Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia : Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis

With modified DNA extraction and Purification protocols, the complete cytochrome b gene sequences (1140 bp) were determined from degraded museum specimens. Molecular analysis and morphological examination of cranial characteristics of the giant flying squirrels of Petaurista philippensis complex (P. grandis, P. hainana, and P. yunanensis) and other Petaurista species yielded new insights into long-standing controversies in the Petaurista systematics. Patterns of genetic variations and morphological differences observed in this study indicate that P. hainana, P. albiventer, and P. yunanensis can be recognized as distinct species, and P. grandis and P. petaurista are conspecific populations. Phylogenetic relationships reconstructed by using parsimony, likelihood, and Bayesian methods reveal that, with P. leucogenys as the basal branch, all Petaurista groups formed two distinct clades. Petaurista philippensis, P. hainana, P. yunanensis, and P. albiventer are clustered in the same clade, while P. grandis shows a close relationship to P. petaurista. Deduced divergence times based on Bayesian analysis and the transversional substitution at the third codon suggest that the retreating of glaciers and upheavals or movements of tectonic plates in the Pliocene-Pleistocene were the major factors responsible for the present geographical distributions of Petaurista groups. (c) 2005 Elsevier Inc. All rights reserved.

Phylogenetic relationships in genus Niviventer (Rodentia : Muridae) in China inferred from complete mitochondrial cytochrome b gene

Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, are a diverse group and have not yet received a thorough molecular phylogenetic analysis. Here, we reconstructed the phylogenetic relatio

Molecular phylogeny of five species of Dremomys (Rodentia : Sciuridae), inferred from cytochrome b gene sequences

Analyses of the mitochondrial cytochrome b gene (1140 bp) showed that Dremomys lokriah, D. pernyi, D. pyrrhomerus, D. rufigenis and D. gularis all are separate species. Dremomys pyrrhomerus showed 8.5% sequence variation from D. rufigenis, and the level o

Differentiation of subspecies of asiatic striped squirrels (Tamiops swinhoei) (Milne-Edwards) (Rodentia : Sciuridae) in China with description of a new subspecies

Based on the pelage characteristics and results of multivariate and univariate analyses, a new subspecies is described in this study, and a taxonomic revision of Tamiops swinhoei from China is presented. In total, 123 specimens of Tamiops swinhoei were in

Geographic variation of the Perny's Long-nosed squirrels (Dremomys pernyi) (Milne-Edwards, 1867) (Rodentia : Sciuridae) from southwestern China based on cranial morphometric variables

A sample of 114 specimens of Dremomys pernyi was investigated, 73 of which had intact skulls and were subjected to multivariate, coefficient of difference (C. D.), and cluster analyses. Results indicate that 4 subspecies (groups) of Dremomys pernyi inhabi

Geographic variation of the Anderson's Niviventer (Niviventer andersoni) (Thomas, 1911) (Rodentia: Muridae) of two new subspecies in China verified with cranial morphometric variables and pelage characteristics

A total of 66 specimens of Niviventer andersoni with intact skulls was investigated on pelage characteristics and cranial morphometric variables. The data were subjected to principal component analyses as well as to discriminant analyses, and measurement

Molecular phylogeny and biogeography of woolly flying squirrel (Rodentia : Sciuridae), inferred from mitochondrial cytochrome b gene sequences

To investigate the genetic diversity between the populations of woolly flying squirrels (Eupetaurus) from the eastern and western extremes of the Himalayas, partial mitochondrial cytochrome b gene sequences (390-810bp) that were determined from the museum specimens were analyzed using maximum parsimony (MP) and maximum likelihood (ML) methods. The molecular data reveal that the two specimens that were collected in northwestern Yunnan (China) are members of the genus Eupetaurus. Reconstructed phylogenetic relationships show that the populations of Eupetaurus in the eastern and western extremes of the Himalayas are two distinct species with significant genetic differences (12%) and diverged about 10.8 million years ago. Eupetaurus is significantly different from Petaurista and Pteromys. The level of estimated pairwise-sequence divergence observed between Eupetaurus and Petaurista or Pteromys is greater than that observed between Eupetaurus and Trogopterus, Belomys, Glaucomys, or Hylopetes. Considering the divergence time of the two Eupetaurus groups, the glaciations and the uplift of the Himalayas and Qinghai-Tibet plateau during the Pliocene-Pleistocene period might be the major factors affecting the present distribution of Eupetaurus along the Himalayas. (C) 2004 Elsevier Inc. All rights reserved.

Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: ( 1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; ( 2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks ( Tamias sibiricus), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (order Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

中国西南部明纹花鼠三个亚种的分化

明纹花鼠是东南亚地区的特有种, 在中国有3 亚种(阿萨姆亚种、滇西亚种、滇南亚种) , 分布于 藏东南、云南西南部和南部。以往主要根据外部形态特征进行分类。为探讨3 亚种头骨性状的差异, 在测量15 个性状的基础上, 运用统计分析软件SPSS 1110 对其可测量性状进行多变量分析。结果及推测如下: ①明纹花 鼠3 个亚种的地位是确定的。②在头骨15 个性状中, 两两亚种之间具有显著差异的性状: 阿萨姆亚种与滇西亚 种有8 个(枕鼻长、吻宽、颧宽、眶间宽、后头宽、鼻骨宽、下齿列、下颌骨高) ; 阿萨姆亚种与滇西亚种有7 个(颅全长、枕鼻长、颧宽、眶间宽、后头宽、下颌高、下颌骨高) ; 滇西亚种与滇南亚种有4 个(吻宽、后头 宽、鼻骨宽、下颌高) 。③滇南亚种与滇西亚种之间的亲缘关系近于两者各自与阿萨姆亚种之间的亲缘关系。

Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background: Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results: To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/ 21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion: Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

澜沧江姬鼠（Apodemus ilex）种群遗传结构及其生物地理分析

澜沧江姬鼠（Apodemus ilex）为小型啮齿类动物，长期以来常被认为是中华姬鼠（A. draco）或长尾姬鼠（A. orestes）的同物异名，但近年基于线粒体Cyt b 的研究证明，该类群与中华姬鼠的遗传距离达到了种间水平，并被认为是一个独立种。本文提取、扩增并测定了来自云南14个地区42个产地156个澜沧江姬鼠的Cyt b 全序列，并将GenBank中的3条澜沧江姬鼠的Cyt b 全序列纳入分析，选取福建武夷山与四川峨眉山的2个中华姬鼠样品的Cyt b 全序列，以及台湾姬鼠、大耳姬鼠、高山姬鼠Cyt b 全序列作为外群，利用贝叶斯法和最大似然法构建系统发育树，并使用Network分析，分子变异分析（AMOVA）分析、错配分析（Mismatch analysis）与Fu`Fs检验等方法，探讨了这些地区澜沧江姬鼠的种群遗传结构，种群动态及生物地理格局。结果表明：云南地区过去被鉴定为中华姬鼠的样品均属于澜沧江姬鼠，澜沧江姬鼠与中华姬鼠间的遗传距离（K2P-ds+v）达到0.091，显著超过姬鼠属内种间差距（0.080），支持澜沧江姬鼠独立种的地位；该种不同地理种群可大致以澜沧江为界分为两大支系，且每个支系又各分为两个亚支系；进一步的AMOVA分析表明遗传变异主要来源于两大支系之间，而错配分析与Fu`Fs检验表明澜沧江姬鼠各地理种群及其两个支系都经历过多次扩张事件，这可能是和冰期与间冰期的轮回交替有关；分子系统树和中介网络图表明地理环境的隔离对于澜沧江姬鼠种群分化存在明显影响，其中澜沧江的阻隔作用最为显著。基于松散分子钟（Relax molecular clock）分析，中华姬鼠和澜沧江姬鼠的分歧时间大约在2.98 Ma（95％HPD: 4.32-1.88），而澜沧江姬鼠则在1.13 Ma（95％HPD: 1.95-0.65）分成两个支系。按照平均分歧时间来看，澜沧江姬鼠两个支系的的分歧事件发生在鄱阳冰期（1.2-0.9 Ma），两个支系内部进一步分化为两支的时间非常接近，分别为：Clade 1中为0.67 Ma （95％HPD: 1.17-0.34）和Clade 2 中为0.64 Ma (95％HPD: 1.17-0.36)，这种隔离种群各自产生分化的时间却非常接近，这提示其分化事件可能是受到古气候如冰期或间冰期的影响所产生。