Genetic structure of diploid-polyploid complex of spined loaches Cobitis (Cypriniformes, Cobitidae) of the Danube delta

The unusually high diversity of spined loache biotypes in Lower Danube was detected by means of biochemical genetic investigation and cytometric analysis of 358 specimens collected in riverbed and eriks. Along with two diploid species (C. elongatoides and C. "tanaitica") six hybrid forms were revealed: diploid C. elongatoides "tanaitica"; triploid C. 2 elongatoides--"tanaitica", C. elongatoides--2 "tanaitica" and C. 2 elongatoides--species-1 and tetraploid C. 3 elongatoides--"tanaitica", C. elongatoides--species-2--2 "tanaitica". Besides that the specimens with recombinant genotypes occured. In spite of the apomictic mode of reproduction the poliploids do not possess the clonal structure but according to the level of polymorphism and the genotype distribution are isomorphous to the parental diploid species. This means that on the contrary to the polyploid cobitids of the Dnieper which have appeared in this catchment area due to the expansion of their home range the polyploid fishes from the Lower Danube reaches are autochtonous and are produced as a result of hybridization with the local diploid species. The process is seemingly going on without any kind of limitations.     

Genetic diversity, origin, and geographic distribution tendencies of biotypes of polyploid spined loaches (Cypriniformes, Cobitidae, Cobitis) in Ukraine

Sixteen of 28 possible biotypes of C. elongatoides-taenia s.lato (C. taenia, C. tanaitica, C. species-1) have been found in Ukrainian waters. Presumably, the biotypes of C. aff. melanoleuca-tanaitica has also been identified. The share of polyploids among Cobitis on average was 65%, where males made up less than 1% with the same ratio among tri- and tetra-polyploids. The absence of amphydiploidy and presence of individuals with recombinant genotype and abnormal electrophoretic specters, whose frequency sometimes is considerable, are attracting increasing interest. There are two centers of polyploid biotypes creation: southern (the Lower Danube) and northern (the Upper Danube, Oder, and Rhine). The C. taenia and C. species-1 type, which is typical for the northwestern basins of Ukraine, participates in the formation of polyploids in the Rhine alongside with C. elongatoides and C. tanaitica. It is determined that biotypes (C. 2(3) elongatoidestanaitica, C. elongatoides-2(3) tanaitica) in comparison with biotypes whose genome includes the chromosome set of C. taenia are limited in distribution towards the East. This is due to the hybridization of females from these biotypes with males of C. taenia afflicted by genetic instability and reduced viability of posterity.     

Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeri Smith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis [ Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade { Philautus odontotarsus Ye & Fei, 1993, [ Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma , so as to correct the paraphyly. Additionally, the monophyly of ' Aquixalus ' is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/ Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 733–749.     

Molecular phylogeny and historical biogeography of Caltha (Ranunculaceae) based on analyses of multiple nuclear and plastid sequences

Caltha is a widely distributed genus in the buttercup family (Ranunculaceae) showing interesting distribution patterns in both hemispheres. Evolutionary history ofCaltha was examined by means of phylogenetic, molecular dating, and historical biogeographic analyses with a more comprehensive sampling than previous studies. The internal transcribed spacer from the nuclear genome and trnL-F and atpB-rbcL regions from the plastid genome were used and analyzed using parsimony and Bayesian methods. Divergence time was estimated using Bayesian dating analyses with multiple fossil calibrations. Historical biogeography was inferred using the Bayes-DIVA method implemented in RASP. We obtained a well-resolved and well-supported phylogeny within the Caltha lineage. Caltha natansPall. diverged first from the genus and the other species grouped into two clades. Our expanded sampling scheme revealed a complicated evolutionary pattern in theC. palustris complex. Caltha sinogracilis W. T. Wang was resolved to be a member of the C. palustris complex, rather than closely related to C. scaposa Hook. f. & Thomson. Caltha rubriflora B. L. Burtt & Lauener was also revealed to be not just a red-flower form of C. sinogracilis. The diversification of the genus began at 50.5 mya (95% high posterior density: 37.1–63.9 mya), and its ancestral range was very probably in the Northern Hemisphere. The South American species may derive from western North American ancestors that dispersed along the western American Cordillera during the Cenozoic era. The vicariance model of the Southern Hemisphere species proposed by a previous study was rejected in this study.     

The historical biogeography of Scabiosa (Dipsacaceae): implications for Old World plant disjunctions

Aim To reconstruct the temporal and biogeographical history of Old World disjunctions in Scabiosa (Dipsacaceae) and the timing of diversification in the Mediterranean Basin, in order to evaluate the importance of biogeographical and climatological history (particularly the onset of a mediterranean climate) in shaping Scabiosa distributions. Location Europe and the Mediterranean Basin, southern Africa and eastern Asia. Methods This study uses maximum‐likelihood and Bayesian phylogenetic analyses of chloroplast DNA (atpB–rbcL, trnL–trnF, trnS–trnG, psbA–trnH) and nuclear ribosomal DNA [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] from 24 out of c. 37 ingroup taxa, beast molecular dating, and the dispersal–extinction–cladogenesis method (Lagrange ) to reconstruct ancestral geographical ranges and the timing of diversification of the major clades of Scabiosa. Results Biogeographical and divergence time reconstructions showed that Scabiosa originated during the Miocene and diversified in Europe, followed by independent movements into Asia and Africa. Several of the major clades were inferred to have radiated sometime between the late Miocene and early Pleistocene, a timeframe that encompasses the onset of the mediterranean climate in Europe. More recent middle–late Pleistocene radiations in the Mediterranean Basin and southern Africa have played a large role in Scabiosa diversification. Main conclusions Members of Scabiosa appear to have capitalized on adaptations to montane and/or dry conditions in order to colonize similar habitats in different biogeographical regions. The formation of the East African Rift mountains is potentially of great importance in explaining the southward migration of Scabiosa. The initial diversification of Scabiosa in Europe during the Miocene is not consistent with the initiation of the mediterranean climate, but may instead be associated with increased aridity and the retreat of subtropical lineages during this time. However, the radiation of some of the major subclades within Scabiosa may have been associated with an emerging mediterranean climate. More recent and rapid radiations in both the Mediterranean Basin and southern Africa highlight the probable importance of Pleistocene climate fluctuations in Scabiosa diversification.     

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.     

从12S rRNA基因序列推测鹭科13种鸟类的系统发生关系

对鹭科12个种的线粒体12S rRNA基因全长约975bp的序列进行了测定,并从GenBank获得黄顶夜鹭12S rRNA基因全序列。比对后的序列长993bp,含363变异位点,288个多态位点,187个简约信息位点。使用邻接法和最大简约法重建的分子系统树将13种鹭聚为2支：第一支包括白鹭、中白鹭、大白鹭、池鹭、牛背鹭、苍鹭、草鹭、夜鹭、黄顶夜鹭,第二支由黄苇渴Gan、黑苇Gan、栗苇Gan、大麻Gan组成。结果提示将鹭科分为鹭亚科和Gan亚科的传统观点是合理的,不支持Payne将鹭科分为日鹭亚科(Ardeinae)、夜鹭亚科(Nycticracinae)、Gan亚科(Botaurinae)和虎鹭亚科(Tigrisomatinae)的观点。进一步的分析表明：白鹭在系统演化中要早于大白鹭和中白鹭分支出来,大白鹭和中白鹭与苍鹭、草鹭和牛背鹭间的亲缘关系较近,而与白鹭较远,支持Sibley(1990)将大白鹭和中白鹭作为独立的大白鹭属(Casmerodius)和中白鹭属(Mesophoyx)的建议;黑Gan、栗苇Gan与黄苇Gan在系统发生中构成一单系群,提示将黑Gan置于苇Gan属(Ixobrychus)是合适的[动物学报49(2)：205—210,2003]。     

Length–weight relationships of six species of the genera Cobitis and Sabanejewia (Cobitidae) in Iranian river systems

Length‐weight relationships (LWRs) were estimated for six spined loach species from Iran. Data were collected between 2010 and 2015. These represent the first reports of length–weight data for five of the species (Cobitis avicennae, Cobitis faridpaki, Cobitis keyvani, Sabanejewia aurata and Sabanejewia caspia) while also providing additional data on the remaining species (Cobitis linea). Five of these species are endemic and the remaining S. caspia, is native to the country. Estimated b values obtained for the studied species ranged from 2.381 for S. aurata to 3.411 for C. keyvani.     

The historical biogeography of sturgeons (Osteichthyes: Acipenseridae): a synthesis of phylogenetics, palaeontology and palaeogeography

Abstract. The historical biogeography of sturgeons is explored using information from palaeogeography, palaeontology and phylogenetic interrelationships. The integration of information from these diverse sources indicates that sturgeons reached a wide Laurasian distribution in the Cretaceous and Tertiary by freshwater and coastal dispersal routes across land connections and along newly forming continental margins. The fossil record also suggests a considerable degree of morphological stasis and also supports an estuarine habit, and perhaps diadromy, as an old and conserved life history trait. While a ‘centre of origin’ for sturgeons remains elusive, phylogenetic relationships indicate that diversification appears to have been associated with fragmentation of biota, and of landmasses and basins, by late Tertiary geological and climatic phenomena, such as orogeny and unequal glaciation over North America, the desiccation of central Asia and alteration of its drainages, and the formation of discrete Ponto-Caspian basins by the fragmentation of the Paratethys. Amphi-oceanic distributions of certain species (Acipenser medirostris Ayres) and sister taxa (e.g. A. oxyrhynchus Mitchill and A. sturio L.) are explained by coastal dispersal and subsequent vicariance by geological (sea-floor spreading and development of new continental margins) and climatic (Pliocene cooling) changes during the Tertiary. An hypothesis is developed for the relationships of the North American sturgeons and their potential relationships with the Siberian sturgeon A. baeri. Late Tertiary climatic and geological phenomena are hypothesized as mediators of vicariance and subsequent diversification of these acipenserids. It appears that although acipenserids are a geologically old group, the historical biogeography of surviving lineages is best explained by more recent geological and climatic changes.     

基于线粒体和核基因序列的蜜蜂属系统发育分析

文章测定了中国分布的蜜蜂属(Apis)5种蜜蜂22个样本的线粒体基因ND2、CO2、16S rRNA以及核基因ITPR的序列,对序列的碱基组成和蜜蜂种间的遗传距离进行了分析。结合下载的蜜蜂属其他4个种的相关序列,采用最大简约法、邻接法和最大似然法重建了蜜蜂属系统发育关系。系统发育分析结果支持蜜蜂属划分为3个类群,即小蜜蜂类群(包括小蜜蜂和黑小蜜蜂)、大蜜蜂类群(包括大蜜蜂和黑大蜜蜂)和穴居蜜蜂类群(西方蜜蜂、东方蜜蜂、沙巴蜂、苏拉威西蜂、绿努蜂),且小蜜蜂类群较早分化。结果还显示,我国海南岛的大蜜蜂和大陆的大蜜蜂之间可能存在较大的遗传分歧。     

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.     

Genetic relationships among the Japanese and Korean striated spined loach complex (Cobitidae: Cobitis) and their phylogenetic positions

The striata complex, a group of spined loaches included in the genus Cobitis and characterized by a striped coloration pattern on the lateral midline, is distributed in rivers in northeastern Asia to western Japan. The complex comprises 2 continental species (Cobitis tetralineata and Cobitis lutheri) and 3 Japanese races of species rank (large race, middle race, and small race), the small race further comprising 6 local forms of subspecific rank (Tokai form, Biwa form, Yodo form, Sanyo form, San-in form, and Kyushu form). Previous karyological studies have revealed that the large race is an allotetraploid, the others being diploid. In this study, mitochondrial (mt) DNA analyses were conducted for 30 diploid populations of the Cobitis striata complex from Japan and Korea to examine: (1) their phylogenetic relationships and the position of the complex among the major lineages of Cobitis; and (2) the genetic relationships among the Japanese and Korean populations. The results, based on cytochrome b sequences (724 base pairs) analyzed with those of the main lineage of European and Japanese Cobitis, indicated that the striata complex should be considered as a monophyletic group, which evolved in northeastern Asia. Initially considered as a subspecies of Cobitis taenia, widely distributed from Europe to Asia, the striata complex does not have a sister-relationship with the former. Although the Korean species C. tetralineata was formerly believed to be closely related to the middle race in Japan, and a second continental species, C. lutheri, closely related to the Kyushu or San-in forms of the small race in Japan, the trees resulting from the present study revealed that the two Korean species were clustered with each other and separated from all Japanese races.     

Phylogenetic relationships and rate of early diversification of Australian Sphenomorphus group scincids (Scincoidea, Squamata)

The Australian Sphenomorphus group is a morphologically and ecologically diverse clade of lygosomine scincids, collectively comprising more than one‐half of the Australian scincid fauna. A previous phylogenetic analysis of mitochondrial 12S and 16S rRNA, and ND4 and adjacent tRNA sequences for a series of Australian Sphenomorphus group scincids recovered several well‐supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage‐level polytomies, I employ ATP synthetase‐β subunit intron sequences and the existing mitochondrial (mt)DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mtDNA and intron sequence data reveal a number of congruent clades, including Anomalopus, Calyptotis, Ctenotus, Lerista, the Eulamprus quoyii group, the Glaphyromorphus crassicaudis group (including Glaphyromorphus cracens, Glaphyromorphus darwiniensis, and Glaphyromorphus fuscicaudis), Glaphyromorphus gracilipes + Hemiergis, Coeranoscincus reticulatus + Ophioscincus truncatus + Saiphos, and Eulamprus amplus + Eulamprus tenuis + Gnypetoscincus + Nangura. The relationships among these clades indicated by the two data sets, however, are generally incongruent. Although this may be partially ascribed to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mtDNA and intron fragments considered, if not essentially simultaneous. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 347–366.     

Phylogenetic relationships of Nembrothinae (Mollusca: Doridacea: Polyceridae) inferred from morphology and mitochondrial DNA

Within the Polyceridae, Nembrothinae includes some of the most striking and conspicuous sea slugs known, although several features of their biology and phylogenetic relationships remain unknown. This paper reports a phylogenetic analysis based on partial sequences of two mitochondrial genes (cytochrome c oxidase subunit I and 16S rRNA) and morphology for most species included in Nembrothinae. Our phylogenetic reconstructions using both molecular and combined morphological and molecular data support the taxonomic splitting of Nembrothinae into several taxa. Excluding one species (Tambja tentaculata), the monophyly of Roboastra was supported by all the phylogenetic analyses of the combined molecular data. Nembrotha was monophyletic both in the morphological and molecular analyses, always with high support. However, Tambja was recovered as para- or polyphyletic, depending on the analysis performed. Our study also rejects the monophyly of "phanerobranch" dorids based on molecular data.     

Phylogenetic relationships and biogeography of midwife toads (Discoglossidae: Alytes)

Aim To devise a robust phylogenetic hypothesis for midwife toads (Alytes: Anura: Discoglossidae) and to discuss its implications for the reconstruction of the biogeographical history of the group. Location Western Palearctic. Methods Analysis of sequences of mitochondrial DNA (cytochrome b and 16S RNA, 861 bp) and 29 characters of cranial osteology of all species and subspecies within Alytes. Results Phylogenetic analyses support a sister group relationship between Alytes dickhilleni and A. muletensis, and of this clade with A. maurus. The monophyly of A. obstetricans is controversial; in particular, the phylogenetic position of A. obstetricans almogavarii is uncertain. The estimated dates for the cladogenetic events within Alytes are congruent with those derived from independent analyses (allozymes), except for the differentiation of A. o. almogavarii and the split between A. dickhilleni and A. muletensis. Main conclusions The phylogeny based on the analysis of morphological and mtDNA data differs from previous hypotheses in the positions of A. o. almogavarii and A. maurus. Events associated with the radiation of Alytes are the formation of large inland saline lakes in Iberia c. 16 Ma and the 11 ° C dramatic decrease in average annual temperature during the Middle–Late Badenian transition c. 14–13.5 Ma (A.cisternasii vs. the ancestor of the remaining clades), the structuring of the Neo‐Pyrenees and the reopening of the Betic Strait c. 10–8 Ma(A. o. almogavarii vs. A. obstetricans and vs. the subgenus Baleaphryne), the opening of the Gibraltar Strait at the end of the Messinian Salinity Crisis at c. 5.3 Ma (A. maurus vs. the ancestor of the A. dickhilleni A. muletensis clade) and a transmarine colonization event at c. 3 Ma (the ancestor of A. muletensis vs. A. dickhilleni). Following the new hypothesis, A. maurus, previously considered a subspecies of A. obstetricans, deserves species status. Second, A. o. almogavarii is a well‐differentiated lineage that was isolated from other A. obstetricans more than c. 5 Ma, but later lost its genetic and specific identity following secondary contact, hybridization and introgression with the main stock. The presence of a marked morphological and genetic diversity within A. obstetricans renders reconstruction of the evolutionary history of the genus more complicated than previously appreciated.     

Mitochondrial DNA diversity and historical biogeography of a wet forest-restricted frog (Litoria pearsoniana) from mid-east Australia

MtDNA sequencing was used to investigate the genetic population structure of Litoria pearsoniana, a wet forest-restricted hylid frog, endemic to southeast Queensland and northeast New South Wales, Australia. L. pearsoniana is regarded as endangered under Queensland legislation. Significant genetic divergence among populations of frogs from different rainforest isolates was identified, but the lack of reciprocal monophyly among adjacent isolates suggests this is the result of a relatively recent disruption to gene flow. A paired catchment study within a single rainforest isolate, the Conondale Range, revealed no substantial genetic structuring, indicating the occurrence of terrestrial dispersal among nearby streams either in the recent past or currently. Two major reciprocally monophyletic clades of mtDNA alleles were identified. These corresponded to two geographical regions separated by the Brisbane River valley; one consisting of the Conondale and D’Aguilar Ranges, and the other of the southern isolates in the Main, Border and Gibraltar Ranges. Sequence divergence between the two regions was more consistent with a late Miocene or Pliocene rather than late Pleistocene separation, and is similar to that found among phylogeographic divisions of rainforest reptiles and amphibians in north Queensland rainforests. The molecular evidence for long-term separation of these two regions is corroborated by the pattern of species turnover in the distributions of species of rainforest-restricted amphibians and reptiles. Bioclimatic modelling suggests that appropriate conditions for L. pearsoniana would have been restricted to isolated refuges in each phylogeographic division under cooler and drier climates, such as predicted for the last glacial maximum. Currently isolated montane areas may have been connected transiently during the past 2000 years. Identification of long-term zoogeographic divisions among southeast Queensland rainforest herpetofauna has important implications for conservation and management. Conservation management of L. pearsoniana should be applied at the scale of major rainforest isolates and the conservation status of the species should be assessed independently north and south of the historical division.     

Scorpions of the genus Odontobuthus Vachon, 1950 (Scorpiones: Buthidae) from Iran: Phylogenetic relationships inferred from mitochondrial DNA sequence data

The molecular phylogeny of the genus Odontobuthus Vachon, 1950 (Scorpiones: Buthidae) in Iran was evaluated using two mitochondrial DNA genes, cytochrome c oxidase, subunit I (COI) and 16S ribosomal RNA (16S rRNA). The molecular phylogenetic analyses were performed using Maximum Parsimony, Maximum Likelihood and Bayesian inference methods. The resulting topologies supported two main clades: the clade comprising Odontobuthus doriae, O. bidentatus, and O. tavighiae, and another one which is the O. tirgari clade. The results clearly presented additional support for the taxonomic validity of the recently described species, O. tirgari and O. tavighiae. In addition, the monophyly of two previously described species O. doriae and O. bidentatus was confirmed. According to the data presented here, three taxonomically valid species belonging to the genus Odontobuthus occur in Iran.     

Phylogenetic relationships and historical biogeography of neotropical parrots (Psittaciformes: Psittacidae: Arini) inferred from mitochondrial and nuclear DNA sequences

Previous hypotheses of phylogenetic relationships among Neotropical parrots were based on limited taxon sampling and lacked support for most internal nodes. In this study we increased the number of taxa (29 species belonging to 25 of the 30 genera) and gene sequences (6388 base pairs of RAG-1, cyt b, NADH2, ATPase 6, ATPase 8, COIII, 12S rDNA, and 16S rDNA) to obtain a stronger molecular phylogenetic hypothesis for this group of birds. Analyses of the combined gene sequences using maximum likelihood and Bayesian methods resulted in a well-supported phylogeny and indicated that amazons and allies are a sister clade to macaws, conures, and relatives, and these two clades are in turn a sister group to parrotlets. Key morphological and behavioral characters used in previous classifications were mapped on the molecular tree and were phylogenetically uninformative. We estimated divergence times of taxa using the molecular tree and Bayesian and penalized likelihood methods that allow for rate variation in DNA substitutions among sites and taxa. Our estimates suggest that the Neotropical parrots shared a common ancestor with Australian parrots 59 Mya (million of years ago; 95% credibility interval (CrI) 66, 51 Mya), well before Australia separated from Antarctica and South America, implying that ancestral parrots were widespread in Gondwanaland. Thus, the divergence of Australian and Neotropical parrots could be attributed to vicariance. The three major clades of Neotropical parrots originated about 50 Mya (95% CrI 57, 41 Mya), coinciding with periods of higher sea level when both Antarctica and South America were fragmented with transcontinental seaways, and likely isolated the ancestors of modern Neotropical parrots in different regions in these continents. The correspondence between major paleoenvironmental changes in South America and the diversification of genera in the clade of amazons and allies between 46 and 16 Mya suggests they diversified exclusively in South America. Conversely, ancestors of parrotlets and of macaws, conures, and allies may have been isolated in Antarctica and/or the southern cone of South America, and only dispersed out of these southern regions when climate cooled and Antarctica became ice-encrusted about 35 Mya. The subsequent radiation of macaws and their allies in South America beginning about 28 Mya (95% CrI 22, 35 Mya) coincides with the uplift of the Andes and the subsequent formation of dry, open grassland habitats that would have facilitated ecological speciation via niche expansion from forested habitats.     

Phylogenetic relationships of bitterlings based on mitochondrial 12S ribosomal DNA sequences

Analysis of the nucleotide sequence of the mitochondrial 12S ribosomal RNA gene of 27 species or sub-species of bitterlings showed that bitterlings comprise an Acheilognathus clade and a Tanakia-Rhodeus clade, partially supporting an earlier classification based on morphology and karyology. The monophyly of Acheilognathus is confirmed, but that of Tanakia and Rhodeus remains poorly resolved. Within the Tanakia–Rhodeus clade, all species or sub-species having a diploid chromosome number of 46 form a monophyletic group. Results support the hypothesis that evolutionary trends of bitterling karyotypes involve reduction from 2 n =48 to either 2 n =44 (by Robertsonian translocation) or 2 n =46 (by non-Robertsonian translocation).