Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

Responses of plants to changes in Qinghai–Tibetan Plateau and glaciations: Evidence from phylogeography of a Sibiraea (Rosaceae) complex

The genetic structure and phylogeographical history of the alpine shrubs Sibiraea angustata (Rosaceae) and Sibiraea laevigata from the Qinghai–Tibetan Plateau (QTP) were investigated to identify alpine plant responses to changes in the QTP and glaciations. Fifty-five populations were analyzed using four chloroplast DNA (cpDNA) regions and (nuclear ribosomal internal transcribed spacer) nrITS sequence data. In all, 21 cpDNA haplotypes and 13 nrITS sequence types were detected. Analyses of the genetic diversity and phylogenetic relationships detected two rarely reported glacial refugia. One was the Yushu–Nangqian area, and the other consisted of the area from the Songpan Plateau to the southeastern margin of the QTP. Sibiraea species populations experienced divergent evolution and founder effects when they recolonized the QTP platform and adjacent high-altitude regions following glaciations. The divergence times of the main lineages and haplotypes were in the range of 1.60–2.58 Ma. The population size of Sibiraea species in the QTP decreased approximately 23-fold during the last 0.12 Ma, indicating that Sibiraea species were significantly affected by environmental changes in the QTP. Therefore, the rapid uplift of the QTP and subsequent glaciations likely played an important role in driving genetic divergence and population size changes of Sibiraea species in the QTP.     

The Quaternary evolutionary history,potential distribution dynamics,and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial,Anisodus tanguticus (Solanaceae)

Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai–Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well‐differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F_ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.     

Genetic diversity and structure of the endangered lady's slipper orchid Cypripedium japonicum Thunb. (Orchidaceae) in Japan

Cypripedium japonicum Thunb. (Orchidaceae), once a common perennial herb, is now designated as endangered throughout most of its distribution due to habitat destruction and fragmentation, and the impacts of horticultural collection. We investigated the genetic characteristics of this species for conservation purposes, using microsatellite markers to examine the genetic diversity and structure of 15 native and 5 ex situ populations in Japan. The results imply that although allelic variation is low in Japanese C. japonicum, sexual reproduction by seed, as well as clonal propagation, may occur in some populations. Both native and ex situ populations were found to be genetically differentiated, indicating that some populations may have experienced recent population declines, genetic fragmentation, or bottlenecks. The degree of genetic drift from the putative ancestral population, inferred through STRUCTURE analysis, was more pronounced in northern populations than in southern populations. Some of the ex situ conserved populations exhibited a low degree of differentiation from ancestral native populations. Our results imply that conservation of C. japonicum in Japan is best supported by maintaining individual populations and their unique genetic characteristics.     

Microsatellite markers indicate genetic differences between cultivated and natural populations of endangered Taxus yunnanensis

Taxus yunnanensis (Taxaceae) is an endangered plant known for its effective natural anti‐cancer metabolite, taxol. To assess the effectiveness of T. yunnanensis ex situ conservation in China, the genetic diversity and genetic structure of nine cultivated and 14 natural populations were compared using 11 polymorphic microsatellite markers. The purpose of this comparison was to determine whether the cultivated populations were genetic representatives of natural types. Among the 14 natural populations studied, three were from Tibet and 11 were from the Hengduan Mountains. There were fewer genetic variations among cultivated populations than among natural populations, but this difference was not significant. However, 23 unique alleles were detected in cultivated populations and 14 were detected in natural populations. Striking differences in genetic structure (G_ST = 0.365) was observed between them. STRUCTURE, AMOVA and cluster analyses also consistently showed a clear genetic separation between the 14 natural and seven cultivated populations. Only five natural populations from the south‐central Hengduan Mountains were genetically represented in two cultivated collections. The reason for the occurrence of distinct genetic differences between cultivated and natural populations and the loss of natural population‐specific alleles in the cultivated populations can be attributed to uneven selection during establishment. These results suggest that the genetic structure of T. yunnanensis may not have been conserved effectively. Based on our study, practical conservation strategies for ex situ preservation of T. yunnanensis have been developed. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 450–461.     

Crumbling diversity: comparison of historical archived and contemporary natural populations indicate reduced genetic diversity and increasing genetic differentiation in the golden-cheeked warbler

Genetic viability of threatened and endangered species is of increasing concern with habitat loss and fragmentation. Valuable assessments of the genetic status of endangered species are difficult in most cases, where only single sample estimates are available. Using historical and contemporary samples, we assessed the impact of both historical and recent demographic changes on population genetics of the endangered golden-cheeked warbler, (Dendroica chrysoparia). Our study documents a steep decline in genetic diversity in an endangered species over a 100-year period, along with concurrent increase in genetic differentiation, and low contemporary effective sizes for all the populations we evaluated. While adding to the growing body of literature that describes the genetic impacts of habitat fragmentation, our study may also serve as an informative guide to future management of endangered species. Our study underlines the importance of long term population genetic monitoring in understanding the full extent of genetic changes in endangered species.     

River islands,refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura,Ranidae) of the Qinghai‐Tibetan Plateau

Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai‐Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re‐treat to south‐eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG‐1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north‐eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.     

Two genetically distinct units of Sinomanglietia glauca (Magnoliaceae) detected by chloroplast PCR‐SSCP

Sinomanglietia glauca is a critically endangered species described from Jiangxi Province in the 1990s. Recently two populations were discovered from Yongshun County of west Hunan Province, about 450 km away from those in Jiangxi. Because of the new findings and the poor reproducibility inherent to RAPD and ISSR markers of previous studies, the population structure of this rare species was reanalyzed with chloroplast PCR‐SSCP (single‐stranded conformation polymorphism), including all of four recorded populations. The results showed that two distinct haplotypes characterized Jiangxi and Hunan populations separately, with no genetic variation occurring within regions. We postulated that this surprising pattern might result from habitat fragmentation and demographic bottlenecks during and/or after the Quaternary glaciation. On the basis of the pronounced genetic structure, two evolutionarily significant units (ESUs) were recommended for effective conservation of S. glauca.     

Genetic variability and the effect of habitat fragmentation in spotted suslik Spermophilus suslicus populations from two different regions

Endangered species worldwide exist in remnant populations, often within fragmented landscapes. Although assessment of genetic diversity in fragmented habitats is very important for conservation purposes, it is usually impossible to evaluate the amount of diversity that has actually been lost. Here, we compared population structure and levels of genetic diversity within populations of spotted suslik Spermophilus suslicus, inhabiting two different parts of the species range characterized by different levels of habitat connectivity. We used microsatellites to analyze 10 critically endangered populations located at the western part of the range, where suslik habitat have been severely devastated due to agriculture industrialization. Their genetic composition was compared with four populations from the eastern part of the range where the species still occupies habitat with reasonable levels of connectivity. In the western region, we detected extreme population structure (F _ST = 0.20) and levels of genetic diversity (Allelic richness ranged from 1.45 to 3.07) characteristic for highly endangered populations. Alternatively, in the eastern region we found significantly higher allelic richness (from 5.09 to 5.81) and insignificant population structure (F _ST = 0.03). As we identified a strong correlation between genetic and geographic distance and a lack of private alleles in the western region, we conclude that extreme population structure and lower genetic diversity is due to recent habitat loss. Results from this study provide guidelines for conservation and management of this highly endangered species.     

Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai‐Tibetan Plateau and its correlation with the Quaternary climate change

The Qinghai‐Tibetan Plateau (QTP) is thought to be more strongly affected by the Quaternary glaciations than most other regions of the same latitude. It would be of great interest to investigate the population genetic structure of organisms distributed on the platform and its correlation with the Quaternary climatic oscillations. Here we used the chloroplast (cp)DNA trnT‐trnF sequence to study genetic variation and phylogeography of Pedicularis longiflora, an alpine herb with extensive distribution on the QTP. Based on a range‐wide sampling comprising 41 populations and 910 individuals, we detected 30 cpDNA haplotypes that were divided into five clades by phylogenetic and network analyses and a strong phylogeographical structure. All haplotypes but one in the three basal clades occur exclusively in the southeast QTP, whereas haplotypes in the young clade V occupy almost the whole species range. In particular, the young haplotype H18 occurs in 420 individuals, even at a frequency of 100% in some QTP platform populations and the Altai population. The haplotype distribution pattern, together with molecular clock estimation and mismatch distribution analysis, suggests that the southeast QTP was either a refuge for P. longiflora during the Quaternary climatic change or is the place of origin of the species. The present wide distribution of the species on the QTP platform has resulted from recent population expansions which could be dated back to 120 000–17 000 years ago, a period mostly before the last glacial maximum. The possible relationships among geographic genetic structure, climatic change and species diversification in Pedicularis are also discussed.     

Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi

In order to devise adequate conservation and management strategies for endangered species, it is important to incorporate a reliable understanding of its spatial population structure, detecting the existence of demographic partitions throughout its geographical range and characterizing the distribution of its genetic diversity. Moreover, in species that occupy fragmented habitats it is essential to know how landscape characteristics may affect the genetic connectivity among populations. In this study we use eight microsatellite markers to analyze population structure and gene flow patterns in the complete geographic range of the endangered rodent Ctenomys porteousi. Also, we use landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. In spite of geographical proximity of the sampling sites (8–27 km between the nearest sites) and the absence of marked barriers to individual movement, strong population structure and low values of gene flow were observed. Genetic differentiation among sampling sites was consistent with a simple model of isolation by distance, where peripheral areas showed higher population differentiation than those sites located in the central area of the species’ distribution. Landscape genetics analysis suggested that habitat fragmentation at regional level has affected the distribution of genetic variation among populations. The distance of sampling sites to areas of the landscape having higher habitat connectivity was the environmental factor most strongly related to population genetic structure. In general, our results indicate strong genetic structure in C. porteousi, even at a small spatial scale, and suggest that habitat fragmentation could increase the population differentiation.     

Demographic history of the Tibetan antelope Pantholops hodgsoni (chiru)

Abstract The Tibetan antelope (chiru, Pantholops hodgsoni), a heavily poached species and symbol of the Qinghai‐Tibetan Plateau (QTP), is noted worldwide for its special calving migration. This species originated in the early Quaternary and it is interesting to know how the following climatic oscillations affected its demographic dynamics in the climate‐sensitive QTP. In this study, we analyzed the mitochondrial D‐loop region from 312 individuals sampled in all of the six major populations. We found high rates of gene flow and little genetic differentiation between populations, suggesting that the calving migration may have homogenized the genetic pool of this species. Both mismatch distribution analyses and coalescent simulations suggested that this species experienced a demographic expansion approximately 600–200 Kyr following the retreat of the large glaciers developed in the QTP at 800–600 Kyr, rather than at the end of the last glacial age, as previously suggested, based on a limited sample size. In addition, we found evidence of a chiru population decrease probably related to the human settings at the QTP during the middle Holocene.     

Allopatric divergence,demographic history,and conservation implications of an endangered conifer <Emphasis Type="Italic">Cupressus chengiana</Emphasis> in the eastern Qinghai-Tibet Plateau

Isolation and demographic history are key factors that affect lineage divergence of tree species in topographic complex areas, such as the Qinghai-Tibet Plateau (QTP), yet few studies have evaluated these factors in a coalescent-based modeling framework. In the present study, we surveyed ten nuclear DNA sequence loci (nDNA) and six nuclear microsatellite loci (nSSR) for an endangered conifer, Cupressus chengiana, throughout its natural range in the eastern QTP. BARRIER analyses revealed a strong genetic barrier between Gansu and Sichuan populations of C. chengiana, and isolation with migration models detected limited gene flow between them, supporting the division of this species into two evolutionary significant units (ESUs). Two independent coalescent-based approaches suggest a Quaternary divergence between ESUs, their consensus age range ((0.09–) 0.59–1.53 (–2.71) Mya) largely overlaps with the time period when the largest glaciation occurred in the QTP. Both demographic inferences, IMa2 and DIYABC, suggest that both ESUs may have experienced a bottleneck or population contraction event during the late Quaternary. A documented massive recent anthropogenic habitat loss and fragmentation may have led to further decrease of the natural distribution of this conifer. We propose that the conservation and management of both natural stands and plantations of C. chengiana should be reconsidered in the light of our findings.     

Phylogeography of Potentilla fruticosa (Rosaceae) in the Qinghai-Tibetan Plateau revisited: a reappraisal and new insights

Background: Most empirical studies to date have suggested that alpine plants in the central Qinghai-Tibetan Plateau (QTP) originated from the south-eastern QTP. However, previous phylogeographcial analysis of Potentilla fruticosa suggested that it diversified in the central QTP, which has also been assumed to have been a glacial refugium, and expanded to the north-eastern regions during the mid-Holocene period.

Aim: We reappraise this claim in the light of information acquired from sampling, haplotyping and analysing additional populations.

Methods: We sequenced the chloroplast trnT-L intergenic spacer of 346 individuals collected from 52 populations. We reconstructed phylogenetic relationships among haplotypes through Bayesian and Network analysis, and used several methods for demographic analysis.

Results: Some common and highly divergent haplotypes were distributed in the central, western and south-eastern QTP. Mismatch and other population genetic analyses applied to our data suggested that a distinct range expansion had occurred between approximately 30,000 and 325,000 years ago (kya).

Conclusions: Besides the possible postglacial expansion in the north-eastern QTP, our results further suggested that the range of the species radically expanded across the whole Plateau before the last glacial maximum (around 18 kya) and the south-eastern, western and central QTP regions had together provided important refugia during recent glacial stages. These findings, in contrast to the previous conclusions, highlight the importance of adequate sampling strategies in phylogeographical studies.     

Pliocene intraspecific divergence and Plio‐Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai‐Tibet Plateau

A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai‐Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with intervariety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modelling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modelling of population‐genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hot spot region.     

Diversity and structure of fragmented populations of a threatened endemic cyprinodontid (Aphanius sophiae) inferred from genetics and otolith morphology: Implications for conservation and management

The assessment of population structure and genetic diversity is crucial for the management and conservation of threatened species. Natural and artificial barriers to dispersal (i.e., gene flow) increase populations’ differentiation and isolation by reducing genetic exchange and diversity. Freshwater ecosystems are highly fragmented because of human activities. Threatened species with small population sizes are more sensitive to habitat fragmentation effects. Here, we investigate the genetic population structure and gene flow among seven populations of Aphanius sophiae in the Kor Basin by using sequences of the complete Cyt b gene and otolith morphometry. The Cyt b gene showed low level of genetic variation, only 4.12% of the identified sites were variable, and 2.42% were parsimony informative. Overall, haplotype diversity was low to moderate and nucleotide diversity was low to extremely low. Fish populations exhibited high levels of genetic differentiation, suggesting limited gene flow among them. These differences were obtained not only among geographically distant populations, but also among neighboring localities. Genetic population structure was supported by the AMOVA analysis and by the haplotype network (only one of 21 haplotypes were shared by two localities). Otolith morphometric analysis was in agreement with genetic results, the two most distant and isolated populations were clearly separated, and genetically close populations showed less differences in morphometry. A significant pattern of isolation by distance was also detected among A. sophiae populations, with genetic distance more correlated with hydrological distance than with geographic distance. Results suggested that limited gene flow due to habitat fragmentation is an important factor contributing to genetic structuring and to the loss of genetic variation of A. sophiae populations. Aphanius sophiae population structure seems to be the result of habitat fragmentation and water pollution, but other factors such as introduced species should be considered. Given the high degree of genetic structuring, the definition of conservation groups is of particular importance for A. sophiae, which should be considered endangered according to the IUCN criteria. Conservation plans must recognize the genetic independence of populations and manage separately preventing the loss of locally adapted genotypes.     

Population structure and genetic variation in the endangered Giant Kangaroo Rat (<Emphasis Type="Italic">Dipodomys ingens</Emphasis>)

Populations of the endangered giant kangaroo rat, Dipodomys ingens (Heteromyidae), have suffered increasing fragmentation and isolation over the recent past, and the distribution of this unique rodent has become restricted to 3% of its historical range. Such changes in population structure can significantly affect effective population size and dispersal, and ultimately increase the risk of extinction for endangered species. To assess the fine-scale population structure, gene flow, and genetic diversity of remnant populations of Dipodomys ingens, we examined variation at six microsatellite DNA loci in 95 animals from six populations. Genetic subdivision was significant for both the northern and southern part of the kangaroo rat’s range although there was considerable gene flow among southern populations. While regional gene diversity was relatively high for this endangered species, hierarchical F-statistics of northern populations in Fresno and San Benito counties suggested non-random mating and genetic drift within subpopulations. We conclude that effective dispersal, and therefore genetic distances between populations, is better predicted by ecological conditions and topography of the environment than linear geographic distance between populations. Our results are consistent with and complimentary to previous findings based on mtDNA variation of giant kangaroo rats. We suggest that management plans for this endangered rodent focus on protection of suitable habitat, maintenance of connectivity, and enhancement of effective dispersal between populations either through suitable dispersal corridors or translocations.     

The uplift of the Qinghai–Tibet Plateau and glacial oscillations triggered the diversification of Tetraogallus (Galliformes,Phasianidae)

The Qinghai–Tibet Plateau (QTP) plays an important role in avian diversification. To reveal the relationship between the QTP uplift and avian diversification since the Late Cenozoic, here, we analyzed the phylogenetic relationship and biogeographical pattern of the genus Tetraogallus (Galliformes, Phasianidae) and the probable factors of speciation in the period of the QTP uplift inferred from concatenated data of four nuclear and five mitochondrial genes using the method of the Bayesian inference. Phylogenetic analysis indicated that T. himalayensis had a close relationship with T. altaicus and conflicted with the previous taxonomy of dark‐bellied and white‐bellied groups. The molecular clock showed that the speciation of Tetraogallus was profoundly affected by the uplift of the QTP and glacial oscillations. Biogeographic analysis suggested that the extant snowcocks originated from the QTP, and the QTP uplift and glacial oscillations triggered the diversification of Tetraogallus ancestor. Specifically, the uplift of the mountain provided a prerequisite for the colonization of snowcocks Tetraogallus as a result of the collision between the Indian and the Arab plates and the Eurasian plate, in which ecological isolation (the glacial and interglacial periods alternate) and geographical barrier had accelerated the Tetraogallus diversification process. Interestingly, we discovered hybrids between T. tibetanus and T. himalayensis for the first time and suggested that T. tibetanus and T. himalayensis hybridized after a second contact during the glacial period. Here, we proposed that the hybrid offspring was the ancestor of the T. altaicus. In conclusion, the uplift of QTP and glacial oscillations triggered the snowcocks colonization, and then, isolation and introgression hybridization promoted diversification.     

Molecular phylogeography and intraspecific divergence of Spiraea alpina (Rosaceae) distributed in the Qinghai-Tibetan Plateau and adjacent regions inferred from nrDNA

The Qinghai-Tibetan plateau (QTP) uplift had a decisive effect on climatic and eco-environmental evolution in East Asia during the Quaternary. In the current study phylogeographic structure and diversification history of Spiraea alpina across the QTP were investigated for the first time based on nuclear internal transcribed spacer. The nuclear internal transcribed spacers (ITS_1a–ITS₄) were generated for a total of 284 individuals distributed within 31 natural populations. A clear phylogeographic structure was found for S. alpina. The results showed that this species colonized in three different glacial refugia during the Quaternary extensive glaciation and expanded during the Interglacial period. Analysis of molecular variance (AMOVA) showed 74.13% genetic diversity among populations and 25.87% genetic variation within populations with distinct phylogeographic structure (F_ST = 0.741*). The estimated divergence time revealed that the main lineages of S. alpina diversified during the Quaternary 1.2–0.6 million years ago. The study concluded that severe climatic oscillations during Quaternary and the uplift of QTP had a profound effect on intraspecific divergence of S. alpina.     

Anthropogenic fragmentation may not alter pre‐existing patterns of genetic diversity and differentiation in perennial shrubs

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird‐pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F′_ST = 0.615 and 0.454; S_p = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long‐term effects of inbreeding in self‐compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self‐compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation.