欧亚大陆广布物种的谱系地理研究:现状与发展趋势

广布物种的地理分布范围涉及欧亚大陆地区,主要分为4种模式:全球分布模式、全北区分布模式、欧亚大陆中高纬度分布模式以及欧亚大陆中低纬度分布模式.通过比较近年来欧亚大陆广布种的谱系地理学的研究结果,总结得出三种谱系地理格局:(ⅰ)"单一组分"格局;(ⅱ)"东-西组分"格局;(ⅲ)"边域组分"格局.本研究分析了欧亚大陆广布种的谱系地理格局形成的成因,主要包括以下三个方面:(ⅰ)物种本身较强的环境耐受力和扩散能力,以及受到人类的贸易、运输、驯养活动的影响;(ⅱ)东-西相异的更新世冰期气候和内陆干旱带来的影响:欧洲在冰期期间大部分区域被冰盖覆盖,物种退到避难所,间冰期物种从避难所向适宜生存的区域扩张,扩张时间大致在末次冰盛期后;亚洲大部分地区的冰期气候相对较为温和,尤其是亚洲东部并没有被大范围冰川覆盖,冰期对这些地区生物的分布格局影响相对较小;此外,由于更新世青藏高原的快速隆升及亚洲夏季风的增强,促进了欧亚大陆内陆干旱带的形成,从而起到长期生态隔离的作用;(ⅲ)边域种化的影响:种群扩散至分布边缘新环境,由于地理或新环境隔离,遗传漂变在小的隔离种群中固定下来,种群间产生遗传分化.通过分析欧亚大陆广布物种在相同地理、地质历史事件下的应对机制的独特性与一致性规律,有助于深入了解广布种在欧亚大陆的地理种群演化及种系发生的形成机制,能够更好地总结、完善整个欧亚大陆生物物种的谱系地理格局的多样性和普遍规律.最后,从大规模核基因组标记的应用和基于物种的生活史特征的预测谱系地理学两个方面对欧亚大陆广布物种的谱系地理学研究提出了展望.     

鸟类分子系统地理学研究进展

分子系统地理学是当代生物地理学的重要分支,是以分子生物学方法重建种内和种上水平的系统发育关系,阐释进化历史,并通过分析近缘生物类群的系统发育关系与其空间和时间分布格局间的相关性构建生物区系历史的研究,是分子生物学与生物地理学结合的产物。中性进化学说和溯祖理论分析的建立,以及线粒体DNA和微卫星标记等分子遗传标记的应用,为分子系统地理学研究的开展提供了理论和实践基础。近年来,分子系统地理方法在鸟类学研究中的应用揭示了许多不同于传统认知的发现,为准确而深入的了解鸟类分子系统地理格局的差异和不同类群的起源中心提供了新颖的证据。目前的研究多从隔离分化说和扩散说的角度对鸟类分子系统地理格局的成因进行分析,而迁徙行为不同对鸟类系统地理格局的影响为成因的解释提供了新的角度。结合区域特点的比较分子系统地理研究,在更广泛的地域和更多类群中开展研究是我国鸟类分子系统地理研究的方向。此外,展望了第二代测序技术对分子生态生物地理研究具有的潜在促进作用。     

陆栖哺乳动物的地理隔离研究进展

地理隔离是驱动物种分布格局形成的主要因素之一。本文回顾和总结了近几十年来地理隔离影响陆栖哺乳动物空间分布的研究成果, 从自然因素和人为因素两方面就地理隔离对物种分布的影响研究进展进行了综述。自然因素包括山脉、水体、沙漠和其他极端环境、气候变化等, 这些要素通常是在陆栖哺乳动物的缓慢演化进程中发挥作用; 人为因素侧重于因人类活动参与导致的物种分布变化, 包括景观结构变化、交通设施建设等, 在短短几百年甚至几十年内, 可以使物种分布特征发生显著变化。地理隔离对陆栖哺乳动物分布的作用是普遍而相对的, 长期存在且处于动态变化中。多种地理隔离因素之间的尺度效应不同, 哺乳动物在适应地理隔离的过程中表现出了生物个体和种群的响应过程。最后, 建议今后重点开展以下几方面的研究: (1)基于历史动物地理学与生态动物地理学, 深入研究地理隔离与动物地理边界形成的原因; (2)微观尺度下, 借助分子生物学和各种组学技术探讨地理隔离对物种遗传和适应机制的影响; (3)借鉴其他动物类群的研究经验, 加强对我国陆生哺乳动物的跟踪监测; (4)以数据驱动为导向, 将动物地理学与数据科学相结合, 以更好地分析动物分布的变迁史。     

植物区系地理研究现状及发展趋势

中国植物区系地理学在植物区系的调查、分布区类型的划分和研究、植物区系分区以及区域植物区系的分析等方面有了丰富的研究积累。但这些研究绝大部分是利用传统方法对植物物种或分类群数据进行统计分析,因此仍处于对区系现象的认识和描述阶段,缺乏空间格局形成过程、形成机制方面的深入探索。此外,还存在植物区系调查薄弱甚至是空白的地区,许多植物标本缺乏详细或精确的信息,植物物种鉴定的准确性还需要提高。同时,随着植物区系地理以及相关学科的快速发展,植物区系地理学的研究步入了多学科交叉融合、综合研究分析的阶段,学科界限趋于模糊。一方面,利用物种信息数据库,融合生态学、古植物学以及地质历史等探讨区系空间地理格局的成因;另一方面,结合系统发育、分子系统进化(甚至到进化基因组学)、生命之树以及分子生物地理学等揭示区系的起源和进化;同时,各学科的快速发展,产生了大量的数据,新的分析方法或新理论的出现和运用,使植物区系地理研究也进入到了大数据时代,进而使得植物区系地理研究由定性的现象认识和描述,逐步深入到了定量地解释区系现象和探索其形成机制的时代。     

新疆同域分布梭梭和白梭梭多样性格局及其形成机制

探究第四纪气候波动和地质事件对古尔班通古特沙漠同域分布的梭梭(Haloxylonammodendron)和白梭梭(H.persicum)分布、分化和演化的影响,对了解旱生植物区系的发展与演化具有重要意义。该研究测定新疆自然分布的19个梭梭种群225个个体和12个白梭梭种群106个个体叶绿体DNA间隔区(trn S-trn G和trn V)序列,整合单倍型网络分析、主坐标分析、分子方差分析、贝叶斯系统发育树、地理加权回归分析揭示种间、种内不同地理种群间的遗传多样性及其环境解释、空间遗传结构,估算种间谱系分化时间,分析群体演化历史。主要结果有:(1)共定义了21个叶绿体单倍型,梭梭和白梭梭聚为独立的支系;(2)接近80%的遗传变异发生于物种间及梭梭种内不同地理种群间,物种间分化发生于上新世晚期至更新世早期,这可能受干旱化加剧和沙漠形成、扩展的共同影响;(3)地理加权回归模型结果显示,环境因子对梭梭和白梭梭遗传多样性的影响存在明显的空间差异性,气候和土壤因子总体上主导梭梭、白梭梭的遗传多样性格局:在古尔班通古特沙漠南缘,气候因子对梭梭和白梭梭均为显著正向作用;在沙漠西南缘,气候因子对白梭梭为...     

青藏高原及其周边地区高山植物谱系地理学研究进展

青藏高原及其周边地区是世界上高山植物最丰富的地区,通过谱系地理学研究可以探讨高山植物演化历史与高原隆升和第四纪冰期的关系。根据对已经报道的36种高山植物的谱系地理分析,其谱系地理模式主要表现为:一、冰期退却到高原边缘的避难所,冰后期回迁到高原面;二、地理隔离造成冰期存在多处避难所(含微型避难所),冰后期发生局域性扩张。青藏高原在晚第三纪的快速隆升促进了物种的分化和成种,而第四纪冰期更是加剧了物种的快速分化,高原隆升和第四纪周期性气候波动是形成青藏高原高山植物现代谱系地理格局的主要原因。横断山脉地区作为第四纪冰期高山植物的主要避难所,在进化生物学和保护生物学方面具有重要启示。最后在物种选择、采样策略、基因片段选择和研究方法等4个方面提出青藏高原地区谱系地理学的研究方向。     

青藏高原兽类分布格局及动物地理区划

通过文献资料检索,依据Wilson和Reeder(2005)主编的兽类分类系统,共收集青藏高原兽类250种,分别隶属10目30科.将青藏高原各自然地理单元作为基本单元,根据兽类分布特点,采用Ward's方法对各基本单元进行聚类,结合自然地理条件,对青藏高原兽类动物地理分布格局进行了研究.结果为:(1)青藏高原的兽类中,古北界物种主要分布在羌塘及高原北部地区,该地区的古北界物种占高原全部古北界物种的88.6%;东洋界物种主要分布在藏南及横断山地区,该地区东洋界物种占高原全部东洋界物种的97.7%.(2)根据聚类分析结果.当连接距离为0.6219-1.0738时,将青藏高原划分为2个动物地理I级区,当连接距离为0.5034-0.6219时,划分为4个动物地理Ⅱ级区,当连接距离为0.2236～0.2684时,划分为7个动物地理Ⅲ级区,当连接距离为0.0930～0.1245时,划分为16个动物地理Ⅳ级区.(3)依据青藏高原兽类地理分布格局特点,结合青藏高原隆升对物种分布和自然生态环境的影响,探讨了高原兽类分布格局成因.研究表明,青藏高原兽类分布格局的形成与高原的自身演化密切相关.     

中国鸟类生物地理学研究回顾与展望

本文回顾总结了中国鸟类生物地理学的产生、发展、重要成果和未来的发展趋势。主要论述了以下五个方面:1.中国动物地理学简史及鸟类生物地理学的萌芽;2.鸟类动物地理区划的发展,并重点论述了岛屿鸟类区系调查与生物地理格局、中国台湾岛和海南岛与大陆鸟类区系的联系以及鸟类特有化现象;3.鸟类多样性的格局、形成与维持,并重点归纳了几种重要的科学假说;4.鸟类的谱系生物地理格局、形成原因及影响因素;5.鸟类生物地理学研究的新进展和未来发展趋势,重点阐述谱系生物地理学的发展、"地理格局-适应-基因"的整合分析方法对中国鸟类多样性格局形成机制的深度解析,指出大数据和组学时代是中国乃至世界鸟类生物地理学的发展趋势。     

多学科融合、多尺度探索——植物区系地理研究的新趋势

<正>植物区系地理学(Floristic Geography)是以植物分类学为基础,从空间格局(地理分布)上来探讨地球上或一定区域内植物的构成及其地理格局形成和起源演化过程的学科。当今的植物区系地理学研究正从两大方面发展:宏观上从地质历史–生态环境–植物群落–植物区系及大尺度空间格局方面探讨区系地理格局的成因;微观上从生命之树–物种形成–分子机制(基因组进化)揭示区系地理成分的     

土壤微生物生物地理学研究进展

生物地理学是研究生物（包括种群、群落等不同层次）地理分布格局及成因的一门交叉学科。微生物生物地理学的研究长期滞后于宏生物地理学。鉴于土壤微生物在调控生物地球化学过程和维持生态系统功能方面的重要作用,对其空间分布格局及形成机制的认识具有十分重要的理论和实际意义。随着分子生物学技术的发展,对微生物多样性的认知日益深入。越来越多的证据表明,土壤微生物群落结构和多样性具有一定的时空分布格局,从而对微生物全球性随机分布的传统观点提出了挑战。对当前土壤微生物生物地理学研究中的一些概念性问题,如微生物物种的定义、微生物多样性的定量测度、对微生物全球性随机分布的争论等,进行了系统评述;以微生物种-面积关系和距离-衰减关系为例对当前最新的土壤微生物生物地理学研究成果进行总结,并初步探讨了土壤微生物群落的地带性分布问题;在传统生物地理学理论的指导下,提出了一个可用于验证土壤微生物空间分布格局形成和机制维持的简单研究框架。这些对今后土壤微生物生物地理学的研究有一定借鉴和指导意义。     

分子系统地理学及其应用

分子系统地理学是20世纪70年代中期伴随着对线粒体DNA的认识而开始酝酿发展的,本文回顾了该学科自诞生以来的发展简史,阐述了其研究内容,着重从3个方面介绍了该领域在其它相关学科中的研究进展,总结了该学科存在的问题,并提出重点应解决的3个问题：1）将细胞器基因与遗传信息更为丰富的核基因相结合;2）合生理论在非平衡种群中的发展应用;3）提高对分化时间估计的精确性。     

Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled.     

The role of phylogeny in desert rodent community assembly

Recent advances in molecular genetics and phylogenetic reconstruction have the potential to transform ecology by providing new insights into the historical evolution of ecological communities. This study by Stevens and collaborators complements decades of previous research on desert rodents, by combining data from a field study and a phylogenetic tree for Mojave Desert rodents to address patterns and processes of community assembly. The number of coexisting rodent species is positively correlated, and the average phylogenetic distance among these species is negatively correlated with perennial plant species richness. As rodent species diversity increases along a gradient of increasing environmental heterogeneity, communities are composed of increasingly related species: there is a consistent pattern of phylogenetic structure from over-dispersed through random to clumped. I discuss this pattern in the light of complementary results of previous studies. This paper is noteworthy for calling attention to still unanswered questions about how the historical events of speciation, colonization, extinction, and trait evolution and their relationship to past climates and vegetation have given rise to current patterns of community organization.     

A new record and an evaluation of the phylogenetic relationships of Abrothrix olivaceus markhami (Rodentia: Sigmodontinae)

Recent phylogenetic studies of the subfamily of cricetid rodents (Sigmodntinae) have validated the taxonomic classification at the tribal level of the Andean Clade. It is possible that some endemic species from Patagonian South America are part of this new tribe, but previous studies have not evaluated this hypothesis due to the difficulty of obtaining samples. In this study, we evaluate the phylogenetic relationships of Akodon markhami (Pine, 1973), a species endemic to the Chilean Patagonia, using individuals recently captured at the type locality of this taxon. Our results indicate that this form of Akodon corresponds to a subspecies of Abrothrix olivaceus, and should be incorporated into the Andean Clade as a geographic race of this widely distributed species on the South American continent. Based on a molecular clock calibration, we dated the origin of this geographic race during the last glacial cycles of the Quaternary, as the result of a vicariant process.     

Marine turtle mitogenome phylogenetics and evolution

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.     

Phylogeographic patterns of steppe species in Eastern Central Europe: a review and the implications for conservation

The phylogeography of species associated with European steppes and extrazonal xeric grasslands is poorly understood. This paper summarizes the results of recent studies on the phylogeography and conservation genetics of animals (20 taxa of beetles, butterflies, reptiles and rodents) and flowering plants (18 taxa) of such, "steppic" habitats in Eastern Central Europe. Most species show a similar phylogeographic pattern: relatively high genetic similarity within regional groups of populations and moderate-to-high genetic distinctiveness of populations from currently isolated regions located in the studied area. This distinctiveness of populations suggests a survival here during glacial maxima, including areas north of the Bohemian Massif-Carpathians arc. Steppic species generally do not follow the paradigmatic patterns known for temperate biota (south-north “contraction–expansion”), but to some extent are similar to those of arctic-alpine taxa. There are three main groups of taxa within Eastern Central Europe that differ in their contemporary distribution pattern, which may reflect historical origin and expansion routes. Present diversity patterns of the studied steppic species suggest that they share a unique genetic signature and distinct assemblages exist in each of the now isolated areas rich in steppic habitats. At least some of these areas probably act as present “interglacial refugia” for steppic species. This study strongly supports the need to protect steppic species throughout their entire ranges in the region, as the continuous destruction of steppic habitats in some areas may lead not only to the disappearance of local populations, but also to the extinction of unique evolutionary units.     

Phylogeography of the Arctic-Alpine Saxifraga oppositifolia (Saxifragaceae) and some related taxa based on cpDNA and ITS sequence variation

Saxifraga oppositifolia (Saxifragaceae) is an important model system for the evolution of Arctic-Alpine plant species. Sequences of the psbA-trnH intergenic spacer of chloroplast DNA and of the internal transcribed spacer region, ITS1-5.8S-ITS2, of the nuclear ribosomal DNA were used to investigate the intraspecific evolution and phylogeography of this species. Samples from nearly the species' entire circumpolar distribution were included in the analysis as well as samples from the closely related taxa S. smalliana from Alaska and S. blepharophylla and S. biflora from the Alps (S. aizoides served as outgroup). These latter taxa showed a low number of parsimony informative characters, in both cpDNA and ITS sequences, which separated them from S. oppositifolia. Two main cpDNA haplotypes were detected within S. oppositifolia, one with a Eurasian distribution and one with an East Asian-North American distribution. This confirmed the existence of two cpDNA lineages with different geographical distributions in this species, which had previously been reported based on a RFLP analysis. The ITS phylogeny was not useful with respect to the intraspecific evolution and phylogeography of S. oppositifolia, because it showed a largely unresolved topology with low statistical support. The cpDNA sequence analysis, however, also suggested a putative long-distance dispersal event. All investigated taxa had cpDNA haplotypes that were congruent with their geographical origin rather than their phylogeny. This could point to putative lineage sorting in S. oppositifolia and related taxa.     

Comparative phylogeography of two open forest frogs from eastern Australia

We investigated the phylogeography of two closely related Australian frog species from open forest habitats, Limnodynastes tasmaniensis and L. peronii , using mitochondrial ND4 sequence data. Comparison of our results with previous work on Litoria fallax allowed us to test the generality of phylogeographic patterns among non-rainforest anurans along the east coast of Australia. In general, there was no strong evidence for congruence between overall patterns of genetic structure in the three species. However, phylogenetic breaks congruent with the position of the Burdekin Gap were detected at some level in all species. As previously noted for closed forest taxa, this area of dry habitat appears to have been an important influence on the evolution of several open forest taxa. There were broad geographic similarities in the phylogenetic structuring of southern populations of L. peronii and L. tasmaniensis. Contrarily, although the McPherson Range has previously been noted to coincide geographically with a major mtDNA phylogenetic break in Litoria fallax this pattern is not apparent in L. peronii or L. tasmaniensis. It appears that major phylogeographic splits within L. peronii and L. tasmaniensis may predate the Quaternary. We conclude that phylogeographies of open forest frogs are complex and more difficult to predict than for rainforest taxa, mainly due to an absence of palæomodels for historical distributions of non-rainforest habitats.     

Evolution of isochores in rodents

The most deviant isochore pattern within mammals was found in rat and mouse; most other mammals possess a different kind of isochore organization called the "general pattern." However, isochore patterns remain largely unknown in rodents other than mouse and rat. To investigate the taxonomic distribution of isochore patterns in rodents, we sequenced the nuclear gene LCAT (lecithin:cholesterol acyltransferase) from 17 rodents species (bringing the total of LCAT sequences in rodent to 19) and compared their GC contents at third codon positions and in introns. We also analyzed an extensive sequence database from rodents other than rat and mouse. All murid LCAT sequences are much poorer in GC than all nonrodent LCAT sequences, and the hamster sequence database shows exactly the same isochore pattern as rat and mouse. Thus, all murids share the same special isochore pattern--GC homogenization. LCAT sequences are GC-poor in hystricomorphs too, but the guinea pig sequence database indicates that large changes in GC content occur without an overall modification of the isochore pattern. This novel mode of isochore evolution is called GC reordering. LCAT sequences also show that the evolution of isochores in sciurids and glirids is nonconservative in comparison with that in nonrodents. Thus, at least two novel patterns of isochore evolution were found. No rodent investigated to date shared the general mammalian pattern.