线粒体DNA（mtDNA）多态性在动物保护生物学中的应用

本文从两个方面论述了mtDNA在动物保护生物学中的应用：一是对物种进行遗传多样性的检 测与管理,二是进行与种群统计学数据相关的遗传分析。前者与保护的长期效益（如进化） 密切相关,而后者则主要用于指导短期管理措施的制定。同时,本文重点论述了mtDNA在进 化显著单位(ESUs)和管理单位(MUs)的认定方面的作用。认定ESUs的目的是隔离管理遗传多 样性,它是一系列系统进化史独特的种群,这种独特性同时表现在mtDNA和核DNA上;MUs是 种群统计意义上的生殖隔离单位,具有独特的等位基因频率,与系统发生结构和遗传分歧水 平无关。ESUs与MUs都是保护生物学中保护与管理的重要基本单位。     

Update of genetic information for the white-clawed crayfish in Spain,with new insights into its population genetics and origin

The white-clawed crayfish is endemic to western and southern Europe and its populations have decreased over recent decades. Spanish populations are generally poorly represented in scientific reports and are usually studied only with a single molecular marker. Here, we use two mitochondrial markers (cytochrome oxidase subunit I and rDNA 16S genes) to examine levels and patterns of genetic structure across the range of the species’ distribution in Spain. Data reveal the existence of two main genetic groups of white-clawed crayfish in Spain with the Ebro basin as a possible contact zone. Processes occurred in historical and recent times, such as genetic drift and translocations, contribute greatly to this genetic structure. Levels of genetic variability and genetic structure of Spanish populations together with demographic inferences suggest that the species established in the Iberian Peninsula, at least since the Late Pleistocene. Knowing the true origin of the Spanish populations is crucial when deciding upon the management policies that should be followed. Given the lack of any clear evidence against its indigenous status, we propose that current protection and conservation measures should be maintained. From a management point of view, we suggest that Spanish population should be considered as a single evolutionary significant unit (ESU) with two management units (MUs) corresponding with the genetic clusters detected in the present study.     

Genetic characterization of Western European noble crayfish populations (<Emphasis Type="Italic">Astacus astacus</Emphasis>) for advanced conservation management strategies

One central goal of conservation biology is to conserve the genetic diversity of species in order to protect their adaptive potential. The main objective of this study was to identify management units (MUs) for the threatened noble crayfish (Astacus astacus) in Western Europe by utilizing sequence and microsatellite analysis to determine populations in need of focused conservation programs. With the analysis of noble crayfish from 31 sampling sites from Belgium, France, The Netherlands and Germany, and further comparison of this data with a European-wide dataset, we propose four distinct MUs: the French Meuse (MU 1), the French Rhine (MU 2), the Belgian Scheldt and Meuse (MU 3) as well as populations from the French Seine (MU 4). This knowledge enables advanced A. astacus conservation management practises in these catchments by distinguishing between outbreeding and inbreeding populations and by preserving the maximum genetic diversity. When required, a high genetic diversity can be conserved by strengthen existing populations via stocking with populations that either bear the most common haplotype or population-specific private haplotypes in order to maintain recent and regional adaptions. Above all, stocking with populations that exhibit haplotypes from outside Western Europe should be avoided in these catchments. This study supports the preservation of the genetic diversity of noble crayfish in Western Europe and provides thus a proposition for advanced conservation management.     

Patterns of chloroplast DNA polymorphism in the endangered polyploid Centaurea borjae (Asteraceae): implications for preserving genetic diversity.

A previous study with amplified fragment length polymorphism (AFLP) fingerprints found no evidence of genetic impoverishment in the endangered Centaurea borjae and recommended that four management units (MUs) should be designated. Nevertheless, the high ploidy (6x) of this narrow endemic plant suggested that these conclusions should be validated by independent evidence derived from non-nuclear markers. Here, the variable trnT-F region of the plastid genome was sequenced to obtain this new evidence and to provide an historical background for the current genetic structure. Plastid sequences revealed little genetic variation; calling into question the previous conclusion that C. borjae does not undergo genetic impoverishment. By contrast, the conclusion that gene flow must be low was reinforced by the strong genetic differentiation detected among populations using plastid sequences (global F_ST = 0.419). The spatial arrangement of haplotypes and diversity indicate that the populations currently located at the center of the species range are probable sites of long-persistence whereas the remaining sites may have derived from a latter colonization. From a conservation perspective, four populations contributed most to the allelic richness of the plastid genome of the species and should be given priority. Combined with previous AFLP results, these new data recommended that five, instead of four, MUs should be established. Altogether, our study highlights the benefits of combining markers with different modes of inheritance to design accurate conservation guidelines and to obtain clues on the evolutionary processes behind the present-day genetic structures.     

Genetic evidence for a recent divergence and subsequent gene flow between Spanish and Eastern imperial eagles

Background  

Dating of population divergence is critical in understanding speciation and in evaluating the evolutionary significance of genetic lineages, upon which identification of conservation and management units should be based. In this study we used a multilocus approach and the Isolation-Migration model based on coalescence theory to estimate the time of divergence of the Spanish and Eastern imperial eagle sister species. This model enables estimation of population sizes at split, and inference of gene flow after divergence.     

Genetic variability among endangered Chinese giant salamanders, Andrias davidianus

The endangered Chinese giant salamander (Andrias davidianus) is endemic to mainland China. Genetic divergence among six populations of the species was investigated by means of isozyme electrophoresis and mitochondrial DNA (mtDNA) sequences. Forty allozyme loci were resolved for all populations; the amount of genetic divergence among populations was comparable to that in other amphibians. mtDNA sequences showed a similar level of divergence. The population from Huangshan is distinct from other populations, indicating the existence of localized divergence. Both allozyme and mtDNA data failed to associate the populations into a pattern corresponding to the three Chinese river systems, which may be the consequence of human relocation. Conservation policies should emphasize the protection of localized populations and cessation of human-facilitated introductions. Future studies should focus on investigating the divergence among localized populations from isolated mountain regions, particularly using more fine-grained techniques such as microsatellite DNA.     

Genetic population structure of the fluvial eight-barbel loach <Emphasis Type="Italic">Lefua</Emphasis> sp. 1 in the three river systems in central Honshu,Japan, revealed by microsatellite DNA markers

The fluvial eight-barbel loach Lefua sp. 1 is an undescribed species distributed from the Kinki to Chugoku districts, Honshu, and also on Shikoku Island, Japan. Genetic relationships among local populations are unclear and management units remain undetermined. To aid conservation, we determined genetic population structures from microsatellite loci for 20 populations from three river systems on Honshu. The genetic diversity within populations is relatively low; the majority has experienced genetic bottlenecks. Statistical analysis revealed significant divergence among river systems suggesting that each should be recognized as a management unit. Any conservation program should consider the populations’ genetic uniqueness.     

Biochemical genetic stock structure of the southern African anchovy, Engraulis capensis Gilchrist

The geographical distributions of inherited biochemical markers were used to measure the amount of genetic isolation between stocks of Namibian and South African anchovy, Engraulis capensis . A contingency-table analysis of allele frequencies for 10 polymorphic protein-coding loci revealed no significant frequency differences between spawning areas. The average Nei genetic distance between samples was 0.0003 and there were no geographic trends in the amount of genetic distance between populations. Average population heterozygosity for 31 loci was 0.115 and this accounted for 99.26% of the total genetic variation. The remaining 0.24% was due to all temporal and spatial differences combined. The observed amount of genetic divergence between populations was used to estimate the amount of migration between spawning areas, using the stepping-stone model of migration. As few as 13 migrants may account for the observed genetic divergence between spawning areas. The validity of using the genetic stock concept in the management of marine fishes is discussed.     

Evolution of rough sculpin (<Emphasis Type="Italic">Cottus asperrimus</Emphasis>) genetic divergence and late Quaternary displacement on the Hat Creek fault,California, USA

The rough sculpin (Cottus asperrimus) is a threatened species whose geographic range in northwestern California, USA is disrupted by Hat Creek fault. We tested whether the fluvial barriers (rapids and waterfalls) produced by this fault have generated significant phylogeographic structure among rough sculpin populations by analyzing variation in microsatellites and mitochondrial DNA. Rough sculpin isolated on either side of Hat Creek fault exhibited significant genetic divergence (microsatellite F _ST = 0.36; mitochondrial uncorrected p distance = 1 %). Independently derived estimates for the date of divergence, based upon a molecular clock and upon the age of slip on the Hat Creek fault are concordant and indicate divergence was initiated about 0.5–1 million years ago. Based upon the findings of our genetic analysis and the Pleistocene geologic history of midsections of the Pit River, we present a model of evolution of rough sculpin genetic divergence and late Quaternary displacement on Hat Creek fault. Our findings reveal that rough sculpin exhibit significant population structure and that two management units should be recognized within the species for future conservation planning.     

Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan

Betula maximowicziana is a long-lived pioneer tree species in Japanese cool temperate forests that plays an important role in maintenance of the forest ecosystem and has high economic value. Here we assess the wide-range genetic structure of 23 natural populations of B. maximowicziana using 11 simple sequence repeat (SSR) loci. Genetic diversity within populations was relatively low in all populations (mean H(E), 0.361; mean allelic richness, 2.80; mean rare allelic richness, 1.02). The population differentiation was also relatively low (F(ST), 0.062). Genetic distance-based and Bayesian clustering analysis revealed that the populations examined here could be divided into a southern group and a northern group. Analysis of rare allelic richness and Bayesian clustering revealed evidence for both southern and northern refugia during the last glacial period. Furthermore, a comparison of regional genetic diversity revealed significant clines in allelic richness. In spatial genetic structure evaluation, significant isolation by distance (IBD) was detected among the 23 populations, but not within regions. Moreover, significant population bottlenecks were found in all populations under infinite allele model (IAM) assumptions. These unusual, significant bottlenecks might be because of the processes of postglacial colonization and the species' characters and/or life history as a long-lived pioneer tree species. The wide-range, regional genetic structure found in this study provides an important baseline for conservation and forest management, including the identification of evolutionarily significant units (ESUs) and/or management units (MUs) of B. maximowicziana.     

Using microsatellite and MHC variation to identify species, ESUs, and MUs in the endangered Sonoran topminnow

Highly variable loci can provide insight into the recognition of species, evolutionarily significant units (ESUs) and management units (MUs). In general, the ESU and MU categories are thought to be reflective of adaptive differences between them. Here we examine this premise by presenting a comprehensive examination of genetic variation for both microsatellite loci and a major histocompatibility complex (MHC) locus, thought to be of adaptive significance, in the endangered Sonoran topminnow. The extent of variation for the microsatellite loci and the MHC gene within the 13 populations of the Gila topminnow is highly correlated, suggesting that nonselective factors have played an important role in influencing variation within and between populations for the MHC locus. Therefore, using all of these loci, we found that the eight natural populations of the Gila topminnow fell into two different ESUs, one of which had four different MUs. The source of the Boyce Thompson sample, a population that was used extensively for restocking, appeared to be Monkey Spring. The source of the Watson Wash population also appeared to be Monkey Spring (or Boyce Thompson). The newly colonized Santa Cruz River population, which had the most genetic variation of any Gila topminnow population, appeared to descend primarily from Sonoita Creek populations. The Yaqui topminnow, presently considered another subspecies of the Sonoran topminnow, was very distinct for both microsatellite (only two of 25 alleles found in the Yaqui were in any of the Gila topminnow samples) and MHC alleles (nonoverlapping sets of alleles for the two groups). As a result, it appeared that the taxonomic status of the two subspecies should be re-evaluated and that full species status for Gila and Yaqui topminnows was appropriate. There was evidence for the importance of long-term selection at the MHC locus in the higher rate of nonsynonymous than synonymous substitution. In addition, there appeared to have been a duplication of the MHC locus that was present in most of the fish in six of the natural populations of the Gila topminnow.     

A Bayesian approach to conservation genetics of Blanding’s turtle (Emys blandingii) in Ontario,Canada

Blanding’s turtle, Emys blandingii, is a globally endangered species with a range centred on the Great Lakes of North America. Several disjunct populations also occur along the East Coast of North America. Previous studies suggest that the Great Lakes portion of the species’ range exhibits panmixia. However, E. blandingii is restricted to relatively small populations in many areas around the Great Lakes. Therefore, panmixia across large geographic distances in this area is unlikely. Here, we apply Bayesian analyses of population structure to samples collected across southern Ontario (N = 97) to test a null hypothesis of panmixia and assess possible management units (MUs), and to estimate rates of gene flow across the study area. Sampled sites in Ontario represent a minimum of four distinct genetic clusters of E. blandingii, which we recommend should be considered as independent MUs. Preliminary evidence suggests that further structure may be present in less robustly sampled areas, which deserve further consideration. Genetic diversity at sampled sites is comparable to that reported for other freshwater turtles. Our comparison between this study and previous work confirms that genetic diversity in E. blandingii is reduced in disjunct eastern populations compared to populations centred on the Great Lakes. Genetic diversity in E. blandingii is not correlated with latitude, and instead may reflect post-glacial dispersal of this species from multiple Pleistocene glacial refugia.     

tossm: an R package for assessing performance of genetic analytical methods in a management context

tossm (Testing of Spatial Structure Methods) is a package for testing the performance of genetic analytical methods in a management context. In the tossm package, any method developed to detect population genetic structure can be combined with a mechanism for creating management units (MUs) based on the genetic analysis. The resulting Boundary-Setting Algorithm (BSA) dictates harvest boundaries with a genetic basis. These BSAs can be evaluated with respect to how well the MUs they define meet management objectives.     

Conservation units based on mitochondrial and nuclear DNA variation among European bullhead populations (Cottus gobio L., 1758) from Flanders, Belgium

In this study, we aimed to delineateevolutionarily significant units (ESUs) andmanagement units (MUs) for the Europeanbullhead in Flanders (Belgium). Therefore, wedetermined the genetic interrelationshipsbetween 11 bullhead populations, using lengthvariation at 7 polymorphic microsatellite lociand sequence variation in the d-loop of themitochondrial DNA (mtDNA). Despite therelatively small geographical scale of ourstudy, the analysis of the d-loop sequencesshows that the Flemish bullhead populationscontain 3 haplotype groups, which can beassigned to 3 previously described EuropeanmtDNA clades. Because of the importantdifferences between these clades, they may bedefined as evolutionarily significant units,which should be managed separately. Analysis ofmicrosatellite data reveals very high degreesof isolation between populations, with theexception of 3 pairwise comparisons whichinvolved adjacent populations. Our data suggestthat the 3 haplotype groups probably qualify asESUs, as they show phylogeographicdifferentiation for mtDNA variants as well assignificant divergence of allele frequencies atnuclear loci. However, one of these units,limited to a single population, may be ofCentral European origin. All populations of theScheldt basin meet the criteria for MUrecognition, since significantly differentmicrosatellite allele frequencies as well asprivate alleles are found. In contrast, geneticdifferentiation among the 3 populations of theMeuse basin is very low.     

Evidence for stabilizing selection and slow divergent evolution of male genitalia in a millipede (Antichiropus variabilis)

It is generally accepted that postcopulatory sexual selection drives rapid divergence of genital morphology among isolated populations. The mode of selection operating upon genitalia can be explored by comparing patterns of population divergence in genetic and genitalic traits. We collected Antichiropus variabilis millipedes from eight localities across the species range. Levels of among-population genetic divergence, at microsatellite loci, and the mitochondrial COI gene were very high. Following geometric morphometric analyses, genital morphology was also found to be highly divergent among the populations surveyed, whereas head morphology had not diverged as markedly. However, pairwise comparisons of F(ST) and P(ST) showed that among-population divergence in both genital and head shape was significantly lower than that experienced by neutral genetic markers. Our results suggest that the genitalia of A. variabilis are currently experiencing a period of stabilizing selection, the mode of selection expected for genitalia that function in species recognition via a "lock-and-key" mechanism. Our results demonstrate that although genital morphology can clearly diverge among genetically isolated populations, divergence is not necessarily as rapid as commonly argued, and continuous directional sexual selection may not always underpin the evolutionary divergence of male genitalia.     

Population mixing and the adaptive divergence of quantitative traits in discrete populations: a theoretical framework for empirical tests

Empirical tests for the importance of population mixing in constraining adaptive divergence have not been well grounded in theory for quantitative traits in spatially discrete populations. We develop quantitative-genetic models to examine the equilibrium difference between two populations that are experiencing different selective regimes and exchanging individuals. These models demonstrate that adaptive divergence is negatively correlated with the rate of population mixing (m, most strongly so when m is low), positively correlated with the difference in phenotypic optima between populations, and positively correlated with the amount of additive genetic variance (G, most strongly so when G is low). The approach to equilibrium is quite rapid (fewer than 50 generations for two populations to evolve 90% of the distance to equilibrium) when either heritability or mixing are not too low (h2 > 0.2 or m > 0.05). The theory can be used to aid empirical tests that: (1) compare observed divergence to that predicted using estimates of population mixing, additive genetic variance/covariance, and selection; (2) test for a negative correlation between population mixing and adaptive divergence across multiple independent population pairs; and (3) experimentally manipulate the rate of mixing. Application of the first two of these approaches to data from two well-studied natural systems suggests that population mixing has constrained adaptive divergence for color patterns in Lake Erie water snakes (Nerodia sipedon), but not for trophic traits in sympatric pairs of benthic and limnetic stickleback (Gasterosteus aculeatus). The theoretical framework we outline should provide an improved basis for future empirical tests of the role of population mixing in adaptive divergence.     

Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis

In the past decade much attention has focused on the role that genetics can play in the formation of management strategies in conservation. Here, we describe genetic diversity in the world''s largest lizard, the Komodo dragon (Varanus komodoensis), examining the evolutionary relationships and population genetic history of the four islands in south-east Indonesia, which form the vast majority of its range. We identify distinct genetic groups for conservation. The population on the island of Komodo shows by far the largest values of genetic divergence and is proposed that it should be a separate conservation management unit. Other populations, surviving either on small islands with substantially reduced genetic variability, or in isolated patches, are identified as particularly vulnerable to stochastic threats and habitat loss. Our results provide an example of how data defining intraspecific levels of genetic divergence can provide information to help management plans, ensure the maintenance of genetic variability across populations and identify evolutionary potential within endangered species.     

DNA marker technology for wildlife conservation

Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care. Molecular markers are versatile tools for identification of populations with genetic crisis by comparing genetic diversities that in turn helps to resolve taxonomic uncertainties and to establish management units within species. The genetic marker analysis also provides sensitive and useful tools for prevention of illegal hunting and poaching and for more effective implementation of the laws for protection of the endangered species. This review summarizes various tools of DNA markers technology for application in molecular diversity analysis with special emphasis on wildlife conservation.     

Genetic diversity and population structure in Tunisian Lavandula stoechas L. and Lavandula multifida L. (Lamiaceae)

The genetic diversity and population structure of 20 Tunisian Lavandula stoechas L. and Lavandula multifida L. populations, from different bioclimates, were analysed by starch gel electrophoresis using seven isozymes. The genetic diversity within populations varied according to species. Variation in L. multifida was higher than that observed for L. stoechas, and exclusive alleles were detected for taxa.

A high differentiation among populations, for each species, estimated by Wright's F-statistics was revealed. The genetic structure of populations from the same bioclimate was substantial. Nei's, R. [1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590] genetic distance among pairs of populations was low. The UPGMA cluster analysis of genetic distance values revealed that populations for each species were not strictly clustered together according to bioclimate or geographic proximity.

For each species, the low genetic divergence among populations and their substantial structure indicate their recent fragmentation due to anthropic pressures. The dendrogram generated from pairwise genetic distance among all populations showed two distinct clusters each corresponding to one species. The high genetic divergence between the two species, based on isozymes, corroborates their taxonomic status, as previously reported using morphological traits. The strategy for the management and conservation of populations should be made for each taxa according to its level of diversity and bioclimate.     

Habent Fata Sua: The Rise and Fall of Garden Plants

Background: Rare cactus in the Americas and other species worldwide are threatened species because of their high level of habitat specialisation, narrow distribution range and continuing population decline.

Aims: To identify management units (MUs) based on genetic variability and demographic structure in order to propose assertive conservation actions for Mammillaria crucigera and to provide a model case study for other species that are under similar threats.

Methods: We genotyped through eight microsatellite loci in 171 individuals and described demographic structures in six populations of this cactus based on plots of 1 m².

Results: Across populations with a mean density of 2.6 m^?2 and a total of ~500 individuals counted, 30% of the individuals were reproductive (diameter >2 cm). The total heterozygosity was low (H_O = 0.54), but the inbreeding coefficient (F_IS = 0.29) and the allele diversity (N_A = 20) were high. Four genetic groups were distinguished, although considering the demographic structure, we propose three MUs.

Conclusions: It is critical to maintain the genetic connectivity within and among MUs, which can only be achieved through cooperation between government authorities and local habitants to halt the degradation and further destruction of the remnant populations. Searching MUs allows the identification of critical areas for conservation issues for all species whose extant populations are in a fragmented landscape.