Quaternary Climatic Oscillations Research Articles

Genetic diversity and population dynamic of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow in Central China.

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single‐copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θ w = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (F st = 0.197). Relatively low long‐distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction‐expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high‐latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae).

Background Bretschneidera sinensis is an endangered relic tree species in the Akaniaceae family and is sporadically distributed in eastern Asia. As opposed to its current narrow and rare distribution, the fossil pollen of B. sinensis has been found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant, and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of B. sinensis will help us to more deeply understand the survival and demographic histories of this relic species.ResultsA total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in B. sinensis. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (Ne) of B. sinensis was found to oscillate greatly in response to Quaternary climatic changes. The Ne of B. sinensis has decreased rapidly in the recent past, making its extant Ne extremely lower. Our additional evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis.ConclusionThis is a detailed report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource may provide critical clues for comparative genomics studies of this family in the future.

Pleistocene climate-driven diversification of plateau zokor (Eospalax baileyi) in the eastern Qinghai-Tibet Plateau

Glacial oscillations and associated tectonic processes during the middle-late Pleistocene are thought to have created a unique pattern of species distribution diversity in the Qinghai-Tibet Plateau (QTP). As a subterranean rodent endemic to the QTP, the impact of these geological events on the genetic diversity and demographic history of plateau zokors (Eospalax baileyi) is worth exploring. In this study, genetic diversity analyses were performed based on two mitochondrial DNA regions and microsatellite markers, representing 370 individuals from five populations on a large scale and six populations on two small scales in the eastern QTP. On a large scale, both mitochondrial DNA and microsatellite markers implied substantial genetic diversity and strong differentiation of the five populations. All sampled populations showed only unique haplotypes and lacked shared haplotypes, revealing the isolated nature of most populations. The genetic differentiation of the plateau zokor was in line with that of the isolate by distance (IBD) model. Mismatch distribution and Bayesian skyline analysis suggested recent demographic expansions highly consistent with glaciation events, and BEAST divergence analysis unveiled southward divergence events originating from the northern populations of the eastern QTP. The genetic structure of the five populations was almost singular. On a small scale, all the populations showed high genetic diversity. However, the analysis of molecular variation (AMOVA) showed less variation among populations; the genetic differentiation of the populations no longer conformed to IBD model, and the genetic information among populations was more heterogenous and similar to those of each other. Overall, our research revealed the genetic differentiation of plateau zokor driven by quaternary climatic oscillation and the variations in the genetic diversity of the plateau zokor at different geographical scales.

Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China.

Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable.

Congruent evolutionary responses of European steppe biota to late Quaternary climate change

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level.

Evolutionary history and colonization patterns of the wing dimorphic grasshopper Dichroplus vittatus in two Argentinean biomes

Quaternary climate oscillations and modification of the environment by humans have played an important role in shaping species distribution and genetic structure of modern species. Here, population genetic parameters were inferred from the analysis of 168 individuals belonging to 11 populations of the South American grasshopper, Dichroplus vittatus, distributed in two Argentinean Biomes (Grassland and Savanna), by sequencing a 543 bp of the mitochondrial COI gene. Overall, we detected considerable haplotype diversity and low nucleotide diversity. AMOVA analyses showed a significant degree of differentiation among Biomes and between populations. Two major mitochondrial lineages can be distinguished. The haplogroup containing the most common haplotype split 17,000 years BP while the haplogroup including the second most common haplotype has a divergence date of about 11,700 years. Approximate Bayesian Computation (ABC) analyses showed that the palaeodemographic scenario that best fitted our data is consistent with a hypothesis of divergence from an ancestral population and subsequent admixture with Grassland-Savanna (South–North) direction. Our results suggest that populations located in both Biomes would derive from a single ancestral population that colonized the region after the Last Glacial Maximum and Grassland would have a more ancestral origin than Savanna. Further, our results emphasize the importance of human-mediated dispersal in the reconfiguration of genetic diversity of species with potential pest capacity.

Population genomic signatures of the oriental fruit moth related to the Pleistocene climates

The Quaternary climatic oscillations are expected to have had strong impacts on the evolution of species. Although legacies of the Quaternary climates on population processes have been widely identified in diverse groups of species, adaptive genetic changes shaped during the Quaternary have been harder to decipher. Here, we assembled a chromosome-level genome of the oriental fruit moth and compared genomic variation among refugial and colonized populations of this species that diverged in the Pleistocene. High genomic diversity was maintained in refugial populations. Demographic analysis showed that the effective population size of refugial populations declined during the penultimate glacial maximum (PGM) but remained stable during the last glacial maximum (LGM), indicating a strong impact of the PGM rather than the LGM on this pest species. Genome scans identified one chromosomal inversion and a mutation of the circadian gene Clk on the neo-Z chromosome potentially related to the endemicity of a refugial population. In the colonized populations, genes in pathways of energy metabolism and wing development showed signatures of selection. These different genomic signatures of refugial and colonized populations point to multiple impacts of Quaternary climates on adaptation in an extant species.

Fragmented habitats and Pleistocene climate shaped diversification of the hoary bamboo rat (Rhizomys pruinosus) in the mountainous plateau of SW China

AbstractThe southwest mountainous region of China has been characterized as one of the worldwide biodiversity hotspots, but mechanisms underlying diversification of organisms in this region are still not clear. We assessed whether fragmented mountainous habitats and Pleistocene climate changes impacted the genetic diversity and diversification patterns of the hoary bamboo rat (Rhizomys pruinosus Blyth), a widely distributed species of rodent in SW China. Genetic diversity analyses were undertaken based on four mitochondrial DNA regions and 12 nuclear microsatellite loci (simple sequence repeats), representing 153 individuals from 24 populations across SW China. Moreover, we investigated correlations between genotype and geographical components, and predicted species distribution models for R. pruinosus under the historical and present climate conditions. Both mitochondrial DNA and simple sequence repeat markers revealed substantial genetic diversity and strong differentiation between populations. Phylogeographical analyses revealed two phylogenetic clades that were consistent with their geographical distributions (eastern and western clades). We inferred that the divergence of R. pruinosus was largely driven by Quaternary climatic oscillations and regionally fragmented mountainous habitats with environmental and geographical heterogeneity. Overall, our study revealed diversification patterns of R. pruinosus—patterns that may be shared by small alpine vertebrates in SW China.

Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex

Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importances on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scales. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.

Genetic variation and cytological diversity in the Urar Brush-tailed Mouse, Calomyscus urartensis Vorontsov & Kartavseva, 1979 (Mammalia: Rodentia) in Lesser Caucasia

The Urar Brush-tailed Mouse, Calomyscus urartensis Vorontsov & Kartavseva, 1979, is distributed in the Lesser Caucasus and is reported only from the type locality in Nakhjivan, Azerbaijan, and two localities in Azerbaijan provinces, Iran. To evaluate genetic structure and karyologic variation a combination of molecular (cytochrome b and cytochrome c oxidase subunit I gene sequences) and cytological approaches were used. Karyologic data highlighted the existence of a population from Khoy, north-western Iran, with differentiated chromosome components 2n=34 and FNa=42. This new population with a distinct Cytb haplotype showed a 2.2% genetic distance from the population from Kordasht, Iran, that located 150 kilometres away from Khoy. Considering time divergence estimation, we propose that vicariance might explain the divergences within C. urartensis that have accumulated by range restriction of populations as a result of Quaternary climate oscillations and glacial refugia.

Highlighted articles for January 2022.

Highlighted articles for January 2022.

Phylogeography and ecological differentiation of strictly Mediterranean taxa: the case of the Iberian endemic Odontites recordonii.

Ecological drivers for genetic differentiation in Mediterranean climates are still underexplored. We have used the strictly Mediterranean endemic Odontites recordonii as a model species to address this question. This species is one of the three Iberian representatives of the O. vernus group, which are morphologically similar. Thus, it was additionally necessary to clarify their phylogenetic relationships. We used amplified fragment length polymorphisms to reveal phylogenetic relationships within O. vernus group, and to reconstruct the phylogeographic patterns within O. recordonii. Additionally, ecological niche models were generated to detect refugia along the Quaternary climatic oscillations. And finally, alleles under natural selection were identified, and correlations between allele presences and environmental variables were calculated in order to shed light on the ecological drivers promoting differentiation. The three species from the O. vernus group were recovered as distinct species. Three genetic groups were found within O. recordonii and a putative refugium was detected for each one. Eighty-one alleles could be under diversifying selection, and 58 alleles showed significant correlations with environmental variables, especially with temperature and precipitation seasonality and summer drought. The three Iberian species of the O. vernus group are reciprocal monophyletic taxa. The three genetic groups of O. recordonii could have been restricted to narrow refugia during the Quaternary and displayed present distributions in accordance with bioclimatic conditions. Temperature and precipitation seasonality and the intensity of summer drought are definitory climatic parameters of Mediterranean-type climates, and they could have acted as drivers of genetic differentiation on O. recordonii.

Phylogeography of Iris loczyi (Iridaceae) in Qinghai-Tibet Plateau revealed by chloroplast DNA and microsatellite markers.

Quaternary climate oscillations and complex topography have tremendous effects on current distribution and genetic structure of species, and hence the Qinghai–Tibet Plateau (QTP), the largest plateau in the world, has become a hotspot for many phylogeographic studies. However, little is known about the phylogeographic pattern of herbaceous plants in QTP. Here, we investigate the genetic diversity, population structure and historical dynamics of Iris loczyi, using five chloroplast DNA (cpDNA) fragments and seven microsatellite markers. A total of 15 populations, and 149 individuals were sampled throughout the QTP. High genetic diversity was detected both in cpDNA (Hd = 0.820) and SSR (Ho = 0.689, He = 0.699). Ten cpDNA haplotypes and 163 alleles were identified. AMOVA and clustering analyses revealed obvious differentiation between regions. The Nst, Gst and Mantel test showed significant phylogeographic structure of I. loczyi. The neutrality test and mismatch distribution analyses indicated that I. loczyi could not have undergone a historical population expansion, but population XS from the Qilian Mountain area could have experienced a local expansion. Bottleneck analyses indicated that I. loczyi had not experienced bottleneck recently. Based on cpDNA and SSR results, the Qilian Mountain area was inferred as a potential glacial refuge, and the southern Tibet valley was considered as a ‘microrefugia’ for I. loczyi. These findings provided new insights into the location of glacial refuges for the species distributed in QTP, and supplemented more plant species data for the response of QTP species to the Quaternary climate.

Distinct Genetic Structure Reflects Ploidy Level Differentiation in Newly Discovered, Extremely Small Populations of Xanthocyparis vietnamensis from Southwestern China

Population genetic assessment is crucial for the conservation and management of threatened species. Xanthocyparis vietnamensis is an endangered species that is currently restricted to karst mountains in southwestern China and Vietnam. This rare conifer was first recorded in 2002 from northern Vietnam and then in 2013 from Guangxi, China, yet nothing is known about its genetic diversity nor ploidy level variation, although previous cytological study suggest that Vietnamese populations are tetraploids. There have been about 45 individuals found to date in Guangxi, China. Here, we genotyped 33 X. vietnamensis individuals using 20 newly developed, polymorphic microsatellite loci, to assess the genetic variability of its extremely small populations. The genetic diversity of X. vietnamensis (H E = 0.511) was lower than that of two other heliophile species, Calocedrus macrolepis and Fokienia hodginsii, which have similar distribution ranges. This is consistent with the signature of a genetic bottleneck detected in X. vietnamensis. Although the population genetic differentiation coefficient across loci is moderate (F ST = 0.125), STRUCTURE analysis revealed two distinct genetic clusters, namely the northern and southern population groups; DAPC analysis grouped the southern populations together in one cluster separate from the northern populations; AMOVA analysis detected a significant genetic differentiation between the two population groups (F RT = 0.089, p < 0.05), and BARRIER analysis detected a genetic barrier between them. Moreover, we detected differentiation in ploidy level between northern and southern populations, sampled individuals from the former and the later are all diploid and tetraploid cytotypes with mean genome sizes of 26.08 and 48.02 pg/2C, respectively. We deduced that heterogeneous geomorphology and historical events (e.g., human deforestation, Quaternary climate oscillations) may have contributed to population fragmentation and small population size in X. vietnamensis. Considering both genetic and ploidy level differentiation, we propose that two different management units (northern and southern) should be considered and a combination of in situ and ex situ conservation measures should be employed to preserve populations of this endangered species in southwestern China in the light of our findings.

Pleistocene climate oscillations and habitat connectivity contributed to avian beta‐diversity in the megadiverse Colombian Paramo ecosystems

AbstractAimThe role of evolutionary history in shaping the patterns of species distributions is generally explored at coarse spatial extents. However, at small spatial extents, the combined effects of history and ecological processes on local diversity has received less attention. We test the relative importance of historical and ecological factors on the spatial distribution of bird taxonomic (TβD) and phylogenetic (PβD) β‐diversity on Paramo ecosystems.LocationSouth‐western Colombia.TaxonAndean bird species.MethodsUsing point occurrence data for 175 bird species recorded in 11 Paramos, we calculated TβD and PβD. We used a lineage through time plot to evaluate the association between bird species richness and the time of Andean uplift and Quaternary climatic oscillations. To capture range dynamics associated with past climate oscillations, we delimited paramos using connectivity matrices based on four distance criteria (i.e. paramos connected at 20, 25, 35 and 55 km apart) to compute Moran's eigenvectors maps. Then, we evaluated the relative importance of altitude, past climatic oscillations, current climate and connectivity on the spatial distribution of avian TβD and PβD.ResultsTwo‐thirds of the bird species in the paramos are recent and emerged after the late Miocene/early Pliocene. The average TβD was four times higher than the average PβD indicating that paramo assemblages harbour distinct, but closely related, species. We found that distribution of β‐diversity had a spatial structure resulting in two groups of paramos – one in the north of our study area containing four paramos and other in the south with seven paramos. This spatial structure together with past climate conditions explained the variation of both TβD and PβD.Main conclusionsOur results are consistent with the hypothesis that patterns of β‐diversity reflect the complex history of Andean region including mountain uplift and climatic oscillations in the Pleistocene. We demonstrated that the integration of different facets of β‐diversity into a community ecology framework provides new insights about the historical and ecological factors responsible for generating the patterns of species distribution.

Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data.

Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.

Stochastic alluvial fan and terrace formation triggered by a high-magnitude Holocene landslide in the Klados Gorge, Crete

Abstract. Alluvial fan and terrace formation is traditionally interpreted as a fluvial system response to Quaternary climate oscillations under the backdrop of slow and steady tectonic activity. However, several recent studies challenge this conventional wisdom, showing that such landforms can evolve rapidly as a geomorphic system responds to catastrophic and stochastic events, like large-magnitude mass wasting. Here, we contribute to this topic through a detailed field, geochronological, and numerical modelling investigation of thick (&gt;50 m) alluvial sequences in the Klados catchment in southwestern Crete, Greece. The Klados River catchment lies in a Mediterranean climate, is largely floored by carbonate bedrock, and is characterised by well-preserved alluvial terraces and inset fans at the river mouth that exceed the volumes of alluvial deposits in neighbouring catchments of similar size. Previous studies interpreted the genesis and evolution of these deposits to result from a combination of Pleistocene sea-level variation and the region's long-term tectonic activity. We show that the &gt;20 m thick lower fan unit, previously thought to be late Pleistocene in age, unconformably buries a paleoshoreline uplifted in the first centuries CE, placing the depositional age of this unit firmly in the late Holocene. The depositional timing is supported by seven new radiocarbon dates that indicate middle to late Holocene ages for the entire fan and terrace sequence. Furthermore, we report new evidence of a previously unidentified valley-filling landslide deposit that is locally 100 m above the modern stream elevation, and based on cross-cutting relationships, it predates the alluvial sequence. Observations indicate the highly erodible landslide deposit as the source of the alluvial fill sediment. We identify the likely landslide detachment area as a large rockfall scar at the steepened head of the catchment. A landslide volume of 9.08×107 m3 is estimated based on volume reconstructions of the mapped landslide deposit and the inferred scar location. We utilise landslide runout modelling to validate the hypothesis that a high-magnitude rockfall would pulverise and send material downstream, filling the valley up to ∼100 m. This partial liquefaction is required for the rockfall to form a landslide body of the extent observed in the valley and is consistent with the sedimentological characteristics of the landslide deposit. Based on the new age control and the identification of the landslide deposit, we hypothesise that the rapid post-landslide aggradation and incision cycles of the alluvial deposits are not linked to long-term tectonic uplift or climate variations but rather stochastic events such as mobilisation of sediment in large earthquakes, storm events, or ephemeral blockage in the valley's narrow reaches. The Klados case study represents a model environment for how stochastically driven events can mimic climate-induced sedimentary archives and lead to deposition of thick alluvial sequences within hundreds to thousands of years, and it illustrates the ultrasensitivity of mountainous catchments to external perturbations after catastrophic events.

Population Demographic History of a Rare and Endangered Tree Magnolia sprengeri Pamp. in East Asia Revealed by Molecular Data and Ecological Niche Analysis

Quaternary climate and environment oscillations have profoundly shaped the population dynamic history and geographic distributions of current plants. However, how the endangered and rare tree species respond to the climatic and environmental fluctuations in the subtropical regions of China in East Asia still needs elucidation. In this study, we collected 36 natural populations of an endangered and rare tree species Magnolia sprengeri Pamp. in subtropical China to determine the demographic history, and modeled the changes of geographic distributions of this species in East Asia based on the MaxEnt ecological niche analyses. In addition, we sequenced three maternally inherited chloroplast DNA fragments (matK, trnH-psbA, and rbcL) for all the natural populations which covered the whole geographic distributions of M. sprengeri. Population genetic analysis showed that the endangered tree species have a low level of chloroplast DNA diversity. However, the genetic variation contribution within populations was greater than that among populations (FST = 0.276), which demonstrated a high level of genetic differentiation. Interestingly, some unique chloroplast DNA haplotypes and higher genetic variations were identified in the Qinling-Daba Mountains, Central China, and Tianmu Mountains of Zhejiang province, East of China in East Asia. Combining with the species distribution modeling, we speculated that these areas might be the potential glacial refugia for the endangered plant M. sprengeri. Phylogeographic analysis demonstrated that the geographic factors (e.g., mountains, rivers, and other isolation barriers) had little effect on the genetic divergence among populations. Ecological niche modeling further revealed that the natural populations of M. sprengeri did not experience significant geographic distribution changes from the last glacial maximum to the present time. These findings are in line with the analysis results of the multimodal mismatch patterns of the chloroplast DNA variations. To protect the endangered species M. sprengeri, in situ and ex situ conservation strategies should be formulated for the natural populations with higher genetic variations.

Glacial connectivity and current population fragmentation in sky islands explain the contemporary distribution of genomic variation in two narrow‐endemic montane grasshoppers from a biodiversity hotspot

AbstractAimCold‐adapted biotas from mid‐latitudes often show small population sizes, harbour low levels of local genetic diversity and are highly vulnerable to extinction due to ongoing climate warming and the progressive shrinking of montane and alpine ecosystems. In this study, we use a suite of analytical approaches to infer the demographic processes that have shaped contemporary patterns of genomic variation in Omocestus bolivari and Omocestus femoralis, two narrow‐endemic and red‐listed Iberian grasshoppers forming highly fragmented populations in the sky island archipelago of the Baetic System.LocationSouth‐eastern Iberia.MethodsWe quantified genomic variation in the two focal taxa and coupled ecological niche models and a spatiotemporally explicit simulation approach based on coalescent theory to determine the relative statistical support of a suite of competing demographic scenarios representing contemporary population isolation (i.e. a predominant role of genetic drift) versus historical connectivity and post‐glacial colonization of sky islands (i.e. pulses of gene flow and genetic drift linked to Pleistocene glacial cycles).ResultsInference of spatial patterns of genetic structure, environmental niche modelling and statistical evaluation of alternative species‐specific demographic models within an approximate Bayesian computation framework collectively supported genetic admixture during glacial periods and post‐glacial colonization of sky islands, rather than long‐term population isolation, as the scenario best explaining the current distribution of genomic variation in the two focal taxa. Moreover, our analyses revealed that isolation in sky islands has also led to extraordinary genetic fragmentation and contributed to reduce local levels of genetic diversity.Main conclusionsThis study exemplifies the potential of integrating genomic and environmental niche modelling data across biological and spatial replicates to determine whether organisms with similar habitat requirements have experienced concerted/idiosyncratic responses to Quaternary climatic oscillations, which can ultimately help to reach more general conclusions about the vulnerability of mountain biodiversity hotspots to ongoing climate warming.

Impact of Quaternary climatic oscillations on phylogeographic patterns of three habitat‐segregated Cerastium taxa endemic to the Dinaric Alps

AbstractAimThe Balkan Peninsula has served as source for the colonisation of large parts of Europe after the Pleistocene, but the processes driving the intraspecific diversification within the Balkan Peninsula are much less understood. To fill this gap, we investigated the phylogeography and evolutionary history of three habitat‐segregated Cerastium taxa endemic to the Dinaric Alps and explored whether they responded differently to the Quaternary climatic oscillations in the Balkan Peninsula.LocationEurope, Balkan Peninsula, Dinaric Alps.TaxonCerastium (Caryophyllaceae, angiosperms).MethodsWe combined climatic niche comparisons and species distribution modelling (SDM) on the one hand, with cytological (relative genome size, RGS) and genetic / genomic approaches such as amplified fragment length polymorphism (AFLP) fingerprinting, phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and plastid (trnT–ndhJ) sequences on the other hand, in order to investigate how the Pleistocene glaciations and the Holocene warming influenced the phylogeographic structure of the studied taxa. SDM was used to reconstruct past, present and future habitat suitability.ResultsDespite nonequivalent climatic niches, we detected climatic niche similarity amongst the three Cerastium taxa. Nonhierarchical K‐means clustering of AFLP data revealed an optimal split into two geographically segregated groups in all three taxa. Genetic divergence between the northwestern and the southeastern populations can be explained by isolation in northern and southern refugia, as suggested by SDM. The ITS and plastid sequences revealed similar, although more complex, patterns of genetic differentiation, and RGS differentiation was mainly geography‐correlated.Main conclusionsDespite the pronounced habitat segregation amongst the studied taxa, their overall phylogeographic structure is similar, suggesting comparable underlying processes and similar responses to the same historical events. However, we anticipate that the three taxa will respond differently to ongoing climate warming.