Revierges?nge ostasiatischer WeidenmeisenParus montanus und ihre mikroevolutive Ableitung

Territorial songs of 4 Asian Willow Tit subspecies namelyParus montanus kamtschatkensis, P. m. songarus, P. m. affinis andP. m. stoetzneri and in addition those of a southern outpost ofP. m. baicalensis are dealt with. These far-eastern subspecies use song types of their own, but nearly identical types may used by different geographical representatives, which are not closely related. The consequences for reconstructing the evolution of the Willow Tit complex by means of acoustical characters are discussed.     

Non-monophyly of the avian genus Seicercus (Aves: Sylviidae) revealed by mitochondrial DNA

The phylogeny of all species and nearly all subspecies of Seicercus and representatives of all subgenera in Phylloscopus was estimated based on two mitochondrial genes. According to the gene tree, and supported by non-molecular data, Seicercus belongs in three separate clades. Two of these include only taxa currently classified as Seicercus , while the third comprises S. xanthoschistos and P. occipitalis . These results suggest that both Seicercus and Phylloscopus are paraphyletic. The gene tree suggests two more cases of non-monophyly: (1) the ' S. burkii complex' is separated into two different clades, one of which also includes S. affinis and S. poliogenys ; (2) two populations of S. affinis intermedius are more closely related to S. affinis ocularis than to a third population of intermedius . A recent proposal to split the ' S. burkii complex' into six species is corroborated, as is the recognition of the taxon cognitus as a colour morph of S. affinis intermedius . Our study also revealed unexpectedly large genetic divergences between three different populations of the monotypic S. poliogenys , indicating the presence of cryptic species. Our results underscore the importance of dense sampling at the specific and infraspecific levels in intrageneric phylogenetic studies.     

Mitochondrial DNA and microsatellite analyses of the genetic status of the presumed subspecies Cervus elaphus montanus (Carpathian red deer)

The possibly distinct Carpathian red deer was compared genetically to other European populations. We screened 120 red deer specimens from Serbia, the Romanian lowland and the Romanian Carpathians for genetic variability using 582 bp of the mitochondrial control region and nine polymorphic nuclear microsatellite loci. The study aimed at a population genetic characterization of the Carpathian red deer, which are often treated as a distinct subspecies (Cervus elaphus montanus). The genetic integrity of the Carpathian populations was confirmed through the haplotype distribution, private alleles and genetic distances. The Carpathian red deer are thus identified as one of the few remaining natural populations of this species, deserving special attention among game and conservation biologists. The history of the populations studied, in particular the introduction of Carpathian red deer into Romanian lowland areas in the 20th century, was reflected by the genetic data.     

Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences

Salamander populations of the Plethodon jordani species complex form a challenging system for applying the general lineage concept of species to diagnose population-level lineages. The present study reports and analyses mitochondrial-DNA haplotypes (∼1200 nucleotide bases from the genes encoding ND2, tRNA^Trp, and tRNA^Ala from 438 salamanders) from 100 populations representing six species of the P. jordani complex ( Plethodon amplus , Plethodon cheoah , Plethodon jordani , Plethodon meridianus , Plethodon metcalfi , and Plethodon montanus ) with comparative analyses of previously published allozymic data to reconstruct the evolutionary history of this group and to diagnose species lineages. Analyses of mitochondrial haplotypic data include nested-cladistic analysis of phylogeography, analysis of molecular variance, hierarchical analysis of nucleotide-diversity measures, and likelihood-based estimates of recent temporal changes in population size. New analyses of allozymic data include multidimensional scaling and principal component analyses, and both data sets are analysed and compared for congruent genetic structure using Mantel correlation tests. These analyses in combination identify the six named species as distinct evolutionary lineages despite sporadic genetic exchanges among them and some discordance between mitochondrial DNA and allozymic markers. Sexual isolation is not complete for any pair of these six species, but they replace each other geographically and appear to block the geographical spreading of their neighbours. The P. jordani complex is a strong study system for investigating the genetic and ecological processes responsible for vicariant speciation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 25–51.     

Molecular phylogenetic analysis of the Grey-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: a case of remarkable genetic divergence in a "species"

The Grey-cheeked Fulvetta, Alcippe morrisonia, is a polytypic species of Quaker babbler (Timaliidae) occurring mainly in highlands from Burma across southern China to Taiwan. To examine gene flow among populations, we sequenced the mitochondrial ND2 gene of 39 individuals of six of the seven subspecies, plus multiple individuals of three outgroup Alcippe species. A lack of shared haplotypes and high FST values suggested no gene flow among populations. The nucleotide divergence between geographically juxtaposed subspecies ranged from 0.8% between Guangdong and Hainan to 9.4% between Yunnan and Vietnam. Phylogenetic analysis of the populations yielded a well resolved tree with two major clades. One clade consisted of the geographically central subspecies schaefferi and davidi, which are located largely in the "Mid-central" zoogeographic region of China's "Oriental" realm. The other clade, the geographically peripheral group, consisted of all other A. morrisonia subspecies, as well as an erstwhile outgroup, the Mountain Fulvetta (Alcippe peracensis annamensis) from central Vietnam. This peripheral group was further divided into two clades, one consisting of taxa occurring in China's "Southwest" zoogeographic region (fratercula and A. p. annamensis), and one occurring in China's "Southern" region (morrisonia, rufescentior, and hueti). These three geographic and phylogenetic groups represent at least four different species based on plumage differences and genetic differentiation. The phylogeny provides the first avian molecular evidence of area relationships among China's zoogeographic zones. It also highlights a remarkable and unexpected amount of genetic divergence and structure in a Sino-Indian "species". If such diversity occurs in other groups of birds with similar distribution, the ramifications are important for conservation planning.     

A mitochondrial-DNA-based phylogeny for some evolutionary-genetic model species of Colias butterflies (Lepidoptera, Pieridae)

We study the phylogenetic relationships among some North American Colias ("sulfur") butterflies, using mitochondrial gene sequences (ribosomal RNA, cytochrome oxidase I+II) totaling about 20% of the mitochondrial genome. We find that (1) the lowland species complex shows a branching order different from earlier views; (2) several montane and northern taxa may be more distinct than in earlier views; (3) one morphologically conservative Holarctic assemblage, C. hecla, is differentiated at the molecular-genetic level into at least three taxa which occupy distinct positions in the phylogeny and are sisters to diverse other taxa. These conclusions, constituting phylogenetic hypotheses, are supported by parsimony, maximum-likelihood, and Bayesian reconstruction algorithms. They are tested formally, by interior branch tests and paired-site tests, against alternative hypotheses derived from conventional species and subspecies naming combinations. In all cases our hypotheses are supported by these tests and the conventional alternatives are rejected. The "barcoding" subset of cytochrome oxidase I sequence identifies only some of the taxa supported by our full data set. Comparison of genetic divergence values among Colias taxa with those among related Pierid butterflies suggests that species radiations within Colias are comparatively younger. This emerging Colias phylogeny facilitates comparisons of genetic polymorphism and other adaptive mechanisms among taxa, thereby connecting micro- and macro-evolutionary processes.     

Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes

Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.     

Phylogeography and population genetic structure of double-crested cormorants (Phalacrocorax auritus)

We examined the genetic structure of double-crested cormorants (Phalacrocorax auritus) across their range in the United States and Canada. Sequences of the mitochondrial control region were analyzed for 248 cormorants from 23 breeding sites. Variation was also examined at eight microsatellite loci for 409 cormorants from the same sites. The mitochondrial and microsatellite data provided strong evidence that the Alaskan subspecies (P. a. cincinnatus) is genetically divergent from other populations in North America (net sequence divergence = 5.85 %; Φ_ST for mitochondrial control region = 0.708; F_ST for microsatellite loci = 0.052). Historical records, contemporary population estimates, and field observations are consistent with recognition of the Alaskan subspecies as distinct and potentially of conservation interest. Our data also indicated the presence of another divergent lineage, associated with the southwestern portion of the species range, as evidenced by highly unique haplotypes sampled in southern California. In contrast, there was little support for recognition of subspecies within the conterminous U.S. and Canada. Rather than genetically distinct regions corresponding to the putative subspecies [P. a. albociliatus (Pacific), P. a. auritus (Interior and North Atlantic), and P. a. floridanus (Southeast)], we observed a distribution of genetic variation consistent with a pattern of isolation by distance. This pattern implies that genetic differences across the range are due to geographic distance, rather than discrete subspecific breaks. Although three of the four traditional subspecies were not genetically distinct, possible demographic separation, habitat differences, and documented declines at some colonies within the regions, suggests that the Pacific and possibly North Atlantic portions of the breeding range may warrant differential consideration from the Interior and Southeast breeding regions.     

Molecular markers of nuclear DNA in the study of evolution and speciation process in an example of "Lacerta agilis complex" (Sauria: Lacertidae)

In order to elucidate the molecular-genetic relations of some Lacerta s. str. lizard populations, subspecies and species in comparison with some other genera we used methods revealing four types of nuclear DNA markers. Among these were taxonprint, RAPD, Inter-MIR-PCR markers and also satellite DNA monomer sequences. The aim was to compare the phylogeny and systematics of this reptilian group based on morphological and molecular criteria. This problem has a general importance for understanding a speciation process. Our results show a good correlation between both approaches when genera and species levels were studied. Systematic status of five subspecies of L. agilis were supported but not in all cases, some subspecies have no meaningful genetic differences by three types of molecular markers, but all of them were differed by RAPD markers. The data confirm the subdivision of L. agilis populations into west and east clades proposed by other authors earlier on the basis of mitochondrial DNA and morphology. The population structure of one of the subspecies--L. agilis exigua, was studied on a number of populations distributed from Ural region up to Kabardino-Balkaria by IMP method. There were no significant differences among these 14 populations investigated. The data testify the rapid distribution of the species after the end of Pleistocene glaciation.     

Genetic diversity among African great apes based on mitochondrial DNA sequences

The mitochondrial DNA D-Loop region was sequenced, analyzed and used as a molecular marker for populations of chimpanzee (Pan troglodytes), bonobo (P. paniscus) and gorilla (Gorilla gorilla and G. beringei), and also compared with data previously reported for these taxa. In Gorilla, a main disjunction between western (G. gorilla) and eastern (G. beringei, including G. b. graueri) species was observed, as well as high mitochondrial diversity within the western species. The genetic distance values within G. gorilla (0.14) were higher than those between subspecies (eastern lowland and mountain 0.12). Likewise, values of genetic diversity within this species (0.05) were higher than those between species (western and eastern lowland gorilla 0.04). Similarly, in genus Pan a main differentiation between western (P. t. verus) and central forms (P. t. troglodytes and P. t. schweinfurthii) was observed. The obtained values of genetic distance and genetic diversity revealed that the central subspecies are closer to each other than either of them is to the western one, while bonobos composed a distinct clade that expresses a well-defined specific identity. The current distribution, phylogeny and levels of genetic diversity in African great ape populations are consistent with the hypothesis that Pleistocene climatic events led to cyclical periods of isolation in forest refugia followed by expansion and dispersal. The implications of this high level of genetic diversity for taxonomic classification, wildlife management and conservation are discussed.     

Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex

We surveyed mitochondrial DNA (mtDNA) sequence variation in short-horned lizards (Phrynosoma douglasi) from throughout western North America and used these data to estimate an intraspecific phylogeny and to assess biogeographic scenarios underlying the geographic structure of lineages in this species. We sequenced 783 base pairs from 38 populations of P. douglasi and three putative outgroups (P. ditmarsi, P. orbiculare, P. platyrhinos). We detected high levels of nucleotide variation among populations and a spatial distribution of mtDNA lineages compatible with major geographic regions. The phylogenetic hypotheses best supported by the data suggest that P. douglasi, as currently described, is paraphyletic with respect to P. ditmarsi. Populations of P. douglasi from the Pacific Northwest (ID, CA, OR, WA) form a monophyletic group that is sister to the subsequent radiation of P. ditmarsi and other P. douglasi clades. These results suggest that divergences within this widespread species are fairly old. We focused on the genetic structure of populations of P. douglasi from a geographic perspective and interpreted the intraspecific phylogeny in light of geologic and climatic changes in western North America during the last 20 million years. The generally high levels of genetic variation found in these population comparisons are in accord with high levels of morphological variation in this species group; however, only in the Pacific Northwest region is there spatial congruence between these phylogenetic results and subspecific ranges based on previous morphological studies. We compared the evolutionary units delineated in this study with previously described subspecies of P. douglasi and evaluated the support (from morphology and mtDNA) for each population lineage in the phylogeny and the implications for the taxonomy of this group.     

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.     

棕颈钩嘴鹛分子系统发育及分类关系初探

棕颈钩嘴鹛(Pomatorhinus ruficollis)各亚种间系统发育关系一直存在分歧。该文测定了棕颈钩嘴鹛10个亚种20个样本的完整线粒体Cyt b和ND2基因序列(共2184bp),以棕颈钩嘴鹛(P.ruficollis)和灰头钩嘴鹛(P.schisticeps)为内群;栗背钩嘴鹛(P.montanus)、棕头钩嘴鹛(P.ochraceiceps)、红嘴钩嘴鹛(P.ferruginosus)和剑嘴鹛(Xiphirhynchus superciliaris)为外群,通过最大简约法、最大似然法以及贝叶斯推断法,构建了棕颈钩嘴鹛亚种间的系统发育树。结果显示:棕颈钩嘴鹛是并系群,灰头钩嘴鹛聚合在其内部;棕颈钩嘴鹛可分为3个地理支序,即中国西南部支序、中国东南部支序和中国中部支序;棕颈钩嘴鹛亚种间系统发育关系与形态特征不完全一致,并澄清了一些分类问题。     

Mitochondrial DNA diversification among the subspecies of the Silver and Kalij Pheasants, Lophura nycthemera and L. leucomelanos, Phasianidae

The taxonomic status of the pheasant superspecies Lophura leucomelanos and Lophura nycthemera has been unclear since 1948. Molecular techniques provided the opportunity to clarify the situation. Using sequences of mitochondrial DNA (800 nucleotides from the D-loop, plus 400 from the cyt b ) from 49 specimens belonging to 10 subspecies (plus two outgroups), we constructed a phylogeny of the subspecies of L. nycthemera and L. leucomelanos . Our data support the monophyly of both species. L. l. lineata and L. l. crawfurdi belong to L. leucomelanos and not to L. nycthemera (suggested by other authors). Our data also confirm a northern locality of origin (Central Buthan) for L. l. moffitti , and have clarified the relationships between subspecies within each species: there are three groups within L. leucomelanos and two within L. nycthemera .     

Radiation and phylogeography in the Japanese macaque, Macaca fuscata

The Japanese macaque (Macaca fuscata) presumably differentiated from eastern rhesus macaque (Macaca mulatta) populations during the Pleistocene and the two species are closely related. In order to analyse speciation and subspeciation events in the Japanese macaque and to describe historical and current relationships among their populations, we sequenced and analysed a fragment of 392bp of mitochondrial DNA (mtDNA) control region in 50 individuals belonging to six populations of Japanese macaque and compared these sequences with 89 eastern rhesus macaque control region sequences from GenBank/EMBL database. There were high genetic similarities between both species and only two positions were fixed within each species, which supports the inclusion of the Japanese macaque in a single species with eastern populations of rhesus macaques. Japanese macaque ancestors colonised Japan after the separation of the two species, estimated at between 0.31 and 0.88 million years ago (Mya). The star-like phylogeny, multimodal mismatch distribution, and lack of correlation between geographic and genetic distances are in accordance with a rapid dispersion of macaques throughout the archipelago after the arrival into Japan. The species shows low genetic variation within populations and high levels of genetic differentiation among populations with no mtDNA haplotype shared across populations. Genetic distances between Yakushima macaques (Macaca fuscata yakui) and any other population of Macaca fuscata fuscata subspecies are comparable to the distances between populations of Honshu, Awajishima, and Kyushu, not supporting the classification of Yakushima macaques as a different subspecies.     

MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF PEROGNATHUS AMPLUS AND PEROGNATHUS LONGIMEMBRIS (RODENTIA: HETEROMYIDAE): A POSSIBLE MAMMALIAN RING SPECIES

Substantiated cases of ring species in mammals are rare. I examined the variation in mitochondrial DNA (mtDNA) of Perognathus amplus and P. longimembris in and around Arizona to test the hypothesis proposed by Hoffmeister (1986) that these two taxa are members of a single ring species demonstrating circular overlap. Through digestion of purified mtDNA from 45 P. amplus and 35 P. longimembris with 16 type II restriction enzymes, I identified 38 distinct haplotypes that belong to eight different evolutionary lineages. I then amplified and directly sequenced a portion of the mitochondrial cytochrome-b region from individuals representative of the lineages identified by restriction fragments, and used these data for phylogeny reconstruction in both a parsimony and neighbor-joining setting. The resulting phylogeny was consistent with the ring hypothesis, but, based on the incompleteness of the ring of subspecies and the apparent timing of evolutionary events in this group, I conclude that P. amplus and P. longimembris are distinct lineages that have completed the speciation process.     

Investigating Concordance among Genetic Data, Subspecies Circumscriptions and Hostplant Use in the Nymphalid Butterfly Polygonia faunus

Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly Polygonia faunus are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of P. faunus and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in P. faunus do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species.     

Evolution and genetic structure of the great tit (Parus major) complex

The great tit complex is divided into four groups, each containing several subspecies. Even though the groups are known to differ markedly on morphological, vocal and behavioural characters, some hybridization occurs in the regions where they meet. The great tit has often been referred to as an example of a ring species, although this has later been questioned. Here, we have studied the genetic structure and phylogenetic relationships of the subspecies groups to clarify the evolutionary history of the complex using control region sequences of the mitochondrial DNA. The subspecies groups were found to be monophyletic and clearly distinct in mitochondrial haplotypes, and therefore must have had long-independent evolutionary histories. This conflicts with the ring species assignment and supports the formation of secondary contact zones of previously temporarily isolated groups. According to the phylogenetic species concept, all the subspecies groups could be considered as separate species, but if the definition of the biological species concept is followed, none of the subspecies groups is a true species because hybridization still occurs.     

Distinct specific status of the Korean brown frog, Rana amurensis coreana (Amphibia: Ranidae)

We used morphological and genetic data to assess the taxonomic status of Rana amurensis coreana and R. a. amurensis. Morphological comparisons revealed these two subspecies to be different from each other in size of body, nature of tubercles on dorsal stripe, degree of development in toe webbing, and condition of lateral spots of trunk. They were also different in sequence of mitochondrial 16S rRNA gene, with genetic distance as large as those observed among different species of brown frogs. Therefore, Korean populations previously considered a subspecies of R. amurensis should be regarded as a distinct species (=R. coreana).     

Phylogenetic reconstruction of the Drosophila obscura group, on the basis of mitochondrial DNA

We have constructed restriction-site maps of the mtDNAs in 13 species and one subspecies of the Drosophila obscura group. The traditional division of this group into two subgroups (affinis and obscura) does not correspond to the phylogeny of the group, which shows two well- defined clusters (the Nearctic affinis and pseudoobscura subgroups) plus a very heterogeneous set of anciently diverged species (the Palearctic obscura subgroup). The mtDNA of Drosophila exhibits a tendency to evolve toward high A+T values. This leads to a "saturation" effect that (1) begets an apparent decrease in the rate of evolution as the time since the divergence of taxa increases and (2) reduces the value that mtDNA restriction analysis has for the phylogenetic reconstruction of Drosophila species that are not closely related.