Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci

Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.     

Microsatellite markers for the Mallorcan midwife toad Alytes muletensis

The highly endangered midwife toad Alytes muletensis occurs only on the Mediterranean island of Mallorca. Little is known about genetic variability and dispersal among the 19 breeding sites (six of which stem from reintroductions) of this amphibian. The value of such information should be high for successful management of this species. We report here the characterization of eight polymorphic microsatellite loci in A. muletensis using individuals from a single population.     

Comparative Population Genetic Structure of the Endangered Southern Brown Bandicoot,Isoodon obesulus,in Fragmented Landscapes of Southern Australia

Genetic connectivity is a key factor for maintaining the persistence of populations in fragmented landscapes. In highly modified landscapes such us peri-urban areas, organisms’ dispersal among fragmented habitat patches can be reduced due to the surrounding matrix, leading to subsequent decreased gene flow and increased potential extinction risk in isolated sub-populations. However, few studies have compared within species how dispersal/gene flow varies between regions and among different forms of matrix that might be encountered. In the current study, we investigated gene flow and dispersal in an endangered marsupial, the southern brown bandicoot (Isoodon obesulus) in a heavily modified peri-urban landscape in South Australia, Australia. We used 14 microsatellite markers to genotype 254 individuals which were sampled from 15 sites. Analyses revealed significant genetic structure. Our analyses also indicated that dispersal was mostly limited to neighbouring sites. Comparisons of these results with analyses of a different population of the same species revealed that gene flow/dispersal was more limited in this peri-urban landscape than in a pine plantation landscape approximately 400 km to the south-east. These findings increase our understanding of how the nature of fragmentation can lead to profound differences in levels of genetic connectivity among populations of the same species.     

Parentage of Overlapping Offspring of an Arboreal-Breeding Frog with No Nest Defense: Implications for Nest Site Selection and Reproductive Strategy

Overlapping offspring occurs when eggs are laid in a nest containing offspring from earlier reproduction. Earlier studies showed that the parentage is not always obvious due to difficulties in field observation and/or alternative breeding tactics. To unveil the parentage between overlapping offspring and parents is critical in understanding oviposition site selection and the reproductive strategies of parents. Amplectant pairs of an arboreal-breeding frog, Kurixalus eiffingeri, lay eggs in tadpole-occupied nests where offspring of different life stages (embryos and tadpoles) coexist. We used five microsatellite DNA markers to assess the parentage between parents and overlapping offspring. We also tested the hypothesis that the male or female frog would breed in the same breeding site because of the scarcity of nest sites. Results showed varied parentage patterns, which may differ from the phenomenon of overlapping egg clutches reported earlier. Parentage analyses showed that only 58 and 25% of the tadpole-occupied stumps were reused by the same male and female respectively, partially confirming our prediction. Re-nesting by the same individual was more common in males than females, which is most likely related to the cost of tadpole feeding and/or feeding schemes of females. On the other hand, results of parentage analyses showed that about 42 and 75% of male and female respectively bred in tadpole-occupied stumps where tadpoles were genetically unrelated. Results of a nest-choice experiment revealed that 40% of frogs chose tadpole-occupied bamboo cups when we presented identical stumps, without or with tadpoles, suggesting that the habitat saturation hypothesis does not fully explain why frogs used the tadpole-occupied stumps. Several possible benefits of overlapping offspring with different life stages were proposed. Our study highlights the importance of integrating molecular data with field observations to better understand the reproductive biology and nest site selection of anuran amphibians.     

独龙江流域鱼类分布特征及其体长与体重的关系(英文)

鱼类主要分布于青藏高原周边,是一群适合于急流生活的科鱼类。在独龙江流域7个点共采集271号鱼类标本(隶属属、属和异齿属),结合各采集点数据绘制大鳍异齿、藏和扁头的分布直方图,结果显示,藏(E. labiatum)在流速较快的独龙江下游各采集点的种群数量较上游高,更适应急流生境。同时研究了这3种鱼类的体长与体重的关系,参数b(W=aLb)的范围在2.8201和3.0131之间,均为异速生长;藏的生长类型最接近等速生长。     

独龙江流域鰋鮡鱼类分布特征及其体长与体重的关系

鰋鮡鱼类主要分布于青藏高原周边,是一群适合于急流生活的鮡科鱼类。在独龙江流域7个点共采集271号鰋鮡鱼类标本（隶属鮡属、鰋属和异齿鰋属）,结合各采集点数据绘制大鳍异齿鰋、藏鰋和扁头鮡的分布直方图,结果显示,藏鰋（E．labiatum）在流速较快的独龙江下游各采集点的种群数量较上游高,更适应急流生境。同时研究了这3种鰋鮡鱼类的体长与体重的关系,参数b（W=aL^b）的范围在2．8201和3．0131之间,均为异速生长;藏鰋的生长类型最接近等速生长.     

独龙江流域(鱼匽)(鱼兆)鱼类分布特征及其体长与体重的关系

(鱼匽)(鱼兆)鱼类主要分布于青藏高原周边, 是一群适合于急流生活的(鱼兆)科鱼类. 在独龙江流域7个点共采集271号(鱼匽)(鱼兆)鱼类标本(隶属(鱼兆)属、(鱼匽)属和异齿(鱼匽)属), 结合各采集点数据绘制大鳍异齿(鱼匽)、藏(鱼匽)和扁头(鱼兆)的分布直方图, 结果显示, 藏(鱼匽)(E. labiatum)在流速较快的独龙江下游各采集点的种群数量较上游高, 更适应急流生境. 同时研究了这3种(鱼匽)(鱼兆)鱼类的体长与体重的关系, 参数b(W=aLb)的范围在2.8201和3.0131之间, 均为异速生长;藏(鱼匽)的生长类型最接近等速生长.     

Factors influencing tadpole deposition site choice in a frog with male parental care: An experimental field study

Parents have evolved a variety of strategies to minimize risks to their offspring, including complex choices regarding suitable rearing sites, based on abiotic and biotic factors, which differentially affect offspring survival. Because availability and quality of these sites are variable, parents may have to choose between immediately available lower‐quality rearing sites or extended search time. In some frog species with larval transport, parents are known to select bodies of water that are free of predators, cannibalistic tadpoles, or intraspecific competitors for larval deposition and rearing sites. We tested whether abiotic factors and the presence of predators and conspecific tadpoles affect tadpole deposition behavior in a population of smooth guardian frog, Limnonectes palavanensis, on the island of Borneo. Females lay eggs on land and males guard them until they hatch; after hatching, tadpoles climb onto the male's back and are subsequently transported to small pools of water on the forest floor, which are scarce and patchily distributed. We estimated the abundance of natural tadpole rearing sites in our study area and conducted experiments using artificial pools to test whether abiotic characteristics of these pools affect the probability of larval deposition. We also performed choice experiments to test whether males of L. palavanensis avoid pools with conspecific tadpoles or predators. Lastly, we tested whether the tadpoles of this species exhibit cannibalism. The abundance of natural deposition sites was low, and males readily used artificial pools for tadpole deposition. Males were less likely to deposit tadpoles in artificial pools located in steep areas, and males did not avoid depositing tadpoles in pools with conspecifics or with experimentally introduced predators. Males exhibited clutch‐partitioning behavior, dividing tadpoles between adjacent artificial pools. Pool availability, rather than the presence of potential competitors or predators in a pool, affects tadpole deposition decisions in this species.     

Genetic structure of red deer population in northeastern Poland in relation to the history of human interventions

We studied the genetic structure of a red deer (Cervus elaphus) population in 8 woodlands of northeastern Poland and 1 in western Belarus and compared it with the documented history of the population in the region. Red deer nearly went extinct in the region in the 18th and 19th centuries. In the mid-19th century, reintroductions began and continued until the mid-1960s. Animals were translocated from various sites in Poland and other European countries. We genotyped 303 individuals using 14 microsatellite loci and sequenced 253 individuals for a fragment of the control region (mitochondrial DNA [mtDNA]). The microsatellite analyses demonstrate that 3 genetically separate subpopulations exist, but 4 according to mtDNA. All haplotypes found in northeastern Poland are closely related to haplotypes from northern and northwestern Europe. The only individuals that could have originated from autochthonous red deer populations, rather than introductions, were found in Napiwoda Forest. The present regional genetic structure of the species is consistent with the known history of red deer translocations. Current patterns of genetic diversity in these populations are determined by the interaction of past human management and contemporary natural migrations. © 2012 The Wildlife Society.     

Genetic differentiation and hybridization in two naturally occurring sympatric trout Salmo spp. forms from a small karstic lake

In this study, multiple molecular markers [genotyping of 12 nuclear microsatellite loci and the protein‐coding gene ldh‐c1* plus sequencing of the mitochondrial DNA (mtDNA) control region] were employed to investigate the genetic structure of the two trout forms, Salmo cettii and Salmo fibreni, inhabiting Lake Posta Fibreno, central Italy. The two forms were found to share a unique mtDNA haplotype, belonging to a widespread Mediterranean haplogroup (AD). Bayesian clustering analyses showed that these two forms correspond to well‐defined autochthonous gene pools. Genetic introgression between the two gene pools, however, was observed, whose frequency appears to correlate with the environmental features of the spawning sites. The interplay of selection for the spawning sites, philopatry and natural selection can be argued to maintain genetic differentiation despite the lack of complete reproductive isolation.     

Genetic support for random mating between left and right‐mouth morphs in the dimorphic scale‐eating cichlid fish Perissodus microlepis from Lake Tanganyika

Population genetic analyses were conducted to investigate whether random mating occurs between left and right‐mouth morphs of the dimorphic scale‐eating cichlid fish Perissodus microlepis from two geographical sites in southern Lake Tanganyika. The mitochondrial and nuclear DNA markers (13 microsatellite loci) revealed no genetic differentiation between left and right morphs (i.e. widespread interbreeding). The observed lack of genetic divergence between the different morphs allowed for the exclusion of the possibility of assortative mating between same morph types. The microsatellite data showed no significant departures of heterozygosity from Hardy–Weinberg equilibrium, suggesting purely random mating between the morphs. Overall, this study indicated no genetic evidence for either assortative or disassortative mating, but it did provide support for the random mating hypothesis. Highly significant, albeit weak, spatial population structure was also found when samples of different morphs were pooled according to geographical sites. An additional analysis of two microsatellite loci that were recently suggested to be putatively linked to the genetic locus that determines the laterality of these mouth morphs did not show any such association.     

The power of the seasons: rainfall triggers parental care in poison frogs

The quality of breeding sites is of great importance for the reproductive success and accordingly the fitness of many animal species. Hence, individuals should decide carefully where to rear their offspring. Often parents have to account for multiple characteristics of habitat quality at once, which in turn might change over time. Specimens confronted with such variability may evolve the ability to display context-dependant decision plasticity. Anuran amphibians breeding in ephemeral pools largely face two risks for their offspring: desiccation and predation. The Neotropical poison frog Ranitomeya variabilis deposits both eggs and tadpoles in phytotelmata. These small tadpole nurseries lower the risk of offspring predation. However, because most poison frog tadpoles are cannibalistic, even these pools need to be surveyed for predators, and parents tend to avoid deposition with conspecifics. We tested if this avoidance behaviour does change in parental R. variabilis depending on seasonal circumstances. Over several months we provided the frogs the option to deposit their eggs or tadpoles in pools that did and did not contain chemical cues of cannibalistic conspecifics, respectively. During the rainy season, frogs strongly avoided conspecific cues for both eggs and tadpoles. Anyway, with the change to the dry season, parental preferences changed such that parent frogs were more likely to deposit tadpoles (but not eggs) in pools containing cues of conspecific tadpoles. We suggest that R. variabilis, a species that typically isolates its cannibalistic offspring, has evolved a plastic feeding behaviour with regard to the risk of phytotelmata desiccation. We interpret that parents provide older tadpoles with younger ‘trophic’ tadpoles in order to accelerate their development and save them from impending desiccation.     

Translocations maintain genetic diversity and increase connectivity in sea otters,Enhydra lutris

Sea otters, Enhydra lutris, were once abundant along the nearshore areas of the North Pacific. The international maritime fur trade that ended in 1911 left 13 small remnant populations with low genetic diversity. Subsequent translocations into previously occupied habitat resulted in several reintroduced populations along the coast of North America. We sampled sea otters between 2008 and 2011 throughout much of their current range and used 19 nuclear microsatellite markers to evaluate genetic diversity, population structure, and connectivity between remnant and reintroduced populations. Average genetic diversity within populations was similar: observed heterozygosity 0.55 and 0.53, expected heterozygosity 0.56 and 0.52, unbiased expected heterozygosity 0.57 and 0.52, for reintroduced and remnant populations, respectively. Sea otter population structure was greatest between the Northern and Southern sea otters with further structuring in Northern sea otters into Western, Central, and Southeast populations (including the reintroduced populations). Migrant analyses suggest the successful reintroductions and growth of remnant groups have enhanced connectivity and gene flow between populations throughout many of the sampled Northern populations. We recommend that future management actions for the Southern sea otter focus on future reintroductions to fill the gap between the California and Washington populations ultimately restoring gene flow to the isolated California population.     

Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations

We examined fine-scale genetic variation among breeding aggregations of the spotted salamander (Ambystoma maculatum) to quantify dispersal, interpopulation connectivity and population genetic structure. Spotted salamanders rely on temporary ponds or wetlands for aggregate breeding. Adequate breeding sites are relatively isolated from one another and field studies suggest considerable adult site fidelity; therefore, we expected to find population structure and differentiation at small spatial scales. We used microsatellites to estimate population structure and dispersal among 29 breeding aggregations in Tompkins County, New York, USA, an area encompassing 1272 km(2). Bayesian and frequency-based analyses revealed fine-scale genetic structure with two genetically defined demes: the North deme included seven breeding ponds, and the South deme included 13 ponds. Nine ponds showed evidence of admixture between these two genetic pools. Bayesian assignment tests for detection of interpopulation dispersal indicate that immigration among ponds is common within demes, and that certain populations serve as sources of immigrants to neighbouring ponds. Likewise, spatial genetic correlation analyses showed that populations < or = 4.8 km distant from each other show significant genetic correlation that is not evident at higher scales. Within-population levels of relatedness are consistently larger than expected if mating were completely random across ponds, and in the case of a few ponds, within-population processes such as inbreeding or reproductive skew contribute significantly to differentiation from neighbouring ponds. Our data underscore the importance of these within-population processes as a source of genetic diversity across the landscape, despite considerable population connectivity. Our data further suggest that spotted salamander breeding groups behave as metapopulations, with population clusters as functional units, but sufficient migration among demes to allow for potential rescue and recolonization. Amphibian habitats are becoming increasingly fragmented and a clear understanding of dispersal and patterns of population connectivity for taxa with different ecologies and life histories is crucial for their conservation.     

用微卫星标记定位小麦T型CMS的恢复基因

以T型细胞质雄性不育系 75 336 9A×恢复系 72 6 9 10的F2 群体作为育性调查和基因定位群体。通过育性分析 ,确定该恢复系含有 2个主效恢复基因 ;结合群分法 ,对恢复基因进行了SSR分子标记定位 ,在 2 30对微卫星引物中 ,微卫星标记Xgwm136和Xgwm5 5 0分别与 2个主效恢复基因连锁。这两个标记与Rf基因之间的遗传距离分别为 6 7cM和 5 1cM ,从而将该恢复基因定位在 1AS、1BS染色体上。     

A serial founder effect model for human settlement out of Africa

The increasing abundance of human genetic data has shown that the geographical patterns of worldwide genetic diversity are best explained by human expansion out of Africa. This expansion is modelled well by prolonged migration from a single origin in Africa with multiple subsequent serial founding events. We discuss a new simulation model for the serial founder effect out of Africa and compare it with results from previous studies. Unlike previous models, we distinguish colonization events from the continued exchange of people between occupied territories as a result of mating. We conduct a search through parameter space to estimate the range of parameter values that best explain key statistics from published data on worldwide variation in microsatellites. The range of parameters we use is chosen to be compatible with an out-of-Africa migration at 50-60Kyr ago and archaeo-ethno-demographic information. In addition to a colonization rate of 0.09-0.18, for an acceptable fit to the published microsatellite data, incorporation into existing models of exchange between neighbouring populations is essential, but at a very low rate. A linear decay of genetic diversity with geographical distance from the origin of expansion could apply to any species, especially if it moved recently into new geographical niches.     

Fine- and regional-scale genetic structure of the exotic ascidian Styela clava (Tunicata) in southwest England, 50 years after its introduction

Styela clava , an ascidian native to the northwest Pacific, was first recorded in the Atlantic at Plymouth, southwest England, in 1953. It now ranges in the northeast Atlantic from Portugal to northern Denmark, and has colonized the east coast of North America. Within the region of first introduction, we aimed to characterize current genetic diversity in the species, elucidate the respective roles of human-aided vs. natural dispersal, and assess the extent of larval dispersal by looking for genetic differentiation at very small scales. Eight sites, mostly marinas, were studied along c . 200 km of coast in southwest England encompassing Plymouth. Five microsatellite loci were genotyped in 303 individuals to analyse gene flow at regional (among sites) and fine (within sites) scales. F -statistics and assignment tests were used to investigate regional genetic structure. At the fine scale, deviation from mutation–drift equilibrium was tested, and isolation by distance and genetic clustering analyses were undertaken. Significant genetic differentiation existed between sites, unrelated to geographical separation; migration between geographically distant marinas was inferred, highlighting the likely importance of human-mediated dispersal in range expansion and occupancy by S. clava . Fine-scale population structure was present within at least four sites, which may be explained by the limited dispersal ability of this ascidian and recruitment from differentiated pools of larvae. Populations in enclosed marinas had higher self-recruitment rates than those in open sites. Some marinas might therefore function as reservoirs of propagules for subsequent spread, whereas others might be sinks for migrants.     

The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation

We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for approximately 90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of 'genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization.     

Gene flow from multiple sources maintains high genetic diversity and stable population history of Common Moorhen Gallinula chloropus in China

In this study, we used mitochondrial control sequences and microsatellite data from 231 Common Moorhen Gallinula chloropus individuals sampled from 19 sites in China to analyse their genetic structure and evolutionary history. High genetic diversity was found for all populations, although microsatellite analysis showed that the genetic diversity in non‐migratory populations was significantly higher than in migratory populations. High gene flow occurred between neighbouring populations, although long‐distance gene flow also occurred. The Huazhong population was the single greatest genetic source for other populations. High gene flow probably led to the shallow genetic structure that we observed. Demographic expansion was found in migratory populations, non‐migratory populations and with all individuals combined. The expansion time for all populations combined was estimated to be 221 000 years ago. The Common Moorhen population grew rapidly during the interglacial before the last glacial maximum (LGM), then remained generally stable from the LGM to the present.     

The effects of gene flow and population isolation on the genetic structure of␣reintroduced wild turkey populations: Are genetic signatures of source populations retained?

To counter losses of genetic diversity in reintroduced populations, species sometimes are reintroduced into networks of populations with the potential to exchange individuals. In reintroduced populations connected by gene flow, patterns of genetic structure initiated by the founding event may become obscured, and populations may eventually follow an isolation-by-distance model of genetic differentiation. Taking advantage of well-documented reintroduction histories of wild turkey populations in Indiana, we assessed the degree to which gene flow among reintroduced populations has obscured genetic signatures left by the founding events. Using a suite of nuclear microsatellite loci and sequence data from the mitochondrial control region, we characterized the level of genetic diversity and degree of genetic structure within and among: (1) reintroduced populations in isolated northern Indiana Fish and Wildlife Areas, (2) reintroduced populations in southern Indiana Fish and Wildlife Areas, where the distribution of populations is more continuous, and (3) source populations used for these reintroductions. We also utilized individual-based assignment tests to determine the relative contribution of source populations to the current distribution of alleles in reintroduced populations. Our results indicate that wild turkey reintroductions in Indiana have left distinct genetic signatures on populations that are detectable even after several decades. Although we found some case-specific evidence for gene flow, particularly in regions where populations are in close proximity, our data indicate on overall paucity of gene flow at a regional scale. Such post-reintroduction genetic monitoring has immediate implications for the design of optimal strategies to reintroduce wildlife for conservation and management.