Molecular Markers Reveal Limited Population Genetic Structure in a North American Corvid,Clark’s Nutcracker (Nucifraga columbiana)

The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark’s nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker’s encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark’s nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark’s nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark’s nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark’s nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.     

Phylogeography and support vector machine classification of colour variation in panther chameleons

Lizards and snakes exhibit colour variation of adaptive value for thermoregulation, camouflage, predator avoidance, sexual selection and speciation. Furcifer pardalis, the panther chameleon, is one of the most spectacular reptilian endemic species in Madagascar, with pronounced sexual dimorphism and exceptionally large intraspecific variation in male coloration. We perform here an integrative analysis of molecular phylogeography and colour variation after collecting high‐resolution colour photographs and blood samples from 324 F. pardalis individuals in locations spanning the whole species distribution. First, mitochondrial and nuclear DNA sequence analyses uncover strong genetic structure among geographically restricted haplogroups, revealing limited gene flow among populations. Bayesian coalescent modelling suggests that most of the mitochondrial haplogroups could be considered as separate species. Second, using a supervised multiclass support vector machine approach on five anatomical components, we identify patterns in 3D colour space that efficiently predict assignment of male individuals to mitochondrial haplogroups. We converted the results of this analysis into a simple visual classification key that can assist trade managers to avoid local population overharvesting.     

THE HISTORICAL PATTERN OF GENE FLOW AMONG MIGRATORY AND NONMIGRATORY POPULATIONS OF PRAIRIE WARBLERS (AVES: PARULINAE)

Within a group of interbreeding organisms, the balance of gene flow among populations and microevolutionary forces acting within populations is expected to result in clinal transitions in the phenotypes possessed by members of differentiated populations. Discontinuous variation between geographically adjacent populations suggests the presence of a significant barrier to gene flow. Here I present genetic evidence for restricted gene flow between migratory and nonmigratory populations of prairie warblers. The nonmigratory form of this species is restricted to coastal mangroves in Florida and is morphologically distinguishable from the typical, migratory form that occurs across the remainder of the eastern United States. Pairs of migratory populations exhibited little population subdivision (Φ_ST ? 0.09), whereas pairs of migratory and nonmigratory populations are much more differentiated (Φ_ST = 0.27–0.42). A phylogenetic analysis of mitochondrial DNA haplotypes did not offer evidence of long-term isolation of migratory and nonmigratory populations. Together with the population genetic analysis, the phylogenetic relationship of haplotypes suggests that isolation between these forms must have arisen relatively recently in their history. Evidence for significant population structure is unexpected, given the geographic proximity of migratory and nonmigratory populations, the capacity for long-distance movements (e.g., migration) by prairie warblers, and several previous studies of population structure in North American birds. However, the findings are consistent with the geographic distribution of morphological and behavioral variation and demonstrate that significant boundaries between populations of vagile organisms may be relatively cryptic.     

Comparative phylogeography of brown (Sula leucogaster) and red-footed boobies (S. sula): The influence of physical barriers and habitat preference on gene flow in pelagic seabirds

To test the hypothesis that both physical and ecological barriers to gene flow drive population differentiation in tropical seabirds, we surveyed mitochondrial control region variation in 242 brown boobies (Sula leucogaster), which prefer inshore habitat, and 271 red-footed boobies (S. sula), which prefer pelagic habitat. To determine the relative influence of isolation and gene flow on population structure, we used both traditional methods and a recently developed statistical method based on coalescent theory and Bayesian inference (Isolation with Migration). We found that global population genetic structure was high in both species, and that female-mediated gene flow among ocean basins apparently has been restricted by major physical barriers including the Isthmus of Panama, and the periodic emergence of the Sunda and Sahul Shelves in Southeast Asia. In contrast, the evolutionary history of populations within ocean basins differed markedly between the two species. In brown boobies, we found high levels of population genetic differentiation and limited gene flow among colonies, even at spatial scales as small as 500 km. Although red-footed booby colonies were also genetically differentiated within ocean basins, coalescent analyses indicated that populations have either diverged in the face of ongoing gene flow, or diverged without gene flow but recently made secondary contact. Regardless, gene flow among red-footed booby populations was higher than among brown booby populations. We suggest that these contrasting patterns of gene flow within ocean basins may be explained by the different habitat preferences of brown and red-footed boobies.     

Genetic population structure of the paper wasp Polistes olivaceus (Hymenoptera: Vespidae) in Bangladesh

Dispersal triggers gene flow, which in turn strongly affects the ensuing genetic population structure of a species. Using nuclear microsatellite loci and mitochondrial DNA (mtDNA), we estimated the genetic population structure of the wasp Polistes olivaceus throughout Bangladesh. The level of population differentiation using nuclear markers (F _ST) appeared to be much lower than that estimated using mtDNA haplotype sequences (Ф_ST), even after correcting for effective population size differences between the two markers. These results suggest a philopatric tendency, in which gynes disperse less than males. We observed no isolation by distance among the study populations at either the nuclear or mtDNA level, suggesting nonequilibrium between gene flow and drift as a result of very frequent interpopulation movement. For the nuclear markers, an individual assignment test showed no genetically and geographically distinct groups. Instead, phylogenetic analyses as well as a minimum spanning network using mtDNA haplotypes consistently revealed two distinct lineages. The distribution of haplotypes indicated western populations with a single lineage and offered clear evidence for restricted gene flow across the Jamuna–Padma–Upper Meghna river system. Mismatch distributions exhibited a unimodal distribution, which along with a starlike haplotype network, suggested a population expansion in lineage I but not in lineage II. Overall, these results suggest that gene flow among populations of P. olivaceus was affected by both female philopatry and a major river system across Bangladesh.     

Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei)

Astyanax has become an important model system for evolutionary studies of cave animals. We investigated correlations of population genetic patterns revealed by microsatellite data and phylogeographic patterns shown by mitochondrial DNA sequences in Mexican cave and surface fish of the genus Astyanax (Characidae, Teleostei) to improve the understanding of the colonization history of this neotropical fish in Central and North America and to assess a recent taxonomic classification. The distribution of nuclear genotypes is not congruent with that of the mitochondrial clades. Admixture analyses suggest there has been nuclear gene flow between populations defined by different mitochondrial clades. The microsatellite data indicate that there was mitochondrial capture of a cave population from adjacent populations. Furthermore, gene flow also occurred between populations belonging to different nuclear genotypic clusters. This indicates that neither the nuclear genotypic clusters nor the mitochondrial clades represent independent evolutionary units, although the mitochondrial divergences are high and in a range usually characteristic for different fish species. This conclusion is supported by the presence of morphologically intermediate forms. Our analyses show that the Trans-Mexican Volcanic Belt limited gene flow, but has been crossed by Astyanax several times. In Yucatán, where obvious geographic barriers are missing, the incongruence between the distribution of nuclear and mitochondrial markers reflects random colonization events caused by inundations or marine transgressions resulting in random phylogeographic breaks. Thus, conclusions about the phylogeographic history and even more about the delimitation of species should not be based on single genetic markers.     

UNUSUAL POPULATION GENETICS OF A PARASITIC NEMATODE: mtDNA VARIATION WITHIN AND AMONG POPULATIONS

Very little is known about the distribution of genetic variance within and among populations of parasitic helminths. In this study we used mitochondrial DNA (mtDNA) restriction fragment analysis to describe the population genetic structure of Ostertagia ostertagi, a nematode parasite of cattle, in the United States. Estimates of within-population mtDNA diversity are 5 to 10 times greater than typical estimates reported for species in other taxa. Although populations are genetically differentiated for a key life–history trait, greater than 98% of the total genetic diversity is partitioned within populations, and the geographic distribution of individual mtDNA haplotypes suggests high gene flow among populations.     

Weak large‐scale population genetic structure in a philopatric seabird,the European Shag Phalacrocorax aristotelis

Quantifying population genetic structure is fundamental to testing hypotheses regarding gene flow, population divergence and dynamics across large spatial scales. In species with highly mobile life‐history stages, where it is unclear whether such movements translate into effective dispersal among discrete philopatric breeding populations, this approach can be particularly effective. We used seven nuclear microsatellite loci and mitochondrial DNA (ND2) markers to quantify population genetic structure and variation across 20 populations (447 individuals) of one such species, the European Shag, spanning a large geographical range. Despite high breeding philopatry, rare cross‐sea movements and recognized subspecies, population genetic structure was weak across both microsatellites and mitochondrial markers. Furthermore, although isolation‐by‐distance was detected, microsatellite variation provided no evidence that open sea formed a complete barrier to effective dispersal. These data suggest that occasional long‐distance, cross‐sea movements translate into gene flow across a large spatial scale. Historical factors may also have shaped contemporary genetic structure: cluster analyses of microsatellite data identified three groups, comprising colonies at southern, mid‐ and northern latitudes, and similar structure was observed at mitochondrial loci. Only one private mitochondrial haplotype was found among subspecies, suggesting that this current taxonomic subdivision may not be mirrored by genetic isolation.     

Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands

The disjunct distribution of forests in the Qinghai-Tibetan Plateau (QTP) and adjacent Helan Shan and Daqing Shan highlands provides an excellent model to examine vegetation shifts, glacial refugia and gene flow of key species in this complex landscape region in response to past climatic oscillations and human disturbance. In this study, we examined maternally inherited mitochondrial DNA (nad1 intron b/c and nad5 intron 1) and paternally inherited chloroplast DNA (trnC-trnD) sequence variation within a dominant forest species, Picea crassifolia Kom. We recovered nine mitotypes and two chlorotypes in a survey of 442 individuals from 32 populations sampled throughout the species' range. Significant mitochondrial DNA population subdivision was detected (G(ST) = 0.512; N(ST) = 0.679), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (N(ST) > GST, P < 0.05). Plateau haplotypes differed in sequence from those in the adjacent highlands, suggesting a long period of allopatric fragmentation between the species in the two regions and the presence of independent refugia in each region during Quaternary glaciations. On the QTP platform, all but one of the disjunct populations surveyed were fixed for the same mitotype, while most populations at the plateau edge contained more than one haplotype with the mitotype that was fixed in plateau platform populations always present at high frequency. This distribution pattern suggests that present-day disjunct populations on the QTP platform experienced a common recolonization history. The same phylogeographical pattern, however, was not detected for paternally inherited chloroplast DNA haplotypes. Two chlorotypes were distributed throughout the range of the species with little geographical population differentiation (G(ST) = N(ST) = 0.093). This provides evidence for highly efficient pollen-mediated gene flow among isolated forest patches, both within and between the QTP and adjacent highland populations. A lack of isolation to pollen-mediated gene flow between forests on the QTP and adjacent highlands is surprising given that the Tengger Desert has been a geographical barrier between these two regions for approximately the last 1.8 million years.     

Population divergence and gene flow in an endangered and highly mobile seabird

Seabirds are highly vagile and can disperse up to thousands of kilometers, making it difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given the great dispersal potential of these petrels, it remains unclear if populations are genetically distinct and which factors may contribute to isolation between them. We sampled petrels from across their range, including individuals from the presumably extirpated Molokai population. We sequenced 524 bp of mitochondrial DNA, 741 bp from three nuclear introns, and genotyped 18 microsatellite loci in order to examine the patterns of divergence in this species and to investigate the potential underlying mechanisms. Both mitochondrial and nuclear data sets indicated significant genetic differentiation among all modern populations, but no differentiation was found between historic samples from Molokai and modern birds from Lanai. Population-specific nonbreeding distribution and strong natal philopatry may reduce gene flow between populations. However, the lack of population structure between extirpated Molokai birds and modern birds on Lanai indicates that there was substantial gene flow between these populations and that petrels may be able to overcome barriers to dispersal prior to complete extirpation. Hawaiian petrel populations could be considered distinct management units, however, the dwindling population on Hawaii may require translocation to prevent extirpation in the near future.     

Mechanisms of population differentiation in seabirds

Despite recent advances in population genetic theory and empirical research, the extent of genetic differentiation among natural populations of animals remains difficult to predict. We reviewed studies of geographic variation in mitochondrial DNA in seabirds to test the importance of various factors in generating population genetic and phylogeographic structure. The extent of population genetic and phylogeographic structure varies extensively among species. Species fragmented by land or ice invariably exhibit population genetic structure and most also have phylogeographic structure. However, many populations (26 of 37) display genetic structure in the absence of land, suggesting that other barriers to gene flow exist. In these populations, the extent of genetic structure is best explained by nonbreeding distribution: almost all species with two or more population-specific nonbreeding areas (or seasons) have phylogeographic structure, and all species that are resident at or near breeding colonies year-round have population genetic structure. Geographic distance between colonies and foraging range appeared to have a weak influence on the extent of population genetic structure, but little evidence was found for an effect of colony dispersion or population bottlenecks. In two species (Galapagos petrel, Pterodroma phaeopygia, and Xantus's murrelet, Synthliboramphus hypoleucus), population genetic structure, and even phylogeographic structure, exist in the absence of any recognizable physical or nonphysical barrier, suggesting that other selective or behavioural processes such as philopatry may limit gene flow. Retained ancestral variation may be masking barriers to dispersal in some species, especially at high latitudes. Allopatric speciation undoubtedly occurs in this group, but reproductive isolation also appears to have evolved through founder-induced speciation, and there is strong evidence that parapatric and sympatric speciation occur. While many questions remain unanswered, results of the present review should aid conservation efforts by enabling managers to predict the extent of population differentiation in species that have not yet been studied using molecular markers, and, thus, enable the identification of management units and evolutionary significant units for conservation.     

Population genetic structure of Bellamya aeruginosa (Mollusca: Gastropoda: Viviparidae) in China: weak divergence across large geographic distances

Bellamya aeruginosa is a widely distributed Chinese freshwater snail that is heavily harvested, and its natural habitats are under severe threat due to fragmentation and loss. We were interested whether the large geographic distances between populations and habitat fragmentation have led to population differentiation and reduced genetic diversity in the species. To estimate the genetic diversity and population structure of B. aeruginosa, 277 individuals from 12 populations throughout its distribution range across China were sampled: two populations were sampled from the Yellow River system, eight populations from the Yangtze River system, and two populations from isolated plateau lakes. We used seven microsatellite loci and mitochondrial cytochrome oxidase I sequences to estimate population genetic parameters and test for demographic fluctuations. Our results showed that (1) the genetic diversity of B. aeruginosa was high for both markers in most of the studied populations and effective population sizes appear to be large, (2) only very low and mostly nonsignificant levels of genetic differentiation existed among the 12 populations, gene flow was generally high, and (3) relatively weak geographic structure was detected despite large geographic distances between populations. Further, no isolation by linear or stream distance was found among populations within the Yangtze River system and no signs of population bottlenecks were detected. Gene flow occurred even between far distant populations, possibly as a result of passive dispersal during flooding events, zoochoric dispersal, and/or anthropogenic translocations explaining the lack of stronger differentiation across large geographic distances. The high genetic diversity of B. aeruginosa and the weak population differentiation are likely the results of strong gene flow facilitated by passive dispersal and large population sizes suggesting that the species currently is not of conservation concern.     

Speciation and population structure in the morphospecies Lutzomyia longipalpis (Lutz & Neiva) as derived from the mitochondrial ND4 gene

Recent studies have suggested that the phlebotomine sand fly Lutzomyia longipalpis (Diptera: Psychodidae), the principal vector of visceral leishmaniasis in the Neotropics, may consist of several allopatric sibling species. Phylogenetic and population genetic analyses of nucleotide variation in a 618-bp fragment of the mitochondrial ND4 gene were carried out on specimens of Lu. longipalpis from several locations in Central and South America. The analyses were concordant with previous findings, indicating that certain allopatric populations of Lu. longipalpis have become sufficiently differentiated as to represent sibling species. Phylogenetic analyses revealed deep genetic divisions between four clades represented by specimens from northern South America, Brazil, Central America, and an isolated Colombian population. Strong differentiation also was observed between certain populations within the first two clades. Partitioning of genetic diversity within and between Central American populations did not show the presence of more than one species in the region. However, distance, even within the 70-km range of the Honduran collection sites, was found to have a remarkably strong effect on gene flow. The highly subdivided population structure may be due to the patchiness of their distribution. F(ST) values comparing a Guatemalan population with several Honduran populations revealed a level of differentiation associated with a negligible rate of gene flow.     

The voyage of an invasive species across continents: genetic diversity of North American and European Colorado potato beetle populations

The paradox of successful invading species is that they are likely to be genetically depauperate compared to their source population. This study on Colorado potato beetles is one of the few studies of the genetic consequences of continent-scale invasion in an insect pest. Understanding gene flow, population structure and the potential for rapid evolution in native and invasive populations offers insights both into the dynamics of small populations that become successful invaders and for their management as pests. We used this approach to investigate the invasion of the Colorado potato beetle (Leptinotarsa decemlineata) from North America to Europe. The beetles invaded Europe at the beginning of the 20th century and expanded almost throughout the continent in about 30 years. From the analysis of mitochondrial DNA (mtDNA) and amplified fragment length polymorphism (AFLP) markers, we found the highest genetic diversity in beetle populations from the central United States. The European populations clearly contained only a fraction of the genetic variability observed in North American populations. European populations show a significant reduction at nuclear markers (AFLPs) and are fixed for one mitochondrial haplotype, suggesting a single successful founder event. Despite the high vagility of the species and the reduction of genetic diversity in Europe, we found a similar, high level of population structure and low gene flow among populations on both continents. Founder events during range expansion, agricultural management with crop rotation, and selection due to insecticide applications are most likely the causes partitioning genetic diversity in this species.     

乔氏新银鱼基于细胞色素b序列的种群遗传结构和种群历史

为促进乔氏新银鱼(Neosalanx jordani)种质资源的保护, 采集了长江流域和淮河流域5个乔氏新银鱼地理种群计129个样本, 利用线粒体细胞色素b基因(Cyt b)全序列作为分子标记, 初步分析了乔氏新银鱼种群的遗传多样性、遗传结构及种群历史动态。研究结果共检测到18个Cyt b单倍型, 发现和其他鱼类相比, 乔氏新银鱼具有较高的单倍型多样性(h, 0.590±0.047), 但核苷酸多样性较低(π, 0.00088±0.00011)。分子变异分析(AMOVA)表明, 乔氏新银鱼5个地理种群内个体间和流域内种群间均存在显著的遗传差异, 而长江流域与淮河流域之间遗传分化不明显, 显示乔氏新银鱼遗传分化与当前水系的分布格局不吻合。结果表明乔氏新银鱼目前的遗传格局主要是由于长距离独立的建群事件、基因流限制以及种群的持续扩张的共同作用而形成的。种群历史动态分析结果显示乔氏新银鱼种群为近期扩张种群, 其大部分变异发生在1.897万年之内, 与最后一次冰期全面消退、海平面上升、长江流域及淮河流域中下游大量湖泊(适宜生境)形成的时间相吻合。建议对现存的乔氏新银鱼种群, 特别是遗传多样性较高的那些种群(如鄱阳湖、太湖及洪泽湖种群)分别保护。     

Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages

We describe the phylogeographic structure of 28 Chinese populations of the cyprinid Opsariichthys bidens across three main Chinese river drainages. Our study is based on the phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 bp). We combined this analysis with population processes inferred from nested clade analysis (NCA) and mismatch distributions. Both analyses showed that Chinese O. bidens consists of five mtDNA lineages (Opsariichthys 1-5) with high genetic divergence among them. Molecular divergences (TrN+G) higher than 20% among the Opsariichthys 1-5 mtDNA lineages suggest a taxonomic underestimation at the species level. About 92% of the genetic variance among samples was explained by differences among Opsariichthys mtDNA lineages. Drainage-restricted haplotypes with high frequencies and moderate nucleotide diversity show that Opsariichthys populations have evolved independently. NCA results were congruent with the phylogeny, and unimodal mismatch distributions with negative Tajima's D values suggest population expansions in some Opsariichthys lineages. The phylogeographic structure of the Opsariichthys 1-5 mtDNA lineages appears to be related to their long-term interruption of gene flow (theta(ST)>0.97). Our results suggested that fragmentation of ancestral ranges might have caused Opsariichthys diversification in Chinese waters. However, current distribution of common haplotypes across the Yangtze and Pearl drainages suggests a recent river connection that could have favoured gene flow across drainages. Overall, the results indicated that the richness of current Asian widespread species might have been underestimated, and that the cyprinid populations of O. bidens in the Yangtze, Pearl and Hai He drainages may correspond to five species.     

Subterranean termite phylogeography reveals multiple postglacial colonization events in southwestern Europe

A long‐standing goal of evolutionary biology is to understand how paleoclimatic and geological events shape the geographical distribution and genetic structure within and among species. Using a diverse set of markers (cuticular hydrocarbons, mitochondrial and nuclear gene sequences, microsatellite loci), we studied Reticulitermes grassei and R. banyulensis, two closely related termite species in southwestern Europe. We sought to clarify the current genetic structure of populations that formed following postglacial dispersal from refugia in southern Spain and characterize the gene flow between the two lineages over the last several million years. Each marker type separately provided a fragmented picture of the evolutionary history at different timescales. Chemical analyses of cuticular hydrocarbons and phylogenetic analyses of mitochondrial and nuclear genes showed clear separation between the species, suggesting they diverged following vicariance events in the Late Miocene. However, the presence of intermediate chemical profiles and mtDNA introgression in some Spanish colonies suggests ongoing gene flow. The current genetic structure of Iberian populations is consistent with alternating isolation and dispersal events during Quaternary glacial periods. Analyses of population genetic structure revealed postglacial colonization routes from southern Spain to France, where populations underwent strong genetic bottlenecks after traversing the Pyrenees resulting in parapatric speciation.     

A multilocus population genetic survey of the greater sage-grouse across their range

The distribution and abundance of the greater sage-grouse (Centrocercus urophasianus) have declined dramatically, and as a result the species has become the focus of conservation efforts. We conducted a range-wide genetic survey of the species which included 46 populations and over 1000 individuals using both mitochondrial sequence data and data from seven nuclear microsatellites. Nested clade and structure analyses revealed that, in general, the greater sage-grouse populations follow an isolation-by-distance model of restricted gene flow. This suggests that movements of the greater sage-grouse are typically among neighbouring populations and not across the species, range. This may have important implications if management is considering translocations as they should involve neighbouring rather than distant populations to preserve any effects of local adaptation. We identified two populations in Washington with low levels of genetic variation that reflect severe habitat loss and dramatic population decline. Managers of these populations may consider augmentation from geographically close populations. One population (Lyon/Mono) on the southwestern edge of the species' range appears to have been isolated from all other greater sage-grouse populations. This population is sufficiently genetically distinct that it warrants protection and management as a separate unit. The genetic data presented here, in conjunction with large-scale demographic and habitat data, will provide an integrated approach to conservation efforts for the greater sage-grouse.     

Population genetic diversity and structure of a naturally isolated plant species, Rhodiola dumulosa (Crassulaceae)

AIMS: Rhodiola dumulosa (Crassulaceae) is a perennial diploid species found in high-montane areas. It is distributed in fragmented populations across northern, central and northwestern China. In this study, we aimed to (i) measure the genetic diversity of this species and that of its populations; (ii) describe the genetic structure of these populations across the entire distribution range in China; and (iii) evaluate the extent of gene flow among the naturally fragmented populations. METHODS: Samples from 1089 individuals within 35 populations of R. dumulosa were collected, covering as much of the entire distribution range of this species within China as possible. Population genetic diversity and structure were analyzed using AFLP molecular markers. Gene flow among populations was estimated according to the level of population differentiation. IMPORTANT FINDINGS: The total genetic diversity of R. dumulosa was high but decreased with increasing altitude. Population-structure analysis indicated that the most closely related populations were geographically restricted and occurred in close proximity to each other. A significant isolation-by-distance pattern, caused by the naturally fragmented population distribution, was observed. At least two distinct gene pools were found in the 35 sampled populations, one composed of populations in northern China and the other composed of populations in central and northwestern China. The calculation of Nei's gene diversity index revealed that the genetic diversity in the northern China pool (0.1972) was lower than that in the central and northwestern China pool (0.2216). The populations were significantly isolated, and gene flow was restricted throughout the entire distribution. However, gene flow among populations on the same mountain appears to be unrestricted, as indicated by the weak genetic isolation among these populations.     

Population structure and gene flow among wild populations of the black muntjac (Muntiacus crinifrons) based on mitochondrial DNA control region sequences

The black muntjac (Muntiacus crinifrons) is a rare species endemic to China and its current distribution is confined to partial mountain ranges in eastern China. To assess the population structure and gene flow among the extant populations, we sequenced a portion of the mitochondrial control region (424 bp) for 47 samples collected from its current three large populations (Huangshan, Tiammushan and Suichang). A total of 18 unique haplotypes were defined based on 22 polymorphic sites. Of these haplotypes, 15 ones were population-specific and only one haplotype was shared among the three populations. Significant genetic differentiation was detected between Suichang and Huangshan populations (?(ST)=0.1677, P<0.001) or between Suichang and Tianmushan populations (?(ST)=0.2002, P<0.001), indicating that the Suichang population may be spatially structured from other two populations along matriline. The Mantel test revealed that this significant differentiation was not driven by geographic distance (P=0.14), implying that genetic divergence of Suichang population might result from recent human disturbances. Phylogenetic analyses suggested the mitochondrial control region haplotypes were split into two well divergent clades (Clade I and Clade II). Interestingly, the two distinct haplotype clades were found to coexist in Suichang area. The nested clade analysis revealed a significant phylogeographic structure among the black muntjac populations (total cladogram: chi2=18.68; P<0.001), which was inferred to result from past fragmentation followed by range expansion. The population expansion was supported by the analysis of mismatch distribution and the tests of neutrality. Therefore, we suggest that the coexistence of distinct haplotypes in Suichang population was induced by historical population expansion after fragmentation and that the current genetic differentiation should be attributed to the reduction of female-mediated gene flow due to recent habitat fragmentation and subsequent loss.