Functional trait and community phylogenetic analyses reveal environmental filtering as the major determinant of assembly of tropical forest tree communities in the Western Ghats biodiversity hotspot in India

Background: Improved understanding of the processes shaping the assembly of tropical tree communities is crucial for gaining insights into the evolution of forest communities and biological diversity. The climate is thought to be the first order determinant of abundance and distribution patterns of tree species with contrasting traits such as evergreen and deciduous leaf phenology. However, the relative role of neutral, and niche-based processes in the evolution of these patterns remain poorly understood.Methods: Here, we perform an integrated analysis of the data on tree species abundance, functional traits and community phylogeny from a network of 96 forest plots, each 1 ha in size, distributed along a broad environmental gradient in the central Western Ghats, India. Then, we determine the relative importance of various process in assembly and structuring of tropical forest communities with evergreen and deciduous leaf phenology.Results: The deciduous leaf phenological trait has repeatedly evolved among multiple distantly related lineages. Tree communities in dry deciduous forests were phylogenetically clustered and showed a low range and variance of functional traits related to light harvesting, reproduction, and growth suggesting niche-based processes such as environmental filtering play a vital role in the assembly of tree communities in these forests. The external factors such as human-mediated disturbance also significantly, but to a lesser extent, influences the species and phylogenetic turnover.Conclusions: These findings revealed that the environmental filtering plays a significant role in assembly of tree communities in the biologically diverse tropical forests in the Western Ghats biodiversity hotspot.

Discovery of a wild,genetically pure Chinese giant salamander creates new conservation opportunities

Effective conservation of threatened biota relies on accurate assessments and scientific guidance.As an unfortunate example,Chinese giant salamanders(Andrias,CGS)remain critically endangered in nature.Misguided conservation efforts,e.g.,commercial propagation and releasing of millions of likely non-indigenous or interspecific hybrids,have further compromised conservation initiatives.Limited information on wild populations of CGS poses a significant conservation challenge.Following 18-month long field monitoring,we now report the discovery of a wild population of CGS in a closed nature reserve in Jiangxi Province,China.Genomic assessments reveal its genetic distinctiveness and do not detect genetic admixture with other species.Based on morphological and molecular evidences,we describe this CGS as a new species Andrias jiangxiensis sp.nov.This is the only known species of CGS today with a genetically pure,reproducing,in situ population.This discovery emphasizes the important role that closed nature reserves play in protecting species,and the necessity of integrating long-term field monitoring and genetic assessments.It sets a new pathway for discovering and conserving endangered species,especially for those biotas that are similarly being extirpated by anthropogenic translocations and overexploitation.

How many species of Apodemus and Rattus occur in China？ A survey based on mitochondrial cyt b and morphological analyses

Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their diversity.We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank.We also tested whether species could be identified using external and craniodental measurements exclusively.Measurements from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological comparisons.We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations.Results demonstrated that nine species of Apodemus and seven species of Rattus,plus a new subspecies of Rattus nitidus,are distributed in China.Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species.The occurrence of Rattus pyctoris in China remains uncertain.

Matrilineal History of the Rana longicrus Species Group(Rana,Ranidae,Anura) and the Description of a New Species from Hunan,southern China

Fieldwork in Jiemuxi National Nature Reserve, Hunan, China, discovered morphologically indis- tinguishable groups of brown frogs that bred at different, exclusive times of the year. A principal components analysis of morphometric data, molecular analyses, and the exclusive breeding season suggested the occurrence of two species. The population that breeds during the winter was found to be an undescribed species and was subsequently described as Rana jiemuxiensis sp. nov. The new cryptic species can be identified from its congeners at the same locality by having a different breeding season and a divergent DNA barcode, Six major lineages of brown frogs were resolved with high nodal support. Rana japonica, R. chaochiaoensis, R. omeimontis, and R. jiemuxiensis have independent maternal lineages. Rana hanlunica and R. maoershanensis have essentially identical maternal lineages and they appear to represent the same species. The validity of the species R. longicrus, R. zhenhaiensis, and R. culaiensis and their genealogical relationships are not resolved and deserve further study. The genealogy indicates that sympatric cryptic lineages probably widely exist in the R. longicrus group. This highlights the importance of future more fine-scaled samplings and the inclusion of nuclear genes.

Reproductive Behavior and Underwater Calls in the Emei Mustache Toad,Leptobrachium boringii

The Emei mustache toad, Leptobrachium boringii （Megophryidae）, is terrestrial but breeds in permanent streams. Primarily, it has a polygynous mating system and polyandry also occurs. The species vigorously defends submerged nest sites. We report on a reproductive study at Mt. Emei, western China conducted in 2004, 2006, 2007, 2009, and 2011 during the breeding season. Males produce both advertisement and courtship calls underwater, and the latter differs from the former in having an additional trill-like last note of low intensity. Females might determine the oviposition location and hence the egg mass location. A low, submissive posture can be adopted by the male to avoid being attacked by other males. When fighting, the maxillary nuptial spines are employed as weapons, and males hold their opponents on their spines with the forelimbs that enlarge during the breeding season. Male body size and the quantity of fight wounds on its ventral side are positively correlated. Satellite male mating might exist in L. boringii. Additionally, underwater calls from another population of this species and a population of L. leishanense generally are similar to those of the population from Mt. Emei.

Phylogenetic Relationships of the Genus Paramesotriton(Caudata: Salamandridae) with the Description of a New Species from Qixiling Nature Reserve, Jiangxi, Southeastern China and a Key to the species

The matrilineal genealogy of the genus Paramesotriton is hypothesized based on DNA sequences from mitochondrial NADH subunit two （ND2） and its flanking tRNAs （tRN^Arp and a partial tRNA^Ala）. The genealogy identifies a highly divergent, unnamed lineage from Qixiling Nature Reserve, Jiangxi, China and places it as the sister taxon of P. chinensis. The newly discovered population differs from other congeners by several features of external morphology including having large clusters of dark brown conical warts on the dorsum of the head, lateral surface of the body and dorsolateral ridges. Its intermittent dorsal vertebral ridge is the same color as other parts of the dorsum and tail narrows gradually from the base to the tip. Further, the new population differs from all congeners by an uncorrected P-distance of more than 9.38% in ND2. Consequently, we describe the new species of Asian warty newt （Salamandridae） as Paramesotriton qixilingensis sp. nov.

A new species of genus Fejervarya (Anura:Dicroglossidae) from northern Thailand

We describe a new species of frog in the dicroglossid genus Fejervarya from Ban Monjong, Omkoi District, Chiang Mai Province, northern Thailand. Analysis of DNA sequence data from the mitochondrial gene 16S, advertisement calls, and morphological distinctiveness support recognition of the new species. Matrilineal genealogy suggests that the new population from Chiang Mai is a sister taxon to the South Asian clade that includes F. syhadrensis, F. granosa, and F. pierreL The new species, Fejervarya chiangmaiensis sp. nov., differs morphologically from its congeners by its relatively small body size and proportions and the presence of dorsal warts and dermal ridges. Discovery of this new species indicates that the biodiversity of amphibians in this region remains underestimated.

Comparative multi-locus assessment of modern Asian newts(Cynops, Paramesotriton, and Pachytriton:Salamandridae) in southern China suggests a shared biogeographic history

Evolutionary biologists are always interested in deciphering the geographic context of diversification,therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region.Here, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asianendemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding,mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern China.Those ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP).Particularly,the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those newts.However,despite differences in realized niches between lineages,there is no evidence for divergence of fundamental niches.Preservation of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of speciation.Based on those results,we advocate a multi-pronged protection strategy for newts in the three genera.

A new species of the genus Xenophrys(Anura:Megophryidae) from northern Thailand

DEAR EDITOR,Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein we report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, which were identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other known congeners, and therefore we describe a new species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.

Matrilineal Genealogy of Hynobius (Caudata:Hynobiidae) and a Temporal Perspective on Varying Levels of Diversity among Lineages of Salamanders on the Japanese Islands

Previous work found that different Japanese lineages of salamanders had quite different levels of species and genetic diversity. Lineages vary from having one to several species and the extent of genetic variation among lineages differs substantially. Most speciose,genus Hynobius contains 18 species and several potential cryptic species. We explore genetic diversity in this genus by combining comprehensive sampling and mitochondrial DNA sequences. Based on this and previous analyses of salamanders,relative times of divergence are employed to evaluate the relationship between age and diversity among the four major lineages whose distributions broadly overlap on the islands. For Hynobius,our analyses are congruent with the previously reported high level of cryptic diversity in morphology and allozymes,particularly in species composed of non-sister matrilines. Both species and genetic diversity correlate with the relative ages of the lineages. This correlation indicates that the variation in levels of diversity can be explained,to a considerable extent,by the hypothesis that older insular lineages have accumulated greater diversity. In addition to the Korean Peninsula,H. leechii might have survived in another Pleistocene glacial refugium north of the peninsula and this refugium provided a source of colonization after the last glacial maximum.

Testing Hypotheses of Pleistocene Population History Using Coalescent Simulations: Refugial Isolation and Secondary Contact in Pseudepidalea raddei (Amphibia: Bufonidae)

The impact of the Quaternary glaciation on eastern China’s local fauna and flora is a topic of considerable interest. We use mitochondrial DNA(mtDNA) sequences and coalescent simulations to test two general biogeographic hypotheses related to the effect of the Pleistocene climatic fluctuations on a widespread, eastern Chinese amphibian, Pseudepidalea raddei. Genealogical reconstructions are made and they detect major western and eastern lineages, which overlap in northwestern China, and possibly indicate the secondary contact of the populations that had entered the region from separate glacial refugia. Coalescent tests rejected alternative hypotheses of fragmentation of either a widespread ancestor or panmixia. The tests instead supported the hypothesis of geographic isolation and a remarkable dispersal pattern in one of the lineages. Though the Pleistocene climatic events are known to have affected the historical distributions and intra-specific divergence of Chinese squamates, coalescent and non-coalescent demographic analyses indicated that the toad P. raddei was not adversely affected by glacial cycling. Presumably, an increase in the amount of climatically mild habitats in East Asia is due to the development of monsoons since the Mid-late Pleistocene is responsible for the relatively mild effects.

A new species of the genus Sinomicrurus(Serpentes:Elapidae)from China and Vietnam

DEAR EDITOR,A new species of Sinomicrurus Slowinski,Boundy,and Lawson,2001 is described herein based on a series of specimens.The new species,Sinomicrurus peinani sp.nov.,occurs in southern China and northern Vietnam.Sinomicrurus peinani sp.nov.is distinguished from its congeners by the following combination of characters:(1)30-35 black crossbands on body and tail;(2)13 dorsal scale rows throughout,all smooth;(3)white belly with black cross-bands or irregular spots;(4)broad white transverse bar on top of head with inverted V-shaped anterior margin,white bar wider than anterior black bar;and(5)frontal V-like,1.3 times as long as wide.In addition,new occurrences of S.houi in Guangxi,China,and Vietnam are discussed.

鼩鼹亚科(Talpidae:Uropsilinae)一新种

2006年至2009年,在四川西南地区开展小型兽类区系调查时,在普格县、美姑县、泸定县、九龙县采获了11号鼩鼹类标本。其外形和头骨形态与其他鼩鼹类一致,但牙齿数量和齿式与已知鼩鼹类不同。这批标本上、下颌牙齿均为9枚,齿式为i2/2,c1/1,pm3/3,m3/3=36,与少齿鼩鼹上颌9枚、下颌8枚(齿式:i2/1,c1/1,pm3/3,m3/3=34)不同,也不同于长吻鼩鼹与贡山鼩鼹(齿式:i2/1,c1/1,pm4/4,m3/3=38)及峨眉鼩鼹(齿式:i2/2,c1/1,pm4/3,m3/3=38)上颌10枚、下颌9枚,而不能归类于现有任何已知鼩鼹类物种。通过线粒体细胞色素b基因构建的系统发育关系显示未归类标本形成一单系群,且与峨眉鼩鼹关系最近,构成姊妹关系。为此,我们认为采自于四川普格县、美姑县、泸定县、九龙县的鼩鼹类标本为鼩鼹亚科一新物种。根据新种上、下颌牙齿数量相等命名为等齿鼩鼹(Uropsilus aequodonenia)。

基于18S基因序列的姬小蜂分子系统发育(英文)

本文基于18S rDNA部分序列,用MP和Baysian方法研究了姬小蜂科的系统发育,对姬小蜂科的单系性及其与其它小蜂科间的关系进行了讨论。姬小蜂亚科、灿姬小蜂亚科和啮姬小蜂亚科形成三个独立的支系,研究结果支持它们各自的单系性,但本结果没有明确姬小蜂科的单系性。研究结果同时还支持瑟姬小蜂族、扁股姬小蜂族和狭面姬小蜂族三个族的地位,但不支持姬小蜂族的地位。姬小蜂科的单系性及其与其它小蜂间的关系还需更多的形态学数据和更多的基因序列来进一步研究[动物学报52 (2) : 288 -301 , 2006]。

基于分子系统学的可疑瑟姬小蜂分类修订及姬小蜂亚科盾纵沟的演化分析(英文)

姬小蜂为寄生蜂的演化研究提供了很好的材料。在姬小蜂分类中,盾纵沟是一个重要性状,曾被用来区分亚科、族、属及种。非同源性相似形态特征的存在使得物种准确鉴定存在困难。从盾纵沟形状上,可疑瑟姬小蜂Cirrospilus ambiguus和双斑潜蝇姬小蜂Diglyphus bimaculatus应介于瑟姬小蜂属Cirrospilus和潜蝇姬小蜂属Diglyphus之间。确定这两种姬小蜂的系统发育位置将有助于分析盾纵沟的演化模式。本文用贝叶斯方法分析了线粒体COⅠ部分序列、核糖体ITS1序列及核糖体28S D2区部分序列等3个基因序列,结果显示可疑瑟姬小蜂应被移到潜蝇姬小蜂属中;研究结果支持潜蝇姬小蜂属是单系,而不支持瑟姬小蜂属是单系。结合28S D2区部分序列的贝叶斯分析结果,分析了在姬小蜂亚科中盾纵沟的演化模式。结果显示,完整且延伸到中胸背板后缘的盾纵沟代表其原始类型;完整且延伸到三角片的盾纵沟类型分别出现在5个独立的枝上,代表了该特征5次独立的演化;不完整的盾纵沟类型出现在4个独立的枝上,表明该类型独立演化了4次。

榕小蜂基因共表达研究(英文)

榕小蜂的雌雄个体之间存在很大表型差异,以至于很难将雌雄个体彼此联系在一起.以对叶榕传粉榕小蜂作为材料,利用"加权基因共表达网络分析"软件(WGCNA),对榕小蜂的基因组和转录组进行分析,结果发现,5个基因共表达模块,分别用蓝色、蓝绿色、棕色、绿色和黄色标识,其中2个模块偏爱在雌蜂中表达,3个模块偏爱在蛹中表达.基因本体(GO)分析发现在蓝绿色和黄色表达模块中发现3个功能富集的基因集合.在蓝绿色基因表达模块中发现2个基因集合,分别与细胞周期和核苷酸结合活性有关;在黄色基因表达模块中发现1个基因结合,与细胞分化有关,尤其是与神经发育有关.

Comparative Skin Histology of Frogs Reveals High-elevation Adaptation of the Tibetan Nanorana parkeri

Adaptations to extreme environmental conditions are intriguing. Animal skin, which directly interacts with external environment, plays diverse and important roles in adaptive evolution. The thin and bare skin of amphibians is sensitive to external environmental conditions and, thus, it facilitates investigations into adaptations for living in extreme environments. Herein, we compare the structures of skin in four anuran species living at elevations ranging from 100 m to 4500 m to assess phenotypic innovations in the skin of Nanorana parkeri, which lives at extremely high elevations. Analyses reveal similar basic skin structures, but N. parkeri differs from the other species by having more epidermal capillaries and granular glands, which correlate highly with responses to hypoxia and/or ultraviolet(UV) radiation. Further intraspecific comparisons from frogs taken at ~4500 m and ~2900 m reveal that all of the changes are fixed. Changes occurring only in the higher elevation population, such as possessing more skin pigments, may represent local adaptations to coldness and/or UV radiation. These results provide a morphological basis for understanding further the molecular adaptations of these frogs.

A new species of the genus Raorchestes(Anura:Rhacophoridae) from Yunnan Province, China

DEAR EDITOR,A new bush frog species, Raorchestes cangyuanensis sp. nov., from Cangyuan, Yunnan Province, China, is described based on morphological and molecular analyses. It differs from all known congeners by a combination of the following characters: body size small, adult snout-vent length (SVL) 16.1–20.0 mm in males (n=3);tympanum indistinct;tips of all fingers and toes expanded into discs with circummarginal grooves;rudimentary webbing between toes;fingers and toes with lateral dermal fringes;inner and outer metacarpal tubercles present;heels meeting when limbs held at right angles to body;crotch with a distinct black patch;discs of fingers and toes orange;male with external single subgular vocal sac and reddish nuptial pad at the base of first finger.

Molecular phylogeny of European and African Barbus and their West Asian relatives in the Cyprininae(Teleostei:Cypriniformes)and orogenesis of the Qinghai-Tibetan Plateau

The phylogenetic relationships of European and African Barbus and their West Asian relatives in Cyprininae remain largely unresolved.Consequently,little is known about the drivers of their evolution,including the possible association of uplifting of the Qinghai-Tibetan Plateau(QTP)with the early divergence of the subfamily.We use complete sequence data of the mitochondrial DNA gene encoding the protein cytochrome b(Cytb)to hypothesize the phylogeny of 85 species belonging to 47 genera in the Cyprininae plus 6 species from the Leuciscinae.We employ 6 other species from Cypriniformes as outgroup taxa and estimate divergence times.Our results indicate that European Barbus sensu stricto lineage including Aulopyge shares a common ancestor with specialized and highly specialized schizothoracins and the genera Cyprinion and Scaphiodonichtys.The common ancestor appears to have originated in the Qinghai-Tibetan Plateau(QTP)region about 19.4–17.8 Ma.Barbus sensu stricto lineage appears to have originated about 16.6–15.5 Ma.Small to medium sized African Barbus sensu lato appear to have had an Oriental origin about 19.1–15.3 Ma and are closely related to Asian Puntius.West Asian Carasobarbus lineage including large African Barbus sensu lato might have originated about 9.94 Ma,also in Oriental Realm and has a close relationship to Asian Neolissochilus and Tor.The large-sized Barbus sensu lato appear to have diverged from Carasobarbus about 7.7 Ma.Finally,the Cyprininae appear to have radiated rapidly into nine lineages and many sublineages from about 27.8 to 17.8 Ma,close to the time of the second-stage tectonic movements of the QTP.Our analyses provide evidence that the uplifting of the QTP drove early diversification of the Cyprininae.Our extensive sampling of species involving all of the important areas results in clear evolutionary scenario for the Cyprininae.

Conserved sequences identify the closest living relatives of primates

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.