Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci

Although homoploid hybridization is increasingly recognized as an important phenomenon in plant evolution, its evolutionary genetic mechanisms are poorly documented and understood. Pinus densata, a pine native to the Tibetan Plateau, represents a good example of a homoploid hybrid speciation facilitated by adaptation to extreme environment and ecological isolation from the parents. Its ecologically and reproductively stabilized nature offers excellent opportunity for studying genetic processes associated with hybrid speciation. In this study, we investigated the levels and patterns of nucleotide variation in P. densata and its putative parents. Haplotype composition, gene genealogies, and the levels and patterns of nucleotide variation gave further support to the hybrid nature of P. densata. Allelic history, as revealed by our data, suggests the ancient nature of the hybrid preceding elevation of the Tibetan Plateau. We detected more deviations from neutrality in P. densata than in the parental species. Thus, at least some of the evolutionary forces that have shaped the genetic variation in P. densata are likely to be different from those acting upon parental species. We speculate that when populations of P. densata invaded new territories, they had elevated rates of response to selection in order to develop traits that help them to survive and adapt in the new environments.     

Reexamining Phylloscopus trochiloides complex as a ring species: a refugial counter‐hypothesis

The idea of ring species has been viewed as a demonstration of the potential for species‐level differentiation produced by isolation by distance in otherwise continuous populations. Although the concept is attractive, the list of empirical examples has narrowed significantly as detailed studies have been carried out. One of the few examples still cited among birds is the warbler species complex Phylloscopus trochiloides, which comprises P. trochiloides sensu stricto, P. plumbeitarsus, and P. nitidus. The ring comprises a series of populations surrounding the Tibetan Plateau in which a species‐level break is apparent at the north end of the ring. Although recent theoretical treatments have indicated that such differentiation is possible in theory, recent genomic analyses indicated multiple differentiated populations around the ring unlikely to have resulted from isolation by distance. Here, we complement the genomic studies to date with paleodistributional projections of ecological niche models that provide further evidence for multiple, isolated refugia around the ring during and since the Late Pleistocene. As such, this group should not be interpreted as exemplifying an isolation‐by‐distance mechanism of speciation, and should no longer be considered as a ring species: genomic and geographic evidence coincide in indicating that its differentiation took place in allopatry.     

Paleodistribution modeling suggests glacial refugia in Scandinavia and out‐of‐Tibet range expansion of the Arctic fox

Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid‐Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.     

Accounting for regional niche variation in habitat suitability models

Ecological niche modeling has become an increasingly important tool to address issues in many fields of basic and applied ecology. The ecological niche space occupied across the geographic range, particularly for wide-ranging species, may vary for a variety of evolutionary and non-evolutionary reasons. However, ecological niche models are often applied over large geographic areas without regard for the potential effects of regional variation in adaptation, environmental conditions and their interactions, and species responses, thus significantly reducing their accuracy and utility. We develop regionally partitioned ecological niche models, using GARP, for the wide-ranging North American tree Gleditsia triacanthos (Fabaceae) . Models were constructed based on known tree occurrences at peripheral and range-centre locations, as well as across the geographic range as a whole.
Our results suggest that the niche space occupied by G. triacanthos varies regionally and that between some regions in particular there may be a complete absence of niche overlap. In particular, while there is some overlap between the niche space occupied by trees in the western and central regions of the range, there appears to be virtually no overlap in the niche space occupied by trees in the south of the range and that occupied by western and central trees. This lack of overlap appears to be driven primarily by regional differences in abiotic conditions, rather than regional adaptation per se. The results of our study have several important implications for the future development of habitat suitability models over large geographic areas. Spatial partitioning of data is clearly necessary to improve predictions of models where regional niche variation occurs. For wide-ranging species in particular, regional differences in ecological characteristics may cause apparent niche variation.     

高山松及其亲本种油松和云南松DHAR基因的功能分化

高山松(Pinus densata)是油松(P. tabulaeformis)与云南松(P. yunnanensis)自然杂交产生的同倍性杂种, 分布于青藏高原东南缘, 占据了油松和云南松两个亲本种都不能正常生长的高海拔地带。为了揭示高山松、油松和云南松脱氢抗坏血酸还原酶(DHAR)基因的组成和功能分化, 分别从高山松、油松和云南松中克隆到2类DHAR基因(DHAR1与DHAR2)。组织表达模式分析表明, 这6个基因在根、韧皮部、叶和芽中均有表达; 通过系统发育分析发现, 高山松在物种形成过程中保留了油松的DHAR1拷贝以及云南松的DHAR2拷贝; 酶学性质分析则表明, 高山松与油松DHAR1蛋白对底物具有相似的催化活性、催化效率、最适pH和热力学稳定性, 但其催化活性比云南松DHAR1蛋白高约300倍。高山松DHAR2蛋白对底物的催化活性和热力学稳定性均高于油松DHAR2蛋白。高山松DHAR基因在生化功能上显示出优于或类似亲本DHAR, 这种优势功能的选择与杂种独特的生态适应性可能有重要的相关性。     

Local adaptation versus historical isolation as sources of melanin‐based coloration in the white‐throated thrush Turdus assimilis

Local adaptation seems to be one of the causes of variation in melanin‐based colors in bird plumages, related mainly to the heterogeneity of the environmental conditions along the distribution of a species. Based on comparisons of genetic (mtDNA sequences), ecological (niche models), and quantitative colorimetric data, we explored variation in plumage coloration of the white‐throated thrush Turdus assimilis, a Mesoamerican species whose dorsal color varies from brown (northern and central Mexico) to dark gray (southern Mexico and Central America). Our results suggest the existence of two major patterns of coloration in this bird, which are congruent with the genetic structure, and comparisons of ecological niche models showed that population's niches were more similar than expected by chance, suggesting that color variation in plumage of T. assimilis is not consequence of local adaptation to different environmental conditions. Our results also showed that a greater geographic distance between populations is correlated with greater colorimetric differences, suggesting that color variation in T. assimilis may be consequence of historical isolation.     

Genetically informed ecological niche models improve climate change predictions

We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species’ ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species’ niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12‐fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change.     

同倍杂交种高山松与亲本种云南松的地理隔离研究

为了探讨横断山区同倍杂交种高山松与其亲本种云南松的地理隔离机制,采用实际的路线踏查方法,调查了高山松和云南松群体的地理分布情况和开花物候特征,并基于7个气象因子进行了聚类分析。调查研究表明高山松和云南松群体分布在不同的地貌类型中,以云南中甸为临界区,沿着金沙江河谷向北分布高山松,向南分布云南松。云南松的开花物候日期明显早于高山松,聚类分析表明两个物种分别聚为一支。在地质历史过程中,高大山系的形成以及海拔的升高将高山松和云南松从地理上隔离开来,两物种的适生区的气象因子的差异造成花期不遇,从而阻碍了两个物种问的基因交流,进而隔离开来。     

Maternal lineages of Pinus densata,a diploid hybrid

Previous morphological, allozyme and chloroplast DNA data have suggested that Pinus densata originated through hybridization between P. tabuliformis and P. yunnanensis. In the present study, sequence and restriction site analyses of maternally inherited mitochondrial nad1 intron were used to detect variation patterns in 19 populations of P. tabuliformis, P. yunnanensis and P. densata. A total of three mitotypes (A, B, C) were detected. All but one of the populations of P. yunnanensis possessed mitotype B while all populations of P. tabuliformis had mitotype A. Pinus densata populations, on the other hand, harboured both mitotypes A and B, which are characteristic of P. tabuliformis and P. yunnanensis, respectively. This result gives strong additional evidence supporting the hybrid origin of this diploid pine. The distribution of mitotypes indicated very different mating compositions and evolutionary history among P. densata populations. It seems that local founder populations and backcrosses may have played important roles in the early establishment of P. densata populations. The uplift of the Tibetan Plateau had a significant impact on the distribution of maternal lineages of P. densata populations.     

Influence of ammonium and nitrate supply on growth,nitrate reductase activity and N-use efficiency in a natural hybrid pine and its parents

Aims Selection of tree species with a high capacity to assimilate N and efficiently utilize N resources would facilitate the success of initial tree seedling establishment in infertile soils. The preference for N forms was tested using three pine species (Pinus densata, Pinus tabuliformis and Pinus yunnanensis). Pinus densata is a natural diploid hybrid between P. tabuliformis and P. yunnanensis .Methods Seedlings of three pine species were supplied with nitrate-N, ammonium-N (at two different pH regimes) or combined ammonium and nitrate as a nitrogen source in perlite culture in a controlled environment.Important findings Seedlings of P. densata had higher total biomass and net photosynthesis when supplied with nitrate-N and ammonium nitrate than with ammonium-N. In parental species, total biomass and net photosynthesis for P. yunnanensis seedlings was higher in ammonium-N than in nitrate-N, whereas the other parental species P. tabuliformis had the highest total biomass among species for all treatments except ammonium with CaCO 3. Most morphological traits in P. densata seedlings were intermediate between its two parental species. However, N-use efficiency and photosynthetic N-use efficiency of P. densata significantly exceeded both parents when supplied with nitrate-N and ammonium nitrate. The results suggested that the diploid hybrid tree species P. densata has a preference for nitrate and is not well adapted to ammonium-N as a sole nitrogen source regardless of the growth medium pH. Based on changes in environmental conditions, such as predicted future temperature increases in high altitude areas associated with climate change, P. densata is likely to be increasingly competitive and have wide adaptation in high altitude regions.     

Song variation in an avian ring species

Abstract.— Divergence of mating signals can occur rapidly and be of prime importance in causing reproductive isolation and speciation. A ring species, in which two reproductively isolated taxa are connected by a chain of intergrading populations, provides a rare opportunity to use spatial variation to reconstruct the history of divergence. I use geographic variation in the song of a likely ring species, the greenish warbler ( Phylloscopus trochiloides ) to reconstruct the microevolutionary steps that occurred during divergence of a trait that is often important in speciation in birds. Populations of a western Siberian ( P. t. viridanus ) and an eastern Siberian ( P. t. plumbeitarsus ) form of the greenish warbler meet, but do not interbreed in central Siberia; these forms are connected by a chain of interbreeding populations extending in a ring to the south around the treeless Tibetan Plateau. I show that: (1) song structure differs greatly between the two Siberian forms, which share the same habitat; (2) song structure changes gradually around the ring; (3) singing behavior is relatively simple in the Himalayas, but becomes increasingly complex to the north, both to the west and east of the Tibetan Plateau; and (4) song varies along independent axes of complexity in the western and eastern south-north clines. By comparing geographic variation in singing behavior and ecological variables, I distinguish among possible causes of song divergence, including selection based on the acoustic environment, stochastic effects of sexual selection, and selection for species recognition. I suggest that parallel south-to-north ecological gradients have caused a greater intensity of sexual selection on song in northern populations and that the stochastic effects of sexual selection have led to divergence in song structure.     

Genetic composition and diploid hybrid speciation of a high mountain pine, Pinus densata, native to the Tibetan plateau

Pinus densata has been suggested to have originated from hybridization events involving P. tabulaeformis and P. yunnanensis. In this study, allozyme differentiation at 12 loci was studied in 14 populations of P. tabulaeformis, P. densata, and P. yunnanensis from China. The observed genetic composition of P. densata supported the hybrid hypothesis and showed varying degrees of contribution from P. yunnanensis and P. tabulaeformis among its populations. These data, together with previous chloroplast DNA results, indicated different evolutionary histories among P. densata populations. To examine the possibility of ongoing hybridization among the three species, we analyzed patterns of linkage disequilibria between allozyme loci in ovule, pollen, and zygote pools. None of these tests suggested that there is significant ongoing gene exchange, implying that populations of P. densata have a stabilized hybrid nature. The normal fertility and high fecundity of P. densata indicate that this hybrid is maintained through sexual reproduction. P. densata represents an example of diploid hybrid speciation in an extreme ecological habitat that is both spatially and ecologically separated from that of its parents.     

Phylogeography of ground tit (Pseudopodoces humilis) based on mtDNA: evidence of past fragmentation on the Tibetan Plateau

Pseudopodoces humilis, a long misclassified terrestrial tit, is the only species of parid whose distribution is limited to treeless terrain and endemic to the Tibetan Plateau. We revealed the phylogeographic structure of the species by using mitochondrial control region, as well as comparing morphological characters. The distinct geographic distributions of two major clades suggest spatial and temporal separations that coincide with important climatic and paleogeographic changes following the uplift of the Tibetan Plateau. Population expansion was inferred for the population at the platform of the Plateau 0.17 million years before present (Ma B.P.), and restricted gene flow with isolation by distance was detected within this region, congruent with expansion occurring after the extensive glacial period. A significant decrease in body size with decreasing altitude was found, possibly indicating selection for larger-sized birds at higher altitude.     

The Pines and Pine Forests of Xizang

Six species of pines are distributed in Xizang. They are: Pinus griffithii McClell., P. armandi Franch. and P. gerardiana Wall. of haploxylon pines and P. densata Mast., P. yttnnanensis French. and P. roxburghii Sarg. of diploxylon pines. According to the relation of these pines with water-temperature conditions, 4 ecological types may be divided: the warm-temp erate and wet type (P. griffithii), the warm-temperate and dry type (P. yunnanensis, P. roxburghii), the temperate-cold and moist type (P. armandi) and the temperate-cold and dry type (P. densata). The composition and structure of every pine community reflect the ecological environments of the given pine in the region. The main pine comnmnity in Xizang are P. griffithii forest and P. densata forest. The P. griffithii forest is distributed on the southern side of Himalayas, while the P. densata forest on the northern side of Himalayas and the southern part of Hengtuan mountains. This indicates that the Himalaya range is a clear boundary and there is difference in water-temperature condition between southern and northern parts. They belong different vegetation regions. The different distribution of other several pine forests reflects the difference of environmental conditions within these two regions. These facts have significance in the investigation of the regularity of vegetation distribution and vegetation division in Xizang. Besides, the vertical distribution of pines cannot be used as a marker to divide the altitudinal belts due to the wide range of adaptation of pines, though there must be regularity of vertical distribution too.     

Recent Geological Events and Intrinsic Behavior Influence the Population Genetic Structure of the Chiru and Tibetan Gazelle on the Tibetan Plateau

The extent to which a species responds to environmental changes is mediated not only by extrinsic processes such as time and space, but also by species-specific ecology. The Qinghai-Tibetan Plateau uplifted approximately 3000 m and experienced at least four major glaciations during the Pleistocene epoch in the Quaternary Period. Consequently, the area experienced concurrent changes in geomorphological structure and climate. Two species, the Tibetan antelope (Pantholops hodgsonii, chiru) and Tibetan gazelle (Procapra picticaudata), both are endemic on the Qinghai-Tibetan Plateau, where their habitats overlap, but have different migratory behaviors: the chiru is inclined to have female-biased dispersal with a breeding migration during the calving season; in contrast, Tibetan gazelles are year-round residents and never migrate distantly. By using coalescence methods we compared mitochondrial control region DNA sequences and variation at nine microsatellite loci in these two species. Coalescent simulations indicate that the chiru and Tibetan gazelle do not share concordant patterns in their genealogies. The non-migratory Tibetan gazelle, that is more vulnerable to the impact of drastic geographic changes such as the elevation of the plateau, glaciations and so on, appears to have a strong population genetic structure with complicated demographic history. Specifically, the Tibetan gazelle population appears to have experienced isolation and divergence with population fluctuations since the Middle Pleistocene (0.781 Ma). However, it showed continued decline since the Upper Pleistocene (0.126 Ma), which may be attributed to the irreversible impact of increased human activities on the plateau. In contrast, the migratory chiru appears to have simply experienced population expansion. With substantial gene flow among regional populations, this species shows no historical population isolation and divergence. Thus, this study adds to many empirical studies that show historical and contemporary extrinsic and intrinsic processes shape the recent evolutionary history and population genetic structure of species.     

应用Maxent生态位模型预测淡水钩虾(甲壳纲,端足目)的分布(英文)

预测物种的适生区对于物种资源的评估、保护以及生物多样性的管理非常重要。由于全球气候变化和人类的过度开发,冷水性无脊椎动物的衰减速度比在陆地和海洋生活的无脊椎动物都要高。目前关于中国淡水钩虾分布方面的研究很少,本研究基于103个地表淡水钩虾的不同分布位点和广布种湖泊钩虾Gammarus lacustris 23个不同分布位点以及32个环境因子数据,使用生态位模型(Maxent)预测了淡水钩虾和湖泊钩虾在我国的适生分布区域。结果显示淡水钩虾非常适合分布在我国的一些偏远山区,如长白山、太行山、横断山、天山、昆仑山和祁连山,而青藏高原的东部、西部边缘地区和南部分布地区、尼泊尔、不丹和朝鲜半岛也是淡水钩虾的潜在适生区域,但淡水钩虾在我国华南、华中和华北的平原地区分布却很少,其在我国的潜在分布区与-10℃和5℃1月平均气温线间的区域相似。淡水钩虾是典型的狭温性物种,在不适宜温度条件下很难存活,这可能也是限制其扩散和存活的关键性因素。     

Pleistocene climatic fluctuations explain the disjunct distribution and complex phylogeographic structure of the Southern Red-backed Salamander, <Emphasis Type="Italic">Plethodon serratus</Emphasis>

The southeastern United States (U.S.) has experienced dynamic climatic changes over the past several million years that have impacted species distributions. In many cases, contiguous ranges were fragmented and a lack of gene flow between allopatric populations led to genetic divergence and speciation. The Southern Red-backed Salamander, Plethodon serratus, inhabits four widely disjunct regions of the southeastern U.S.: the southern Appalachian Mountains, the Ozark Plateau, the Ouachita Mountains, and the Southern Tertiary Uplands of central Louisiana. We integrated phylogenetic analysis of mitochondrial DNA sequences (1399 base pairs) with ecological niche modeling to test the hypothesis that climate fluctuations during the Pleistocene drove the isolation and divergence of disjunct populations of P. serratus. Appalachian, Ozark, and Louisiana populations each formed well-supported clades in our phylogeny. Ouachita Mountain populations sorted into two geographically distinct clades; one Ouachita clade was sister to the Louisiana clade whereas the other Ouachita clade grouped with the Appalachian and Ozark clades but relationships were unresolved. Plethodon serratus diverged from its sister taxon, P. sherando, ~5.4 million years ago (Ma), and lineage diversification within P. serratus occurred ~1.9–0.6 Ma (Pleistocene). Ecological niche models showed that the four geographic isolates of P. serratus are currently separated by unsuitable habitat, but the species was likely more continuously distributed during the colder climates of the Pleistocene. Our results support the hypothesis that climate-induced environmental changes during the Pleistocene played a dominant role in driving isolation and divergence of disjunct populations of P. serratus.     

A Dispersal and Vicariance Analysis of the Genus Caragana Fabr.

The genus Caragana Fabr., consisting of approximately 70 species, has a temperate Asian distribution and occurs mainly in the drought and cold regions of the northwestern and southwestern Tibetan Plateau of China. The distribution pattern of the genus was investigated using dispersal-vicariance analysis （DIVA）, The results indicate that vicariance versus dispersal plays a major role in the evolution of the genus and that short-distance dispersal also exists. There is no fossil record of this genus. Therefore, Caragana is inferred as an advanced taxon in terms of its limited temperate Asian distribution. Based on the morphological variation and ecological adaptation in Caragana, the generic speciation is postulated to be related to the uplifting of the Tibetan Plateau and to the increasing arid conditions of Central Asian lands since the Neogene. The Mongolian Plateau and the Tibetan Plateau are hypothesized as the barriers of vicariance between East Asia and western Central Asia.     

Analyzing niche stability and biogeography of Late Ordovician brachiopod species using ecological niche modeling

Gauging the potential impacts of environmental change on the geographic distributions of species is a central area of modern biogeographic analysis, often involving complex models of species–environment interactions. The geographic distribution of fossil species can also provide a framework to test the impact of environmental change on biogeography and ecological niches of species, yet few paleontological analyses have attacked this question in deep time. Herein we present a quantitative biogeographic analysis to examine the stability of ecological niches and geographic ranges of rhynchonelliform brachiopods during an interval of sea level change preserved in Upper Ordovician strata of the Cincinnati Arch.The intensive sampling, excellent preservation, and numerous prior paleoecological and sedimentological analyses within the tri-state region of Kentucky, Indiana, and Ohio provide a robust framework for detailed paleobiogeographic study. Quantitative biogeographic modeling methods incorporating GIS (Geographic Information Systems) are utilized in order to spatially analyze the geographic ranges of brachiopod species of the Corryville and Mt. Auburn Formations of the C3 (uppermost Maysvillian) depositional sequence.This study employs the ecological niche modeling program GARP (Genetic Algorithm using Rule-set Prediction) to predict the geographic distribution of eight brachiopod species during three time slices within the C3 sequence. This method estimates a species’ geographic range by modeling the ecological niche of the species based on a set of known species occurrence data coupled with environmental data inferred from sedimentologic proxies. Once environmental tolerances for a species are modeled; the species is predicted to occur wherever its preferred set of environmental conditions occurs within the study region.Distributional patterns were reconstructed for three time slices during the C3 sequence. Recovered range predictions were quantitatively analyzed for evidence of temporal range changes. Results indicate that average species range within the study area decreased and species tracked their preferred niche with high fidelity during the transition from the early to middle portions of the C3 depositional sequence, an interval of rapid relative sea level change. However, during the transition from the middle to late portions of the sequence, gradual shallowing within the basin and development of discontinuous habitat patches correlates with niche evolution of five of the eight species modeled. The average area a species occupied within the basin increased during this interval, but there is a mixed response including both increases and decreases in range size within the study group. In general, the species that exhibit niche evolution increased their geographic range size while those that continue to track their niche with high fidelity experience a decrease in geographic range size. During the latter half of the C3 sequence, previously continuous habitats become fragmented, thereby isolating individual populations and providing a mechanism for niche evolution. The rate of sea level change and the corresponding fragmentation of previously continuous habitats into isolated patches appear to be the primary controls on both mean geographic range size and relative degree of niche evolution.