Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super‐volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co‐distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target‐capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction‐site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full‐likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid‐Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.     

Phylogeography and ecological niche modelling in Eugenia uniflora (Myrtaceae) suggest distinct vegetational responses to climate change between the southern and the northern Atlantic Forest

In this study, we evaluate phylogeographic patterns and predictions of ecological niche modelling (ENM) for Eugenia uniflora (Myrtaceae), a widely distributed taxon in the Atlantic forest domain, to understand the effect of past climatic oscillations on the demographic history of this species. An analysis of phylogeographic population structure and demography was conducted on E. uniflora from 46 localities in natural environments across the distribution range of the species based on three plastid markers. ENM was also performed to predict suitable environments and areas of dramatic decrease in future suitability for the species under distinct representative concentration pathways (RCPs). Eugenia uniflora exhibited higher haplotype and nucleotide diversity in the southern part of its distribution than in the northern part. Two divergent lineages were revealed in the phylogenetic analysis of haplotypes, with an estimated divergence at c. 4.9 Mya. The populations in the northern and central regions of the range probably experienced population growth, whereas populations in the southern region are marked by historical demographic stability. ENM results indicate that the distribution of E. uniflora was fragmented in cool periods and was broader and more connected during warm periods during Pleistocene. The results suggest distinct evolutionary histories in southern to northern populations, indicating region‐specific responses to changes.     

Palaeodistribution modelling and genetic evidence highlight differential post‐glacial range shifts of a rain forest conifer distributed across a latitudinal gradient

Aim We examine the range expansion/contraction dynamics during the last glacial cycle of the late‐successional tropical rain forest conifer Podocarpus elatus using a combination of modelling and molecular marker analyses. Specifically, we test whether distributional changes predicted by environmental niche modelling are in agreement with (1) the glacial maximum contractions inferred from the southern fossil record, and (2) population genetic‐based estimates of range disjunctions and demographic dynamics. In addition, we test whether northern and southern ranges are likely to have experienced similar expansion/contraction dynamics. Location Eastern Australian tropical and subtropical rain forests. Methods Environmental niche modelling was completed for three time periods during the last glacial cycle and was interpreted in light of the known palynology. We collected 109 samples from 32 populations across the entire range of P. elatus. Six microsatellite loci and Bayesian coalescence analysis were used to infer population expansion/contraction dynamics, and five sequenced loci (one plastid and four nuclear) were used to quantify genetic structure/diversity. Results Environmental niche modelling suggested that the northern and southern ranges of P. elatus experienced different expansion/contraction dynamics. In the northern range, the habitat suitable for P. elatus persisted in a small refugial area during the Last Glacial Maximum (LGM, 21 ka) and then expanded during the post‐glacial period. Conversely, in the south suitable habitat was widespread during the LGM but subsequently contracted. These differential dynamics were supported by Bayesian analyses of the population genetic data (northern dispersal) and are consistent with the greater genetic diversity in the south compared with the north. A contact zone between the two genetically divergent groups (corresponding to the Macleay Overlap Zone) was supported by environmental niche modelling and molecular analyses. Main conclusions The climatic fluctuations of the Quaternary have differentially impacted the northern and southern ranges of a broadly distributed rain forest tree in Australia. Recurrent contraction/expansion cycles contributed to the genetic distinction between northern and southern distributions of P. elatus. By combining molecular and environmental niche modelling evidence, this unique study undermines the general assumption that broadly distributed species respond in a uniform way to climate change.     

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. F_ST outlier analysis revealed that promoter, 5′‐UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within‐population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.     

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS‐trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.     

Population genetic structure of the endangered crayfish Austropotamobius pallipes in France based on microsatellite variation: biogeographical inferences and conservation implications

1. One important goal in conservation biology is to characterise evolutionary lineages within endangered species before management decisions are taken. Here, we assess population differentiation in the freshwater crayfish Austropotamobius pallipes, an endangered species endemic to western Europe and provide valuable information for the conservation of French populations. 2. Analysis of five microsatellite loci in 44 populations revealed very different within population levels of genetic diversity (0.000 < H₀ < 0.564). Two groups, corresponding to northern and southern French populations, showed a high degree of genetic differentiation in both allele frequencies and allele sizes. Comparison of these results with previous studies of A. pallipes strongly suggests that the divergence between northern and southern populations could have occurred during the last glaciation period of the Pleistocene from one Atlantic and one Mediterranean refuge. 3. Evidence for genetic admixture between these two lineages was revealed by correspondence analyses in southern populations, probably as the result of artificial translocations. 4. French populations appeared significantly differentiated among the different river drainages and were highly structured within rivers. The impact of population size, population bottlenecks and founder events on the population genetic differentiation are discussed. 5. Based on these results, we propose the designation of two evolutionarily significant units for A. pallipes in France. Our data also support the maintenance of separate demographic management strategies for crayfish inhabiting different river systems. However, genetic analyses will have to be combined with demographic and ecological data for sustainable conservation programmes.     

Genetic population structure in horse chestnut (Aesculus hippocastanum L.): effects of human‐mediated expansion across Europe

The geographical distribution of existing populations of horse chestnut (Aesculus hippocastanum L.) in Europe is determined by past demographic events during the Quaternary. In the present study we evaluate the imprints that northward expansions originated from common ancestry at southern Europe may have left on the present patterns of genetic variation for horse chestnut across the continent. Genetic diversity and levels of population structure in a European south–north gradient, ranging from the Balkans to the Scandinavian Peninsula, were determined with Amplified Fragment Length Polymorphism (AFLP) markers in 159 loci. A family of rarefaction techniques for the estimation of gene diversity was used to exclude potential confounding effects as a result of the unequal sample sizes. The results indicate that northern populations are not more genetically depleted than southern populations, thus suggesting that diversity for this species is not correlated with latitudinal distribution. Detailed hypotheses based on prediction models for different historical events associated with human‐mediated spread of cultivation are examined for a better understanding of the current genetic patterns of regional differentiation.     

Evolutionary history of a widespread tree species Acer mono in East Asia

East Asia has the most diverse temperate flora in the world primarily due to the lack of Pleistocene glaciation and the geographic heterogeneity. Although increasing phylogeography studies in this region provided more proofs in this issue, discrepancies and uncertainty still exist, especially in northern temperate deciduous broad‐leaved and coniferous mixed forest region (II). And a widespread plant species could reduce the complexity to infer the relationship between diversity and physiographical pattern. Hence, we studied the evolution history of a widespread temperate tree, Acer mono, populations in region II and the influence of physiographic patterns on intraspecific genetic diversity. Analyses of chloroplast sequences and nuclear microsatellites indicated high levels of genetic diversity. The diversity distribution was spatially heterogeneous and a latitudinal cline existed in both markers. The spatial distribution pattern between genetic diversity within A. mono and the diversity at species level was generally consistent. Western subtropical evergreen broad‐leaved forest subregion (IVb) had a unique ancient chloroplast clade (CP3) and a nuclear gene pool (GP5) with dominance indicating the critical role of this area in species diversification. Genetic data and ecological niche model results both suggested that populations in region II disappeared during the last glacial maximum (LGM) and recovered from south of Changbai Mt. and the Korean Peninsula. Two distribution centers were likely during the LGM, one in the north edge of warm temperate deciduous broad‐leaved forest region (III) and another in the south edge of region III. This was reflected by the genetic pattern with two spatially independent genetic groups. This study highlights the key role of region III in sustaining genetic diversity in the northern range and connecting diversity between southern and northern range. We elucidated the diversity relationship between vegetation regions which could facilitate the understanding of biodiversity origin and maintenance in East Asia.     

Allozyme diversity and history of distribution expansion in the maritime perennial plant Hedyotis strigulosa (Rubiaceae), distributed over the wide latitudes in the Japanese Archipelago

Allozyme diversity was examined in 30 populations of the maritime perennial plant Hedyotis strigulosa var. parviflora , which is distributed from subtropical islands to the central mainland of Japan. Genetic diversity within populations tended to be larger in southern island populations than in northern mainland populations. In the southern part of the distribution, the population size is generally large and populations are distributed more continuously than in the northern area, resulting in the larger effective size of southern populations as a whole. These factors play a major role in maintaining greater genetic diversity in the southern populations. By contrast, genetic diversity in the northern populations is very low, probably resulting from bottlenecks of population establishments during recolonization from refugial area to the northern areas. Geographically close populations were located near each other in the multidimensional scaling and the phenogram based on genetic distances, suggesting that gene flow among remote populations is rather limited. The pattern of genetic diversity in H. strigulosa var. parviflora is likely caused by the distribution expansion of the species; in the last glacier era, the species was restricted to the southern area; its advance to the northern area is relatively recent. Another variety endemic only to the Daito Islands, H. strigulos a var. luxurians , has lower genetic diversity than H. strigulosa var. parviflora and has genetically diverged from H. strigulosa var. parviflor a.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 679–688.     

The population demography of Betula maximowicziana,a cool‐temperate tree species in Japan,in relation to the last glacial period: its admixture‐like genetic structure is the result of simple population splitting not admixing

Conservation of the local genetic variation and evolutionary integrity of economically and ecologically important trees is a key aspect of studies involving forest genetics, and a population demographic history of the target species provides valuable information for this purpose. Here, the genetic structure of 48 populations of Betula maximowicziana was assessed using 12 expressed sequence tag–simple sequence repeat (EST‐SSR) markers. Genetic diversity was lower in northern populations than southern ones and structure analysis revealed three groups: northern and southern clusters and an admixed group. Eleven more genomic‐SSR loci were added and the demographic history of these three groups was inferred by approximate Bayesian computation (ABC). The ABC revealed that a simple split scenario was much more likely than isolation with admixture, suggesting that the admixture‐like structure detected in this species was due to ancestral polymorphisms. The ABC analysis suggested that the population growth and divergence of the three groups occurred 96 800 (95% CI, 20 500–599 000) and 28 300 (95% CI, 8700–98 400) years ago, respectively. We need to be aware of several sources of uncertainty in the inference such as assumptions about the generation time, overlapping of generations, confidence intervals of the estimated parameters and the assumed model in the ABC. However, the results of the ABC together with the model‐based maps of reconstructed past species distribution and palaeoecological data suggested that the modern genetic structure of B. maximowicziana originated prior to the last glacial maximum (LGM) and that some populations survived in the northern range even during the LGM.     

Range-wide phylogeography of the European temperate-montane herbaceous plant Meum athamanticum Jacq.: evidence for periglacial persistence

Aim  The aim of this study is to analyse the genetic population structure of Meum athamanticum Jacq. in order to explore the alternative hypotheses (1) that the central and northern highland populations are the result of post-glacial recolonization from southern refugia, and the disjunct distribution of M. athamanticum can be explained by modern ecological conditions, or (2) that extant populations north of the Alps and Pyrenees persisted in situ during glacial periods.
Location  Europe.
Methods  Variation of amplified fragment length polymorphisms (AFLPs) was analysed for 23 populations from the entire range of the species. We used band-based approaches and methods based on allele frequencies to measure genetic diversity and to identify population structure.
Results  Our analyses reveal a north–south differentiation within M. athamanticum . High levels of genetic diversity, as well as private fragments, are found in populations both north and south of the Alps. Differentiation among populations is lower in the northern than in the southern population group, and significant isolation-by-distance is found only in the latter group.
Main conclusions  Our results indicate that M. athamanticum survived the last ice age in multiple refugia throughout its contemporary range and did not expand into areas north of the Alps from southern refugia. We found evidence that regional-scale migration in northern, formerly periglacial, parts of the species range has resulted in the intermingling of populations. In contrast, southern populations are characterized by long-term isolation. The south-west Alps represent an area where immigration and mixing of populations from northern and southern refugia appears to have taken place.     

Evolutionary history of Scinax treefrogs on land‐bridge islands in south‐eastern Brazil

Aim We investigated how Pleistocene refugia and recent (c. 12,000 years ago) sea level incursions shaped genetic differentiation in mainland and island populations of the Scinax perpusillus treefrog group. Location Brazilian Atlantic Forest, São Paulo state, south‐eastern Brazil. Methods Using mitochondrial and microsatellite loci, we examined population structure and genetic diversity in three species from the S. perpusillus group, sampled from three land‐bridge islands and five mainland populations, in order to understand the roles of Pleistocene forest fragmentation and sea level incursions on genetic differentiation. We calculated metrics of relatedness and genetic diversity to assess whether island populations exhibit signatures of genetic drift and isolation. Two of the three island populations in this study have previously been described as new species based on a combination of distinct morphological and behavioural characters, thus we used the molecular datasets to determine whether phenotypic change is consistent with genetic differentiation. Results Our analyses recovered three distinct lineages or demes composed of northern mainland São Paulo populations, southern mainland São Paulo populations, and one divergent island population. The two remaining island populations clustered with samples from adjacent mainland populations. Estimates of allelic richness were significantly lower, and estimates of relatedness were significantly higher, in island populations relative to their mainland counterparts. Main conclusions Fine‐scale genetic structure across mainland populations indicates the possible existence of local refugia within São Paulo state, underscoring the small geographic scale at which populations diverge in this species‐rich region of the Atlantic Coastal Forest. Variation in genetic signatures across the three islands indicates that the populations experienced different demographic processes after marine incursions fragmented the distribution of the S. perpusillus group. Genetic signatures of inbreeding and drift in some island populations indicate that small population sizes, coupled with strong ecological selection, may be important evolutionary forces driving speciation on land‐bridge islands.     

Genetic diversity,genetic structure and phylogeography of the Iberian endemic Gypsophila struthium (Caryophyllaceae) as revealed by AFLP and plastid DNA sequences: connecting habitat fragmentation and diversification

Iberian gypsum outcrops are highly fragmented and ecologically challenging environments for plant colonization. As gypsophytes occur exclusively in such habitats, they are ideal models for the study of both the effects of habitat fragmentation and selection on population genetic diversity and structure. In this study, we used amplified fragment length polymorphism (AFLP) and plastid DNA sequences to investigate the phylogeographical history of the Iberian plant Gypsophila struthium (Caryophyllaceae), a widespread endemic restricted to Iberian gypsum outcrops. Gypsophila struthium consists of two subspecies that differ in the architecture of their inflorescence and have mostly allopatric ranges. Gypsophila struthium subsp. struthium occurs in central, eastern and south‐eastern Iberia, whereas G. struthium subsp. hispanica occurs in northern and eastern areas. AFLPs revealed low but significant genetic differentiation between the subspecies, probably as a result of a recent diversification during the Pliocene–Pleistocene. In the geographical contact zone between the taxa, the Bayesian analyses revealed populations with mixed ancestries and genetic clusters predominantly of one or the other subspecies, indicating incomplete reproductive barriers between them. Plastid DNA haplotypes revealed strong geographical structure and testified to processes of isolation by distance and continuous range expansion for some haplotype clades. The Bayesian analyses of the population structure of AFLP data and nested clade phylogeographical analysis (NCPA) of plastid haplotypes revealed that the putative ancestral range corresponded to central and eastern populations of G. struthium subsp. struthium, with those lineages contributing through more recent expansion to increased genetic diversity and structure of the south‐eastern and eastern ranges of this subspecies and to the diversification of G. struthium subsp. hispanica in northern and eastern gypsum outcrops. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 654–675.     

Genetic diversity within and between remnant populations of the endangered calcareous grassland plant <Emphasis Type="Italic">Globularia bisnagarica</Emphasis> L.

Changes in agricultural production methods over the last century have caused a massive reduction and fragmentation of the area of European semi-natural grasslands. It remains unclear whether small and isolated grassland fragments can support viable plant populations in a sustainable way. In our study area in southern Belgium, the extent of calcareous grasslands was reduced from c. 650 ha in 1775 to less than 30 ha in 2004. We used AFLP markers to quantify the effects of present and historical grassland fragmentation on the genetic structure of 27 populations of the rare perennial plant species Globularia bisnagarica. Given the mixed breeding system of the species and the relatively small area of the studied system, the populations were characterized by high genetic differentiation (F _st range: 0.42–0.48; Φ_st=0.53). A Mantel test revealed significant isolation by distance of the populations. Average within population genetic diversity, measured as expected heterozygosity or gene diversity, was low (H _j =0.081) and was negatively related to population isolation. This suggests more gene flow into less isolated populations. Population size and local habitat characteristics did not significantly influence population genetic diversity. Both, high selfing rates in G. bisnagarica and a population genetic response to habitat fragmentation may explain our findings. Finally, a clear geographical clustering was observed, with cluster membership partially explainable by historical grassland connectivity. If populations indeed started to differentiate after fragmentation, this process was not (yet) strong enough to erase the genetic similarity between fragments that historically belonged to the same large grassland fragment.     

Phylogeography of an estuarine mysid, Neomysis integer (Crustacea, Mysida), along the north-east Atlantic coasts

Aim The brackish water mysid, Neomysis integer, is one of the most common mysid species along the coasts of the north‐east Atlantic. In the present study, the phylogeographical patterns were examined throughout the distribution range of N. integer. In particular, the latitudinal trends in genetic diversity and the distribution of genetic variation were examined in order to elucidate the imprints of the Pleistocene glaciations. Location North‐east Atlantic coasts from the Baltic Sea to the south of Spain. Methods A total of 461 specimens from 11 populations were analysed by means of single‐stranded conformation polymorphism analysis combined with DNA sequencing of a fragment of the mitochondrial cytochrome c oxidase I gene. The genetic structure was examined by using a progression of phylogenetic, demographic and population genetic analyses to elucidate not only the geographical structure, but also the evolutionary history producing that structure. Results The levels of genetic diversity were relatively uniform throughout the distribution range, with the exception of a decline at the northern and southern edges of distribution. A high heterogeneity was observed between the populations analysed (global Φ_ST = 0.787). This is caused by the disparate distribution of the cytochrome oxidase I haplotypes, with several population‐specific haplotypes. A clear genetic break (2.4% sequence divergence) occurred between the southernmost Guadalquivir population and all other populations. Main conclusions The present study corroborates the expectations of the genetic patterns typically observed in an estuarine species. The within‐population variability was low, whereas a significant (moderate to high) divergence was observed between populations. Phylogeographical analysis revealed that northern populations within the English Channel, North Sea and Baltic Sea are characterized by several widespread haplotypes, while the Irish population and all sites south of the Bay of Biscay consist solely of unique haplotypes. This pattern, combined with the relative high levels of genetic diversity, could be indicative for the presence of a glacial refugium in the English Channel region. Under this scenario N. integer must have survived the Last Glacial Maximum in the palaeoriver system present in that region.     

Genetic diversity assessment of bittersweet (Solanum dulcamara,Solanaceae) germplasm using conserved DNA‐derived polymorphism and intron‐targeting markers

Bittersweet (Solanum dulcamara), a European native weed, is widespread across a variety of habitats and often occurs as a coloniser of open, disturbed, ephemeral environments or wetlands, although it is also found in mountain habitats and on forest edges. As recent studies have shown the potential utility of the species in plant breeding programs, we assembled a collection of bittersweet germplasm from natural populations found in Europe. This collection was analysed with conserved DNA‐derived polymorphism (CDDP) and intron‐targeting (IT) markers to assess genetic diversity found within and among the populations. We found that there is limited genetic variability within the collected S. dulcamara accessions, with a greater proportion of allelic variation distributed among populations and considerably greater population structure at higher regional levels. Although bittersweet is an outcrossing species, its population structure might be affected by its perennial self‐compatible nature, reducing genetic diversity within regional populations and enhancing inbreeding leading to high interpopulation or spatial differentiation. We found that populations have been separated by local selection of alleles, resulting in regional differentiation. This has been accompanied by concurrent loss of genetic diversity within populations, although this process has not affected species‐level genetic diversity. Germplasm collecting strategies should be aimed at preserving overall genetic diversity in bittersweet nightshade by expanding sampling to southern Europe and to smaller regional geographic levels in northern and central Europe.     

Phylogeography of the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico

We quantify the population divergence processes that shaped population genetic structure in the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a northern population with a broad distribution across Hidalgo, Puebla, and Veracruz. The multilocus nuclear data and mtDNA both supported a Late Pleistocene increase in effective population size, and the nuclear data revealed low levels of unidirectional gene flow from the widespread northern population into the southern and western populations. Populations of S. bicanthalis experienced different demographic histories during the Pleistocene, and phylogeographical patterns were similar to those observed in many co‐distributed highland taxa. Although we recommend continuing to recognize S. bicanthalis as a single species, future research on the evolution of viviparity could gain novel insights by contrasting physiological and genomic patterns among the different populations located across the highlands of south‐eastern Mexico. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 852–865.     

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.     

喀斯特退化天坑不同坡向植物群落系统发育与功能性状结构

喀斯特退化天坑地下森林主要分布在不同坡向的倒石坡上,探究环境过滤、竞争排斥和随机过程在天坑地下森林群落构建中的作用,有助于揭示天坑物种避难所价值,为天坑植物多样性的保护及坑外地表生态恢复提供科学的参考。以云南沾益深陷塘退化天坑为例,综合运用功能性状生态学和系统发育方法,研究不同坡向植物群落的土壤环境特征、功能性状变异、系统发育信号及系统发育多样性。研究表明：（1）不同坡向土壤环境差异较大,相对于南坡和北坡而言,东坡的土壤环境变异程度最大。（2）各坡向具有不同的优势种群,其中壳斗科植物种群多度较大,在北坡和东坡的黄背栎（Quercus pannosa）种群数量较大,在南坡则是青冈（Cyclobalanopsis glauca）多度最大。各优势物种功能性状在不同坡向存在差异,整体上变异程度中等,但南坡优势物种变异程度最大。（3）叶宽、长宽比、叶厚度、比叶面积具有较强且显著的系统发育信号（K>1,P<0.05）,性状进化过程中受遗传因素影响较大;而叶长、叶面积、叶干重、叶干物质含量、最大树高系统发育信号弱（K<1）,性状进化过程中受生境因素影响较大。（4）各坡向植物群落构建过程由生态位理论的环境过滤和竞争排斥作用主导,坡向从北坡-东坡-南坡的转变过程中,植物群落构建中环境过滤作用逐渐减小,竞争排斥作用逐渐增大。北坡可能较长时间内都是以旱生型植物为主要建群种,而南坡则可能最终演替成亚热带湿润气候型的顶极群落。     

Population genetics analysis of the origin of the Oriental fruit fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae), in northern Yunnan Province, China

We examined genetic variation in the Oriental fruit fly, Bactrocera dorsalis (Hendel), using six populations in two regions of Yunnan Province, China, to determine the distribution and likely mechanism for the dispersal of this fly. A 501‐bp portion of the mitochondrial cytochrome oxidase gene was sequenced from a minimum of eight individuals from each population, and 43 haplotypes were observed in the six Bactrocera dorsalis populations. When comparing the genetic diversity of populations in the northern and southern regions, which differ with respect to elevation, climate and plant phenology, we found a significantly greater haplotype diversity in the southern region (permutation test; P < 0.05), suggesting that the northern populations, those at Kunming and Qujing, probably originated from somewhere in the southern region. F_ST and number of pairwise differences revealed a high level of differentiation between the Panxi population and the other populations (permutation test; P < 0.05). Although the difference was marginally insignificant, the Shuitang population seemed to have differentiated from both northern populations. The Mantel test did not detect any isolation due to geographic distance. An amova analysis found that 2.56% of the variance was caused by the Panxi population. Haplotype network analysis showed that none of the six populations had a specific genetic lineage. Together, these analyses suggest that long‐distance dispersal has occurred for this species, and the species most probably took advantage of both a mountain pass and prevailing air currents. The Panxi population was significantly isolated from the others, probably because of its distinguishing habitat features, host plants or the recent reduction of the population size.