Ontogenetic and evolutionary trends in the tooth enamel features in Craseomys voles (Arvicolinae,Rodentia)

In Craseomys rufocanus and Craseomys rex, the age-related and species differences in thickness and microstructure of the first lower molars (ml) have been identified and studied. The results suggest that the enamel dimensional and microstructural features may serve as additional indicators of the vole tooth evolutionary stage within a single phyletic lineage.     

Mitochondrial and nuclear DNA phylogenies reveal a complex evolutionary history in the Australasian robins (Passeriformes: Petroicidae)

The Australasian robins (Petroicidae) comprise a relatively homogeneous group of small to medium-sized insectivorous birds. Their center of diversity is Australia and New Guinea (40 species) but seven species have managed to colonize geographically distant islands such as Tanimbar, New Britain, New Zealand, New Caledonia, Norfolk Island, Vanuatu, Solomon Islands, Fiji and Samoa. To resolve the evolutionary relationships within the Petroicidae, we here present the results of a phylogenetic analysis of sequence data from two mitochondrial genes (ND2, CO1) and one nuclear intron (β-Fibrinogen intron 5) for all 14 genera and 40 of the 46 currently recognized species. All phylogenetic analyses identified six primary lineages, treated here as subfamilies, within the Petroicidae: (1) Eopsaltriinae comprising Eopsaltria (excluding E. flaviventris), Tregellasia, Peneothello, Melanodryas, Poecilodryas and Heteromyias; (2) Drymodinae comprising Drymodes; (3) Microecinae comprising Microeca, Monachella and Eopsaltria flaviventris; (4) Petroicinae comprising Petroica and Eugerygone; (5) Pachycephalopsinae comprising Pachycephalopsis; and (6) Amalocichlinae comprising Amalocichla. The genera Eopsaltria, Microeca, Peneothello and Poecilodryas were found to be paraphyletic. Based on assessments of phylogenetic branching patterns and/or DNA divergence it also was apparent that Eopsaltriaaustralis, Tregellasialeucops, Melanodryascucullata, Heteromyiasalbispecularis, Drymodessupercilious and Microecaflavigaster may each comprise more than one species. The Petroicidae display a complex biogeographical history involving repeated radiations both within, and across Australia and New Guinea. It appears that dispersal into smaller islands such as New Britain, Tanimbar and the South Pacific has only been undertaken by species with a "flycatcher" body form.     

Systematics of snow voles (Chionomys, Arvicolinae) revisited

To elucidate the evolutionary history of snow voles, genus Chionomys, we studied the phylogeography of Chionomysnivalis across its range and investigated its relationships with two congeneric species, Chionomysgud and Chionomysroberti, using independent molecular markers. Analyses were based on mitochondrial (~940 bp cyt b) and Y-chromosomal (~2020 bp from three introns) genetic variation. Our data provide conclusive evidence for a Caucasian and Middle Eastern origin for the three species and a subsequent westward expansion of C.nivalis. In addition, we discuss the taxonomic status of the genus Chionomys in relation to the genus Microtus.     

Phylogeny of Oriental voles (Rodentia: Muridae: Arvicolinae): molecular and morphological evidence

The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.     

Climatic niche conservatism and ecological opportunity in the explosive radiation of arvicoline rodents (Arvicolinae,Cricetidae)

Climatic niche conservatism shapes patterns of diversity in many taxonomic groups, while ecological opportunity (EO) can trigger rapid speciation that is less constrained by the amount of time a lineage has occupied a given habitat. These two processes are well studied, but limited research has considered their joint and relative roles in shaping diversity patterns. We characterized climatic and biogeographic variables for 102 species of arvicoline rodents (Arvicolinae, Cricetidae), testing the effects of climatic niche conservatism and EO on arvicoline diversification as lineages transitioned between biogeographic regions. We found that the amount of time a lineage has occupied a precipitation niche is positively correlated with diversity along a precipitation gradient, suggesting climatic niche conservatism. In contrast, shift in diversification rate explained diversity patterns along a temperature gradient. Our results suggest that an indirect relationship exists between temperature and diversification that is associated with EO as arvicoline rodents colonized warm Palearctic environments. Climatic niche conservatism alone did not fully explain diversity patterns under density‐dependence, highlighting the additional importance of EO‐related processes in promoting the explosive radiation in arvicoline rodents and shaping diversity pattern among biogeographic regions and along climatic gradients.     

Conflicting phylogenies of Larix (Pinaceae) based on cytoplasmic and nuclear DNA

The phylogeny of Larix species was studied using chloroplast DNA RFLPs and nuclear ITS sequences and AFLPs. The study resolved the sister relationships between the Eurasian and Asian species and the monophyletic origin of each major geographic group. It also provides strong evidence for an early splitting of American Larix from other species in the genus. The discrepancy between phylogenies based on chloroplast DNA and nuclear DNA, previously observed by Qian et al. [Can. J. For. Res. 25 (1995) 1197], is confirmed. Various explanations for the incongruence between chloroplast DNA and nuclear DNA are discussed, and a tentative reconstruction of Eurasian Larix phylogeography is proposed.     

Phylogeography and mitochondrial DNA (mtDNA) diversity in North American collared lemmings (Dicrostonyx groenlandicus)

Variation in the nucleotide sequence of the mitochondrial control region (250 bp) and the cytochrome b region (870 bp) was examined in collared lemmings (Dicrostonyx groenlandicus) from 19 localities in northern Alaska and the Canadian Arctic. The division of D. groenlandicus in two phylogeographical groups with limited divergence across the Mackenzie River is consistent with the separation of this species in more than one refugial area located to the northwest of the Laurentide ice sheet during the last glaciation. Populations of D.groenlandicus from formerly glaciated areas are no less variable than those in nonglaciated areas. Instead, the low intrapopulation and intraregional diversity estimates in D. groenlandicus are probably a result of regional bottleneck events due to range contractions during Holocene warming events. These results are consistent with findings previously reported on collared lemmings (D. torquatus) from the Eurasian Arctic.     

Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data

The phylogenetic relationships of the African lungfish (Protopterus dolloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapods were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelancanth clade was favored by maximum parsimony (although this result is dependent on which transition:transversion weights are applied), and a lungfish + tetrapod clade was supported by neighbor-joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of the third alternative, the coelacanth + tetrapod sister group relationship. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the complete mitochondrial sequence data were combined with nuclear 28S rRNA gene data, a lungfish + coelacanth clade was supported by maximum parsimony and maximum likelihood, but a lungfish + tetrapod clade was favored by neighbor-joining. The seeming conflicting results based on different data sets and phylogenetic methods were typically not statistically strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differences in rate of evolution of the different mitochondrial genes (slowly evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster substitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the lineages back in the Devonian, rather than base compositional biases among taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.     

Cryptic variation in mole voles Ellobius (Arvicolinae,Rodentia) of Mongolia

The mole vole subgenus Ellobius is currently considered to include three species: Ellobius talpinus (distributed from SE Europe and Turkmenistan through Kazakhstan to SW Siberia), Ellobius alaicus (S Tianshan, Pamir-Alay) and Ellobius tancrei (East and West Central Asia, from the Amu-Darya to Mongolia and N China). A study focusing on the genetic variation in Ellobius from Mongolia was conducted using one mitochondrial and three nuclear markers. Two divergent allopatric lineages endemic to East Central Asia were revealed. The first lineage occurs from Dzungaria eastwards to central Mongolia and represents E. tancrei sensu stricto. The second lineage is found in East Gobi only and corresponds to a taxon described as Ellobius orientalis, which has been traditionally treated as a subspecies of E. tancrei. However, molecular and chromosome data indicate that orientalis is related not to E. tancrei but to E. talpinus, which is separated from the former by a distribution gap of ~2,000 km. The taxonomic status of the East Gobi mole vole is ambiguous, and its genetic distance from E. talpinus s. str. falls into the range characteristic for closely related vole species or semi-species. According to molecular estimates, the two taxa have been isolated since the late Middle Pleistocene. A similar divergence is observed between the East and West Central Asian lineages of E. tancrei. E. alaicus is placed as sister to the latter rendering E. tancrei sensu lato paraphyletic. The revealed phylogeographic pattern implies that East Central Asia was colonized by mole voles through multiple eastward dispersal events.     

Multilocus phylogeny and taxonomy of East Asian voles Alexandromys (Rodentia,Arvicolinae)

Phylogenetic relationships, taxonomy and nomenclature issues within East Asian voles Alexandromys were addressed using comprehensive species samples, including all 12 valid species of the genus, and multilocus analysis. We examined the mitochondrial cytochrome b (cytb) gene and three nuclear genes in 36 specimens. Additionally, we examined a data set of 106 specimens using only the cytb gene. Our results did not confirm the aggregation of A. kikuchii, A. montebelli and A. oeconomus into a separate clade, namely the subgenus Pallasiinus. Analysis of incomplete lineage sorting using JML software highlighted both the cases of mitochondrial introgression and incomplete lineage sorting within the genus. Thus, the sister position of A. sachalinensis and A. maximowiczii in mitochondrial trees could be explained by mitochondrial introgression, while the sister position of A. limnophilus and A. fortis in mitochondrial trees could be successfully explained by incomplete lineage sorting. Very short genetic distances, together with an absence of monophyly, of the three species, A. evoronensis, A. mujanensis and A. maximowiczii, is supported by multiple morphological data, which indicates that these three taxa should be one species—A. maximowiczii. Analysis of genetic distances and tree topology revealed that three species of short‐tailed voles—A. middendorffii, A. mongolicus and A. gromovi—are more closely related to each other than to other established species of Alexandromys. The lacustrine vole, A. limnophilus, is closely related to the group of short‐tailed voles. Analysis of the type specimens of limnophilus and flaviventris confirmed that these taxa form one species together with A. l. malygini. Our results suggest that the mountains of western Mongolia are inhabited by a new taxon of short‐tailed voles of the same rank as middendorffii, mongolicus and gromovi—A. m. alpinus ssp. n.     

Parallel evolution in eight-barbel loaches of the genus Lefua (Balitoridae, Cypriniformes) revealed by mitochondrial and nuclear DNA phylogenies

The evolutionary history of eight-barbel loaches of the genus Lefua contains important phylogenetic information that will aid in resolution of the faunal formations and evolutionary histories of Japanese and East Asian freshwater fishes. Our sequencing of the mitochondrial D-loop region in a large number of samples allowed construction of the most comprehensive phylogeny of these loaches to date; we demonstrated monophyly of five Lefua species and identified populations of Lufua. sp. and Lefua echigonia. Loaches inhabiting the Tokai region in Japan were morphologically and ecologically indistinguishable from Lefua sp. However, they were included in the L. echigonia lineage. We determined a novel phylogeny by sequencing the nuclear ribosomal S7 subunit and showed that nuclear DNA phylogeny essentially matched the mitochondrial DNA phylogeny. Loaches from the Tokai region were part of the L. echigonia lineage, indicating parallel evolution between Tokai loaches and Lefua sp. in western Japan. We presented the most robust phylogeny to date using concatenated mitochondrial and nuclear sequences. The wealth of molecular information allowed us to speculate on evolutionary processes in the genus Lefua.     

Phylogeographic structure and mitochondrial DNA variation in true lemmings (Lemmus) from the Eurasian Arctic

The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochrome b region. These data are used to reveal the vicariant history of Lemmus , and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non-glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial-interglacial periods were crucial in the vicariant history of Lemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non-glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.     

Genetic diversity of Chionomys genus (Mammalia, Arvicolinae) and comparative phylogeography of snow voles

In the present study, the genetic polymorphism of the Chionomys genus was examined based on the sequencing of the mitochondrial cytb gene and two nuclear exons, including GHR exon 10 and BRCA1 exon 11. The distinct subdivision of the genus of snow voles into five lineages, including Ch. nivalis, Ch. gud, Ch. roberti, and Ch. aff. nivalis from Turkey, as well as Ch. aff. gud from Turkey, was demonstrated. The branching order in the trees constructed based on the data for different genes was ambiguous, which was probably the consequence of recent and rapid radiation of the major lineages from a common ancestor. However, the data of the mitochondrial and nuclear gene analyses definitely indicated that the genetic and taxonomic diversity of the Chionomys genus was higher than it was expected before. The genetic divergence of some populations was so deep that they probably deserved the statuses of independent species. Despite that the range of the European snow vole Ch. nivalis is larger and more fragmented than the Gudaur vole Ch. gud, the latter species with its relatively small range, which is limited to the Caucasian and Pontic Mountains, was characterized by a similarly expressed phylogenetic structure. At the same time, Robert’s vole Ch. roberti was less structured genetically than the first two species. The data obtained supported the Near Eastern, rather than the European origin of the Chionomys genus.     

DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys)

The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 bp in length. Our data were compatible with the proposal of three domains (extended terminal associated sequences [ETAS], central, conserved sequence blocks [CSB]) within the control region. The most conserved region in the control region was the central domain (12% of nucleotide positions variable), whereas in the ETAS and CSB domains, 22% and 40% of nucleotide positions were variable, respectively. Tandem repeats were encountered only in the ETAS domain of Clethrionomys rufocanus. This tandem repeat found in C. rufocanus was 24 bp in length and was located at the 5' end of the control region. Only two of the proposed CSB and ETAS elements appeared to be supported by our data; however, a "CSB1-like" element was also documented in the ETAS domain.     

Diversification of the North American shrub genus Ceanothus (Rhamnaceae): conflicting phylogenies from nuclear ribosomal DNA and chloroplast DNA

Ceanothus comprises ～55 morphologically and ecologically diverse species of woody perennials endemic to North America. Interpretations of the natural history of Ceanothus have served as a general model of evolution for woody perennials with simple entomophilous pollination systems, but these interpretations lacked explicit phylogenetic context. We used cladistic analysis of sequences of the chloroplast-encoded matK and the internal transcribed spacers (ITS) and 5.8S coding region of nuclear ribosomal DNA (nrDNA) to reconstruct the phylogeny of Ceanothus. The nuclear and organellar phylogenies exhibited very low levels of both topological and character congruence. Subgenera Ceanothus and Cerastes are monophyletic sister taxa in both phylogenies, but both data sets suffer from a lack of resolution below the level of subgenus. Lack of taxonomic congruence between the two data sets may be a result of introgression and/or lineage sorting. The ITS tree was accepted as the better estimate of a species phylogeny for Ceanothus, on the assumption that nuclear markers are less prone to introgression. Three of five polytypic species in the ITS data set were paraphyletic, and four of six polytypic species in the matK data set were paraphyletic. This study demonstrates the degree to which matched independent data sets can produce conflicting summaries of evolutionary history.