三峡大坝下游残存疏花水柏枝种群结构和动态

在三峡大坝下游的湖北宜都关洲设立1个40 m×40 m的固定样地,利用高度分级,比较2008与2009年两年间的疏花水柏枝（Myricaria laxiflora）种群数量动态,并运用点格局的Ripley＇s K函数分析了其空间格局变化及种群更新特征。结果表明,疏花水柏枝幼苗数量较少,种群更新存在一些障碍。空间分布格局与空间尺度及植株的大小密切相关。种群总体呈集群分布,各大小级多在9 m时出现最大的聚集强度,随着大小级的增加,聚集强度有减弱的趋势。幼苗与中株有较强的正关联。由于种群现有生境变化较大,应考虑迁地保护,并对原生种群加强长期动态监测;同时,开展疏花水柏枝适应机理研究,实施科学保护。     

三峡濒危植物疏花水柏枝的回归引种和种群重建

疏花水柏枝分布于三峡库区原海拔70～155m的消落带,三峡工程修建后它将丧失其全部生境而成为濒危植物。实验结果显示其种子在土壤含水量大于10%以上时开始萌发,以土壤含水量达到饱和状况时萌发最好。种子萌发与定居阶段对土壤水分条件的严格要求使得疏花水柏枝分布区十分狭小。回归引种和种群重建是拯救该物种的主要手段。三峡工程修建后库区内新的消落带将形成夏旱冬淹的水节律,完全不同于库区原有消落带所具有的冬旱夏淹的水节律,不适于作为疏花水柏枝种群的迁移地。相比之下库区淹没区以上各支流消落带的生态环境与疏花水柏枝原有生境较为接近,适于作其新的生境。种群遗传多样性、年龄结构、分布格局、繁殖与扩展等生物学特性是种群持续发展的基础,文章以此为依据,对疏花水柏枝种群重建与管理中的相关问题进行了分析讨论。认为疏花水柏枝种群恢复与重建中目前所面临的主要问题是如何增强被隔离的种群间的基因交流、促进种群的种子扩散与萌发、协调新建种群与当地物种的关系、营造有利于新建种群定居与生长的生态环境。重建种群的管理应结合疏花水柏枝的生长发育节律和移栽地的生态环境条件来开展,要有效地监控种群的生长发育动态,合理地在隔离种群间相互引种,适时地进行水分管理,并对周围植被适度控制。     

Cladogenesis and phylogeography of the lizard Phrynocephalus vlangalii (Agamidae) on the Tibetan plateau

Phrynocephalus vlangalii is restricted to dry sand or Gobi desert highlands between major mountain ranges in the Qinghai (Tibetan) Plateau. Mitochondrial DNA (mtDNA) sequence (partial ND2, tRNA(Trp) and partial tRNA(Ala)) was obtained from 293 Phrynocephalus sampled from 34 sites across the plateau. Partitioned Bayesian and maximum parsimony phylogenetic analyses revealed that P. vlangalii and two other proposed species (P. erythrus and P. putjatia) together form a monophyletic mtDNA clade which, in contrast with previous studies, does not include P. theobaldi and P. zetangensis. The main P. vlangalli clade comprises seven well-supported lineages that correspond to distinct geographical areas with little or no overlap, and share a most recent common ancestor at 5.06 +/- 0.68 million years ago (mya). This is much older than intraspecific lineages in other Tibetan animal groups. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruption of maternal gene flow. A combined approach based on tests of population expansion, estimation of node dates, and significance tests on clade areas indicated that phylogeographical structuring has been primarily shaped by three main periods of plateau uplift during the Pliocene and Pleistocene, specifically 3.4 mya, 2.5 mya and 1.7 mya. These periods corresponded to the appearance of several mountain ranges that formed physical barriers between lineages. Populations from the Qaidam Basin are shown to have undergone major demographic and range expansions in the early Pleistocene, consistent with colonization of areas previously covered by the huge Qaidam palaeolake, which desiccated at this time. The study represents one of the most detailed phylogeographical analyses of the Qinghai Plateau to date and shows how geological events have shaped current patterns of diversity.     

Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes

The phylogeographical patterns and population genetic structures of Varicorhinus barbatulus in Taiwan were investigated based on genetic diversity of 34 allozyme loci and nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mtDNA. Allozyme and mtDNA analyses revealing evident geographical structuring suggest limited gene flow between populations (F(ST)=0.511 and 0.791, respectively). Low genetic variability within populations (P=5.56%; He=0.018) based on allozymes and significantly negative Tajima's D statistics based on mtDNA suggest that most populations in Taiwan may have originated from a small number of founders followed by demographic expansion. The gene genealogy of mtDNA identified six lineages corresponding to major drainages that were separated by the geological barriers due to vicariant events. A minimum spanning network based on nucleotide substitutions reflects divergence from populations of the Miao-li Plateau to northern and southern regions of the island. In contrast to a previous hypothesis that suggests an early invasion to eastern part of Taiwan prior to the lifting of central mountain range some one million years ago, the mtDNA genealogy and molecular dating reveal very recent colonization of the eastern population. Nested clade analyses revealing significant associations between genetic structure and geographical division identify past fragmentation and range expansion as major phylogeographical events that shaped the geographical distribution of this species in Taiwan.     

Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird

Phylogeographical studies of Nearctic songbirds conducted to date have yielded unexpectedly low levels of genetic differentiation and weak phylogeographical structure in mitochondrial DNA lineages as compared with species studied in Neotropical areas. Factors leading to this pattern may include (i) gene flow, (ii) population expansions from bottlenecked populations, and (iii) selective sweeps. Here we provide evidence for the role played by Pleistocene postglacial population expansions on the phylogeography of MacGillivray's warbler (Oporornis tolmiei), a long-distance migratory bird. Samples from 12 breeding localities in the temperate USA were compared with those from two localities in north-eastern Mexico. The former showed evidence of a Late Pleistocene population expansion as indicated by low haplotype and nucleotide diversity, a star-like phylogeny of alleles, and a mismatch distribution indicating a sudden increase in effective population size. By contrast, the Mexican population showed high levels of genetic diversity and a mismatch distribution as expected for a population unaffected by sudden demographic change. Haplotypes from the two regions formed two distinct phylogroups which separated roughly one million years ago according to a conventional molecular clock for songbirds. This study provides support for the Pleistocene expansion hypothesis in MacGillivray's warbler and suggests that postglacial expansion of bottlenecked populations is responsible for the lack of variation and structure reported for most North American songbird species.     

Phylogenetic Origin of Phyllolobium with a Further Implication for Diversification of Astragalus in China

Astragalus is a species-rich genus occurring in the western arid habitats in China and its diversification and infrageneric relationships in this region remain unclear. In the present study, based on molecular data, we aim to (i) test whether Phyllolobium (previously treated as a subgenus Pogonophace in Astragalus ) should be warranted; and (ii) date the origin of Phyllolobium and probable diversification of Astragalus sensu stricto (s.s.). We sequenced five species from Phyllolobium first and collected all related sequences from the genus, Astragalus s.s and their close relatives ( Oxytropis and Caragana etc.). Our phylogenetic analyses suggested that all species of Phyllolobium comprise a monophyletic sister-group to genera of the subtribe Coluteinae. Molecular dating suggested that Phyllolobium and Astragalus s.s. originated around 8 and 10 million years ago. These two estimates are highly consistent with the intense uplifts of the Qinghai-Tibetan Plateau inferred from geological evidence. In addition, one section of Pogonophace (Sect. Robusti) was estimated to originate 2.5 million years ago and this section with a tendency for dry habitats seems to be evidence of Asian intensified aridity resulting from the intense uplift of the Qinghai-Tibetan Plateau.     

基于叶绿体基因序列rbcL-accD研究莛子藨的分子遗传多样性和谱系地理结构

莛子藨是莛子藨属的一种多年生草本植物,主要分布在青藏高原东北部及邻近高山地区和日本,为东亚特有种。本文基于叶绿体DNA基因间隔区rbcL-accD序列,对莛子藨物种水平的序列特征、分子遗传多样性和谱系地理结构进行研究。分析结果发现该区域莛子藨种群的遗传变异主要来自于居群间（72.28%）,优势单倍型（H2）广泛分布,特有单倍型分散在多个居群。居群间遗传分化系数N_STST,没有检测到显著谱系地理结构,而且居群间基因流较低（N_m=0.096）,青藏高原及其邻近地区特殊地形和生态环境造成的地理隔离或者生境异质化可能是现有单倍型分布格局形成的原因。种群动态历史分析显示莛子藨经历过不显著的种群选择或者扩张事件,综合分析推测莛子藨居群应该是在间冰期或者冰期后从不同避难所扩散形成现在的分布格局,具体避难所还需进一步深入研究才能确认。     

Phylogeography and introgressive hybridization of the ground beetle Carabus yamato in Japan based on mitochondrial gene sequences

To study the phylogeography of the ground beetle Carabus yamato in Japan, we compared 1,020-bp sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene from 373 specimens from 37 localities with those of three parapatric species (C. albrechti, C. kimurai, and C. japonicus) that might share mitochondrial lineages with C. yamato through introgressive hybridization. We found 81 haplotypes from C. yamato. Of these, 17 haplotypes were considered to be of an introgressed lineage from C. albrechti, based on the phylogeny and geographic distribution. In addition, one haplotype of C. kimurai was likely an introgressant from C. yamato. Putative introgression events among the four species were restricted to these two directional cases. We analyzed the phylogeography of C. yamato using nested clade phylogeographical analysis and population genetic parameters. The mitochondrial lineages of C. yamato were estimated to have diverged no more than approximately 1.12 million years ago, implying that the estimated historical events occurred after the Early Pleistocene. Carabus yamato was inferred to have experienced a contraction of its distribution range, followed by recent range expansion. Populations in the western and eastern regions, segregated by Ise Bay and the Nobi and Okazaki Plains, diverged in the mitochondrial clades. The northern and most western populations possessed one clade only (except an introgressed lineage), whereas eastern and some southwestern populations possessed several diverged clades, which were considered to be ancestral; these populations may have been associated with refugia during glacial periods.     

中国水柏枝属植物的地理分布、濒危状况及其保育策略

水柏枝属(MyricariaDesv.)植物主要分布于中国青藏高原及其邻近地区,为欧亚温带高山植物类群,多为河岸带植物,是分布区湿地生态系统和荒漠生态系统的重要组分。为评价这些特殊生态系统关键植物的分布及受威胁现状,对中国水柏枝属植物的地理分布和濒危状况进行了调查。调查发现,该属中国分布的11个分类群均受到生存胁迫,其中疏花水柏枝即将成为野外灭绝种,宽叶水柏枝已属极危种,心叶水柏枝为濒危种,秀丽水柏枝、泽当水柏枝、小花水柏枝、卧生水柏枝和匍匐水柏枝为渐危种,具鳞水柏枝、三春水柏枝和宽苞水柏枝为受胁种。结果表明,以水利建设为主的人为干扰和土地沙化、气温升高带来的环境改变是导致该属植物生存胁迫的主要原因。最后探讨了水柏枝属这类河岸带湿地和荒漠生境植物的保育策略。     

Palaeoclimatic changes explain Anatolian mountain frog evolution: a test for alternating vicariance and dispersal events

Holarctic biodiversity has been influenced by climatic fluctuations since the Pliocene. Asia Minor was one of the major corridors for postglacial invasions in the Palearctic. Today this area is characterized by an extraordinarily rich fauna with close affiliation to European, Asian and Indo-African biota. However, exact scenarios of range expansion and contraction are lacking. Using a phylogeographical approach we (i). identify monophyletic lineages among Anatolian mountain frogs and (ii). derive a spatio-temporal hypothesis for the invasion process in Anatolia. We sequenced 540 bp of the mitochondrial 16S rRNA gene from 40 populations of mountain frogs from Anatolia, the Elburz Mountains and the Caucasus. Our samples comprise all known species and subspecies: Rana macrocnemis macrocnemis, R. m. tavasensis, R. m. pseudodalmatina, R. camerani and R. holtzi. They include the type localities of four of these taxa. We used a nested clade analysis (NCA) to infer historical and recurrent events that account for the observed geographical distribution of haplotypes. None of the extant species is monophyletic. Based on a molecular clock calibration using homologous sequences of Western Palearctic water frogs of the same genus, we estimated that a basic radiation into three lineages c. 2 Mya was followed by several dispersal and fragmentation events. The geographical distribution of resident and widespread haplotypes allows us to infer and date scenarios of range expansion and fragmentation that are aligned with dramatic climatic oscillations that have occurred during the last 600000 years. Consequently, Pliocene and Pleistocene climatic oscillations triggered the evolution of Anatolian mountain frogs through an interplay of vicariance and dispersal events.     

Phylogeography and evolution of two closely related oak species (<Emphasis Type="Italic">Quercus</Emphasis>) from north and northeast China

Orographic and climatic influences during the Pleistocene have had a crucial role on interspecific divergence and population demography during speciation. However, associations between demographic histories of closely related species and related climatic events, especially in north and northeast China, are still underexplored. Genetic analyses with four chloroplast DNA and two nuclear genes and species distribution modeling were used for two closely related oak species (Quercus liaotungensis and Quercus mongolica) to test if their interspecific divergence and phylogeographical histories were possibly related to the Pleistocene-era climatic events. Potential divergence of the two oak species was estimated at about 0.92–2.15 Ma. Species distribution models and genetic data showed varying phylogeographical histories and spatial population structures between the two oaks, leading to different patterns of interspecific gene flow between the chloroplast and nuclear genes. The results indicate that speciation event between the two species is recent and may have been triggered by geological and climatic fluctuations linked to the upheavals of the Qinghai-Tibetan Plateau at the Pliocene/Pleistocene boundary. The two closely related oaks possess varying population demography during the interglacial-glacial climatic oscillations of the Quaternary, probably due to the various niche adaptations among different distribution ranges across their species trajectories.     

High interpopulation genetic differentiation and unidirectional linear migration patterns in Myricaria laxiflora (Tamaricaceae), an endemic riparian plant in the Three Gorges Valley of the Yangtze River

Myricaria laxiflora is restricted to the riverbanks of the Yangtze River valley and will be completely lost owing to the construction of the Three Gorges Dam. Genetic diversity and structure of nine natural and one ex situ populations were investigated using amplified fragment length polymorphisms (AFLPs). A moderate level of gene diversity was found in natural populations, while the ex situ population had the highest. The F statistics calculated by different approaches consistently revealed a high genetic differentiation among natural populations, contributing >45% of the total gene diversity. The Bayesian-based analysis differentiated nine independent populations in accordance with the sites sampled. Estimates of gene flow by F(ST) and coalescent-based simulation analysis indicated a restricted recurrent gene exchange among populations (Nm = 0.290-0.401), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. The migration pattern in M. laxiflora is best explained by a classical metapopulation model, but with a unique unidirectional direction underlined by hydrochoric force that drove dispersal of seeds and propagules from upstream toward downstream populations. Previous efforts in preserving genomic integrity in ex situ conservation were evaluated, and the results provide valuable information to formulate conservation guidelines for successfully reintroducing M. laxiflora to the wild.     

Tracing an invasion: landbridges, refugia, and the phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus)

Abstract Pleistocene fragmentation of the Amazonian rainforest has been hypothesized to be a major cause of Neotropical speciation and diversity. However, the role and even the reality of Pleistocene forest refugia have attracted much scepticism. In Amazonia, previous phylogeographical studies have focused mostly on organisms found in the forests themselves, and generally found speciation events to have predated the Pleistocene. However, molecular studies of open-formation taxa found both north and south of the Amazonian forests, probably because of vicariance resulting from expansion of the rainforests, may provide novel insights into the age of continuous forest cover across the Amazon basin. Here, we analyse three mitochondrial genes to infer the phylogeography of one such trans-Amazonian vicariant, the Neotropical rattlesnake (Crotalus durissus), which occupies primarily seasonal formations from Mexico to Argentina, but avoids the rainforests of Central and tropical South America. The phylogeographical pattern is consistent with gradual dispersal along the Central American Isthmus, followed by more rapid dispersal into and across South America after the uplift of the Isthmus of Panama. Low sequence divergence between populations from north and south of the Amazon rainforest is consistent with mid-Pleistocene divergence, approximately 1.1 million years ago (Ma). This suggests that the Amazonian rainforests must have become fragmented or at least shrunk considerably during that period, lending support to the Pleistocene refugia theory as an important cause of distribution patterns, if not necessarily speciation, in Amazonian forest organisms. These results highlight the potential of nonforest species to contribute to an understanding of the history of the Amazonian rainforests themselves.     

密度对濒危物种疏花水柏枝幼苗存活与生长的影响

疏花水柏枝(Myricarialaxiflora)原产于三峡库区长江干流的河滩,三峡水库的蓄水淹没了其所有的野生种群,使之濒临绝灭。通过一系列的密度处理实验,我们研究了不同密度下疏花水柏枝幼苗的存活率、幼苗总生物量、地下生物量、地上生物量、一级枝数、二级枝数、一级枝长度的变化,揭示了密度对一年生幼苗存活与生长的影响。结果显示,随着密度的增加,疏花水柏枝种群内部的竞争加剧,幼苗的死亡率增加,特别是当密度大于250ind./m2时,死亡率显著上升,上述体现植株生长状况的各指标值也随密度的增加而显著减小。表明疏花水柏枝一年生幼苗的存活与生长受到密度的影响。文中还建立了密度影响下疏花水柏枝各构件部分生长发育的回归模型,解释了密度对它们的调节作用。最后对疏花水柏枝种群重建中的相关问题进行了分析讨论,以求为回归引种实践提供参考。     

Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the southern Andes

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000-13,000 years ago). Neutrality tests and the "g" parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats.     

Impact of Plio-Pleistocene arid cycling on the population history of a southwestern Australian frog

Southwestern Australia is regarded as a global biodiversity hotspot. The region contains a high number of endemic species, ranging from Gondwanan relicts to much more recently evolved plant and animal species. Myobatrachid frogs are diverse in southwestern Australia, and while we know they have speciated in situ in the southwest, we know little about the temporal and geographical patterning of speciation events. Crinia georgiana is an ideal subject to test hypotheses concerning the effect of climatic history on southwestern Australian anurans, as it is an old lineage with a broad distribution covering the entire region. We compiled an extensive phylogeographical data set based on 1085 bp of the mitochondrial gene ND2 for 68 individuals from 18 sites across the species' range. Two major genetic clades were identified which were largely confined to the high rainfall and southeast coastal biogeographical zones, respectively. The clades appear to have diverged around the Plio-Pleistocene border (1.26-1.72 million years ago), concordant with increasing intensity and frequency of arid climate cycles. Subsequent phylogeographical structure appears to have developed primarily during the Pleistocene climatic fluctuations that also have been integral in generating species diversity in the endemic southwestern Australian flora. Phylogeographical analyses identified several dispersal routes, possible refugial areas within the range of the species and also regions of secondary contact. Dispersal routes identified may now be closed to the species because of habitat destruction and salinity problems in inland regions, posing concerns about the evolutionary potential of the species in light of predicted climate change.     

Great genetic differentiation among populations of Meconopsis integrifolia and its implication for plant speciation in the Qinghai-Tibetan Plateau

The complex tectonic events and climatic oscillations in the Qinghai-Tibetan Plateau (QTP), the largest and highest plateau in the world, are thought to have had great effects on the evolutionary history of the native plants. Of great interest is to investigate plant population genetic divergence in the QTP and its correlation with the geologic and climatic changes. We conducted a range-wide phylogeographical analysis of M. integrifolia based on the chloroplast DNA (cpDNA) trnL-trnF and trnfM-trnS regions, and defined 26 haplotypes that were phylogenetically divided into six clades dated to the late Tertiary. The six clades correspond, respectively, to highly differentiated population groups that do not overlap in geographic distribution, implying that the mountain ranges acting as corridors or barriers greatly affected the evolutionary history of the QTP plants. The older clade of M. integrifolia only occurs in the southwest of the species' range, whereas the distributions of younger clades extend northeastward in the eastern QTP, suggesting that climatic divergence resulting from the uplift of the QTP triggered the initial divergence of M. integrifolia native to the plateau. Also, the nrDNA ITS region was used to clarify the unexpected phylogenetic relationships of cpDNA haplotypes between M. integrifolia and M. betonicifolia. The topological incongruence between the two phylogenies suggests an ancestral hybridization between the two species. Our study indicates that geographic isolation and hybridization are two important mechanisms responsible for the population differentiation and speciation of Meconopsis, a species-rich genus with complex polyploids.     

三峡库区两种特有植物天然生境与迁地生境土壤特征的比较

对库区特有的濒危植物荷叶铁线蕨、疏花水柏枝天然生境和迁地保护区生境及其土壤性质进行了调查分析和比较,结果表明：荷叶铁线蕨适宜于温暖湿润且排水良好的条件下发育的酸性淋溶土,养分含量高,多为粘土。疏花水柏枝适宜于亚热气候下弱碱性、养分含量低的冲积性砂砾质初育土、能耐一定程度的盐分。中国科学院武汉植物研究所内的迁地保护区土壤为湖滨沉积物上发育的中性粘土、主要养分和盐分含量介于两种天然生境土壤之间。微量元     

Historic range dynamics in Kaiser's mountain newt (Neurergus kaiseri): Insights from phylogeographic analyses and species distribution modeling

Vulnerable Kaiser''s mountain newt, Neurergus kaiseri, is endemic to highland streams, springs, and pools of the southwestern Zagros mountain, Iran. The present study aimed to use an integration of phylogeographical and species distribution modeling (SDM) approaches to provide new insights into the evolutionary history of the species throughout Quaternary climate oscillations. The phylogeographical analysis was followed by analyzing two mitochondrial DNA (mt‐DNA) markers including 127 control region (D‐loop) and 72 NADH dehydrogenase 2 (ND2) sequences from 15 populations in the entire species range that were obtained from GenBank. Potential recent and past distribution (the Last Glacial Maximum, LGM, 21 Kya and the Mid‐Holocene, 6 Kya) reconstructed by ensemble SDM using nine algorithms with CCSM4, MIROC‐ESM, and MPI‐ESM‐P models. N. kaiseri displayed two distinct lineages in the northern and southern regions that diverged in the Early‐Pleistocene. The demographics analysis showed signs of a slight increase in effective population size for both northern and southern populations in the Mid‐Pleistocene. Biogeography analysis showed that both vicariance and dispersal events played an important role in the formation of recent species distribution of N. kaiseri. Based on SDM projection onto paleoclimatic data, N. kaiseri displayed a scenario of past range expansion that followed by postglacial contraction. The models showed that the distribution range of the species may have shifted to a lower altitude during LGM while with amelioration of climatic during Mid‐Holocene to recent conditions caused the species to shift to the higher altitude. The findings of the current study support the hypothesis that the Zagros mountains​ may be acting as climatic refugia and play an important role in the protection of isolated populations during climate oscillations.     

Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States

Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species' range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus' range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum approximately 12,000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajima's D and patterns associated with location-specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.