线粒体DNA 序列分析在中国水域真海豚物种鉴定中的初步应用

真海豚包括长喙真海豚( Delphinus capensis) 和短喙真海豚( D. delphis) 2 种, 而中国水域的真海豚到底是哪一个种或是否同时有两个种的存在, 并不清楚。本研究测定了12 头中国水域真海豚mtDNA 控制区(control region) 366 bp 和细胞色素b (cytochrome b , cyt b) 基因336 bp 的序列, 并与已发表的其它真海豚的序列合并分析,初步鉴定中国水域真海豚的分类地位。结果表明, 中国水域的真海豚与东太平洋的长喙真海豚有相同的鉴别位点, 且两者之间的核苷酸歧异度(控制区: 1.93 ±0.22 % , cyt b 基因: 0.68 ±0.19 %) 显著低于与短喙真海豚之间的差异(控制区: 2.92 ±0.41 % , cyt b 基因: 0.95 ±0.27 %) 。通过MEGA (molecular evolutionary genetic analysis) 软件中的邻接法(neighbor joining) 进行的系统发生分析中, 中国水域的真海豚与长喙真海豚聚成一支, 有明显较近的亲缘关系。因此, 中国水域的真海豚在分类上应归属于长喙真海豚。     

Genetic differentiation among recently diverged delphinid taxa determined using AFLP markers

In the mid-1990s, a new common dolphin species (Delphinus capensis) was defined in the northeast Pacific using morphological characters and mitochondrial DNA (mtDNA) sequences. This species is sympatric with a second species, Delphinus delphis; morphological differences between the two are slight and it is clear they are closely related. Does the phenotypic distinction result from only a few important genes or from large differences between their nuclear genomes? We used amplified fragment length polymorphism (AFLP) markers to broadly survey the nuclear genomes of these two species to examine the levels of nuclear divergence and genetic diversity between them. Furthermore, to create an evolutionary context in which to compare the level of interspecific divergence found between the two Delphinus taxa, we also examined two distinct morphotypes of the bottlenose dolphin (Tursiops truncatus). A nonmetric multidimensional scaling analysis clearly differentiated both Delphinus species, indicating that significant nuclear genetic differentiation has arisen between the species despite their morphological similarity. However, the AFLP data indicated that the two T. truncatus morphotypes exhibit greater divergence than D. capensis and D. delphis, suggesting that they too should be considered different species.     

The use of carcasses for the analysis of cetacean population genetic structure: a comparative study in two dolphin species

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans.     

Evolution of mating isolation between populations of Drosophila ananassae

Prezygotic mating isolation has been a major interest of evolutionary biologists during the past several decades because it is likely to represent one of the first stages in the transition from populations to species. Mate discrimination is one of the most commonly measured forms of prezygotic isolation and appears to be relatively common among closely related species. In some cases, it has been used as a measure to distinguish populations from subspecies, races, and sister species, yet the influences of various evolutionary mechanisms that may generate mate discrimination are largely unknown. In this study, we measured the level and pattern of mate discrimination among 18 populations of a cosmopolitan drosophilid species, Drosophila ananassae , from throughout its geographical range and its sister species, Drosophila pallidosa, which has a restricted geographical distribution in the South Pacific Islands. In addition, we measured genetic differentiation between all 18 populations using mitochondrial DNA polymorphism data. Mate discrimination varies considerably throughout the species range, being higher among populations outside the ancestral Indonesian range, and highest in the South Pacific. Our results suggest that colonization and genetic differentiation may have an influence on the evolutionary origin of mate discrimination. Our phylogeographical approach clarifies the ancestral relationships of several populations from the South Pacific that show particularly strong mate discrimination and suggests that they may be in the early stages of speciation. Furthermore, both the genetic and behavioral results cast doubt on the status of D. pallidosa as a good species.     

Population structure and genetic diversity in tristylous Narcissus triandrus: insights from microsatellite and chloroplast DNA variation

We investigated cpDNA sequence and nuclear microsatellite variation among populations of the wild daffodil Narcissus triandrus to examine the role of historical vs. contemporary forces in shaping population structure, morphological differentiation and sexual-system evolution. This wide-ranging heterostylous species of the Iberian Peninsula is largely composed of two allopatric varieties (vars. cernuus and triandrus), and populations with either stylar trimorphism or dimorphism. Dimorphic populations only occur in var. triandrus, are mainly restricted to the northwestern portion of the species range, and uniformly lack the mid-styled morph (M-morph). Chloroplast DNA (cpDNA) sequence variation revealed strong geographical structuring and evidence for a fragmentation event associated with differentiation of the two varieties. In var. triandrus, population fragmentation, restricted gene flow and isolation-by-distance were also inferred. Significant differences in genetic diversity and population structure between the two varieties likely reflect historical and contemporary differences in demography and gene flow among populations. Discordance between cpDNA markers and both microsatellite and morphological variation indicate that hybridization has occurred between the two varieties at contact zones. There were no differences in genetic diversity or population structure between dimorphic and trimorphic populations, and chloroplast haplotypes were not associated with either sexual system, indicating transitions in morph structure within each maternal lineage. M-morph frequencies were positively correlated with differentiation at microsatellite loci, indicating that the evolutionary processes influencing these neutral markers also influence alleles controlling the style morphs.     

Leaf morphological and genetic divergence in populations of Drimys (Winteraceae) in Chile

The genus Drimys is distributed in Chile from semi-arid zones to sub-Antarctic forests; there are three species of this tree, D. andina, D. confertifolia and D. winteri, the latter with varieties chilensis and winteri. Northern populations are found in small disjunct natural refuges, specifically mountain cloud forests and the bottom of ravines. The size and continuity of populations are greater in the south, where wetter conditions prevail. Morphological differences between populations have been observed, particularly between the northern populations of Fray Jorge and Talinay. This observation, led to the following questions: a) what is the level of morphological and genetic divergence among the populations of Drimys in Chile? and b) do the populations from Fray Jorge/Talinay, currently classified as D. winteri var. chilensis, differ genetically from the other populations of this variety? To answer these questions, we collected leaf samples from 37 populations of all Chilean Drimys, performed leaf morphology analysis and estimated genetic divergence using RAPD markers. We found a high degree of leaf morphological and genetic divergence between the populations of Fray Jorge/Talinay and the other Chilean species of Drimys. The morphological and genetic divergence among varieties of D. winteri was greater than that among the species of Drimys, which may indicate problems with their taxonomic classification.     

Patterns of genetic differentiation in Thamnophis and Taricha from the Pacific Northwest

Aim The co‐evolutionary interaction between the common garter snake, Thamnophis sirtalis, and the rough‐skinned newt, Taricha granulosa, takes place throughout much of the Pacific Northwest (North America). The biogeography of the Pacific Northwest has been heavily influenced by the last Pleistocene glaciation, which reached a maximum as late as 14,000 yr bp . We researched: (1) what type of population structure is present for garter snakes and newts, (2) whether the population structure of these species is consistent with a Pleistocene glaciation hypothesis, and (3) how population structure and migration possibly affect co‐evolution between these species. Location The Pacific Northwest of North America, specifically northern California, Oregon and Washington in the USA. Methods We sampled approximately 20 populations for each species from three different transects. Using microsatellite markers and tissue samples from both species, we quantified the population structure for both species. Individual‐based assignment tests were used to estimate contemporary migration rates. Results Both Th. sirtalis and Ta. granulosa exhibited little genetic differentiation among our study sites, even among those separated by large distances. Significant population structure was detected on multiple geographic scales. Differences in population structure were observed among transects and between garter snake and newt transects. Contemporary migration rate estimates indicate high levels of genetic exchange between populations. Main conclusions Prior to this study, little was known about the fine‐scale population structure of either species in this region. Patterns of population structure for garter snakes and newts reflect a shared biogeographical history affected by the Pleistocene glaciation in the Pacific Northwest. Both species apparently migrate frequently between populations, thus potentially retarding the process of adaptive co‐evolution. We find that populations from a northern coastal transect (Washington) are most likely to be locally adapted.     

GENETIC AND MORPHOLOGICAL DIVERGENCE AMONG MORPHOTYPES OF THE ISOPOD EXCIROLANA ON THE TWO SIDES OF THE ISTHMUS OF PANAMA

Excirolana braziliensis is a dioecious marine isopod that lives in the high intertidal zone of sandy beaches on both sides of Central and South America. It possesses no larval stage and has only limited means of adult dispersal. Indirect estimates of gene flow have indicated that populations from each beach exchange less than one propagule per generation. Multivariate morphometrics have discovered three morphs of this species in Panama, two of them closely related and found on opposite sides of Central America (“C morph” in the Caribbean and “C′ morph” in the eastern Pacific), the third found predominantly in the eastern Pacific (“P morph”). Though the P and C′ morphs are seldom found on the same beach, they have overlapping latitudinal ranges in the eastern Pacific. A related species, Excirolana chamensis, has been described from the Pacific coast of Panama. Each beach contains populations that remain morphologically and genetically stable, but a single drastic change in both isozymes and morphology has been documented. We studied isozymes and multivariate morphology of 10 populations of E. braziliensis and of one population of E. chamensis. Our objective was to assess the degree of genetic and morphological variation, the correlation of divergence on these two levels of integration, the phylogenetic relationships between morphs, and the possible contributions of low vagility, low gene flow, and occasional extinction and recolonization to the genetic structuring of populations. Genetic distance between the P morph, on one hand, and the other two morphotypes of E. braziliensis, on the other, was as high as the distance between E. braziliensis and E. chamensis. Several lines of evidence agree that E. chamensis and the P morph had diverged from other morphs of E. braziliensis before the rise of the Panama Isthmus separated the C and C′ forms, and that the P morph constitutes a different species. A high degree of genetic differentiation also exists between populations of the same morph. On the isozyme level, every population can be differentiated from every other on the basis of at least one diagnostically different locus, regardless of geographical distance or morphological affiliation. Morphological and genetic distances between populations are highly correlated. However, despite the high degree of local variation, evolution of E. braziliensis as a whole has not been particularly rapid; divergence between the C and C′ morphs isolated for 3 million yr by the Isthmus of Panama is not high by the standard of within-morph differentiation or by comparison with other organisms similarly separated. Alleles that are common in one population may be absent from another of the same morph, yet they appear in a different morph in a separate ocean. The high degree of local differentiation, the exclusive occupation of a beach by one genotype with rare arrival of foreign individuals that cannot interbreed freely with the residents, the genetic stability of populations with infrequent complete replacement by another genetic population, and the sharing by morphs of polymorphisms that are not shared by local populations, all suggest a mode of evolution concentrated in rare episodes of extinction and recolonization, possibly coupled with exceptional events of gene flow that help preserve ancestral variability in both oceans.     

Genomic variation patterns of subspecies defined by phenotypic criteria: Analyses of the mangrove species complex,Avicennia marina

Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation are expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina (Forssk.) Vierh. of the Indo-West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, whereas the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species-like patterns in some respects and population-like patterns in others. We propose that the subspecies designated in A. marina are informative in predicting genetic divergences and useful in making conservation decisions.     

中国南方茶棍蓟马地理种群遗传分化分析

【目的】基于mtDNA COI和COⅡ的联合序列,探讨中国南方茶棍蓟马Dendrothrips minowai地理种群的遗传多样性与遗传分化。【方法】利用MEGA 6.0, DnaSP 5.10和Arlequin 3.5.2.2等软件对中国南方茶棍蓟马8个地理种群遗传多样性、遗传分化、基因流、分子变异及地理距离与遗传距离的相关性进行分析,并推断群体演化历史。【结果】茶棍蓟马mtDNA COI和COⅡ序列均具有明显的AT偏好性,COI和COⅡ联合序列的长度为1 146 bp,共有22个单倍型。中国南方茶棍蓟马总群体遗传多样性较高,表现出高单倍型多样性(Hd=0.924)和低核苷酸多样性(π=0.00600)。8个地理种群总群体的遗传分化程度高(F_ST=0.84830),基因交流水平低(Nm=0.040),群体可能由于遗传漂变而发生明显分化。AMOVA分析显示,茶棍蓟马种群的遗传变异主要来自组间种群(F_CT=0.84922);Mantel检测显示地理距离与遗传距离存在显著的正相关(r=0.5029, P<0.01)。中性检验结果表明,除云南两个地理种群外的其他地理种群近期可能经历了种群扩张。【结论】中国南方茶棍蓟马地理种群遗传多样性较高,具有明显的遗传分化,基因交流较少;地理距离可能是影响茶棍蓟马地理种群遗传分化的主要因素之一。     

Microsatellite variation among diverging populations of Drosophila mojavensis

Divergence and speciation may occur by various means, depending on the particular history, selective environments, and genetic composition of populations. In Drosophila mojavensis, a good model of incipient speciation, understanding the population genetic structure within this group facilitates our ability to understand the context in which reproductive isolation among populations is developing. Here we report the genetic structure and relationships of D. mojavensis populations at nuclear loci. We surveyed 29 populations throughout the distribution of D. mojavensis for four microsatellite loci to differentiation among populations of this species. These loci reveal four distinct geographical regions of D. mojavensis populations in the south-western United States and north-western Mexico--(i) Baja California peninsula (Baja), (ii) Sonora, Mexico-southern Arizona, United States (Sonora), (iii) Mojave Desert and Grand Canyon (Mojave), and (iv) Santa Catalina Island (Catalina). While all regions show strong isolation, Mojave and Catalina are highly diverged from other regions. Within any region, populations are largely homogenous over broad geographical distances. Based on the population structure, we find clear geographical barriers to gene flow appear to have a strong effect in isolating populations across regions for this species.     

Population structure in African Drosophila melanogaster revealed by microsatellite analysis

Tropical sub-Saharan regions are considered to be the geographical origin of Drosophila melanogaster. Starting from there, the species colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic scenario, African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, limited information is available on the genetic structure of African populations. We used X chromosomal microsatellite variation to study the population structure of D. melanogaster populations using 13 sampling sites in North, West and East Africa. These populations were compared to six European and one North American population. Significant population structure was found among African D. melanogaster populations. Using a Bayesian method for inferring population structure we detected two distinct groups of populations among African D. melanogaster. Interestingly, the comparison to cosmopolitan D. melanogaster populations indicated that one of the divergent African groups is closely related to cosmopolitan flies. Low, but significant levels of differentiation were observed for sub-Saharan D. melanogaster populations from West and East Africa.     

Strong intraspecific variation in genetic diversity and genetic differentiation in Daphnia magna: the effects of population turnover and population size

Theory predicts that genetic diversity and genetic differentiation may strongly vary among populations of the same species depending on population turnover and local population sizes. Yet, despite the importance of these predictions for evolutionary and conservation issues, empirical studies comparing high‐turnover and low‐turnover populations of the same species are scarce. In this study, we used Daphnia magna, a freshwater crustacean, as a model organism for such a comparison. In the southern/central part of its range, D. magna inhabits medium‐sized, stable ponds, whereas in the north, it occurs in small rock pools with strong population turnover. We found that these northern populations have a significantly lower genetic diversity and higher genetic differentiation compared to the southern/central populations. Total genetic diversity across populations was only about half and average within‐population diversity only about a third of that in southern/central populations. Moreover, an average southern population contains more genetic diversity than the whole metapopulation system in the north. We based our analyses both on silent sites and microsatellites. The similarity of our results despite the contrasting mutation rates of these markers suggests that the differences are caused by contemporary rather than by historical processes. Our findings show that variation in population turnover and population size may have a major impact on the genetic diversity and differentiation of populations, and hence may lead to differences in evolutionary processes like local adaptation, hybrid vigour and breeding system evolution in different parts of a species range.     

Inverse relationship between F and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure

Microsatellites have proved to be useful for the detection of weak population structure in marine fishes and other species characterized by large populations and high gene flow. None the less, uncertainty remains about the net effects of the particular mutational properties of these markers, and the wide range of locus polymorphism they exhibit, on estimates of differentiation. We examined the effect of varying microsatellite polymorphism on the magnitude of observed differentiation in a population survey of walleye pollock, Theragra chalcogramma. Genetic differentiation at 14 microsatellite loci among six putative populations from across the North Pacific Ocean and Bering Sea was weak but significant on large geographical scales and conformed to an isolation-by-distance pattern. A negative relationship was found between locus variability and the magnitude of estimated population subdivision. Estimates of F(ST) declined with locus polymorphism, resulting in diminished power to discriminate among samples, and we attribute this loss to the effects of size homoplasy. This empirical result suggests that mutation rates of some microsatellite loci are sufficiently high to limit resolution of weak genetic structure typical of many marine fishes.     

Widespread geographical distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika

The spectacularly diverse cichlid fish species flocks of the East African Rift Lakes have elicited much debate on the potential evolutionary mechanisms responsible for the origin of these adaptive radiations. An historical perspective on population structure may offer insights into the processes driving population differentiation and possibly speciation. Here, we examine mitochondrial DNA (mtDNA) sequence variation in two endemic species of rock-dwelling cichlids, Simochromis babaulti and S. diagramma , from Lake Tanganyika. Phylogeographic analyses were used to infer what factors might have been important in the genetic structuring of Simochromis populations. Patterns of mtDNA differentiation in Simochromis were compared to those of other rock-dwelling cichlids to distinguish between competing hypotheses concerning the processes underlying their evolution. In striking contrast to previous findings, populations of Simochromis , even those separated by up to 300 km, were found to share mitochondrial DNA haplotypes. There is no correspondence between mtDNA genealogies and the geographical distribution of populations. Only S. babaulti , but not S. diagramma was found to have a significant association between genetic and geographical distance. These phylogeographic patterns suggest that the evolutionary effects of abiotic and biotic factors shaping population genetic structure may differ substantially even among closely related species of rock-dwelling cichlids. Physical events and barriers to gene flow that are believed to have had a major impact on the geographical distribution and intralacustrine speciation of Tropheus do not seem to have equally strongly affected its close relative Simochromis . These findings emphasize that no single mechanism can be responsible for the formation of population structure, speciation, and the adaptive radiation of all cichlid fishes.     

Genetic differentiation and phylogeographical structure of the Brachionus calyciflorus complex in eastern China

Spatio-temporal patterns and processes of genetic differentiation in passively dispersing zooplankton are drawing much attention from both ecologists and evolutionary biologists. Two opposite phylogeographical scenarios have already been demonstrated in rotifers, which consist of high levels of genetic differentiation among populations even on small geographical scales on the one hand and the traditionally known cosmopolitanism that is associated with high levels of gene flow and long-distance dispersal via diapausing stages on the other hand. Here, we analysed the population genetic structure and the phylogeography of the Brachionus calyciflorus species complex in eastern China. By screening a total of 318 individuals from ten locations along a 2320-km gradient and analysing samples from two growing seasons, we aimed at focusing on both small- and large-scale patterns. We identified eight cryptic species and verified species status of two of these by sexual reproduction tests. Samples in summer and winter yielded different cryptic species. The distribution patterns of these genetically distinct cryptic species were diverse across eastern China, from full cosmopolitanism to local endemism. The two most abundant cryptic species BcWIII and BcSW showed a pattern of strong genetic differentiation among populations and no significant isolation by distance. Long-distance colonization, secondary contact and recent range expansion are probably responsible for the indistinct pattern of isolation by distance. Our results suggest that geographical distance is more important than temporal segregation across seasons in explaining population differentiation and the occurrence of cryptic species. We explain the current phylogeographical structure in the B. calyciflorus species complex by a combination of recent population expansion, restricted gene flow, priority effects and long-distance colonization.     

Genetics, behaviour and chemical recognition of the invading ant Pheidole megacephala

Introduced species often become ecologically dominant, displacing native species and posing a serious threat to ecosystem function and global biodiversity. Ants are among the most widespread and damaging alien species; introductions are often accompanied by population-level behavioural and genetic changes contributing to their success. We investigated the genetic structure, chemical profile and nestmate recognition in introduced populations of the invasive big-headed ant, Pheidole megacephala, in Australia. Behavioural analyses show that workers are not aggressive towards conspecifics from different nests, even at large geographical scales (up to 3000 km) and between populations encompassing a wide range of environmental conditions. By contrast, interactions with workers of other species invariably result in agonistic behaviours. Genetic analyses reveal that populations have low genetic diversity. No genetic differentiation occurs among nests of the same population; differentiation between populations, though significant, remains weak. Chemical analyses indicate that cuticular lipids are similar between colonies of a population, and that differentiation between populations is low. Altogether, these results indicate that the big-headed ant P. megacephala forms a large unicolonial population across northern/eastern Australia.