Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in g...Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderrna ruficeps, and compare results to previous studies that examined this species across China's Mainland and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations （Nepal, Tibet, Myanmar, Yunnan）, rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood [Current Zoology 61 （5）： 901-909, 2015].展开更多
The impact of the Quaternary glaciation on eastern China’s local fauna and flora is a topic of considerable interest. We use mitochondrial DNA(mtDNA) sequences and coalescent simulations to test two general biogeogra...The impact of the Quaternary glaciation on eastern China’s local fauna and flora is a topic of considerable interest. We use mitochondrial DNA(mtDNA) sequences and coalescent simulations to test two general biogeographic hypotheses related to the effect of the Pleistocene climatic fluctuations on a widespread, eastern Chinese amphibian, Pseudepidalea raddei. Genealogical reconstructions are made and they detect major western and eastern lineages, which overlap in northwestern China, and possibly indicate the secondary contact of the populations that had entered the region from separate glacial refugia. Coalescent tests rejected alternative hypotheses of fragmentation of either a widespread ancestor or panmixia. The tests instead supported the hypothesis of geographic isolation and a remarkable dispersal pattern in one of the lineages. Though the Pleistocene climatic events are known to have affected the historical distributions and intra-specific divergence of Chinese squamates, coalescent and non-coalescent demographic analyses indicated that the toad P. raddei was not adversely affected by glacial cycling. Presumably, an increase in the amount of climatically mild habitats in East Asia is due to the development of monsoons since the Mid-late Pleistocene is responsible for the relatively mild effects.展开更多
Quaternary geological events,glacial cycles,and climate fluctuations have a profound influence on the evolutionary history and population dynamics of many species.Mountain ungulates offer an ideal model for researchin...Quaternary geological events,glacial cycles,and climate fluctuations have a profound influence on the evolutionary history and population dynamics of many species.Mountain ungulates offer an ideal model for researching these historical processes.In this study,three taxa of mountain ungulates(Capricornis,Naemorhedus,and Muntiacus),which share overlapping ecological niches and similar life-history strategies,were selected to analyze the impact of historical events on their evolution and population dynamics.Specimens were collected from naturally deceased individuals during multiple field expeditions,as well as from forest police seizures,and included skulls,skins,and dried meat.Mitochondrial genomes(mitogenomes)were used as molecular markers.Analyses indicated that the evolutionary divergence of these mountain ungulates was primarily driven by five major uplift phases of the Qinghai-Xizang Plateau and a series of glaciation events.Results also indicated the formation of multiple refugia in the East Himalaya-Hengduan Mountains(EHHM)during the Quaternary.Four species—C.sumatraensis,N.cranbrooki,N.evansi,and M.gongshanensis—were selected for detailed analyses of historical population dynamics.Notably,population expansions were detected for all species,with the expansions of N.cranbrooki,N.evansi,and M.gongshanensis occurring during the early to mid-Holocene,likely due to warmer and more humid climatic conditions.In contrast,the population expansion of C.sumatraensis occurred in the late Holocene,driven by forest retreat and increased human activities such as settlement and grazing.Additionally,and most importantly,we obtained molecular samples of N.cranbrooki in Xizang,China,for the first time,and also confirmed the distribution of N.cranbrooki in Xizang rather than being limited to northern Myanmar.Overall,these findings provide evidence that N.cranbrooki is distributed in Xizang,also offer novel insights into the connections between Quaternary environmental change and species differentiation,refugia formation and population dynamics of mountain ungulates in the EHHM region.展开更多
Climate refugia can serve as a remnant habitat or stepping stones for species dispersal under climate warming.The largest freshwater lake by surface area,Lake Superior,USA and Canada,serves as a model system for under...Climate refugia can serve as a remnant habitat or stepping stones for species dispersal under climate warming.The largest freshwater lake by surface area,Lake Superior,USA and Canada,serves as a model system for understanding cooling-mediated local refugia,as its cool water temperatures and wave action have maintained shoreline habitats suitable for southern disjunct populations of arctic-alpine plants since deglaciation.Here,we seek to explain spatial patterns and environmental drivers of arctic-alpine plant refugia along Lake Superior’s shores,and assess future risk to refugia under moderate(+3.5℃)and warmest(+5.7℃)climate warming scenarios.First,we examined how the interactive effects of summer surface water temperatures and wind affected onshore temperatures,resulting in areas of cooler refugia.Second,we developed an ecological niche model for the presence of disjunct arctic-alpine refugia(pooling 1253 occurrences from 58 species)along the lake’s shoreline.Third,we fit species distribution models for 20 of the most common arctic-alpine disjunct species and predicted presence to identify refugia hotspots.Finally,we used the two climate warming scenarios to predict changes in the presence of refugia and disjunct hotspots.Bedrock type,elevation above water,inland distance,July land surface temperature from MODIS/Terra satellite and near-shore depth of water were the best predictors of disjunct occurrences.Overall,we predicted 2236 km of the shoreline(51%)as disjunct refugia habitat for at least one species under current conditions,but this was reduced to 20% and 7% with moderate(894 km)and warmest(313 km)climate change projections.展开更多
Given the reality of climate-driven migration,the net effectiveness of existing spatially fixed protected areas(PAs)to biodiversity conservation is expected to decline,while the potential of non-PA habitats(non-PAs,i....Given the reality of climate-driven migration,the net effectiveness of existing spatially fixed protected areas(PAs)to biodiversity conservation is expected to decline,while the potential of non-PA habitats(non-PAs,i.e.,natural,altered,or artificial ecosystems that are not formally designated as PAs)for biodiversity conservation is gaining attention.However,the contribution of non-PAs to biodiversity conservation remains poorly understood.With the aim of comprehensively assessing the effectiveness of non-PAs as transient refugia and steppingstones during future climate-change-induced migration of species in China,a six-metric integrated framework was applied and statistics of these metrics for PAs and non-PAs are compared.Results reveal that,a greater area of non-PAs has a low velocity of climate change(VoCC)compared to that of PAs,and can therefore serve as temporary refugia for species.The disappearing climate index(DCI)and novel climate index(NCI)results show that some 17%of the subdivided climate classes within the PAs have changed.However,the displacement index(DI)results imply that nearly half(48.98%)of the PAs need non-PAs to provide transient refugia for climate-driven migration of species in PAs.The higher ratio of effective steppingstones measured using the climate corridor score(CCS)and landscape current flow(LCF)further emphasizes that non-PAs play a more significant role as steppingstones for climate driven migration than do PAs in terms of both their structural and functional connectivity.Our research further demonstrates that a conservation approach that improves connectivity among PAs and considers Other Effective area-based Conservation Measures(OECMs)is essential for long-term biodiversity adaptation to climate change.展开更多
Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible...Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L.in China.In total,220 individuals from 12 populations in China and three populations outside China were analyzed,representing the largest number of populations studied by molecular markers to date.Nineteen haplotypes were produced and haplotype A was found in all populations.Populations in south-western China,including WC,JF,PX,and SP,contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.7714 to 0.8676.The TM population from China also showed a high genetic diversity(H=0.8485).Most of the genetic variation existed within populations and the differentiation among populations was low(GsT=0.2).According to haplotype distribution and the historical record,we suggest that populations of G.biloba have been subjected to extensive human impact,which has compounded our attempt to infer glacial refugia for Ginkgo.Nevertheless,the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.展开更多
基金We thank Nikki Boggess, who assisted in labwork. Fieldwork in Vietnam was facilitated by Dr. Le Mahn Hung, and supported by the National Geographic Committee for Research and Exploration. Fieldwork in China was supported by the National Science Foundation （DEB-0344430 to ATP）. The laboratory portions of this work were supported by the National Science Foundation （DEB-0743576 to RGM）. We thank recordists who shared their Stachyris/Cyanoderma recordings on Xeno-canto.
文摘Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderrna ruficeps, and compare results to previous studies that examined this species across China's Mainland and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations （Nepal, Tibet, Myanmar, Yunnan）, rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood [Current Zoology 61 （5）： 901-909, 2015].
基金supported by the Director Foundation of Experimental Centre, Shenyang Normal University (Syzx1104)a Visiting Professorship for Senior International Scientists from the Chinese Academy of Sciences to Robert W. MURPHYsupported by a Discovery Grant of the Natural Sciences and Engineering Research Council of Canada (A3148)
文摘The impact of the Quaternary glaciation on eastern China’s local fauna and flora is a topic of considerable interest. We use mitochondrial DNA(mtDNA) sequences and coalescent simulations to test two general biogeographic hypotheses related to the effect of the Pleistocene climatic fluctuations on a widespread, eastern Chinese amphibian, Pseudepidalea raddei. Genealogical reconstructions are made and they detect major western and eastern lineages, which overlap in northwestern China, and possibly indicate the secondary contact of the populations that had entered the region from separate glacial refugia. Coalescent tests rejected alternative hypotheses of fragmentation of either a widespread ancestor or panmixia. The tests instead supported the hypothesis of geographic isolation and a remarkable dispersal pattern in one of the lineages. Though the Pleistocene climatic events are known to have affected the historical distributions and intra-specific divergence of Chinese squamates, coalescent and non-coalescent demographic analyses indicated that the toad P. raddei was not adversely affected by glacial cycling. Presumably, an increase in the amount of climatically mild habitats in East Asia is due to the development of monsoons since the Mid-late Pleistocene is responsible for the relatively mild effects.
基金supported by the National Natural Science Foundation of China(32360133,31901080)Transboundary Cooperation on Biodiversity Research and Conservation in Gaoligong Mountains(No.E1ZK251)Major Science and Technique Programs in Yunnan Province(Grant No.202102AA310055)。
文摘Quaternary geological events,glacial cycles,and climate fluctuations have a profound influence on the evolutionary history and population dynamics of many species.Mountain ungulates offer an ideal model for researching these historical processes.In this study,three taxa of mountain ungulates(Capricornis,Naemorhedus,and Muntiacus),which share overlapping ecological niches and similar life-history strategies,were selected to analyze the impact of historical events on their evolution and population dynamics.Specimens were collected from naturally deceased individuals during multiple field expeditions,as well as from forest police seizures,and included skulls,skins,and dried meat.Mitochondrial genomes(mitogenomes)were used as molecular markers.Analyses indicated that the evolutionary divergence of these mountain ungulates was primarily driven by five major uplift phases of the Qinghai-Xizang Plateau and a series of glaciation events.Results also indicated the formation of multiple refugia in the East Himalaya-Hengduan Mountains(EHHM)during the Quaternary.Four species—C.sumatraensis,N.cranbrooki,N.evansi,and M.gongshanensis—were selected for detailed analyses of historical population dynamics.Notably,population expansions were detected for all species,with the expansions of N.cranbrooki,N.evansi,and M.gongshanensis occurring during the early to mid-Holocene,likely due to warmer and more humid climatic conditions.In contrast,the population expansion of C.sumatraensis occurred in the late Holocene,driven by forest retreat and increased human activities such as settlement and grazing.Additionally,and most importantly,we obtained molecular samples of N.cranbrooki in Xizang,China,for the first time,and also confirmed the distribution of N.cranbrooki in Xizang rather than being limited to northern Myanmar.Overall,these findings provide evidence that N.cranbrooki is distributed in Xizang,also offer novel insights into the connections between Quaternary environmental change and species differentiation,refugia formation and population dynamics of mountain ungulates in the EHHM region.
基金supported by the Natural Sciences and Engineering Research Council of Canada(RGPIN-2019-06040).
文摘Climate refugia can serve as a remnant habitat or stepping stones for species dispersal under climate warming.The largest freshwater lake by surface area,Lake Superior,USA and Canada,serves as a model system for understanding cooling-mediated local refugia,as its cool water temperatures and wave action have maintained shoreline habitats suitable for southern disjunct populations of arctic-alpine plants since deglaciation.Here,we seek to explain spatial patterns and environmental drivers of arctic-alpine plant refugia along Lake Superior’s shores,and assess future risk to refugia under moderate(+3.5℃)and warmest(+5.7℃)climate warming scenarios.First,we examined how the interactive effects of summer surface water temperatures and wind affected onshore temperatures,resulting in areas of cooler refugia.Second,we developed an ecological niche model for the presence of disjunct arctic-alpine refugia(pooling 1253 occurrences from 58 species)along the lake’s shoreline.Third,we fit species distribution models for 20 of the most common arctic-alpine disjunct species and predicted presence to identify refugia hotspots.Finally,we used the two climate warming scenarios to predict changes in the presence of refugia and disjunct hotspots.Bedrock type,elevation above water,inland distance,July land surface temperature from MODIS/Terra satellite and near-shore depth of water were the best predictors of disjunct occurrences.Overall,we predicted 2236 km of the shoreline(51%)as disjunct refugia habitat for at least one species under current conditions,but this was reduced to 20% and 7% with moderate(894 km)and warmest(313 km)climate change projections.
基金financially supported by the National Key R&D Program of China(Grants No.2022YFC3802604,2022YFF1303102)the Global Engagement for Strategic Partnership project of Nanjing University.
文摘Given the reality of climate-driven migration,the net effectiveness of existing spatially fixed protected areas(PAs)to biodiversity conservation is expected to decline,while the potential of non-PA habitats(non-PAs,i.e.,natural,altered,or artificial ecosystems that are not formally designated as PAs)for biodiversity conservation is gaining attention.However,the contribution of non-PAs to biodiversity conservation remains poorly understood.With the aim of comprehensively assessing the effectiveness of non-PAs as transient refugia and steppingstones during future climate-change-induced migration of species in China,a six-metric integrated framework was applied and statistics of these metrics for PAs and non-PAs are compared.Results reveal that,a greater area of non-PAs has a low velocity of climate change(VoCC)compared to that of PAs,and can therefore serve as temporary refugia for species.The disappearing climate index(DCI)and novel climate index(NCI)results show that some 17%of the subdivided climate classes within the PAs have changed.However,the displacement index(DI)results imply that nearly half(48.98%)of the PAs need non-PAs to provide transient refugia for climate-driven migration of species in PAs.The higher ratio of effective steppingstones measured using the climate corridor score(CCS)and landscape current flow(LCF)further emphasizes that non-PAs play a more significant role as steppingstones for climate driven migration than do PAs in terms of both their structural and functional connectivity.Our research further demonstrates that a conservation approach that improves connectivity among PAs and considers Other Effective area-based Conservation Measures(OECMs)is essential for long-term biodiversity adaptation to climate change.
基金the National Basic Research Program of China(973 Program2007CB411605)the National Natural Science Foundation of China(30670139,30300020).
文摘Variations in the trnK region of chloroplast DNA were investigated in the present study using polymerase chain reactionrestriction fragment length polymorphism to detect the genetic structure and to infer the possible glacial refugia of Ginkgo biloba L.in China.In total,220 individuals from 12 populations in China and three populations outside China were analyzed,representing the largest number of populations studied by molecular markers to date.Nineteen haplotypes were produced and haplotype A was found in all populations.Populations in south-western China,including WC,JF,PX,and SP,contained 14 of the 19 haplotypes and their genetic diversity ranged from 0.7714 to 0.8676.The TM population from China also showed a high genetic diversity(H=0.8485).Most of the genetic variation existed within populations and the differentiation among populations was low(GsT=0.2).According to haplotype distribution and the historical record,we suggest that populations of G.biloba have been subjected to extensive human impact,which has compounded our attempt to infer glacial refugia for Ginkgo.Nevertheless,the present results suggest that the center of genetic diversity of Ginkgo is mainly in south-western China and in situ conservation is needed to protect and preserve the genetic resources.
基金Supported by the National Natural Science Foundation of China, Grant Nos. 30470125, 40671066the Knowledge Innovation Project of Chinese Academy of Sciences, Grant No. KSCX2-SW-132.
