite markers that reduce the problem of stutter in DNA analysis. These new markers, along with three of the existing markers (two microsatellites and the SRY gender marker) were optimised in a single multiplex reaction that will reduce the time and cost of future northern hairy-nosed wombat hair censuses. We tested this new multiplex on 277 non-invasively collected hairs. One locus was rejected due to null-allele issues. The remaining nine microsatellite loci had two or three alleles. Genotype frequencies in the sample of detected individuals did not differ significantly from Hardy-Weinberg equilibrium and there was no evidence of linkage disequilibrium. This new multiplex provides comparable power to distinguish individuals, fewer issues with stutter artefacts and a reduced time and cost of analysis. It will be useful for future population censuses and long-term monitoring of individuals once they have been scored in previously genotyped and assigned samples. The endangered northern hairy-nosed wombat (Lasiorhinus krefftii) has been monitored via remote sampling and genetic techniques since 2000, thus avoiding the detrimental effects on the animals of trapping. We have developed eight new microsatellite markers, specifically designed to reduce the time, cost and error rates of future northern hairy-nosed wombat hair censuses. [ABSTRACT FROM AUTHOR]

Conservation of frogs is of global concern, owing to declines resulting from habitat destruction, global climate change, and disease. Knowledge of genetic variation in frog species is therefore desirable for the identification of management units. Here we surveyed mitochondrial DNA sequence variation in the Tasmanian endemic hylid frog Litoria burrowsae, which is infected by chytrid fungus, Batrachochytrium dendrobatidis, and may be declining. Neither phylogeographic structure nor deep phylogenetic divergence was detected in the species, although its populations were highly differentiated with respect to haplotype frequencies. The low-haplotype diversity in L. burrowsae suggests a recent bottleneck in the species, and population genetic structuring may reflect isolation by distance as well as founder effects associated with range expansion. Three putative management units were identified that require verification based on nuclear DNA variation and adaptation to local environments. Knowledge of intraspecific genetic variation is desirable for the identification of management units. We surveyed mitochondrial DNA sequences in the Tasmanian endemic frog Litoria burrowsae. Although phylogeographic structure was absent, populations were highly differentiated in haplotype frequencies, with a signature of 'isolation by distance'. Three putative management units were identified. [ABSTRACT FROM AUTHOR]

Across North America, anthropogenically induced habitat fragmentation has led to a severe decline in populations of black-tailed prairie dogs ( Cynomys ludovicianus). Although the area occupied by black-tailed prairie dogs in Chihuahua, northwestern Mexico, also has recently declined, this site remains comparatively unaffected by human disturbance. Cytochrome- b sequences and 10 nuclear microsatellite loci were analyzed across 13 colonies to test if due to large size, absence of plague, and protected status, the black-tailed prairie dogs from Janos possess relatively high levels of genetic variation and low genetic structure; or if recent population decline and peripheral effects result in relatively low genetic variation and high genetic structure. Analysis suggests moderate mitochondrial genetic variation relative to other sciurids, and not significantly different nuclear genetic variation relative to other populations of prairie dogs. Furthermore, in accordance to black-tailed prairie dog social organization, genetic structure among local populations was significant, and within-colony variation was higher than among-colony variation for both markers. FST was higher for mitochondrial than for nuclear DNA related to female philopatry and male-biased gene flow. Finally, a negative correlation between genetic differentiation as a function of colony area and population size found for nuclear microsatellite loci suggests an increased effect of genetic drift in smaller and less-dense colonies because of recent habitat fragmentation. In conclusion, despite being a peripheral and declining population, Janos black-tailed prairie dogs retained genetic variation that has been maintained by their social structure and dispersal pattern. En Norte América, la fragmentación del hábitat inducida por el hombre ha provocado una reducción considerable de las poblaciones de perros llaneros de cola negra ( Cynomys ludovicianus). Aunque el área ocupada por las colonias de perros llaneros en Chihuahua, al noroeste de México, también se ha reducido recientemente, esta población ha sido menos afectada por la perturbación humana. Se analizaron secuencias del citocromo b ( Cytb) y 10 microsatélites nucleares en 13 colonias para poner a prueba si la población de perros llaneros de cola negra de Janos posee niveles de variación genética relativamente altos y baja estructura genética debido a su gran tamaño, ausencia de peste y estatus de protección; o si la disminución poblacional reciente y los efectos periféricos han resultado en la presencia de baja variación y alta estructura genética. Los análisis sugieren que la variación genética mitocondrial es moderada con relación a otros sciúridos y que la variación genética nuclear no es significativamente distinta en relación a otras poblaciones de perros llaneros. Además, de acuerdo con la organización social de los perros llaneros de cola negra, la estructura genética entre poblaciones locales fue significativa y la variación hacia el interior de las colonias fue mayor que entre las colonias para ambos marcadores. Con relación a la filopatría de las hembras y la dispersión sesgada hacia los machos, la FST fue mayor para el ADN mitocondrial que para el ADN nuclear. Finalmente, para los marcadores nucleares se encontró una correlación negativa entre la diferenciación genética y el área de la colonia y el tamaño poblacional, lo que sugiere un incremento en el efecto de la deriva génica en las colonias más pequeñas y menos densas como resultado de la fragmentación del hábitat reciente. En conclusión, la estructura social y el patrón de dispersión ha mantenido la variación genética de los perros llaneros de cola negra de Janos a pesar de considerarse una población periférica y en declive. [ABSTRACT FROM AUTHOR]

Purpose: This study was performed to evaluate the potential association of the tumor necrosis factor alpha inducible protein 3gene ( TNFAIP3) polymorphisms with Fuchs' heterochromic iridocyclitis (Fuchs' Syndrome) in a Chinese Han population. Methods: Five single-nucleotide polymorphisms (SNPs), rs10499194, rs610604, rs7753873, rs5029928 and rs9494885 of TNFAIP3 were genotyped in 225 Fuchs' syndrome patients and 651 healthy controls using a PCR-restriction fragment length polymorphism assay. All control subjects were matched ethnically and geographically with the patients. Genotype counts in patients and controls were analyzed by the χ2 test. Results: All genotypic and allelic frequencies of the tested TNFAIP3 polymorphisms were in Hardy-Weinberg equilibrium. The genotypic and allelic frequencies of rs10499194, rs610604, rs7753873, rs5029928 and rs9494885 of TNFAIP3 were not different between patients with Fuchs' syndrome and controls. Conclusions: Our results suggest that rs10499194, rs610604, rs7753873, rs5029928 and rs9494885 of TNFAIP3 are not associated with Fuchs' syndrome in a Chinese Han population. [ABSTRACT FROM AUTHOR]

Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ‘tetricus complex’. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. [ABSTRACT FROM AUTHOR]

The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale ( Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci ( MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci. [ABSTRACT FROM AUTHOR]

To test the hypothesis that different drivers shape the diversity and biogeography of the total and active bacterial community, we examined the bacterial community composition along two transects, one from the inner Pearl River estuary to the open waters of the South China Sea ( SCS) and the other from the Luzon Strait to the SCS basin, using 454 pyrosequencing of the 16S r RNA and 16S r RNA gene (V1-3 regions) and thereby characterizing the active and total bacterial community, respectively. The diversity and biogeographic patterns differed substantially between the active and total bacterial communities. Although the composition of both the total and active bacterial community was strongly correlated with environmental factors and weakly correlated with geographic distance, the active bacterial community displayed higher environmental sensitivity than the total community and particularly a greater distance effect largely caused by the active assemblage from deep waters. The 16S r RNA vs. r DNA relationships indicated that the active bacteria were low in relative abundance in the SCS. This might be due to a high competition between active bacterial taxa as indicated by our community network models. Based on these analyses, we speculate that high competition could cause some dispersal limitation of the active bacterial community resulting in a distinct distance-decay relationship. Altogether, our results indicated that the biogeographic distribution of bacteria in the SCS is the result of both environmental control and distance decay. [ABSTRACT FROM AUTHOR]

Current population genetic models fail to cope with genetic differentiation for species with large, contiguous and heterogeneous distribution. We show that in such a case, genetic differentiation can be predicted at equilibrium by circuit theory, where conductance corresponds to abundance in species distribution models ( SDMs). Circuit- SDM approach was used for the phylogeographic study of the lepidopteran cereal stemborer Busseola fusca Füller ( Noctuidae) across sub- Saharan Africa. Species abundance was surveyed across its distribution range. SDMs were optimized and selected by cross-validation. Relationship between observed matrices of genetic differentiation between individuals, and between matrices of resistance distance was assessed through Mantel tests and redundancy discriminant analyses ( RDAs). A total of 628 individuals from 130 localities in 17 countries were genotyped at seven microsatellite loci. Six population clusters were found based on a Bayesian analysis. The eastern margin of Dahomey gap between East and West Africa was the main factor of genetic differentiation. The SDM projections at present, last interglacial and last glacial maximum periods were used for the estimation of circuit resistance between locations of genotyped individuals. For all periods of time, when using either all individuals or only East African individuals, partial Mantel r and RDA conditioning on geographic distance were found significant. Under future projections (year 2080), partial r and RDA significance were different. From this study, it is concluded that analytical solutions provided by circuit theory are useful for the evolutionary management of populations and for phylogeographic analysis when coalescence times are not accessible by approximate Bayesian simulations. [ABSTRACT FROM AUTHOR]

Landscape genetics has tremendous potential for enhancing our understanding about landscape effects on effective dispersal and resulting genetic structures. However, the vast majority of landscape genetic studies focus on effects of the landscape among sampling locations on dispersal (i.e. matrix quality), while effects of local environmental conditions are rather neglected. Such local environmental conditions include patch size, habitat type or resource availability and are commonly used in (meta-) population ecology and population genetics. In our opinion, landscape genetic studies would greatly benefit from simultaneously incorporating both matrix quality and local environmental conditions when assessing landscape effects on effective dispersal. To illustrate this point, we first outline the various ways in which environmental heterogeneity can influence different stages of the dispersal process. We then propose a three-step approach for assessing local and matrix effects on effective dispersal and review how both types of effects can be considered in landscape genetic analyses. Using simulated data, we show that it is possible to correctly disentangle the relative importance of matrix quality vs. local environmental conditions for effective dispersal. We argue that differentiating local and matrix effects in such a way is crucial for predicting future species distribution and persistence, and for optimal conservation decisions that are based on landscape genetics. In sum, we think it is timely to move beyond purely statistical, pattern-oriented analyses in landscape genetics and towards process-oriented approaches that consider the full range of possible landscape effects on dispersal behaviour and resulting gene flow. [ABSTRACT FROM AUTHOR]

Genetic variation within species is commonly structured in a hierarchical manner which may result from superimposition of processes acting at different spatial and temporal scales. In organisms of limited dispersal ability, signatures of past subdivision are detectable for a long time. Studies of contemporary genetic structure in such taxa inform about the history of isolation, range changes and local admixture resulting from geographically restricted hybridization with related species. Here we use a set of 139 transcriptome-derived, unlinked nuclear single nucleotide polymorphisms (SNP) to assess the genetic structure of the Carpathian newt (Lissotriton montandoni, Lm) and introgression from its congener, the smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of Lm populations likely originated from separate refugia, both located in the Eastern Carpathians. The colonization of the present range in north-western and south-western directions was accompanied by a modest loss of variation; admixture between the two groups has occurred in the middle of the Eastern Carpathians. Local, apparently recent introgression of Lv alleles into several Lm populations was detected, demonstrating increased power for admixture detection in comparison to a previous study based on a limited number of microsatellite markers. The level of introgression was higher in Lm populations classified as admixed than in syntopic populations. We discuss the possible causes and propose further tests to distinguish between alternatives. Several outlier loci were identified in tests of interspecific differentiation, suggesting genomic heterogeneity of gene flow between species. [ABSTRACT FROM AUTHOR]

The coat color of mammals is determined by the melanogenesis pathway, which is responsible for maintaining the balance between black-brown eumelanin and yellow-reddish pheomelanin. It is also believed that the color of the bovine muzzle is regulated in a similar manner; however, the molecular mechanism underlying pigment deposition in the dark-muzzle has yet to be elucidated. The aim of the present study was to identify melanogenesis-associated genes that are differentially expressed in the dark vs. light muzzle of native Korean cows. Using microarray clustering and real-time polymerase chain reaction techniques, we observed that the expression of genes involved in the mitogen-activated protein kinase (MAPK) and Wnt signaling pathways is distinctively regulated in the dark and light muzzle tissues. Differential expression of tyrosinase was also noticed, although the difference was not as distinct as those of MAPK and Wnt. We hypothesize that emphasis on the MAPK pathway in the dark-muzzle induces eumelanin synthesis through the activation of cAMP response element-binding protein and tyrosinase, while activation of Wnt signaling counteracts this process and raises the amount of pheomelanin in the light-muzzle. We also found 2 novel genes (GenBank No. NM-001076026 and XM-588439) with increase expression in the black nose, which may provide additional information about the mechanism of nose pigmentation. Regarding the increasing interest in the genetic diversity of cattle stocks, genes we identified for differential expression in the dark vs. light muzzle may serve as novel markers for genetic diversity among cows based on the muzzle color phenotype. [ABSTRACT FROM AUTHOR]

In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep. [ABSTRACT FROM AUTHOR]

The genetic study of animal populations has become a valuable tool in conservation programs, particularly of those species that are endangered. Different population parameters can be determined in both captive and wild animals to assess their genetic status and long-term viability. In Mexico, different genetic tools have been used in the three species of nonhuman primates to assess, reinforce or test different biological aspects that have been determined by observations and field work. Among others, taxonomic and biogeographic aspects, differentiation and population structures, patterns of kinship and social systems have been made to know and understand the biology of the species and direct conservation and survival strategies of the genus Alouatta in Mexico. [ABSTRACT FROM AUTHOR]

Pleistocene climate cycles and glaciations had profound impacts on taxon diversification in the Boreal Forest Biome. Using population genetic analyses with multilocus data, we examined diversification, isolation, and hybridization in two sibling species of tree squirrels ( Tamiasciurus douglasii and Tamiasciurus hudsonicus) with special attention to the geographically and genetically enigmatic population of T. hudsonicus on Vancouver Island, Canada. The two species differentiated only about 500,000 years ago, in the Late Pleistocene. The island population is phylogenetically nested within T. hudsonicus according to our nuclear analysis but within T. douglasii according to mitochondrial DNA. This conflict is more likely due to historical hybridization than to incomplete lineage sorting, and it appears that bidirectional gene flow occurred between the island population and both species on the mainland. This interpretation of our genetic analyses is consistent with our bioclimatic modeling, which demonstrates that both species were able to occupy this region throughout the Late Pleistocene. The divergence of the island population 40,000 years ago suggests that tree squirrels persisted in a refugium on Vancouver Island at the last glacial maximum, 20,000 years ago. Our observations demonstrate how Pleistocene climate change and habitat shifts have created incipient divergence in the presence of gene flow. [ABSTRACT FROM AUTHOR]

Genetic drift (GD) randomly impacts small breeds and imported populations. Therefore, it can impact policies that affect conservation of animal genetic resources. This paper evaluates GD for a population of Meishan pigs imported into the United States and explores the ramifications of GD on access and benefit sharing of genetic resources under the Nagoya Protocol (NP) of the United Nations' Convention on Biological Diversity. The NP was motivated by concerns about fair and equitable benefit sharing of genetic resources across life forms. In this experiment, 35 microsatellite markers were used to quantify the level of GD that occurred between Meishan pigs (Meishan-China; n = 22) imported into the United States in the late 1980s and contemporary Meishan (Meishan-US; n = 42), which have been randomly bred since importation. The Meishan-US consisted of 2 subpopulations (Meishan-MARC and Meishan-ISU). Five other breeds were also included in the analysis to serve as reference populations: Fengjing and Minzhu, which were imported with Meishan-China, and Duroc, Berk-shire, and Yorkshire from the United States. Mean shift in allele frequency was 0.11 (SE = 0.019) due to GD for Meishan-US vs. Meishan-China with some loci having changed allele frequencies by greater than 0.20. Principle coordinate analysis confinned divergence among the Meishan populations. Model-based clustering tended to place the U.S. and Chinese breeds into 2 distinct clusters, likely due to differences in allele frequencies between U.S. and Chinese breeds. Contemporary Meishan-US has become differentiated from the original imported animals due to GD. Attributing future performance of Meishan-US to Meishan-China, as set forth by NP, is problematic due to GD. As an imported breed becomes established there will be an increasing number of breeders who may have different selection goals and private treaty contracts will govern the exchange of stock between them. Therefore, considering biological phenomena and social dynamics simultaneously draws into question whether a rigorous access and benefit sharing protocol as envisioned in the NP will be operational. [ABSTRACT FROM AUTHOR]

Genotoxic chemicals, through damage and alteration of the genetic material of wild organisms, pose significant threats to the persistence of wild animal populations. Their damaging effects can ultimately impair the health of the ecosystem and its provision of services to human society. Bird species are good candidates for the role of sentinels of the effects of genotoxins, thanks to (i) the diversity of their ecological niches, (ii) their ubiquity across environments, (iii) their conspicuousness, abundance and approachability, together with (iv) their well-known life histories and the availability of historical data series. Avian diversity increases the likelihood that adequate model species be available for monitoring genotoxicants and assessing their impact. This paper reviews the methods utilized by genetic ecotoxicological studies of wild birds, highlighting their benefits and shortcomings. It also summarizes the genetic ecotoxicological studies so far conducted. In spite of a paucity of studies, several classes of genotoxicants have already been investigated across a variety of species and environments, thus supporting the versatility of birds as monitors of genotoxic contamination. Future technical advancements and applications are suggested, with particular reference to the analysis of mutational events, gene expression and methylation patterns. Finally, I argue that the development of avian genetic ecotoxicology will contribute to the understanding of natural variation in the underlying machinery for coping with DNA damage and oxidative stress, both of which are increasingly recognized as proximate factors in the evolution of life history adaptations. [ABSTRACT FROM AUTHOR]

The Qinghai-Tibet Plateau (QTP) is well known for being of great importance in the evolution of montane species due to its unique geological history and landform configuration, climate complexity, and diversified habitats. The effect of environmental changes since the Quaternary on species diversification, population genetic structure, and demography under environmental change can be studied using phylogenetic and phylogeographical approaches. Birds are the most well-studied group of all terrestrial vertebrates with regard to their response to climatic changes over time. Herein, we briefly review the species diversification of birds in response to the uplift of the QTP, focusing on summarizing the different phylogeographical patterns of birds on the Plateau, its southeastern margin, and the Eastern Himalayas and the reasons underlying these patterns. Speciation was found to be closely related to the uplift of the QTP, with different patterns of intraspecific processes: (1) no divergence within a single refuge was identified in a restricted semi-continuous area of the eastern margin of the Plateau; (2) two divergent lineages with separated refugia were located at the south-eastern and north-eastern margins of the plateau; and (3) multiple divergent lineages within subregions were found in the Eastern Himalayas. Glacial movements and induced climate change are considered to be key factors in shaping these different patterns. The species distributed mainly in the heavily ice-covered platform regions of the Plateau experienced population expansion following the retreat of the extensive glaciations, whereas the species distributed on the ice-free edges of the plateau maintained their population size at a stable level. Demographic stresses on the edge species might have been mitigated by the milder climate in comparison to their platform-distributed counterparts. Various behavioral and ecological characteristics, including dispersal capacity, habitat preference, and elevation specificity, along with evolutionary history might have helped to shape these different phylogeographical patterns. [ABSTRACT FROM AUTHOR]