Genetic structure in a montane mayfly Baetis bicaudatus (Ephemeroptera: Baetidae), from the Rocky Mountains, Colorado

1. Populations of a number of sub‐tropical stream insect species have been found to show unexpected patterns of genetic variation, with more differences between samples from the same stream than between whole streams or between subcatchments. Many samples also showed deviations from Hardy–Weinberg proportions. It has been proposed that these patterns result from limited numbers of matings contributing to a given stream reach, because adults emerge throughout the year, and low levels of larval drift between reaches. These patterns may be less likely in a northern hemisphere montane species with synchronous emergence of adults and high levels of drift. We tested the hypothesis that patterns of genetic variation in a montane mayfly from the Rocky Mountains, Colorado, would reflect a pattern of ‘isolation by distance’ with samples from the same creek being more similar than samples from different creeks and that deviations from Hardy–Weinberg proportions would be minimal. 2. Based on allozyme variation, the hypothesis of minimal deviations from Hardy–Weinberg proportions was not supported and there was no evidence of isolation by distance. Nevertheless the levels of differentiation among samples from within the same stream were less than those reported for most subtropical species. 3. Results from analysis of a fragment of the cytochrome oxidase gene (subunit 1) revealed contrasting patterns. The levels of genetic differentiation were an order of magnitude higher between streams than among samples within streams. In addition, although there was no significant isolation by distance effect overall, a nested clade analysis provided evidence for restricted gene flow with isolation by distance for some clades. 4. We suggest that these contrasting results may reflect the differences in male and female dispersal patterns. While differentiation at nuclear gene markers (allozymes) give information about both male and female dispersal, mitochondrial DNA markers reflect only female dispersal. We suggest that in this species, female dispersal may be more restricted, perhaps mostly along stream channels, whereas male dispersal is more widespread. An alternative explanation for the different results is the different evolutionary rates of the mitochondrial and nuclear markers.     

云南中华按蚊的遗传变异和种群结构

为了掌握云南省各地中华按蚊种群间的遗传变异和种群结构特征,测序并分析了采自云南9个样本点5个种群组的89头中华按蚊的线粒体COII基因。结果表明这些中华按蚊种群的COII基因序列平均单倍型多样性指数和核苷酸多样性指数分别为h=0.933,π=0.00406,共有51个变异位点,占分析的739个碱基总数的6.9%;定义了39个单倍型,有2个频率最高的单倍型H1和H9,分别占个体序列数的20.2%和12.4%;系统发育分析表明单倍型与地理位置没有明显的对应关系,单倍型网络图显示大部分单倍型分布没有明显的亲缘地理格局,主要以单倍型H1、H9、H4、H33和H2为中心呈星状分布,但元江和元阳构成的种群组(YU)单倍型存在明显地域分布特征;AMOVA结果表明种群组间遗传变异为12.58%,达到显著水平(P=0.04888),地理种群组间具有明显种群遗传结构。不同地区两两种群组间的Fst值和Nm值显示大部分种群组间存在基因交流,没有形成明显的遗传分化,但YU种群组和其他种群组间缺乏明显的基因交流,这主要是因为哀牢山的阻隔,使云南东西部形成两种不同的气候,产生了明显的遗传分化;歧点分布图显示为明显单峰分布,中性检测结果均为显著负值,说明云南省的中华按蚊种群在近期经历过复杂的种群扩张事件。掌握中华按蚊遗传多样性及分化特征,对中华按蚊及疟疾控制具有重要的作用。     

Genetic signatures of parental contribution in black and white populations in Brazil

Two hundred and three individuals classified as white were tested for 11 single nucleotide polymorphisms plus two insertion/deletions in their Y-chromosomes. A subset of these individuals (n = 172) was also screened for sequences in the first hypervariable segment of their mitochondrial DNA (mtDNA). In addition, complementary studies were done for 11 of the 13 markers indicated above in 54 of 107 black subjects previously investigated in this southern Brazilian population. The prevalence of Y-chromosome haplogroups among whites was similar to that found in the Azores (Portugal) or Spain, but not to that of other European countries. About half of the European or African mtDNA haplogroups of these individuals were related to their places of origin, but not their Amerindian counterparts. Persons classified in these two categories of skin color and related morphological traits showed distinct genomic ancestries through the country. These findings emphasize the need to consider in Brazil, despite some general trends, a notable heterogeneity in the pattern of admixture dynamics within and between populations/groups.     

澜沧江老挝纹胸鮡Cytb基因的序列变异与遗传结构分析

老挝纹胸鮡是分布于澜沧江流域的一种特有鱼类,喜激流底栖生活。为了解其各地理种群间的遗传结构与遗传变异,文章分析了129尾采自澜沧江8条支流水系的老挝纹胸鮡mtDNA细胞色素b基因1 138 bp的序列变异,共发现16个多态性位点,定义了15个单倍型。澜沧江老挝纹胸鮡遗传变异较低,平均单倍型多样性指数和核苷酸多样性指数分别是h=0.299,π=0.299,有3个种群甚至没有变异,分子变异方差分析结果表明各种群内变异大于各种群间变异,种群间没有差异。对老挝纹胸鮡所有种群进行的单倍型错配分布呈现单峰型,中性检验结果均为负值(Tajima’s D=?2.36965,P<0.02;Fu’s Fs=?20.975,P<0.05)表明,澜沧江老挝纹胸鮡自然种群可能经历过近期的种群扩张事件。     

Genetic structure among populations in the endemic Hawaiian Plantago lineage: insights from microsatellite variation

Endemic Hawaiian species in the genus Plantago show considerable morphological and ecological diversity. Despite their variation, a recent phylogenetic analysis based on DNA sequence data showed that the group is monophyletic and that sequence variation among species and morphotypes is low. This lack of sequence polymorphisms resulted in an inability to resolve species and population affinities within the most recently derived clade of this lineage. To assess species boundaries, population genetic structure and interpopulation connectivity among the morphologically and ecologically distinct populations within this clade, genetic variation was examined using eight microsatellite loci. Within‐population genetic diversity was found to be lowest in the Maunaiu, Hawai'i population of the endangered P. hawaiensis, and highest in the large P. pachyphylla population from 'Eke, West Maui. Isolation by distance across the range of populations was detected and indicated restricted dispersal. This result is likely to be attributable to few interisland dispersal events in the evolutionary history of this lineage. Genetic differentiation within islands tended to be higher among populations occurring in contrasting bog and woodland habitats, suggesting ecological barriers to gene flow and the potential role of ecological divergence in population diversification. Overall, these results are consistent with findings from phylogenetic analysis of the entire lineage. Our data bring new insights regarding patterns of dispersal and population genetic structure to this endemic and endangered group of island taxa. As island environments become increasingly fragmented, information of this type has important implications for the successful management of these fragile populations and habitats.     

Genetic variation and recent population history of the tropical gar Atractosteus tropicus Gill (Pisces: Lepisosteidae)

The tropical gar Atractosteus tropicus belongs to one of the few extant lineages of early bony fishes. The genetic variation detected both within and among 11 natural populations of A. tropicus in Mesoamerica along with the implications for their recent history are presented. Sequences from cytochrome b (307 bp) and cytochrome oxidase subunit II (607 bp) were used as data sources. Apparently, the populations of this fish have decreased in size because of anthropogenic pressures, such as habitat degradation and destruction. The observed values for nucleotide diversity (0·0016 ± 0·0018) and haplotype diversity (0·477 ± 0·302) suggest low levels of genetic variation. Nonetheless, most of the populations studied are currently in a period of genetic stasis. Recent isolation by distance, reduced gene flow and translocation were inferred as the processes maintaining this stasis. Phylogenetic analyses showed reciprocal monophyly between the haplotypes from Guatemala and the other populations. This, together with the observed genetic variation, suggests that the Guatemalan haplotypes might represent a new species. The haplotypes, other than those from Guatemala, exhibited a geographic pattern consistent with two main reproductive populations, one from the Pacific and the other from the Gulf of Mexico–Caribbean slope of Mesoamerica. Pleistocene glacial and interglacial periods might be responsible for moulding the heterogeneity in the genetic structure observed during this study.     

Genetic variation and population structure ofCarex breviculmis (Cyperaceae) in Korea

We determined the genetic diversity and population structures ofCarex breviculmis (Cyperaceae) populations in Korea, using genetic variations at 23 allozyme loci.C. breviculmis is a long-lived herbaceous species that is widely distributed in eastern Asia. A high level of genetic variation was found in 15 populations. Twelve enzymes revealed 23 loci, of which 11 were polymorphic (47.8%). Genetic diversity at the speciesand population levels were 0.174 and 0.146, respectively. Total genetic diversity (H_T = 0.363) and within-population genetic diversity (H_s = 0.346) were high, whereas the extent of the population divergence was relatively low (G_ST = 0.063). Deviation from random mating (Fis) within the 15 populations was 0.206. An indirect estimate of the number of migrants per generation(Nm = 3.69) indicated that gene flow was extensive among Korean populations of this species. Analysis of fixation indices revealed a substantial heterozygote deficiency in some populations and at some loci. Genetic identity between popu-lations was high, exceeding 0.956.     

Genetic structure among continental and island populations of gyrfalcons

Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub-Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (F(ST)). With the microsatellite results, significant population structure (F(ST), principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1-16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial-age refugium to their current circumpolar distribution. Additional sampling of gyrfalcons from Fennoscandia and Russia throughout Siberia is necessary to test putative gene flow between Norway and Alaska and Canada as suggested by this study.     

Molecular ecology of social behaviour: analyses of breeding systems and genetic structure

Molecular genetic studies of group kin composition and local genetic structure in social organisms are becoming increasingly common. A conceptual and mathematical framework that links attributes of the breeding system to group composition and genetic structure is presented here, and recent empirical studies are reviewed in the context of this framework. Breeding system properties, including the number of breeders in a social group, their genetic relatedness, and skew in their parentage, determine group composition and the distribution of genetic variation within and between social units. This group genetic structure in turn influences the opportunities for conflict and cooperation to evolve within groups and for selection to occur among groups or clusters of groups. Thus, molecular studies of social groups provide the starting point for analyses of the selective forces involved in social evolution, as well as for analyses of other fundamental evolutionary problems related to sex allocation, reproductive skew, life history evolution, and the nature of selection in hierarchically structured populations. The framework presented here provides a standard system for interpreting and integrating genetic and natural history data from social organisms for application to a broad range of evolutionary questions.     

Genetic relatedness and disrupted social structure in a poached population of African elephants

We use genetic measures of relatedness and observations of female bonding to examine the demographic signature of historically heavy poaching of a population of free-ranging African elephants. We collected dung samples to obtain DNA and observed behaviour from 102 elephant families over a 25-month period in 2003–2005 in Mikumi National Park, Tanzania. Poaching reduced the population by 75% in the decade prior to the 1989 ivory trade ban; park records indicate that poaching dropped significantly in Mikumi following the ban. Using 10 microsatellite loci, DNA was genotyped in 203 elephants and pair-wise relatedness was calculated among adult females within and between groups. The Mikumi population is characterized by small group size, considerable variation in group relatedness, females with no first-order adult relatives and females that form only weak social bonds. We used gene-drop analysis and a model of a genetically intact pedigree to compare our observed Mikumi group relatedness to a simulated genetically intact unpoached expectation. The majority of groups in Mikumi contain 2 to 3 adults; of these, 45% were classified as genetically disrupted. Bonding, quantified with a pair-wise association index, was significantly correlated with relatedness; however only half of the females formed strong bonds with other females, and relatedness was substantially lower for a given bond strength as compared to an unpoached population. Female African elephants without kin demonstrated considerable behavioural plasticity in this disturbed environment, grouping with other females lacking kin, with established groups, or remaining alone, unable to form any stable adult female-bonds. We interpret these findings as the remaining effect of poaching disturbance in Mikumi, despite a drop in the level of poaching since the commercial trade in ivory was banned 15 years ago.     

Genetic structure in Orchesella cincta (Collembola): strong subdivision of European populations inferred from mtDNA and AFLP markers

Population genetic structure is determined both by current processes and historical events. Current processes include gene flow, which is largely influenced by the migration capacity of a species. Historical events are, for example, glaciation periods, which have had a major impact on the distribution of many species. Species with a low capacity or tendency to move about or disperse often exhibit clear spatial genetic structures, whereas mobile species mostly show less spatial genetic differentiation. In this paper we report on the genetic structure of a small, wingless arthropod species (Orchesella cincta: Collembola) in Europe. For this purpose we used mtDNA COII sequences and AFLP markers. We show that large genetic differences exist between populations of O. cincta, as expected from O. cincta's winglessness and sedentary lifestyle. Despite the fact that most variability was observed within populations (59%), a highly significant amount of AFLP variation (25%) was observed between populations from northwestern Europe, central Europe and Italy. This suggests that gene flow among regions is extremely low, which is additionally supported by the lack of shared mtDNA alleles between regions. Based on the genetic variation and sequence differences observed we conclude that the subdivision occurred long before the last glaciation periods. Although the populations still interbreed in the lab, we assume that in the long term the genetic isolation of these regions may lead to speciation processes.     

Genetic variation and population structure in the endangered greater horseshoe bat Rhinolophus ferrumequinum

Following a dramatic decline last century, the British population of the endangered greater horseshoe bat Rhinolophus ferrumequinum is highly fragmented. To examine the consequences of fragmentation and limited dispersal on patterns of genetic structure and variation, we used microsatellite markers to screen bats from around 50% of the known maternity colonies in Britain, and two areas from continental Europe. Analyses revealed that Welsh and English colonies were genetically isolated. This, and lower variability in Britain than north France, may result from either genetic drift, or the species' colonization history. Gene flow among most neighbouring colonies was not generally restricted, with one exception. These findings have important implications for the ongoing conservation management of this species.     

Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers

The genetic variation of the critically endangered Corfu killifish (Valencia letourneuxi), an endemic freshwater fish species of the western Balkans, was assessed for nine populations sampled in eight water systems in western continental Greece, the Peloponnese and the Ionian Island of Corfu, using mitochondrial and microsatellite markers. The analyses were based on data from three mtDNA regions (D‐loop, COI and 16S rRNA sequences) and 14 microsatellite loci. Samples from the congeneric species Valencia hispanica and the phylogenetically closely related species Aphanius fasciatus were also used in the study as outgroups. Both the mitochondrial and the microsatellite analyses revealed three distinct population groupings associated with the geographical distribution of the populations: one southern group occupying rivers draining to the Patraikos Gulf, the second one including the populations flowing into the Amvrakikos Gulf and the third, more northern group, including the other populations from rivers in Corfu Island and Epirus flowing into the Ionian Sea. Within these groupings there is limited genetic differentiation between populations; in addition, there is reduced intrapopulation genetic variation, evidenced by low heterozygosity values, number of alleles and haplotype diversity. In terms of taxonomic implications and appropriate management actions for conservation, our data suggest that the major population groups should be regarded at least as three distinct conservation units (CUs), with translocation and restocking actions to take place only within the geographical range of the CU concerned. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 334–349.     

Microsatellite variation in a social insect

We undertook a study to explore the potential of microsatellite loci as genetic markers for investigating kinship patterns in a social waspParachartergus colobopterus. A plasmid library with small inserts was screened for several oligonucleotide repeat motifs. Positive clones were sequenced and several were selected for further work. PCR primers were constructed that would amplify the tandem repeat region and a number of female wasps were scored for variation in the number of tandem repeats at these loci. The five amplified loci were far more variable than allozymes, with an average heterozygosity of 0.35. This work was supported by NSF Grants BSR-9021514 and IBN-9210051.     

Genetic variability and demographic history of Anguilla mossambica (Peters, 1852) from continental Africa and Madagascar

In this study, population genetic and demographic parameters were inferred using sequence data from 151 individuals of Anguilla mossambica originating from continental south and south-east Africa and Madagascar. The analyses were based on a 532 bp segment of the mitochondrial cytochrome b gene. The absence of genetic structuring was observed thereby supporting the hypothesis of panmixia for the endemic A. mossambica. The overall nucleotide diversity π = 0.002 and the haplotype diversity reached h = 0.691. Significant negative values from several tests of neutrality and mismatch analysis pointed to fluctuating historical population sizes. Bayesian averaging resulted in higher support for population growth models vs. a constant population-size model. Population decline and subsequent growth most likely predated the last glacial and were probably related to extended periods of extreme drought followed by wetter and more stable hydroclimate between 150 and 75,000 years before present (kBP). According to this scenario the female effective population size has increased since 110 kBP by c. two orders of magnitude to a recent level of about 650,000 (219,317–2,292,000).     

Genetic structure and divergence of tench Tinca tinca European populations

The tench Tinca tinca is a freshwater species with human-mediated translocations, aquaculture interest and limited information on its genetic structure. mtDNA sequencing analysis of control region and two genes in 50 individuals from five European populations identified two phylogroups, with greater variability than that reported until now, and a hybridization zone in the Danube River region. Restriction analyses of additional samples reveal the complicated genetic structure characteristics of tench's wild and translocated populations, supporting future breeding practices.     

Genetic variation and structure in Scandinavian red deer (Cervus elaphus): influence of ancestry,past hunting,and restoration management

In the 19^th century, the red deer (Cervus elaphus) population in Sweden experienced a rapid decline in numbers and distribution. A small population was, however, remnant in the southernmost province (Skåne) of the country, presumably corresponding to the nominate form of red deer (Cervus elaphus elaphus Linnaeus, 1758). After management, reintroductions, and supplementary release during the 20^th century the Swedish C. elaphus population recovered. The recovery was partially uncontrolled, and included introductions of C. elaphus of continental origin. In northern central Sweden (Jämtland) the current C. elaphus population may stem from natural colonization from Norway and/or from specimens of Swedish origin that have escaped from enclosures. To evaluate the status of the current, partially separated populations, we investigated variation at microsatellite markers in 157 C. elaphus specimens from ten locations in Sweden and Norway. Analyses suggest that the highest‐likelihood phylogenetic structure among the individuals sampled is described four distinct genetic clusters: (1) animals from the province of Västergötland in south‐western Sweden; (2) deer from the southernmost province of Skåne; (3) deer from the provinces Jämtland, Blekinge, and Västmanland; and (4) Norwegian deer. Cervus elaphus from a captive herd at the Skåne Zoo cluster with deer from Skåne or deer from Västergötland, depending on the method of analysis. A number of populations in Sweden may genetically match the nominate form of red deer (C. e. elaphus). The recently established C. elaphus population in Jämtland seems to stem mainly from escapees from enclosures, with a mixed ancestry from the wild remnant population in Skåne and continental deer, whereas the influx from Norway is minor, if any. Our results show the need for a detailed assessment of genetic differentiation, and emphasize the value of local management plans when planning and managing introductions. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 43–53.     

When gender matters: new insights into the relationships between social systems and the genetic structure of human populations

Due to its important effects on the ecological dynamics and the genetic structure of species, biologists have long been interested in gender‐biased dispersal, a condition where one gender is more prone to move from the natal site. More recently, this topic has attracted a great attention from human evolutionary geneticists. Considering the close relations between residential rules and social structure, gender‐biased dispersal is, in fact, regarded as an important case study concerning the effects of socio‐cultural factors on human genetic variation. It all started with the seminal paper by Mark Seielstad, Erich Minch and Luigi Luca Cavalli Sforza from Stanford University (Seielstad et al. 1998). They observed a larger differentiation for Y‐chromosome than mitochondrial DNA between extant human populations, purportedly a consequence of the prevalence of long‐term patrilocality in human societies. Subsequent studies, however, have highlighted the need to consider geographically close and culturally homogeneous groups, disentangle signals due to different peopling events and obtain unbiased estimates of genetic diversity. In this issue of Molecular Ecology, not only do Marks et al. (2012) adopt an experimental design which addresses these concerns, but they also take a further and important step forward by integrating the genetic analysis of two distant populations, the Basotho and Spanish, with data regarding migration rates and matrimonial distances. Using both empirical evidence and simulations, the authors show that female‐biased migration due to patrilocality might shape the genetic structure of human populations only at short ranges and under substantial differences in migration rates between genders. Providing a quantitative framework for future studies of the effects of residential rules on the human genome, this study paves the way for further developments in the field. On a wider perspective, Marks et al.'s work demonstrates the power of approaches which integrate biological, cultural and demographic lines of evidence in the study of relations between social and genetic structures of human populations.     

Social structure and indirect genetic effects: genetics of social behaviour

The social environment modulates gene expression, physiology, behaviour and patterns of inheritance. For more than 50 years, this concept has been investigated using approaches that include partitioning the social component out of behavioural heritability estimates, studying maternal effects on offspring, and analysing dominance hierarchies. Recent advances have formalized this ‘social environment effect’ by providing a more nuanced approach to the study of social influences on behaviour while recognizing evolutionary implications. Yet, in most of these formulations, the dynamics of social interactions are not accounted for. Also, the reciprocity between individual behaviour and group‐level interactions has been largely ignored. Consistent with evolutionary theory, the principles of social interaction are conserved across a broad range of taxa. While noting parallels in diverse organisms, this review uses Drosophila melanogaster as a case study to revisit what is known about social interaction paradigms. We highlight the benefits of integrating the history and pattern of interactions among individuals for dissecting molecular mechanisms that underlie social modulation of behaviour.