Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai‐Tibetan plateau

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai‐Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai‐Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford’s snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5–0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023–0.018 Ma). A single refugium was identified in a restricted semi‐continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present‐day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.     

The elevation history of the Tibetan Plateau and its implications for the Asian monsoon

The determination of the evolving palaeoaltitude of the Tibetan Plateau since the India-Eurasia collision underpins our understanding of how orography in central Asia affects the intensity of the monsoon and hence global climate change. Palaeoaltitudes, however, cannot be measured directly and need to be inferred from proxy observations that are usually model-dependent. Differing tectonic models for the behaviour of the lithosphere during continental collision have contrasting implications for the elevation of the plateau. However, two techniques recently employed for determining palaeo-elevation are independent of tectonic models, the first involving the variation with altitude of oxygen isotopes in precipitation and the second involving the change of leaf morphology with moist static energy of the atmosphere.Elevation studies have focused on southern Tibet, largely due to the relative ease of access to the region. There is a remarkable unanimity amongst the diverse techniques applied that the altitude of the southern plateau has not significantly changed since at least the mid Miocene (ca. 15 Ma) arguing for an onset of the monsoon system during or before the early Miocene. A range of tectonic studies suggest that the northern and eastern parts of the plateau are younger geomorphological features, but there are few quantitative constraints of the timing of elevation from these regions of Tibet. Since both the elevation and the surface area of the plateau impact on atmospheric circulation, palaeoaltitude studies need to be extended to chart the increasing areas of elevated land surface through time.     

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

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

The Eocene climate of China,the early elevation of the Tibetan Plateau and the onset of the Asian Monsoon

Eocene palynological samples from 37 widely distributed sites across China were analysed using co‐existence approach to determine trends in space and time for seven palaeoclimate variables: Mean annual temperature, mean annual precipitation, mean temperature of the warmest month, mean temperature of the coldest month, mean annual range of temperature, mean maximum monthly precipitation and mean minimum monthly precipitation. Present day distributions and observed climates within China of the nearest living relatives of the fossil forms were used to find the range of a given variable in which a maximum number of taxa can coexist. Isotherm and isohyet maps for the early, middle and late Eocene were constructed. These illustrate regional changing patterns in thermal and precipitational gradients that may be interpreted as the beginnings of the modern Asian Monsoon system, and suggest that the uplift of parts of the Tibetan Plateau appear to have taken place by the middle to late Eocene.     

Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai–Tibet Plateau: homoploid hybrid origin and Pleistocene expansion

Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai–Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and P. wilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and P. purpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well‐established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between P. purpurea and P. wilsonii, while variation at the nuclear se1364 gene suggested P. purpurea was more closely related to P. likiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that P. purpurea originated by homoploid hybrid speciation from P. wilsonii and P. likiangensis. The ABC analysis dated the origin of P. purpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by P. likiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from P. wilsonii such that it came to possess both mtDNA and cpDNA of P. wilsonii. The estimated parameters indicated that following its origin, P. purpurea underwent an expansion during/after the largest Pleistocene glaciation recorded for the QTP.     

青藏高原高寒荒漠区藏羚生态廊道识别及其保护状况评估

青藏高原高寒荒漠区是以藏羚、藏野驴和野牦牛等为代表的濒危有蹄类野生动物全球的主要分布区域,然而该区域高速公路、铁路等基础设施建设所带来的人为干扰,往往对上述濒危有蹄类迁徙廊道产生干扰及阻隔效应.基于最小费用距离路径原理及其Linkage Mapper模型,本研究模拟识别了青藏高原高寒荒漠区藏羚种群的潜在廊道分布,并依据主要自然保护区(阿尔金、可可西里和羌塘)和廊道之间的关系,将潜在廊道划分为封闭廊道(保护区内部廊道)、连通廊道(保护区之间廊道)、开放廊道(保护区与其外部非保护区区域之间廊道)和外部廊道（保护区区域之外的廊道）4种类型,并比较了它们的空间分布特征及其受扰状况.结果表明：尽管青藏高原高寒荒漠区有蹄类生境及其廊道总体保护状况仍相对较好,但日益增强的人为干扰对连接主要保护区之间部分廊道生态功能的干扰和影响不容忽视;目前划片分区式保护区管理模式不利于对以藏羚羊为代表的濒危有蹄类迁徙廊道进行有效的整体性保护,未来需要建立基于生态完整性和廊道连通性,整合上述3大保护区,建立青藏高原高寒荒漠保护区网络体系,打破保护区间的行政边界割裂和管理体系分割,通过建立保护区之间信息、资源共享以及保护措施的统一协调机制,实现整个高寒荒漠区生态系统、高原珍稀濒危物种的统一保护管理,提升高寒荒漠保护区的整体保护效率.     

青藏高原钻叶龙胆的遗传分化与种群动态历史研究

青藏高原是全球生物多样性中心之一,是研究物种形成和适应性进化的热点地区.龙胆属小龙胆组(Gen-tiana section Chondrophyllae s.l.)占整个龙胆属物种数目的 近一半,以青藏高原为分化中心,但组内物种的遗传分化及其影响因素并不清楚.该研究以小龙胆组青藏高原特有植物——钻叶龙胆(G.hayna...     

青藏高原高寒荒漠区藏羚适宜生境识别及其保护状况评估

藏羚作为青藏高原高寒荒漠区濒危有蹄类动物的典型代表,其生境保护对于维持其种群存续具有重要意义.本文考虑食物、地形、水系等藏羚关键生境因子及道路、居民点等人为干扰因子,基于生境适宜性模型,对青藏高原高寒荒漠区藏羚的潜在及有效生境适宜性进行了模拟分析.同时,基于保护比例及单位面积对适宜生境的捕获效率,评估了研究区内阿尔金山、可可西里和羌塘国家级自然保护区及其各功能分区的保护情况.结果表明： 青藏高原高寒荒漠区潜在和有效适宜生境面积分别为2.84×10⁵和2.08×10⁵ km²,人为干扰造成的生境退化达16.1%.其中,阿尔金山、可可西里和羌塘保护区所覆盖的潜在适宜生境面积分别为2.01×10⁴、3.13×10⁴和1.26×10⁵ km²;考虑道路、居民点等人为干扰因素,其有效适宜生境面积分别为1.75×10⁴、2.81×10⁴和9.95×10⁴ km²,上述干扰因素导致的生境减损率分别为12.9%、10.2%和21.1%,表明羌塘道路、居民点等人为干扰相对较严重.尽管目前该区域3大保护区保护了藏羚2/3以上的适宜生境,体现了良好的保护效率,但仍存在一定游离于保护体系之外的保护空缺.在保护区功能区划水平上,除核心区外,缓冲区和实验区的保护比例和保护效率也不容忽视.为强化对藏羚等濒危有蹄类的保护,有必要在保护区和功能分区水平上对现有保护体系进行优化调整,减少保护空缺、优化功能分区,提高保护体系对生境保护的有效性,并预先保护物种适应气候变化的潜在庇护所.     

Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of Rhodiola sect. Prainia in the southern Qinghai–Tibetan Plateau

There are two long‐standing biogeographic hypotheses regarding the glacial survival of plant species in the Qinghai–Tibetan Plateau (QTP): the in situ survival hypothesis and the tabula rasa hypothesis. We tested these two hypotheses in a phylogeographic study of Rhodiola sect. Prainia, a monophyletic section with ecologically divergent lineages. Molecular data from the nuclear internal transcribed spacer, six plastid markers and 13 nuclear microsatellite loci were analyzed for 240 individuals from 19 populations of this section. Environmental data were used to analyze the niches of major phylogenetic lineages within this section and to model changes in their distributions since the Last Glacial Maximum (LGM). We found that Rhodiola sect. Prainia consists of three evolutionary lineages: all populations of R. stapfii, R. prainii populations at the southern edge of the QTP, and R. prainii populations in the interior part of the QTP. During the LGM, the survival of R. prainii in the interior part of the QTP corresponded with the in situ survival hypothesis, while R. stapfii most probably survived the LGM in a manner corresponding with the tabula rasa hypothesis. The evolutionary history of different lineages of this section was shaped by topography, climate change, and lineage‐specific habitat preferences.     

Holocene climate and vegetation in the Milford drainage basin,Maine, U.S.A., and their implications for human history

A 9200 ¹⁴C year fossil pollen record from a small kettle lake in central Maine, northeast U.S.A., records the development of nearby upland vegetation throughout the Archaic, Ceramic, and Historic periods of human history. The Early Archaic period (9000 to 8000 B.P.) began as open woodland dominated by Picea, Populus, and Larix, which was replaced by Pinus forest. During the Middle Archaic (8000-6000 B.P.) Tsuga-dominated forest, which developed ca. 7400 B.P., was followed by Pinus forest (ca. 6400 B.P.). The Late Archaic (6000-3000 B.P.) was a period of great transition; Tsuga forest developed again ca. 5700 B.P., but was abruptly replaced by northern hardwood forest ca. 4700 B.P. That Late Archaic expansion of hardwoods would have provided better forage for beaver. Coincidentally, boreal wetland mammals such as beaver (Castor canadensis) and muskrat (Ondatra zibethicus) increase in faunal assemblages of local archaeological sites, while remains of anadromous fish decrease. We postulate that the apparent increase in human populations throughout the region during the Late Archaic may be attributed to an increase in the resource base within both upland and wetland areas resulting from the development of hardwood forest in response to climatic cooling.     

An evaluation of government‐recommended stocking systems for sustaining pastoral businesses and ecosystems of the Alpine Meadows of the Qinghai‐Tibetan Plateau

China introduced the “Retire Livestock and Restore Grassland” policy in 2003. It was strengthened in 2011 by additional funding for on‐farm structures. On the Qinghai‐Tibetan Plateau (QTP), fences were erected, livestock excluded from degraded areas, rotational stocking introduced, nighttime shelters were built, forages grown, and seed sown. However, the effectiveness of these actions and their value to Tibetan herders has been questioned. We conducted a sheep stocking experiment for 5 years in an Alpine Meadow region of the QTP to evaluate stocking options recommended by Government. Cold and warm season stocking each at three rates (0, 8, and 16 sheep/ha) and continuous stocking at 0 and 4 sheep/ha were compared. We measured live weights of sheep, plant species richness and evenness, root biomass and carbon (C), nitrogen (N) and phosphorus (P) contents of the 0–10 cm of soil. We found that resting grassland from stocking during the warm season for later cold season stocking significantly reduced plant species richness and evenness and root biomass but not soil C, N, and P. During cold season stocking, live weights of sheep declined whether at a stocking rate of 8 or 16 per ha. In contrast, sheep continuously stocked on grassland at 4 per ha gained weight throughout both the warm and cold seasons and plant species richness and evenness were maintained. Warm season stocking at 8 and 16 sheep/ha increased plant species richness and root biomass but reduced plant species evenness. Resting these alpine grasslands from stocking in the warm season has adverse consequences for plant conservation. Fencing from stocking in the warm season is not justified by this study; all grassland should be judiciously stocked during the warm season to maintain plant species richness. Neither resting nor stocking during the cold season appears to have any adverse consequences but sheltering and in‐door feeding of sheep during the cold season may be more profitable than cold season stocking with use of open nighttime yards.     

Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia

The association between demographic history, genealogy and geographical distribution of mitochondrial DNA cytochrome b haplotypes was studied in the wood lemming (Myopus schisticolor), a species that is closely associated with the boreal forest of the Eurasian taiga zone from Scandinavia to the Pacific coast. Except for a major phylogeographic discontinuity (0.9% nucleotide divergence) in southeastern Siberia, only shallow regional genetic structure was detected across northern Eurasia. Genetic signs of demographic expansions imply that successive range contractions and expansions on different spatial scales represented the primary historical events that shaped geographical patterns of genetic variation. Comparison of phylogeographic structure across a taxonomically diverse array of other species that are ecologically associated with the taiga forest revealed similar patterns and identified two general aspects. First, the major south-north phylogeographic discontinuity observed in five out of six species studied in southeastern Siberia and the Far East implies vicariant separation in two different refugial areas. The limited distribution range of the southeastern lineages provides no evidence of the importance of the putative southeastern refugial area for postglacial colonization of northern Eurasia by boreal forest species. Second, the lack of phylogeographic structure associated with significant reciprocal monophyly and genetic signatures of demographic expansion in all nine boreal forest animal species studied to date across most of northern Eurasia imply contraction of each species to a single refugial area during the late Pleistocene followed by range expansion on a continental scale. Similar phylogeographic patterns observed in this taxonomically diverse set of organisms with different life histories and dispersal potentials reflect the historical dynamics of their shared environment, the taiga forest in northern Eurasia.     

Genetic diversity,evolutionary history and implications for conservation of the lion (Panthera leo) in West and Central Africa

Aim In recent decades there has been a marked decline in the numbers of African lions (Panthera leo), especially in West Africa where the species is regionally endangered. Based on the climatological history of western Africa, we hypothesize that West and Central African lions have a unique evolutionary history, which is reflected by their genetic makeup. Location Sub‐Saharan Africa and India, with special focus on West and Central Africa. Method In this study 126 samples, throughout the lion’s complete geographic range, were subjected to phylogenetic analyses. DNA sequences of a mitochondrial region, containing cytochrome b, tRNAPro, tRNAThr and the left part of the control region, were analysed. Results Bayesian, maximum likelihood and maximum parsimony analyses consistently showed a distinction between lions from West and Central Africa and lions from southern and East Africa. West and Central African lions are more closely related to Asiatic lions than to the southern and East African lions. This can be explained by a Pleistocene extinction and subsequent recolonization of West Africa from refugia in the Middle East. This is further supported by the fact that the West and Central African clade shows relatively little genetic diversity and is therefore thought to be an evolutionarily young clade. Main conclusions The taxonomic division between an African and an Asian subspecies does not fully reflect the overall genetic diversity within lions. In order to conserve genetic diversity within the species, genetically distinct lineages should be prioritized. Understanding the geographic pattern of genetic diversity is key to developing conservation strategies, both for in situ management and for breeding of captive stocks.