Differentiation under isolation and genetic structure of Sardinian hares as revealed by craniometric analysis,mitochondrial DNA and microsatellites

Hares (Lepus capensis Linnaeus 1758) were probably introduced into Sardinia in historical times. Previous studies indicated North Africa as the most likely source area but did not exclude the occurrence of hybridization events with continental brown hares (L. europaeus Pallas 1778) perhaps introduced for hunting purposes. We implemented both morphometric and genetic approaches to verify the genetic isolation of the Sardinian population. Specifically, we conducted a multivariate analysis of craniometric data and analysed 461 bp of the mitochondrial control region and 12 autosomal microsatellites in Sardinian hares, using North African cape hares and European brown hares as reference populations. Sardinian hares displayed a peculiar skull shape. In agreement, both nuclear and mitochondrial markers remarked the distinctiveness of this population. Observed and expected heterozygosity were 0.52 and 0.61, while haplotype and nucleotide diversity were 0.822 and 0.0129. Self‐assignment based on Bayesian cluster analysis was high (average membership 0.98), and no evident signs of introgression from continental brown hares were found. Our results support the hypothesis that the Sardinian hares have been introduced from North Africa, remained genetically isolated since the founding event and evolved independently from the source population. This long‐lasting isolation and the consequent genetic drift resulted in a differentiation, perhaps accompanied by an adaptation to local environmental conditions.     

Complex patterns of genetic variability in populations of the New World screwworm fly revealed by mitochondrial DNA markers

Abstract.  Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), the New World screwworm fly, is an important agent of traumatic myiasis, which is endemic in the Neotropical region and which has great economic impact on the development of the livestock industry. International efforts have been aimed at designing programmes to control and eradicate this species from endemic areas. Thorough knowledge of the population genetics of an insect pest is a fundamental component to ensuring the success of a pest management strategy because it enables the determination of an appropriate geographic scale for carrying out effective treatments. This study undertook an analysis of mtDNA polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) in 34 populations of C. hominivorax from 10 countries, encompassing almost all the current distribution of the species. Results showed high levels of mitochondrial DNA variability (π= 2.9%) and a complex pattern of population genetic structure for this species. Significant population structure (> st = 0.5234) and low variability were found in Caribbean populations, suggesting that, in general, islands constitute independent evolutionary entities connected by restricted gene flow. By contrast, high variability and low, but significant, differentiation was found among mainland populations (> st = 0.0483), which could not be attributed to geographic distance. Several processes may be acting to maintain the observed patterns, with different implications for establishing control programmes.     

Mitochondrial DNA variation in European populations of Silurus glanis

Mitochondrial DNA diversity of 13 wild Silurus glanis populations (covering the entire range of the species) and eight hatchery populations was investigated. PCR-RFLP analysis of four regions of mitochondrial DNA (cytochrome b, control region, ND-5/6) was used. Nineteen haplotypes were found. Thirteen of them were private. The proportion of total genetic diversity attributable to population differentiation was almost 80%. Despite the existence of significant differentiation between populations for mtDNA variation, no consistent pattern of geographic structuring was revealed and nucleotide divergence among S. glanis populations was low. These phenomena are discussed with regard to the impact of glaciation events. The domesticated stocks show less genetic diversity than natural ones, possibly due to their mode of management. Analysis of three European catfish species S. glanis, S. aristotelis and Silurus triostegus (sampled in the Euphrates river) revealed several endonucleases which produced restriction phenotypes diagnostic for the three species.     

Landscape location affects genetic variation of Canada lynx (Lynx canadensis)

The effect of a population's location on the landscape on genetic variation has been of interest to population genetics for more than half a century. However, most studies do not consider broadscale biogeography when interpreting genetic data. In this study, we propose an operational definition of a peripheral population, and then explore whether peripheral populations of Canada lynx (Lynx canadensis) have less genetic variation than core populations at nine microsatellite loci. We show that peripheral populations of lynx have fewer mean numbers of alleles per population and lower expected heterozygosity. This is surprising, given the lynx's capacity to move long distances, but can be explained by the fact that peripheral populations often have smaller population sizes, limited opportunities for genetic exchange and may be disproportionately affected by ebbs and flows of species' geographical range.     

Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis

Widespread hunting had fragmented and severely reduced elephant populations in South Africa by 1900. Elephant numbers increased during the 1900s, although rates of recovery of individual populations varied. The Kruger National Park elephant population increased rapidly, to more than 6000 by 1967, with recruitment boosted by immigration from Mozambique. The Addo Elephant National Park population was reduced to 11 elephants in 1931 and remains relatively small (n = 325). Loss of genetic variation is expected to occur whenever a population goes through a bottleneck, especially when post-bottleneck recovery is slow. Variation at nine polymorphic microsatellite loci was analysed for Kruger and Addo elephants, as well as museum specimens of Addo elephants shot prior to the population bottleneck. Significantly reduced genetic variation and heterozygosity were observed in Addo in comparison to Kruger (mean alleles/locus and H(E): Addo 1.89, 0.18; Kruger 3.89, 0.44). Two alleles not present in the current Addo population were observed in the museum specimens. Addo elephants represent a genetic subset of the Kruger population, with high levels of genetic differentiation resulting from rapid genetic drift. The Kruger population is low in genetic diversity in comparison to East African elephants, confirming this population also suffered an appreciable bottleneck.     

Loss of genetic variability in reintroduced roach (Rutilus rutilus) populations

Genetic variation at five microsatellite loci and in mtDNA was surveyed in reintroduced and 'control' populations of roach ( Rutilus rutilus ) in Sweden. Microsatellite allelic richness and allele size ranges were significantly reduced in reintroduced populations, and mtDNA diversity was nearly significantly reduced in reintroduced populations. These measures of genetic variability were strongly correlated with lake characteristics that influence population size and food availability.     

High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant F(ST) values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters.     

Phylogeography and population history of the endangered golden sun moth (Synemon plana) revealed by allozymes and mitochondrial DNA analysis

A combination of allozyme and mitochondrial DNA markers were used to determine the contribution of recent and ancient causes of patterns of genetic variation within and among 46 populations of the endangered golden sun moth, Synemon plana. Allozyme analysis grouped the 46 populations into 5 major genetic clusters that corresponded closely with geographic location following a classic isolation-by-distance model. Phylogenetic analysis of 14 mtDNA haplotypes revealed two reciprocally monophyletic groups. One of these groups (containing 4 geographically distant populations) was clearly identified by allozyme analysis and represents a distinct evolutionary unit. The remaining 4 allozyme groups were not distinguishable by mtDNA analysis. The evidence suggests that the populations within these groups derived from a small founding population that underwent rapid demographic expansion in ancient times. This was followed by more recent population bottlenecks resulting from habitat fragmentation associated with the widespread introduction of agriculture into the region. The generally low levels of allozyme and nucleotide diversity within these populations support this hypothesis. This revised version was published online in July 2006 with corrections to the Cover Date.     

Increase of genetic variation over time in a recently founded population of great reed warblers (Acrocephalus arundinaceus) revealed by microsatellites and DNA fingerprinting

Genetic similarity within pairs of individuals was examined using both 10 polymorphic microsatellite loci and multi-locus DNA fingerprinting profiles in a semi-isolated population of great reed warblers at Lake Kvismaren, south Central Sweden, in 1987-1993. The population was founded by a few individuals in 1978, followed by a gradual increase in numbers until 1988, since when the population has remained relatively stable with about 60 breeding birds. We have previously found that high genetic similarity between pair-mates in the population during the early part of the study period reduced egg hatching success, and hence reproductive success. The measures of pairwise genetic similarity, microsatellite allele sharing and DNA fingerprinting band sharing, were highly correlated with pedigree-based relatedness. Both microsatellite and DNA fingerprinting similarities between pair-mates declined significantly over the study period, and the pattern was most pronounced in the DNA fingerprinting data. Analyses restricted to the microsatellite data showed that the average annual microsatellite similarity between pairwise combinations of individuals, as well as individual homozygosity in males, declined significantly over the study period, and that several immigrants carrying novel alleles entered the population during the study. Hence, the temporal decline in genetic similarity of mates in the population is probably a consequence of increased immigration, facilitated by the recent expansion of the species in the region. These results suggest that the population has now recovered genetically, or is in the process of recovering, from a recent founder event.     

Genetic variation in Lake Erie yellow perch (Percaflavescem) demonstrated by mitochondrial DNA analysis

Restriction fragment length polymorphism analysis of yellow perch ( Perca flavescens ) mitochondrial DNA from a Lake Erie population revealed seven variants in 22 fish (nucleon diversity 0.481). These fish were collected from an area where previous studies using allozymes had failed to reveal any genetic variation.     

草鱼野生群体遗传变异的微卫星分析

利用12个微卫星标记, 对来自长江水系(邗江、吴江、九江、石首、木洞和万州)、珠江水系(肇庆)和黑龙江水系(嫩江)的8个草鱼野生地理群体进行了遗传多样性及遗传结构等分析。遗传多样性分析显示, 12个微卫星位点均为高度多态位点(PIC=0.755~0.930), 8个草鱼野生群体显示出较高的遗传多样性水平(Ho=0.839~0.893), 其中长江水系的6个群体和肇庆群体的多样性水平高于嫩江群体。瓶颈效应分析显示, 嫩江、肇庆群体及2个长江上游群体(木洞、万州)近期出现了瓶颈效应, 群体数量发生下降。群体间遗传分化指数F^ST及AMOVA分析显示, 群体间出现极显著遗传分化(P<0.01), 整体分化水平较低(F^ST<0.05)。遗传距离分析结果显示, 长江水系的6个群体与肇庆群体遗传距离较近, 与嫩江群体较远; 基于此的UPGMA聚类树显示, 长江水系下游、中游和上游的群体依次聚类, 然后与肇庆群体聚类, 最后与嫩江群体聚类, 遗传距离与地理距离呈现出较强的正相关性。遗传结构分析显示, 所有样本被划分为5个理论群, 肇庆和嫩江群体中个体的遗传结构相对独立, 而长江上游、中游和下游群体中个体的遗传结构则存在一定程度的混杂。综上所述, 中国草鱼野生资源具有较高的遗传多样性, 地理群体间存在遗传分化, 具有进一步遗传改良的潜力; 但部分群体出现的瓶颈效应也需要引起重视。     

Low levels of mitochondrial DNA variation among central and southern European Esox lucius populations

Low levels of mitochondrial DNA variation were observed among pike Esox lucius populations from major drainage systems of Europe. Populations from the Italian peninsula including southern Switzerland were genetically distinct from other samples.     

Contrasting patterns of mitochondrial and microsatellite genetic structure among Western European populations of tawny owls (Strix aluco)

A recent study of mitochondrial phylogeography of tawny owls (Strix aluco) in western Europe suggested that this species survived the Pleistocene glaciations in three allopatric refugia located in Iberia, Italy, and the Balkans, and the latter was likely the predominant source of postglacial colonization of northern Europe. New data from seven microsatellite loci from 184 individual owls distributed among 14 populations were used to assess the genetic congruence between nuclear and mitochondrial DNA (mtDNA) markers. Microsatellites corroborated the major phylogeographical conclusions reached on the basis of the mtDNA sequences, but also showed important differences leading to novel inferences. Microsatellites corroborated the three major refugia and supported the Balkan origin of northern populations. When corrected for differences in effective population size, microsatellites and mtDNA yielded generally congruent overall estimates of population structure (N*ST=0.12 vs. RST=0.16); however, there was substantial heterogeneity in the RST among the seven nuclear loci that was not correlated with heterozygosity. Populations representing the Balkans postglacial expansion interact with populations from the other two refugia forming two clines near the Alps and the Pyrenees. In both cases, the apparent position of the contact zones differed substantially between markers due to the genetic composition of populations sampled in northern Italy and Madrid. Microsatellite data did not corroborate the lower genetic diversity of northern, recently populated regions as was found with mtDNA; this discrepancy was taken as evidence for a recent bottleneck recovery. Finally, this study suggests that congruence among genetic markers should be more likely in cases of range expansion into new areas than when populations interact across contact zones.     

Temporal variation in the genetic structure of host-associated populations of the small ermine moth Yponomeuta padellus (Lepidoptera, Yponomeutidae)

Temporal changes in allele frequencies were studied in host-associated populations of the small ermine moth Yponomeuta padellus. At one site, populations from three host plants (Sorbus aucuparia, Amelanchier larnarckii , and Crataegus spp.) were sampled annually during a four-year-period and analysed with 20 polymorphic allozyme markers. At two other sites, allele frequencies at 5- 6 enzyme loci of Y. padellus populations from two different host plants were also tested for consistency over a 13-year-pcriod. Significant allele frequency changes occurred in the short-term analysis, whereas allele frequencies remained relatively stable through time in the long-term analyses. Furthermore, allele frequencies of Y. padellus populations from Crataegus spp. were relatively stable compared to the other host populations. The role of the agents responsible for the observed patterns is discussed.     

TEMPORAL CHANGE OF MITOCHONDRIAL DNA HAPLOTYPE FREQUENCIES AND FEMALE EFFECTIVE SIZE IN A BROWN TROUT (SALMO TRUTTA) POPULATION

We report data on genetic drift of mitochondrial DNA (mtDNA) haplotypes in a natural brown trout (Salmo trutta) population in Sweden. Large temporal frequency shifts were observed over the 14 consecutive year classes studied. The observed rate of drift was used to estimate the effective size of the population. This effective size applies to the female segment of the population as mtDNA is maternally inherited. The magnitude of mtDNA haplotype frequency change is compared with the corresponding allele frequency changes at 14 allozyme loci in the same population. The female effective size is estimated as 58, which is approximately half the effective size of 97 for the total population (both sexes) previously obtained from the shifts of allozyme allele frequencies.     

Introduced Swedish Canada geese (Branta canadensis) have low levels of genetic variation as revealed by DNA fingerprinting

The Swedish, Finnish and Norwegian population of Canada geese (Branta canadensis), now amounting to some 30–50 000 birds, was founded by only five individuals. We used DNA fingerprinting to assess the level of genetic variability in minisatellite loci of Swedish Canada geese from two northern areas. For comparison, we estimated the minisatellite variability in lesser white-fronted geese (Anser erythropus), barnacle geese (Branta leucopsis) and a reintroduced stock of Canadian giant Canada geese (Branta canadensis maxima). The mean similarity between Swedish Canada geese was 0.76 ± 0.15, which is higher than recorded for any other natural bird population. The high similarity implies that a fourfold increase of homozygosity has taken place in this population. The probable cause for the loss of variation is the low number of birds originally introduced and a history of repeated translocations, leading to a sequence of founder events. As a consequence of the high similarity, it has not been possible to use DNA fingerprinting for determination of parenthood in the population studied.     

Breeding origin and migration pattern of dunlin (Calidris alpina) revealed by mitochondrial DNA analysis

The large-scale migration of birds has been studied extensively by recoveries of ringed birds. However, there is very little ringing data from the arctic breeding grounds of waders. Here, the migration pattern of the dunlin, Calidris alpina, is studied with population genetic markers, using haplotype frequencies to estimate the breeding origin of migrating and wintering populations. Polymerase chain reaction (PCR) and restriction analysis of DNA from the mitochondrial control region was used to study the breeding origins of morphologically similar winter populations in the western Palaearctic, and to describe the population structure of the dunlin during winter. Also migrating dunlin from various stopover sites in Europe, Africa and Asia, were analysed with respect to their mitochondrial DNA (mtDNA) haplotypes. The genetic markers clearly show that the dunlin has a parallel migration system, with populations breeding in the western Palaearctic wintering mainly in the western part of the wintering range, and dunlin populations breeding further east wintering further east. The results also show that the distance between breeding and wintering area increases eastwards in this region.     

Differentiation among populations with migration, mutation, and drift: implications for genetic inference

Populations may become differentiated from one another as a result of genetic drift. The amounts and patterns of differentiation at neutral loci are determined by local population sizes, migration rates among populations, and mutation rates. We provide exact analytical expressions for the mean, variance, and covariance of a stochastic model for hierarchically structured populations subject to migration, mutation, and drift. In addition to the expected correlation in allele frequencies among populations in the same geographic region, we demonstrate that there is a substantial correlation in allele frequencies among regions at the top level of the hierarchy. We propose a hierarchical Bayesian model for inference of Wright's F-statistics in a two-level hierarchy in which we estimate the among-region correlation in allele frequencies by substituting replication across loci for replication across time. We illustrate the approach through an analysis of human microsatellite data, and we show that approaches ignoring the among-region correlation in allele frequencies underestimate the amount of genetic differentiation among major geographic population groups by approximately 30%. Finally, we discuss the implications of these results for the use and interpretation of F-statistics in evolutionary studies.     

Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations

This study describes complete control region sequences of mitochondrial DNA (mtDNA) from 117 Ethiopian cattle from 10 representative populations, in conjunction with the available cattle sequences in GenBank. In total, 79 polymorphic sites were detected, and these defined 81 different haplotypes. The haplotype and nucleotide diversity of Ethiopian cattle did not vary among the populations studied. All mtDNA sequences from Ethiopian cattle converged into one main maternal lineage (T1) that corresponds to African Bos taurus cattle. According to the results of this study, no zebu mtDNA haplotypes have been found in Ethiopia, where the most extensive hybridization took place on the African continent.