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.     

中国四种鼯鼠的头骨形态学(英文)

针对长期以来有关鼯鼠分类地位的争议,该研究基于查看、测取60号鼯鼠成体头骨(每号头骨测取26个可量性状)共计1560个数据,运用多变量、单变量分析方法,对鼯鼠属(Petaurista)中的P.yunanensis,P.philippensis,P.hainana以及P.petaurista头骨可测量数据进行了统计学分析,以探讨上述4种鼯鼠的头骨形态差异以及P.yunanensis和P.hainana的分类地位。结果显示:(1)上述可测量头骨性状在该4种鼯鼠中不存在性二型现象;(2)上述4种鼯鼠在所测量的头骨性状上两两间均存在显著差异;(3)P.philippensis与P.hainana之间的头骨形态差异程度远大于P.yunanensis与P.philippensis之间的差异。该结果在宏观统计分析水平上为上述4种鼯鼠的种地位有效性提供了佐证,与前人基于分子水平(mtDNA)的种地位有效性研究结果相似。     

Phylogeography of two sympatric giant flying squirrel subspecies,Petaurista alborufus lena and P. philippensis grandis (Rodentia: Sciuridae), in Taiwan

To test the association between Pleistocene forest dynamics relative to elevation and the population dynamics of arboreal small mammals, we examined the phylogeographical predictions for the genetic structure of the red and white giant flying squirrel (Petaurista alborufus lena) and the Indian giant flying squirrel (P. philippensis grandis) using complete mitochondrial control region sequences. Both giant flying squirrels are endemic subspecies to Taiwan and are sympatric in much of their range. In the phylogenetic analyses, we included 35 specimens of P. alborufus lena collected from 20 localities and five specimens with unknown sampling localities. Also, we phylogenetically examined 32 specimens of P. philippensis grandis from 18 localities and three specimens with unknown sampling localities. We identified 36 haplotypes of P. alborufus lena and 33 haplotypes of P. philippensis grandis. Although we did not recognize major phylogroups, we found several minor phylogroups in both subspecies, suggesting similar evolutionary histories. Phylogeographical and demographic tests showed distributions of these two subspecies expanded into coniferous and mixed forests that developed during glaciation in Taiwan's lowlands and middle lands. This suggests that these two Petaurista subspecies shifted elevation from mountainous areas to lowlands during glaciation. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 404–419.     

Phylogenetic relationships among bumble bees (Bombus, latreille) inferred from mitochondrial cytochrome b and cytochrome oxidase I sequences

We conducted a molecular study intending to derive an estimate of the relationships within the genus Bombus (bumble bees) by comparing the mitochondrial cytochrome b and cytochrome oxidase I (COI) genes from 19 species, spanning 10 of approximately 16 European subgenera and 3 subgenera from North and South America. Our trees differ from the most recent classifications of bumble bees. Although bootstrap values for deep branches are low, our sequences show significant data structure and low homoplasy, and all trees share some groups and patterns. In all cases, the subgenus Bombus s. str. clusters among the most derived bumble bees, contrary to other molecular studies. In all trees, B. funebris is the sister taxon of B. robustus, and in five of the six trees, B. wurflenii is the sister taxon to this clade. B. nevadensis is basal to the other species in the analysis of the cytochrome b gene, but appears to be among the most derived according to the analysis of the COI region. The species representing the subgenera Thoracobombus and Fervidobombus are consistently among the earliest diverged. Species that appear in very different positions in different trees are B. nevadensis, B. mesomelas, B. balteatus, and B. hyperboreus. All subgenera with two representatives in our analysis are apparently monophyletic except Fervidobombus, Melanobombus, and Pyrobombus. The groups formed by pocket makers and non-pocket makers within Bombus also appear to be paraphyletic, and therefore some subgenera may not accurately reflect phylogeny.     

Phylogeography of the Japanese giant flying squirrel, Petaurista leucogenys (Rodentia: Sciuridae): implication of glacial refugia in an arboreal small mammal in the Japanese Islands

To test the association between temperate forest dynamics and glacial refugia for arboreal small mammals, we studied the phylogeography of the Japanese giant flying squirrel ( Petaurista leucogenys ) using complete mitochondrial cytochrome b gene sequences (1140 bp). This squirrel is endemic to three of Japan's main islands: Honshu, Shikoku, and Kyushu. We examined 58 specimens of P. leucogenys collected from 40 localities in Japan. Additionally, two individuals with unknown sampling localities were included in phylogenetic analyses. There were 54 haplotypes of P. leucogenys. We found five major phylogroups (Northern, Central, South-eastern, South-western, and Southern). These phylogroups may have originated from glacial refugia during the Late Pleistocene. After the last glaciation, the Northern phylogroup, widely distributed in eastern Japan, could have extensively expanded northward from its refugia. By contrast, in western Japan, population expansion was restricted to western Japan. All members of four phylogroups existed in western Japan during glaciations. The complicated phylogeographical pattern of P. leucogenys populations originating from western Japan may have resulted from the long history.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 47–60.     

Genetic tests of rapid parallel speciation of flightless birds from an extant volant ancestor

Prior to the extinction wave that followed the human colonization of Oceania, flightless rails (Aves: Rallidae) were among the largest radiations of island birds, and perhaps the most species-rich example of convergent evolution in vertebrates. Insular flightless species are thought to have evolved from extant, volant species that colonized from continental sources and rapidly followed parallel adaptive pathways to flightlessness. The present study provides the first test of this model of speciation using genetic data sampled throughout the range of a putative ancestral species. Mitochondrial control region sequences from 71 individuals of the Gallirallus philippensis species complex reveal essentially no geographic structure within archipelagos and only weak structure among archipelagos, with no major genetic breaks except for birds sampled in the Philippines. Demographic tests of coalescent models support a recent rapid expansion into Oceania (including Australia) out of the Philippines approximately 20 000 years ago. The estimated coalescence of G. philippensis mitochondrial alleles approximately 33 000 years ago closely corresponds to the expansion of humans into the archipelagoes of Near Oceania, suggesting that humans may have facilitated its colonization by exterminating flightless competitors and clearing lowland forests. Phylogenetic analyses that included all G. philippensis haplotypes and samples from 11 single-island endemic flightless species of Gallirallus indicate that G. philippensis is polyphyletic, but is not the ancestor of most of its flightless congeners, as previously thought. Nuclear gene sequences (β-actin inron 3) suggest that G. philippensis polyphyly is at least partly due to hybridization. The flightless condition evolves in rails before reproductive isolation is complete.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 601–616.     

Genetic differentiation of the gobies Gymnogobius castaneus and G. taranetzi in the region surrounding the sea of Japan as inferred from a mitochondrial gene genealogy

The phylogenetic relationships between gobies of the genus Gymnogobius were analyzed using mitochondrial cytochrome b gene sequences, focusing on the species currently classified as G. taranetzi and G. castaneus that occur in Japan, South Korea, and Russia. Gobies of the two species collected at 12 localities in Japan, South Korea, and Russia formed a monophyletic clade (called the "castaneus species complex" here) with G. breunigii as the sister clade. Within the species complex, six lineages were recognized: (L1) G. castaneus from the Akigawa River, Tokyo, Japan; (L2) G. castaneus from Yuza, Yamagata, Japan; (L3) G. taranetzi from Russia and South Korea; (L4) G. castaneus from the Tonegawa River, Chiba, Japan; (L5a) G. taranetzi from Shimane, Japan; and (L5b) G. castaneus + G. taranetzi from the Japan Sea coast of northern Japan. The two local lineages of G. castaneus (L1 and L2) are highly divergent from the others. The Japanese populations of G. taranetzi have diverged from the continental G. taranetzi populations, while one mitochondrial lineage (L5b) is shared with G. castaneus of northeast Japan. Therefore, the current species G. taranetzi and G. castaneus as defined morphologically are polyphyletic, necessitating a taxonomic revision. The genetic differentiation of isolated local lineages and the evolution of taranetzi-and castaneus-type gobies have likely occurred repeatedly in brackish/freshwater habitats around the Sea of Japan. We discussed the time of divergence for these gobies based on a tree with the molecular clock assumption.     

Ancient DNA analysis reveals woolly rhino evolutionary relationships

With ancient DNA technology, DNA sequences have been added to the list of characters available to infer the phyletic position of extinct species in evolutionary trees. We have sequenced the entire 12S rRNA and partial cytochrome b (cyt b) genes of one 60-70,000-year-old sample, and partial 12S rRNA and cyt b sequences of two 40-45,000-year-old samples of the extinct woolly rhinoceros (Coelodonta antiquitatis). Based on these two mitochondrial markers, phylogenetic analyses show that C. antiquitatis is most closely related to one of the three extant Asian rhinoceros species, Dicerorhinus sumatrensis. Calculations based on a molecular clock suggest that the lineage leading to C. antiquitatis and D. sumatrensis diverged in the Oligocene, 21-26 MYA. Both results agree with morphological models deduced from palaeontological data. Nuclear inserts of mitochondrial DNA were identified in the ancient specimens. These data should encourage the use of nuclear DNA in future ancient DNA studies. It also further establishes that the degraded nature of ancient DNA does not completely protect ancient DNA studies based on mitochondrial data from the problems associated with nuclear inserts.     

芍药属牡丹组基于形态学证据的系统发育关系分析

对芍药属牡丹组Paeonia L.sect.Moutan DC.（全部野生种）40个居群进行了基于形态学证据的系统学分析,试图建立组内种间的系统发育关系。利用PAUP （4.0）计算机程序分别构建了建立在25个形态学性状基础上的所有研究类群的距离树（UPGMA、NJ）和最大简约树（MP）。所得树的拓扑结构基本一致,差异只发生在距离树和简约树之间,在由形态和细胞学关系都很近的5个种（牡丹P.suffruticosa、矮牡丹P.jishanensis、卵叶牡丹P.qiui、紫斑牡丹P.rockii和凤丹P.o     

Molecular phylogenetics of Iberian wall lizards (Podarcis): is Podarcis hispanica a species complex?

Phylogenetic relationships between species and morphotypes of Podarcis wall lizards from the Iberian Peninsula and north Africa were estimated using partial 12S rRNA and cytochrome b mitochondrial DNA sequences. All species except Podarcis hispanica form monophyletic units. P. hispanica is paraphyletic, although all identified morphotypes are monophyletic. These morphotypes represent highly divergent lineages showing 10-15% pairwise sequence divergence with the cytochrome b gene. The data suggest that P. hispanica is a species complex. We recommend using P. hispanica* until additional sampling delimits the number and ranges of species currently referred to P. hispanica. P. carbonelli, which has recently been raised to species status, is confirmed as a genetically distinct form. P. atrata is genetically distinct, but much more closely related to some populations of P. hispanica than previously thought.     

Phylogeny and zoogeography of six squirrel species of the genus sciurus (mammalia, rodentia), inferred from cytochrome B gene sequences

To investigate the phylogenetic relationships between the New World Sciurus and the Old World Sciurus and their biogeographic history, the partial mitochondrial cytochrome b gene sequences (1,040 base pairs) were analyzed on six Sciurus species: S. aberti, S. carolinensis, S. lis, S. niger, S. stramineus, and S. vulgaris. Phylogenetic trees (maximum parsimony, neighbor-joining, and maximum likelihood methods) commonly showed two groups with high bootstrap values (73-100%): one consisting of the New World Sciurus and the other consisting of the Old World Sciurus. Genetic distances among the New World Sciurus species were remarkably larger than that between two Sciurus species of the Old World, suggesting the earlier radiation of the New World Sciurus than the Old World Sciurus.     

Taxonomic relationships and sampling effects among Lepilemuridae and Lemuridae using a partial cytochrome b gene

Partial cytochrome b sequences were used to study relationships between three Lepilemuridae species (Lepilemur dorsalis, L. septentrionalis and L. leucopus) and other Lemuridae species. L. dorsalis were subdivided into two sub-groups, according to their capture area (Nosy-Be island and Sahamalaza peninsula). Relationships deduced from phylogenetic trees as well as genetic distances lead to the classification of the Lepilemurs analysed here into separate species. These Lepilemurs form a monophyletic clade which is the sister clade of all other Lemurs used in this study. Reconstructions using randomly chosen sequences and step by step addition of sequences indicate that phylogenetic results for closely related species need to be analysed with caution, if only a small number of sequences are used to obtain them.     

朱鹮线粒体DNA的分子系统发育

朱Huan是一种濒危鸟类。过度开发和栖息地的破坏导致了朱Huan日本种群的绝灭,而在中国目前也仅存一野生种群。本文利用NJ法和最大简约法分析了鹳形目鸟类977bp的线粒体DNA细胞色素b基因的部分序列,以期从DNA水平上阐明朱Huan的系统地位。结果表明,朱Huan与彩Huan和非洲琶鹭组成一姐妹群;NJ法分析得出的结果与DNA杂交分析结果一致,即((Huan科,鹭科),鹳科);而最大简约法分析的结果则与形态学结果一致,即((鹭科,鹳科),Huan科)。同时,这两种系统树上较低的置信度,认为部分是由于可用细胞色素b基因序列的有限所致。     

Phylogenetic and taxonomic heterogeneity of Cryptococcus humicolus by analysis of the sequences of the internal transcribed spacer regions and 18S rDNA, and the phylogenetic relationships of C. humicolus, C. curvatus, and the genus Trichosporon

The phylogenetic and taxonomic heterogeneity of a rare opportunistic yeast pathogen, Cryptococcus humicolus, was revealed by analysis of the sequence of the internal transcribed spacer (ITS) region. Sixteen strains of C. humicolus showed a wide diversity in their ITS sequences. In addition, their 18S rDNA sequences were determined and used to analyze the phylogenetic relationships among C. humicolus and related yeasts. On trees constructed by the Neighbor-Joining and Maximum Parsimony methods, C. humicolus strains were phylogenetically closely related to each other with the exception of one strain, and they clustered with C. curvatus and Trichosporon species with high bootstrap values. Three C. humicolus strains obtained from humans belonged to the group of Trichosporon serotype I species. The results suggest that C. humicolus is a genetically heterogeneous species which should be reclassified on the basis of DNA sequence data.     

Relative patterns and rates of evolution in heron nuclear and mitochondrial DNA

Mitochondrial cytochrome b sequence data from 15 species of herons (Aves: Ardeidae), representing 13 genera, were compared with DNA hybridization data of single-copy nuclear DNA (scnDNA) from the same species in a taxonomic congruence assessment of heron phylogeny. The two data sets produced a partially resolved, completely congruent estimate of phylogeny with the following basic structure: (Tigrisoma, Cochlearius, (((Zebrilus, (Ixobrychus, Botaurus)), (((Ardea, Casmerodius), Bubulcus), ((Egretta thula, Egretta caerulea, Egretta tricolor), Syrigma), Butorides, Nycticorax, Nyctanassa)))). Because congruence indicated similar phylogenetic information in the two data sets, we used the relatively unsaturated DNA hybridization distances as surrogates of time to examine graphically the patterns and rates of change in cytochrome b distances. Cytochrome b distances were computed either from whole sequences or from partitioned sequences consisting of transitions, transversions, specific codon site positions, or specific protein-coding regions. These graphical comparisons indicated that unpartitioned cytochrome b has evolved at 5-10 times the rate of scnDNA. Third-position transversions appeared to offer the most useful sequence partition for phylogenetic analysis because of their relatively fast rate of substitution (two times that of scnDNA) and negligible saturation. We also examined lineage-based rates of evolution by comparing branch length patterns between the nuclear and cytochrome b trees. The degree of correlation in corresponding branch lengths between cytochrome b and DNA hybridization trees depended on DNA sequence partitioning. When cytochrome b sequences were not partitioned, branch lengths in the cytochrome b and DNA hybridization trees were not correlated. However, when cytochrome b sequences were reduced to third-position transversions (i.e., unsaturated, relatively fast changing data), branch lengths were correlated. This finding suggests that lineage-based rates of DNA evolution in nuclear and mitochondrial genomes are influenced by common causes.     

Phylogeographic analysis of the cornsnake (Elaphe guttata) complex as inferred from maximum likelihood and Bayesian analyses

Most phylogeographic studies have used maximum likelihood or maximum parsimony to infer phylogeny and bootstrap analysis to evaluate support for trees. Recently, Bayesian methods using Marlov chain Monte Carlo to search tree space and simultaneously estimate tree support have become popular due to its fast search speed and ability to create a posterior distribution of parameters of interest. Here, I present a study that utilizes Bayesian methods to infer phylogenetic relationships of the cornsnake (Elaphe guttata) complex using cytochrome b sequences. Examination of the posterior probability distributions confirms the existence of three geographic lineages. Additionally, there is no support for the monophyly of the subspecies of E. guttata. Results suggest the three geographic lineages partially conform to the ranges of previously defined subspecies, although Shimodaira-Hasegawa tests suggest that subspecies-constrained trees produce significantly poorer likelihood estimates than the most likely trees reflecting the evolution of three geographic assemblages. Based on molecular support, these three geographic assemblages are recognized as species using evolutionary species criteria: E. guttata, Elaphe slowinskii, and Elaphe emoryi [phylogeographic, maximum likelihood, maximum parsimony, bootstrap, Bayesian, Markov chain Monte Carlo, cornsnake, Cytochrome b, geographic lineages, E. guttta, E. slowinskii, and E. emoryi].     

Molecular Characterization of Tree Peony Germplasm Using Sequence-Related Amplified Polymorphism Markers

This study examined 63 tree peony specimens, consisting of 3 wild species and 63 cultivars, using sequence-related amplified polymorphism (SRAP) markers for the purpose of detecting genomic polymorphisms. Bulk DNA samples from each specimen were evaluated with 23 SRAP primer pairs. Among the 296 different amplicons, 262 were polymorphic. The maximum parsimony, neighbor-joining, and unweighted pair-group method using arithmetic average trees were largely in congruence. In the three trees, the wild species Paeonia ludlowii and P. delavayi formed separate clusters with strong bootstrap support, and P. ostii was closely related to all cultivars. The cultivars were divided into groups with various corresponding bootstrap values. The genetic similarity among the genotypes ranged from 0.02 to 0.73. These results demonstrate that SRAP markers are effective in detecting genomic polymorphisms in the tree peony and should be useful for linkage map construction and molecular marker assisted selection breeding. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular phylogenetic relationships of pond frogs distributed in the Palearctic region inferred from DNA sequences of mitochondrial 12S ribosomal RNA and cytochrome b genes

The evolutionary relationships of pond frogs distributed in the Far East and Europe were investigated by analyses of nucleotide sequences of mitochondrial 12S ribosomal RNA (12S rRNA) and cytochrome b (cyt b) genes. The nucleotide sequences of a 412-bp segment of the 12S rRNA gene and a 534-bp segment of the cyt b gene were determined by the PCR-direct sequencing method using 19 frogs belonging to six species and one subspecies distributed in the Palearctic region. Phylogenetic trees were constructed by the neighbor-joining and maximum-likelihood methods using Rana catesbeiana or Xenopus laevis as an outgroup. The 412-bp segment of the 12S rRNA gene contained 65 variable sites including gap sites, and the 534-bp segment of the cyt b gene contained 160 variable sites. The nucleotide sequence divergences of the 12S rRNA gene were 0.25-4.83% within the Far Eastern frogs, 0.25-6.22% within the European frogs, and 8.74-11.24% between the Far Eastern and the European frogs, whereas those of the cyt b gene were 3.64-14.73% within the Far Eastern frogs, 0.38-14.42% within the European frogs, and 16.53-23.58% between the Far Eastern and the European frogs. Although most nucleotide substitutions were at the third codon position of the cyt b gene and were silent mutations, 4 amino acid replacements occurred within the Far Eastern frogs, 4 within the European frogs, and 11 between the Far Eastern and the European frogs. The phylogenetic trees constructed from the nucleotide sequence divergences showed slightly different topologies for the 12S rRNA and cyt b genes. R. esculenta from Ukraine was closely related to R. lessonae from Luxembourg in both the 12S rRNA and the cyt b gene sequences.     

MONOPHYLY OF THE GENUS CLOSTERIUM AND THE ORDER DESMIDIALES (CHAROPHYCEAE, CHLOROPHYTA) INFERRED FROM NUCLEAR SMALL SUBUNIT rDNA DATA

We newly sequenced the nuclear-encoded small subunit (SSU) rDNA coding region for 21 taxa of the genus Closterium. The new sequences were integrated into an alignment with 13 known sequences of conjugating green algae representing six traditional families (i.e. Zygnemataceae, Mesotaeniaceae, Gonatozygaceae, Peniaceae, Closteriaceae, and Desmidiaceae) and five known charophycean sequences as outgroups. Both maximum likelihood and maximum parsimony analyses supported with high bootstrap values one large clade containing all placoderm desmids (Desmidiales). All the Closterium taxa formed one clade with 100% bootstrap support, indicating their monophyly, but not paraphyly, as suggested earlier. As to the taxa within the genus Closterium , we found two clades of morphologically closely related taxa in both maximum likelihood and maximum parsimony trees. They corresponded to the C. calosporum species complex and the C. moniliferum-ehrenbergii species complex. It is of particular interest that the homothallic entity of C. moniliferum v. moniliferum was distinguished from and ancestral to all other entities of the C. moniliferum-ehrenbergii species complex. Superimposing all 50 charophycean sequences on the higher order SSU rRNA structure model of Closterium , we investigated degrees of nucleotide conservation at a given position in the nucleotide sequence. A characteristic "signature" structure to the genus Closterium was found as an additional helix at the tip of V1 region. In addition, eight base deletions at the tip of helix 10 were found to be characteristic of the C. calosporum species complex, C. gracile , C. incurvum , C. pleurodermatum , and C. pusillum v. maius. These taxa formed one clade with an 82% bootstrap value in maximum parsimony analysis.     

Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences

To set the stage for historical analyses of the ecology and behavior of tree swallows and their allies (genus Tachycineta), we reconstructed the phylogeny of the nine Tachycineta species by comparing DNA sequences of six mitochondrial genes: Cytochrome b (990 base pairs), the second subunit of nicotinamide adenine dinucleotide dehydrogenase (839 base pairs), cytochrome oxidase II (85 base pairs), ATPase 8 (158 base pairs), tRNA-lysine (73 base pairs), and tRNA-methionine (25 base pairs). The phylogeny consisted of two main clades: South and Central American species ((T. stolzmanni, T. albilinea, T. albiventris), (T. leucorrhoa, T. meyeni)), and North American and Caribbean species (T. bicolor, (T. thalassina, T. euchrysea, T. cyaneoviridis)). The genetic distances among the species suggested that Tachycineta is a relatively old group compared to other New World swallow genera. One interesting biogeographic discovery was the close relationship between Caribbean and western North American taxa. This historical connection occurs in other groups of swallows and swifts as well. To reconstruct the phylogeny, we employed Bayesian as well as traditional maximum-likelihood methods. The Bayesian approach provided probability values for trees produced from the different genes and gene combinations, as well as probabilities of branches within those trees. We compared Bayesian and maximum-likelihood bootstrap branch support and found that all branches with Bayesian probabilities > or = 95% received bootstrap support >70%.