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1.
The phylogenetic relationships between western Palaearctic Zamenis and Rhinechis ratsnakes have been troubled, with recent estimates based on the supermatrix approach questioning their monophyly and providing contradictory results. In this study, we generated a comprehensive molecular data set for Zamenis and closely related ratsnakes to assess their phylogenetic and systematic relationships and infer their spatial and temporal modes of diversification. We obtained a fully resolved and well‐supported phylogeny, which is consistent across markers, taxon‐sets and phylogenetic methods. The close phylogenetic relationship between Rhinechis and Zamenis is well‐established. However, the early branching pattern within this clade, and the position of R. scalaris and Z. hohenackeri, remains poorly supported. The Persian ratsnake Z. persicus is sister to the Mediterranean species Z. situla, Z. longissimus and Z. lineatus, of which Z. situla is sister to a clade containing the latter two species. These results are consistent with a recent phylogenomic study on ratsnakes based on hundreds of loci. Whereas, topological tests based on our data and evidence from such phylogenomic study strongly rejected previous phylogenetic estimates based on the supermatrix approach and demonstrate that these “mega‐phylogenies”, with hundreds of taxa and high levels of missing data, have recovered inconsistent relationships with spurious nodal support. Biogeographical and molecular dating analyses suggest an origin of the ancestor of Rhinechis and Zamenis in the Aegean region with early cladogenesis during the Late Miocene associated with the Aegean arch formation and support a scenario of east‐to‐west diversification. Finally, while we have little morphological and phylogenetic evidence for the distinctiveness between Rhinechis and Zamenis, a classification of them in a single genus, and the designation of Zamenis scalaris (Schinz, 1822), reflects better their evolutionary relationships.  相似文献   

2.
Inferring the evolutionary history of a group of species can be challenging given the many factors involved. In recent years, the increased availability of sequences of multiple genes per species has spurred the development of new methodologies to analyse multilocus data sets. Two approaches that analyse such data are concatenated supermatrix and coalescent-based species-tree analyses. In this study, we used both of these methods to infer the phylogenetic relationships of Iberian species of the genus Squalius from one mitochondrial and six nuclear genes. We found mitonuclear discordance in the phylogenetic relationships of the group. According to the mitochondrial gene analysis, all species were recovered as monophyletic except S. pyrenaicus; besides, in the concatenated supermatrix analysis of the nuclear markers, this species resolved as polyphyletic with three divergent evolutionary lineages. The coalescent-based nuclear species-tree analysis rendered a well-resolved phylogeny compared with the supermatrix analysis, which was unable to discern between S. carolitertii, S. castellanus and one of the evolutionary lineages of S. pyrenaicus. This result is likely due to the better integration of population uncertainty in the coalescent approach. Furthermore, Bayesian multilocus species delimitation analyses based on a BPP approach strongly supported the distinct nuclear lineages as different species. Nevertheless, the supermatrix analysis was able to obtain well-supported relationships in the divergent lineages with low numbers of individuals. Our study highlights the usefulness of different analytical methodologies to obtain a more complete picture of the evolutionary history of taxa, especially when discordant patterns among genes are found.  相似文献   

3.
Phylogenetic relationships of populations and species within Potamorrhaphis, a genus of freshwater South American needlefishes, were assessed using mitochondrial cytochrome b sequences. Samples were obtained from eight widely distributed localities in the Amazon and Orinoco rivers, and represented all three currently recognized species of Potamorrhaphis. The phylogeny of haplotypes corresponded imperfectly to current morphological species identities: haplotypes from P. guianensis, the most widespread species, did not make up a monophyletic clade. Geography played a strong role in structuring genetic variation: no haplotypes were shared between any localities, indicating restricted gene flow. Possible causes of this pattern include limited dispersal and the effects of current and past geographical barriers. The haplotype phylogeny also showed a complex relationship between fishes from different river basins. Based on the geographical distribution of clades, we hypothesize a connection between the middle Orinoco and Amazon via rivers of the Guianas. More ancient divergence events may have resulted from Miocene alterations of river drainage patterns. We also present limited data for two other Neotropical freshwater needlefish genera: Belonion and Pseudotylosurus. Pseudotylosurus showed evidence of substantial gene flow between distant localities, indicating ecological differences from Potamorrhaphis.  相似文献   

4.
Phylogenetic analyses were conducted on cytochrome b sequence data of the most geographically and taxonomically broad sampling of Cavia taxa to date. Primary objectives included providing the first extensive molecular phylogenetic framework for the genus, testing the taxonomic and systematic hypotheses of previous authors and providing insight into the evolutionary and biogeographic history of the genus. Support was found for the morphologically defined species C. aperea, C. tschudii, C. magna and C. fulgida and the taxonomic placement of taxa previously subject to conflicting taxonomic opinions (e.g. C. nana, C. anolaimae and C. guianae) was further resolved. Additionally, we elevate the Ecuadorian C. a. patzelti to species status, restrict the distributional limits and suggest taxonomic affiliations of some C. tschudii subspecies, and provide strong evidence for the geographic origin of guinea pig domestication. Finally, we provide an estimated evolutionary timeline for the genus Cavia, which appears to extend well into the late Miocene.  相似文献   

5.
The genus Lessonia Bory de Saint‐Vincent is distributed solely in the Southern Hemisphere, with four species found in South America and five in Australasia. Our goal was to determine the evolutionary relationships between the Lessonia species of the two disjunct areas and hypothesize dispersal patterns and timing of radiation. We combined mitochondria, plastid and nuclear markers in a comprehensive dataset from multiple individuals per known species. Furthermore, for some species we added samples from multiple populations to take account of their widespread distribution over known bioregions. In all analyses the Australasian Lessonia formed a monophyletic group and in most analyses the South American species form a paraphyletic grade. Delimitations of the accepted species are highly supported except for L. variegata J. Agardh and L. nigrescens Bory de Saint‐Vincent. We showed for the first time four lineages for the New Zealand endemic Lessonia variegata with an unexpected high level of genetic differentiation. Our analysis cannot resolve whether the dispersal of the common ancestor of this genus was from the Americas to Australasia or vice versa. Molecular clock analysis suggested that a sudden radiation took place in Australasia c. 3.5 Mya when almost all Australasian species diverged within a time frame of only 35 000 years.  相似文献   

6.
The genus Oryctophileurus is reviewed and its validity is supported by a combination of the following apomorphic characters: a single cephalic horn with lateral carina, pronotal cavity with ocellate punctures and two teeth or tubercles close behind the anterior pronotal margin. The male of Oryctophileurus varicosus Prell, 1934, is described for the first time. A new species, Oryctophileurus guerrai Perger & Grossi sp. n., from subhumid Tucuman-Bolivian forest in the Southern Bolivian Andes is described. The new species is distinguished from its closest relative, O. armicollis Prell, 1911, by a narrower distance between the inner teeth of the dorsal pronotal protuberances and a reduced area of weakly developed ocellate punctures above the posterolateral pronotal margin. The occurrence of Oryctophileurus species in areas of endemism along the eastern slope of the tropical Andes suggests that these populations represent biogeographic “relicts”, and the discovery of Oryctophileurus guerrai sp. n. in the southern Bolivian Andes suggests that this area is underrated with respect to insect diversity and endemism.  相似文献   

7.
Previous studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ-petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ-petA, and ITS dataset, and the combinedrbcL, trnL-F, matK/trnK, psbJ-petA, and ITS dataset. Based on the tree-based comparisons, blast searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ-petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which Beckwithia–Cyrtorhyncha, Kumlienia, andPeltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus-level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.  相似文献   

8.
DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and “song babblers”), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using mitochondrial and nuclear loci. The sister group to Leiothrichidae is composed of the Pellorneidae (“jungle babblers”) plus the genus Alcippe. Within Leiothrichidae, four strongly supported primary clades (A–D) are recovered. Clade A includes Grammatoptila, Laniellus and Cutia. Clade B includes a large group of laughingthrushes, all of them classified in Trochalopteron. In Clade C, the two laughingthrushes endemic to southern India, T. fairbanki and T. cachinnans, which have recently been proposed to be placed in the newly erected genus Montecincla, form a sister clade to the group comprising the “song babblers” (Lioptila, Leiothrix, Heterophasia, Minla, Liocichla, Actinodura, Chrysominla, Siva, and Sibia). Clade D includes the African babblers (Turdoides, Phyllanthus, Kupeornis), Asian relatives (Argya, Acanthoptila, Chatarrhaea) and all remaining laughingthrushes (Garrulax). The time estimates suggest that the early diversification of the Leiothrichidae occurred in the mid‐Miocene, a period that corresponds to the diversification of many passerine groups in Asia. A revised taxonomic classification of the family is proposed in the light of these results.  相似文献   

9.
The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model‐based estimation of ancestral regions indicates that Hakea began diversifying in the Mediterranean biome of southern Australia in the Middle Eocene–Early Oligocene, and dispersed repeatedly into other biomes across the continent. We infer around 47 shifts between biomes. Frequencies of shifts between pairs of biomes are usually similar to those expected from their geographic connectedness or climatic similarity, but in some cases are substantially higher or lower than expected, perhaps reflecting how readily key physiological traits can be modified to adapt lineages to new environments. The history of frequent biome‐shifting is reflected in the structure of present‐day assemblages, which tend to be more phylogenetically diverse than null‐model expectations. The case of Hakea demonstrates that the radiation of large plant clades across wide geographic areas need not be constrained by dispersal limitation or conserved adaptations to particular environments.  相似文献   

10.
We present a comprehensively sampled three‐gene phylogeny of the monophyletic Forcipulatacea, one of three major lineages within the crown‐group Asteroidea. We present substantially more Southern Hemisphere and deep‐sea taxa than were sampled in previous molecular studies of this group. Morphologically distinct groups, such as the Brisingida and the Zoroasteridae, are upheld as monophyletic. Brisingida is supported as the derived sister group to the Asteriidae (restricted), rather than as a basal taxon. The Asteriidae is paraphyletic, and is broken up into the Stichasteridae and four primary asteriid clades: (1) a highly diverse boreal clade, containing members from the Arctic and sub‐Arctic in the Northern Hemisphere; (2) the genus Sclerasterias; (3) and (4) two sister clades that contain asteriids from the Antarctic and pantropical regions. The Stichasteridae, which was regarded as a synonym of the Asteriidae, is resurrected by our results, and represents the most diverse Southern Hemisphere forcipulatacean clade (although two deep‐sea stichasterid genera occur in the Northern Hemisphere). The Labidiasteridae is artificial, and should be synonymized into the Heliasteridae. The Pedicellasteridae is paraphyletic, with three separate clades containing pedicellasterid taxa emerging among the basal Forcipulatacea. Fossils and timing estimates from species‐level phylogeographic studies are consistent with prior phylogenetic hypotheses for the Forcipulatacea, suggesting diversification of basal taxa in the early Mesozoic, with some evidence for more widely distributed ranges from Cretacous taxa. Our analysis suggests a hypothesis of an older fauna present in the Antarctic during the Eocene, which was succeeded by a modern Antarctic fauna that is represented by the recently derived Antarctic Asteriidae and other forcipulatacean lineages. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 646–660.  相似文献   

11.
In recent decades, the field of historical biogeography has become increasingly divorced from evolutionary biology, ecology, and studies of species richness. In this paper, we explore the evolutionary causes of patterns of biogeography and species richness in Northern Hemisphere treefrogs, combining phylogenetics, ancestral area reconstruction, molecular dating methods, and ecological niche modeling. We reconstructed phylogenetic relationships among 58 hylid taxa using data from two mitochondrial genes (12S, ND1) and two nuclear genes (POMC, c-myc). We find that parallel patterns of species richness have developed in Europe, Asia, and in two separate clades of North American hylids, with the highest richness at midtemperate latitudes (30-35 degrees) on each continent. This pattern is surprising given that hylids overall show higher species richness in the New World tropics and given many standard ecological explanations for the latitudinal diversity gradient (e.g., energy, productivity, mid-domain effect). The replicate pattern in Holarctic hylids seems to reflect specialized tolerance for temperate climate regimes or possibly the effects of competition. The results also suggest that long-range dispersal between continental regions with similar climatic regimes may be easier than dispersal between geographically adjacent regions with different climatic regimes. Our results show the importance of ecology and evolution to large-scale biogeography and the importance of large-scale biogeography to understanding patterns of species richness.  相似文献   

12.
13.
In this article, our knowledge of the geographic distribution of Grania species is expanded by describing seven new species, G rania bekkouchei sp. nov. , G rania brasiliensis sp. nov. , G rania capensis sp. nov. , G rania chilensis sp. nov. , G rania cryptica sp. nov. , G rania hinojosai sp. nov. , and G rania simonae sp. nov. , from poorly investigated regions of the Southern Hemisphere, plus two new species, G rania carolinensis sp. nov. and G rania unitheca sp. nov. , from off the east coast of the USA. An immature achaetous specimen that we call Grania cf. levis was also included. The newly generated data were combined with a previously published data set in order to update the hypothesis of phylogenetic relationships among Grania species. All new species except G . cryptica sp. nov. are supported by both morphological and molecular data. In addition, we find that G . chilensis sp. nov. is structured in at least four distinct populations along the Chilean coast. The species described from South Africa form a monophyletic clade where two are morphologically indistinguishable but diverging in both mitochondrial and nuclear ribosomal genes, and thus we describe them as different species, G . bekkouchei sp. nov. and G . cryptica sp. nov. Among the North Carolinian species, G . unitheca sp. nov. is indicated as a close relative of Grania monospermatheca Erséus & Lasserre, 1976, and G . carolinensis sp. nov. is indicated as a close relative of G. cf. levis. The updated phylogeny is strongly concordant with geographical species distributions, thus supporting a low level of dispersal within this genus, as has previously been hypothesized. © 2015 The Linnean Society of London  相似文献   

14.
Panochthus and Glyptodon are the Pleistocene Glyptodontidae having the greatest range of latitudinal distribution and elevation in South America. The most recent revisions of Panochthus recognized its high taxonomic diversification mainly distributed in the Chaco-Pampean region of Argentina, Uruguay, southern Bolivia and southern and north-eastern Brazil, while the Andean records are poorly known. This contribution aims: (a) to describe a new species of Panochthus from the Pleistocene of the surroundings of Potosi (Bolivia), which represents one of the highest known elevation records for fossil Xenarthra; (b) to carry out a phylogenetic analysis in order to test its location in Panochthus and relationship to some allied genera; (c) to discuss some palaeobiogeographical and morphological implications. The results show that, in agreement with previous studies, Panochthus is a natural group, being Propanochthus the sister taxa. This conclusion agrees, at least in part, with the original interpretation of Burmeister, who recognized Pr. bullifer as belonging to Panochthus. The genera Nopachtus and Phlyctaenopyga are more closely related to some ‘Plohophorini’ than to the clade Propanochthus + Panochthus. Within Panochthus, this new species occupies a relatively basal position as a sister taxon of the clade composed of P. tuberculatus, P. intermedius, and P. greslebini.http://zoobank.org/lsid:zoobank.org:pub:5A766550-DBCA-4C4A-BDB8-602E500E4954  相似文献   

15.
Species of the cyprinid genus Gobio Cuvier, 1816 are widely distributed in freshwater lakes and rivers in Turkey, which is a hotspot for freshwater fish diversity and endemism. The mitochondrial 16S, coxI and cytb genes were sequenced for 217 individuals representing 15 species of Gobio from Turkey. A total of 23 haplotypes were identified for each mitochondrial gene. The genetic distance matrices show that Turkish Gobio species are clustered into three groups (northwestern, central and northeastern Anatolia). Phylogenetic trees constructed with combined dataset by using maximum parsimony, maximum likelihood and Bayesian inference methods revealed that the Turkish Gobio species belongs to three well-supported groups in accordance with their geographic distribution: Group I comprises species found in Central Anatolia, Group II species ranging from eastern Thrace to western Anatolia (northwestern Group) and Group III contains only one species from Western Transcaucasia (northeastern Group). The estimated divergence times between the three Gobio groups, calculated using a conventional 1% rate of mutation for a fish mitochondrial cytb gene per million years, coincide with the late Miocene period in which the tectonic uplift of Anatolia and global climate fluctuations occurred. The relatively low genetic distance between Gobio species in the Turkish Lake District indicate that they are not good species.  相似文献   

16.
17.
The long-term isolation of South America during most of the Cenozoic produced a highly peculiar terrestrial vertebrate biota, with a wide array of mammal groups, among which caviomorph rodents and platyrrhine primates are Mid-Cenozoic immigrants. In the absence of indisputable pre-Oligocene South American rodents or primates, the mode, timing and biogeography of these extraordinary dispersals remained debated. Here, we describe South America's oldest known rodents, based on a new diverse caviomorph assemblage from the late Middle Eocene (approx. 41 Ma) of Peru, including five small rodents with three stem caviomorphs. Instead of being tied to the Eocene/Oligocene global cooling and drying episode (approx. 34 Ma), as previously considered, the arrival of caviomorphs and their initial radiation in South America probably occurred under much warmer and wetter conditions, around the Mid-Eocene Climatic Optimum. Our phylogenetic results reaffirm the African origin of South American rodents and support a trans-Atlantic dispersal of these mammals during Middle Eocene times. This discovery further extends the gap (approx. 15 Myr) between first appearances of rodents and primates in South America.  相似文献   

18.
Interrelationships among 10 extant species of the Neotropical electric fish Sternopygus are inferred from phylogenetic analysis of 66 morphological characters, including features of pigmentation, body proportions, meristics and osteology. A total of 287 lots containing 677 specimens were examined. The important findings of this study are: (1) S. branco is the most basal species unique among congeners in being restricted to whitewater rivers in the Central Amazon Basin, (2) S. sp. ‘cau’ from the Rio Caura of Venezuela is the sister taxon to (S. obtusirostris + S. astrabes), (3) S. castroi is a junior synonym of S. astrabes, (4) S. macrurus is the sister taxon to (S. arenatus + S. xingu + S. aequilabiatus species group) and (5) S. arenatus is the sister taxon to (S. xingu + S. aequilabiatus species group). A key to the adults of Sternopygus species is provided. Several features of S. astrabes previously thought to be plesiomorphic are now considered derived, including: short body cavity, paedomorphic cranial osteology, and the habitat restriction to terra firme streams. Sternopygus species assemblages in the Pacific (trans‐Andean) and Atlantic (cis‐Andean) slopes of northwestern South America are not monophyletic and do not result exclusively from local or regional radiations. The clade composed of S. macrurus, S. arenatus, S. xingu and the S. aequilabiatus species group is inferred to predate the Middle Miocene uplift of the Eastern Cordillera (c. 11.8–12.2 Ma). As currently recognized S. macrurus is the most widely distributed and most eurytopic gymnotiform species, inhabiting all hydrogeographical regions of tropical South America and most lowland aquatic habitats. Other Sternopygus species have much more restricted geographic and ecological distributions. Perceptions of phylogenetic patterns in Sternopygus are shown to be highly sensitive to taxon sampling.  相似文献   

19.
Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia Landrein (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. However, relationships within Diabelia remain elusive. In this study, we reconstructed the phylogeny of Diabelia and inferred historical biogeography and evolutionary patterns based on nuclear and plastid sequences from target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: Diabelia serrata (Siebold & Zucc.) Landrein, Diabelia tetrasepala (Koidz.) Landrein, Diabelia sanguinea (Makino) Landrein, Diabelia stenophylla (Honda) Landrein, and Diabelia spathulata (Siebold & Zucc.) Landrein. Species network analyses revealed that Diabelia tetrasepala is likely the result of a hybridization event. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent vicariance and dispersal events between Japan and Korea, and between Japan and China. Overall, our results support the division of Diabelia into five main clades and the recognition of five species in the genus. This research provides new insights into the species delimitation and speciation processes of taxonomically complex lineages such as Diabelia.  相似文献   

20.
The Permian terebratulids of Eurasia are revised. The taxonomic composition of the Permian terebratulids of the Russian Platform, Northern Caucasus, Transcaucasia, northern and southeastern Pamirs, and northern China (Inner Mongolia) is elucidated. Fifty-one species (13 described here as new), 21 genera (3 described here as new), 7 families, and 6 superfamilies are described. During the progress of the study, the author (Smirnova, 2004a, 2004b, 2006a, 2006b) and Smirnova and Grunt (2002, 2003a, 2003b) described for the first time 19 species, nine genera, two families, and one superfamily. Morphofunctional analysis reveals a great diversity of internal structures, of the time of their appearance in the ontogeny, and of their taxonomic significance. Ontogenetic study reveals phylogenetic relationships between the Permian and Meso-Cenozoic terebratulids, the presence of the superfamilies Terebratuloidea and Loboidothyroidea in the Permian, and a new type of brachidium ontogeny characterizing the superfamily Compositelasmatoidea. This book is intended for paleontologists and biologists interested in problems of taxonomy and phylogeny, and includes 5 plates, 80 figures, and 75 bibliographic references.  相似文献   

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