Song dialects do not restrict gene flow in an urban population of the orange-tufted sunbird, <Emphasis Type="Italic">Nectarinia osea</Emphasis>

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. In this study, we test the hypothesis that song dialect, a culturally transmitted trait, is related to the population genetic structure of the orange-tufted sunbird, Nectarinia osea. To address this, we compared mitochondrial DNA (mtDNA) sequence variation together with allele frequencies at five microsatellite loci from an urban population of sunbirds exhibiting two distinct song dialects on a microgeographic scale. Our findings reveal no association between dialect membership and genetic composition. All genetic measures, from both mitochondrial and nuclear DNA, indicate high levels of gene flow between both dialect populations. The low F _ST values obtained from mtDNA and microsatellite analysis imply that the variation among dialects does not account for more than 2%, at best, of the overall genetic variation found in the entire population. These measures fall well within the range of similar measures obtained in other studies of species exhibiting vocal dialects, most of which fail to detect any dialect-based genetic differentiation. The persistence of dialects in the orange-tufted sunbird may thus best be explained by dispersal of individuals across dialect boundaries and possibly from surrounding areas, followed by postdispersal vocal matching. Because genetic structuring appears weaker than cultural structure in this species, we discuss the behavioral mechanisms underlying dialect maintenance in the presence of apparent gene flow.     

Patterns of Genetic Diversity in Remaining Giant Panda Populations

Abstract: The giant panda ( Ailuropoda melanoleuca ) is among the more familiar symbols of species conservation. The protection of giant panda populations has been aided recently by the establishment of more and better-managed reserves in existing panda habitat located in six mountain ranges in western China. These remaining populations are becoming increasingly isolated from one another, however, leading to the concern that historic patterns of gene flow will be disrupted and that reduced population sizes will lead to diminished genetic variability. We analyzed four categories of molecular genetic markers (mtDNA restriction-fragment-length polymorphisms [RFLP], mtDNA control region sequences, nuclear multilocus DNA fingerprints, and microsatellite size variation) in giant pandas from three mountain populations (Qionglai, Minshan, and Qinling) to assess current levels of genetic diversity and to detect evidence of historic population subdivisions. The three populations had moderate levels of genetic diversity compared with similarly studied carnivores for all four gene measures, with a slight but consistent reduction in variability apparent in the smaller Qinling population. That population also showed significant differentiation consistent with its isolation since historic times. From a strictly genetic perspective, the giant panda species and the three populations look promising insofar as they have retained a large amount of genetic diversity in each population, although evidence of recent population reduction—likely from habitat loss—is apparent. Ecological management to increase habitat, population expansion, and gene flow would seem an effective strategy to stabilize the decline of this endangered species.     

Evidence for restricted gene flow over small spatial scales in a marine snapping shrimp <Emphasis Type="Italic">Alpheus angulosus</Emphasis>

Despite the apparent absence of geographic barriers, connectivity among marine populations may be restricted by, for example, ecological or behavioral mechanisms. In such cases, populations may show genetic differentiation even over relatively small spatial scales. Here, mitochondrial sequence data from the cytochrome oxidase I (COI) gene and seven polymorphic microsatellite markers were used to investigate fine geographic scale population genetic structure in the snapping shrimp Alpheus angulosus, a member of the A. armillatus species complex, from collections in Florida, Jamaica, and Puerto Rico carried out from 1999 to 2005. The COI data showed a deep divergence that separated these samples into two mitochondrial clades, but this divergence was not supported by the microsatellite data. The COI data reflect past population divergence not reflected in extant population structure on the whole genome level. The microsatellite data also revealed evidence for moderate population structure between populations as close as ∼10 km, and no evidence for isolation by distance, as divergences between near populations were at least as strong as those between more broadly separated populations. Overall, these data suggest a role for restricted gene flow between populations, though the mechanisms that reduce gene flow in this taxon remain unknown.     

Analysis of global and local population stratification of finless porpoises <Emphasis Type="Italic">Neophocaena phocaenoides</Emphasis> in Chinese waters

The existence of three distinct populations is widely accepted for the finless porpoise (Neophocaena phocaenoides) in Chinese waters: the Yellow Sea, Yangtze River, and South China Sea populations. Here, we use nine species-specific microsatellite loci, the complete mitochondrial DNA control region (912 bp), and the complete mitochondrial cytochrome b gene (1,140 bp) to further investigate potential population stratification in the Yellow Sea using 147 finless porpoise samples from the Bohai Sea and adjacent northern Yellow Sea, two regions that were largely underrepresented in previous genetic studies. Our F-statistics analyses confirm the previously described three populations, but further demonstrate significant genetic differentiation between the [Bohai + northern Yellow] Sea and the southern Yellow Sea. On the other hand, median-joining network analyses do not exhibit well-differentiated haplotype groups among different geographic populations, suggesting the existence of shared ancestral haplotypes. Levels of microsatellite diversity are moderate to high (mean H _E = 0.794) among the 147 [Bohai + northern Yellow] Sea finless porpoises and no recent bottleneck was detected, whereas mtDNA control region and cytochrome b gene diversity is low to moderate. The microsatellite genotypic and mtDNA haplotypic data also confirm the presence of mother-calf pairs in single-net bycatch cases. The results presented here highlight the necessity to treat the [Bohai + northern Yellow] Sea population (highly impacted by anthropogenic threats) as a separate Management Unit.     

Genetic structure of Patagonian toothfish (Dissostichus eleginoides) populations on the Patagonian Shelf and Atlantic and western Indian Ocean Sectors of the Southern Ocean

The genetic structure of Patagonian toothfish populations in the Atlantic and western Indian Ocean Sectors of the Southern Ocean (SO) were analysed using partial sequences of the mitochondrial 12S rRNA gene and seven microsatellite loci. Both haplotype frequency data (F _ST>0.906, P<0.01) and microsatellite genotype frequency data (F _ST=0.0141–0.0338, P<0.05) indicated that populations of toothfish from around the Falkland Islands were genetically distinct from those at South Georgia (eastern Atlantic Sector SO), around Bouvet Island (western Atlantic Sector SO) and the Ob Seamount (western Indian Ocean Sector of the SO). Genetic differentiation between these populations is thought to result from hydrographic isolation, as the sites are separated by two, full-depth, ocean-fronts and topographic isolation, as samples are separated by deep water. The South Georgia, Bouvet and Ob Seamount samples were characterised by an identical haplotype. However, microsatellite genotype frequencies showed genetic differentiation between South Georgia samples and those obtained from around Bouvet Island and nearby seamounts (F _ST=0.0037, P<0.05). These areas are separated by large geographic distance and water in excess of 3,000 m deep, below the distributional range of toothfish (<2,200 m). No significant genetic differentiation was detected between samples around Bouvet Island and the Ob Seamount although comparisons may have been influenced by low sample size. These localities are linked by topographic features, including both ridges and seamounts, that may act as oceanic “stepping stones” for migration between these populations. As for other species of deep-sea fish, Patagonian toothfish populations are genetically structured at the regional and sub-regional scales.     

Influence of contrasting larval developmental types upon the population-genetic structure of cheilostome bryozoans

For many sedentary or sessile benthic marine invertebrates the planktonic duration of the larval stage is believed to be a key determinant of the magnitude of genetic differences between populations. An obvious dichotomy in dispersal potential exists within cheilostome bryozoans that develop from either (1) a cyphonautes larva that spends several weeks in the plankton or (2) a brooded coronate larva that settles soon after release from the adult colony. This study characterises the pattern of variation at allozyme loci among British populations of four species of bryozoan—two species with cyphonautes and two with coronate larvae. There is some variation in the estimates of genetic differentiation among similarly separated populations that may be a consequence of non-equilibrium genetic conditions arising from sporadic migration, possibly through dispersal by rafting on macroalgae by mature colonies. Despite this, however, both the level of genetic differentiation between populations and the pattern of migrant exchange correlate with the larval developmental mode. Bryozoan species that brood coronate larvae show higher levels of genetic heterogeneity between populations and significant isolation by distance genetic structure while, by contrast, distance has little or no effect upon the amount of genetic differentiation among populations of bryozoans with cyphonautes larvae. For cheilostome bryozoans, therefore, it appears that genetic differentiation between populations is directly associated with the type of larval development. These data are discussed also with respect to levels of gene diversity and the geological pattern of cheilostome bryozoan species diversity.     

Mitochondrial DNA variation and population genetic structure of the blue crab<Emphasis Type="Italic"> Callinectes sapidus</Emphasis> in the eastern United States

The genetic population structure of red grouper, Epinephelus morio (Valenciennes), and scamp, Mycteroperca phenax Jordan and Swain, from the southeastern U.S. Atlantic coast and the Gulf of Mexico was examined using nuclear microsatellite DNA markers in order to test the null hypothesis of panmixia throughout this range. Physical and biological data indicate that relatively isolated populations of these fish exist. Genetic variation was assessed at four microsatellite loci in red grouper and six loci in scamp. The fish were collected on different dates between 1991 and 2001. The microsatellite loci were highly polymorphic, with an average expected heterozygosity of 0.75 in red grouper and 0.68 in scamp. Heterozygote deficiencies (significant deviations from Hardy–Weinberg equilibrium, HWE) were found at two of four loci in all red grouper samples except the eastern Gulf of Mexico, and for all red grouper combined. In contrast, all loci conformed to HWE in the separate scamp samples. Minimal genetic differences distinguished southeastern U.S. Atlantic or Mexican red grouper from other localities, and no indication of genetic differentiation was observed in scamp. This large-scale genetic homogeneity may be attributed to ongoing gene flow and/or historical contact between present-day populations. For management purposes, genetic homogeneity does not necessarily imply a single stock. Because larval dispersal may be sufficient to homogenize gene frequencies but not to replenish depleted stocks, other data must be considered in the management of these species.Electronic Supplementary Material Supplementary material is available in the online version of this article at .Communicated by J.P. Grassle, New Brunswick     

Population structure of the wreckfish Polyprion americanus determined with microsatellite genetic markers

 We examined population structure in the wreckfish, Polyprion americanus, by assaying six microsatellite loci in 422 individuals collected throughout the geographic range. Eighteen hapuku, P. oxygeneios, were assayed at the same loci for use as an outgroup. Expected heterozygosities ranged from 0.49 to 0.88 and averaged 0.66. Allele-frequency distributions at those loci indicated that samples from the eastern North Atlantic, western North Atlantic and the Mediterranean were genetically similar, confirming the pattern seen in a previous analysis of mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs). Both mtDNA and microsatellite studies differentiated northern and southern wreckfish stocks. However, in contrast to the mtDNA studies, allelic variation at microsatellite loci clearly differentiated wreckfish from two Southern Hemisphere locations, Brazil and the South Pacific. Far more genetic variation was observed at microsatellite loci than with mtDNA RFLPs (haplotype diversity averaged 0.01), and we saw more evidence of population structure with the microsatellite loci. The differentiation between southern and northern wreckfish supports the distribution records, which indicate that wreckfish do not occur in the tropics. Temperature profiles and current patterns throughout the southern oceans apparently also prevent significant gene flow between the South Pacific and Brazilian samples. Received: 29 January 2000 / Accepted: 27 June 2000     

Population variation in the mitochondrial cytochrome b gene of the orange roughy Hoplostethus atlanticus and the hoki Macruronus novaezelandiae

To describe the genetic relationship among regional populations of two commercially valuable species of marine fish, the orange roughy Hoplostethus atlanticus and the hoki Macruronus novaezelandiae, the mitochondrial (mt) DNA haplotypes of 59 individuals were defined by direct sequencing of the cytochrome b gene. Samples of orange roughy were collected on four fishing grounds around New Zealand, one off the west coast of Tasmania and one near South Africa from 1990–1991. Samples from hoki were collected on three fishing grounds around New Zealand and one off Tasmania during the same period. An average of 252 nucleotides were sequenced from each of 32 orange roughy and an average of 372 nucleotides from each of 27 hoki. Sequence variation allowed the definition of 9 unique orange roughy haplotypes and 5 hoki haplotypes. Genetic variation, as measured by both average sequence divergence and haplotype diversity, was high in the orange roughy (nucleotide diversity=0.590%, haplotype diversity=0.782) and low in the hoki (nucleotide diversity=0.076%, haplotype diversity=0.279) relative to a similar survey of the Atlantic cod, Gadus morhua. Differences in haplotype frequencies of orange roughy from New Zealand, Tasmania and South Africa were not significant, and the most common haplotype was found in similar frequencies in these three geographically distant regions. Differences in haplotype frequencies between the New Zealand and Tasmanian samples of hoki were significant, suggesting restricted gene flow between these two regions. The contrasting patterns of low but regionally subdivided genetic variation in the hoki versus high but geographically undifferentiated genetic variation in the orange roughy may be attributed to the low fecundity, slow maturation and long lifespan of the orange roughy relative to the hoki.     

Conservation Genetics of the Black Rhinoceros (Diceros bicornis), I: Evidence from the Mitochondrial DNA of Three Populations

Abstract: A drastic decline in the number of black rhinoceroses ( Diceros bicornis ), primarily as a result of poaching places this species in imminent danger of extinction. The remaining black rhinos are divided into small, isolated populations that are vulnerable to demographic extinction, disease epidemics, genetic drift and inbreeding. Some conservationists have suggested minimizing these threats by moving as many animals as possible from different isolated populations to a few safe "rhino sanctuaries." To examine the possible long-term genetic consequences of such a strategy, we focused our efforts on determining the level of genetic differences among the remaining black rhino populations by examining restriction fragment length polymorphisms of the rapidly evolving mitochondrial DNA molecule. The 23 black rhinos in our survey, including animals from three geographic regions and two named subspecies, showed very little mitochondrial DNA differentiation. Only 4 out of 18 restriction enzymes revealed any mtDNA polymorphism, and the average estimated percent sequence divergence between the four mtDNA genotypes observed as 0.17%. Mitochondrial DNA divergence between the two named subspecies, D. b. minor and D. b. michaeli , was estimated to be only 0.29%. These results indicate a very close genetic relationship among the black rhinos in our survey. Thus, the mitochondrial DNA data suggest that within national boundaries, the black rhino populations we sampled may be considered single populations for breeding purposes, which might increase the species' probability of survival.     

Relationship of Genetic Variation to Population Size in Wildlife

Genetic diversity is one of three levels of biological diversity requiring conservation. Genetic theory predicts that levels of genetic variation should increase with effective population size. Soulé (1976) compiled the first convincing evidence that levels of genetic variation in wildlife were related to population size, but this issue remains controversial. The hypothesis that genetic variation is related to population size leads to the following predictions: (1) genetic variation within species should be related to population size; (2) genetic variation within species should be related to island size; (3) genetic variation should be related to population size within taxonomic groups; (4) widespread species should have more genetic variation than restricted species; (5) genetic variation in animals should be negatively correlated with body size; (6) genetic variation should be negatively correlated with rate of chromosome evolution; (7) genetic variation across species should be related to population size; (8) vertebrates should have less genetic variation than invertebrates or plants; (9) island populations should have less genetic variation than mainland populations; and (10) endangered species should have less genetic variation than nonendangered species. Empirical observations support all these hypotheses. There can be no doubt that genetic variation is related to population size, as Soulé proposed. Small population size reduces the evolutionary potential of wildlife species.     

Fragmentation of Landscape as a Cause for Genetic Subdivision in Bank Voles

Abstract: We studied the barrier effects of various roadways on the genetic subdivision of bank vole (Clethrionomys glareolus) populations. Allele frequencies, genetic variability, and genetic distances of natural populations were calculated based on polymorphism of seven microsatellite markers. We compared bank vole populations in control areas without such barriers with animals from both sides of a country road, a railway, and a highway. Using F and R statistics, we demonstrated significant population subdivision in bank vole populations separated by the highway, but not in populations on either side of the other roadways or in the control area. Correlations between geographic and genetic distances were revealed by an extended method based on a Mantel analysis. This allowed us to measure genetic barrier effects and express them as additional geographic distances. For instance, statistically significant differences in allele frequencies in all seven loci examined existed among populations in southern Germany and Switzerland, which are separated by the Rhine River and Lake Constance. The real geographic distance between bank vole populations in Konstanz and those in Lengwil, Switzerland, was 6 km. According to this analysis the genetic barrier effect of the Rhine could be defined as an additional distance of 7.7 km. This study shows for the first time that not only old geographic barriers but also more recent fragmentation of landscape by, for example, highways has an important effect on gene flow and the genetic substructuring of populations, which should be considered in future environmental impact assessments.     

Human Impacts on Drainages of the Mesa Central, Mexico, and Its Genetic Effects on an Endangered Fish, Zoogoneticus quitzeoensis

Abstract:  The Mesa Central of Mexico is of special conservation interest due to its high richness of freshwater fish species, of which the goodeines are one of the most representative groups. Through an integrated approach, we determined conservation priorities for goodeine populations. We based our recommendations on the genetic diversity (variation in five microsatellite DNA loci) in 10 populations of Zoogoneticus quitzeoensis and on an analysis of ecological (e.g., presence of exotic species), social (e.g., political situation), and environmental (e.g., pollution) information for 52 historical occurrence points for species in the genus Zoogoneticus . Patterns of genetic erosion and genetic diversity indices were closely associated with human impact. Recent bottleneck events were most evident in the populations from remnants of the lakes drained at the beginning of the twentieth century. We identified seven operational conservation units (OCUs), all of which should be conserved because they contain unique portions of the total variation of the species. Special attention needs to be given to increase genetic variability, recover population sizes, and reestablish contact among populations within OCUs. It is imperative to create an integrative and effective approach for the recovery and conservation of the freshwater fish diversity of Central Mexico that is based on social and natural sciences.     

Microsatellite variation and significant population genetic structure of endangered finless porpoises (Neophocaena phocaenoides) in Chinese coastal waters and the Yangtze River

The finless porpoise (Neophocaena phocaenoides) inhabits a wide range of tropical and temperate waters of the Indo-Pacific region. Genetic structure of finless porpoises in Chinese waters in three regions (Yangtze River, Yellow Sea, and South China Sea) was analyzed, including the Yangtze finless porpoise which is widely known because of its highly endangered status and unusual adaptation to freshwater. To assist in conservation and management of this species, ten microsatellite loci were used to genotype 125 individuals from the three regions. Contrary to the low genetic diversity revealed in previous mtDNA control region sequence analyses, relatively high levels of genetic variation in microsatellite profiles (H _E = 0.732–0.795) were found. Bayesian clustering analysis suggested that finless porpoises in Chinese waters could be described as three distinct genetic groups, which corresponded well to population “units” (populations, subspecies, or species) delimited in earlier studies, based on morphological variation, distribution, and genetic analyses. Genetic differentiation between regions was significant, with F _ST values ranging from 0.07 to 0.137. Immigration rates estimated using a Bayesian method and population ancestry analyses suggested no or very limited gene flow among regional types, even in the area of overlap between types. These results strongly support the classification of porpoises in these regions into distinct evolutionarily significant units, including at least two separate species, and therefore they should be treated as different management units in the design and implementation of conservation programmes.     

山西高原油松种群遗传多样性

用酸性聚丙烯酰胺凝胶电泳（A-PAGE）技术，分析了山西高原9个油松种群在醇溶蛋白水平上的遗传多样性。135份材料共分离出23条带，其中3条为共有带，多态性高达86．95％。全部材料共出现53种带型，9个不同油松种群的带型有差异，同一种群不同个体的带型也有所不同，说明山西高原的油松在遗传上已产生一定程度分化，在醇溶蛋白水平上呈现出遗传多态性。从供试材料的带型计算出油松遗传分化系数为0．1547。即在种群间的变异占总变异的15．47％，种群内变异为84．53％，大部分的遗传变异存在于种群内，但种群间的分化程度在松属树种中也属于较高水平。根据23个多态位点计算遗传相似系数和遗传距离，进行聚类分析，将山西高原9个油松种群聚为3个类群。     

Local variation of within-host clonal diversity coupled with genetic homogeneity in a marine trematode

Despite their ubiquity and importance to intertidal ecosystems, information is currently lacking regarding the genetic diversity of trematode parasites within coastal organisms and the distribution of their genetic variation among intertidal habitats. In this study, we quantified the clonal diversity of the coastal marine trematode Maritrema novaezealandensis within Zeacumantus subcarinatus snail hosts from three coastal bays in Otago Harbour, New Zealand, using five microsatellite loci to determine if differences exist in the frequency of occurrence of multi-clone infections. In addition, we examined gene flow among M. novaezealandensis collected from the three bays. The frequency of mixed-clone infections varied fourfold among bays and no genetic differentiation was detected among intertidal bays. Across the coastal bays studied, M. novaezealandensis comprises a single population that is potentially infecting multiple Z. subcarinatus populations with varying life history traits.     

Lower genetic diversity in the limpet <Emphasis Type="Italic">Patella caerulea</Emphasis> on urban coastal structures compared to natural rocky habitats

Human-made structures are increasingly found in marine coastal habitats. The aim of the present study was to explore whether urban coastal structures can affect the genetic variation of hard-bottom species. We conducted a population genetic analysis on the limpet Patella caerulea sampled in both natural and artificial habitats along the Adriatic coast. Five microsatellite loci were used to test for differences in genetic diversity and structure among samples. Three microsatellite loci showed strong Hardy–Weinberg disequilibrium likely linked with the presence of null alleles. Genetic diversity was significantly higher in natural habitat than in artificial habitat. A weak but significant differentiation over all limpet samples was observed, but not related to the type of habitat. While the exact causes of the differences in genetic diversity deserve further investigation, these results clearly point that the expansion of urban structures can lead to genetic diversity loss at regional scales.     

Evaluating Genetic Diversity Associated with Propagation-Assisted Restoration of American Shad

Abstract: We investigated the conservation of genetic diversity during a restoration program for American shad ( Alosa sapidissima ) in Virginia ( U.S.A.). Restoration entailed capture of wild Pamunkey River shad broodstock followed by production and release of hatchery-reared fry to supplement the nearly extinct James River shad population. To assess the baseline genetic diversity of donor and recipient populations, we used five tri- and tetra-nucleotide microsatellite loci to test for genetic heterogeneity among yearly subsamples from both rivers and between early- and late-spawning shad from the donor population. Tests for allelic heterogeneity between James River and Pamunkey shad subsamples yielded no significant genetic differentiation (χ ² = 14.72, p = 0.132 and χ ² = 10.24, p = 0.440, respectively). We detected no significant genetic divergence between early- and late-spawning adults in Pamunkey River spawning aggregations in either year. The donor and recipient populations exhibited significant genetic differentiation (χ ² = 27.4, p = 0.003), however, indicating that the stocking program carries a risk of outbreeding depression. Because the two river populations are genetically divergent, replenishment of the James population with Pamunkey fry may be detectable in the future as heterozygote deficits and linkage disequilibria in the James River population. In an analysis of broodstock and their hatchery-reared progeny, microsatellites proved efficient for family analysis, unambiguously determining the parentage of 100% of the hatchery-reared fry studied. Genetic analysis indicated that breeding procedures may result in high levels of reproductive variance.     

利用RAPD标记分析卧龙自然保护区不同海拔沙棘种群的遗传变异

从1800m到3400m五个海拔连续取样,用RAPD分子标记研究了卧龙自然保护区中国沙棘种群的遗传结构和遗传变异.用11条寡核苷酸引物,扩增得到151个重复性好的位点,其中143个多态位点,多态率达94.7%.在5个沙棘种群中,总遗传多样性值(HT)为0.289,B种群内的遗传多样性值为0.315,这完全符合沙棘这种多年生、远交的木本植物高遗传变异的特性.5个种群内遗传多样性随海拔升高呈低—高—低变异趋势,在2200m海拔处的B种群遗传多样性达最大值0.315,3400m海拔处的E种群则表现最小,仅0.098.5个种群间的遗传分化值GST=0.406,也即是说有40.6%的遗传变异存在于种群间,59.4%存在种群内.1800m海拔处的A种群与其他种群的明显分离是造成种群间遗传分化大的原因.UPGMA聚类图和PCoA散点图分别进一步确证了5个种群间关系和所有个体间的关系.最后,经过Mantel检测,遗传距离与海拔表现了明显的相关性(r=0.646,P=0.011).