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1.
We report analyses of complete DNA sequences of the mitochondrial cytochrome b (1146 bp), 12S rRNA (974 bp), partial control region (371 bp) loci, and the nuclear protamine P1 (616 bp) gene from all but one species (Sminthopsis butleri) of the dasyurid marsupial tribe Sminthopsini, as well as several outgroups. Parsimony analyses of combined nuclear and mitochondrial data suggest that Antechinomys is sister to a clade consisting of Sminthopsis and Ningaui. Parsimony, maximum-likelihood, and mixed-model distance analyses consistently resolve several species groups within Sminthopsis. The Macroura group includes S. macroura, S. virginiae, S. douglasi, and S. bindi; S. butleri is also included here on the basis of partial 12S rRNA sequences. S. crassicaudata is resolved as sister to the Macroura clade. The Murina group includes S. murina, S. leucopus, S. gilberti, S. dolichura, and S. archeri. S. griseoventer and S. aitkeni are resolved as a clade, and there is moderate support for a group consisting of the genetically divergent species S. psammophila, S. hirtipes, S. youngsoni, and S. ooldea (possibly along with S. longicaudata and S. granulipes). Compositions of species groups are partially congruent with clades previously proposed on the basis of morphological data. Radiations within Sminthopsini appear to be coincident with major environmental changes since the mid-Miocene.  相似文献   

2.
We studied the phylogenetic relationships among Japanese Leptocarabus ground beetles, which show extensive trans-species polymorphisms in mitochondrial gene genealogies. Simultaneous analysis of combined nuclear data with partial sequences from the long-wavelength rhodopsin, wingless, phosphoenolpyruvate carboxykinase, and 28S rRNA genes resolved the relationships among the five species, although separate analyses of these genes provided topologies with low resolution. For both the nuclear gene tree resulting from the combined data from four genes and a mitochondrial cytochrome oxidase subunit I (COI) gene tree, we applied a Bayesian divergence time estimation using a common calibration method to identify mitochondrial introgression events that occurred after speciation. Three mitochondrial lineages shared by two or three species were likely subject to introgression due to interspecific hybridization because the coalescent times for these lineages were much shorter than the corresponding speciation times estimated from nuclear gene sequences. We demonstrated that when species phylogeny is fully resolved with nuclear gene sequence data, comparative analysis of nuclear and mitochondrial gene trees can be used to infer introgressive hybridization events that might cause trans-species polymorphisms in mitochondrial gene trees.  相似文献   

3.
The Macaronesian islands are well known for their unique endemic floras of woody plants. Many of these unusual plant groups provide important novel resources for bark and wood boring beetles which breed in dead or moribund parts of their host plants. The bark beetle genus Liparthrum exploits a wide range of unusual host plants and has its highest proportion of species living on the Macaronesian Islands. We used DNA sequences of the mitochondrial Cytochrome Oxidase I gene and the nuclear Elongation Factor 1 alpha gene, and morphological characters, to estimate the phylogenetic relationships among species endemic to these archipelagos, and to trace the evolution of host-plant use. All parsimony and Bayesian analyses of the combined data, and maximum likelihood analyses of the molecular data, showed that species associated with Euphorbia are monophyletic. We also found genetic and subtle morphological evidence for three cases of cryptic speciation in one polyphyletic species associated with different Euphorbia plants, showing that high levels of host specialisation can occur also in insects breeding in older and very dry, dead plant tissues.  相似文献   

4.
Phylogenetic relationships among the 12 recognized fish species in the New World genus Centropomus (Pisces, Centropomidae) were analyzed using allozyme electrophoresis and 618 bp of the mitochondrial DNA 16S ribosomal RNA (rRNA) gene. Molecular phylogenetic trees were generally consistent with previously published partial hypotheses based on morphological evidence. However, previously undefined sister group relationships between major species groups were resolved using molecular data, and phylogenetic hypotheses for Centropomus based on 16S rRNA sequences were better supported than were allozyme-based hypotheses. The high level of congruence among the trees inferred from the nuclear and mitochondrial characters provided a firm phylogenetic basis for analysis of ecological diversification and molecular evolution in the genus. Compared to basal Centropomus species, members of the most nested species group were significantly larger in body size and occupied a marine niche only peripherally utilized by their congeners. We also observed substitution rate heterogeneity among 16S rRNA lineages; in contrast to expectations based on "metabolic rate" and "generation interval" models, relative substitution rates were faster than expected for the group of large-bodied snooks. Using the Pliocene rise of the Central American isthmian marine barrier to calibrate rates of 16S ribosomal gene evolution in Centropomus, we found that the rates for the genus were similar to those reported for higher vertebrates. Analysis of the three sets of transisthmian geminate taxa in Centropomus indicated that two of the pairs were probably formed during the Pliocene rise of the isthmus while the third pair diverged several million years earlier.  相似文献   

5.
Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes   总被引:10,自引:0,他引:10  
We present a most comprehensive phylogenetic analysis of the family Cichlidae. New data analyzed include mitochondrial 16S rRNA sequences and two nuclear loci (Tmo-M27 and Tmo-4C4) for a large taxonomic sampling with emphasis on South American species. We also incorporate a published morphological data set for a total evidence analysis. Character congruence among mitochondrial (74 taxa) and nuclear data (50 taxa) was high. However, partition-homogeneity tests suggest significant heterogeneity among molecular and morphological data. In agreement with results obtained from molecular data alone, total evidence analysis (1,460 characters for 34 taxa) supports a robust phylogenetic hypothesis for the family Cichlidae that is congruent with drift-vicariance events associated with the fragmentation of Gondwana. Our analyses confirm the placement of Malagasy/Indian cichlids as the most basal lineages, with a sister-group relationship to the monophyletic African and Neotropical clades. Total evidence suggests that the controversial African genus Heterochromis is at the base of the African radiation. Among more than 50 Neotropical genera analyzed, Retroculus is identified as the basal taxon, with successive branching of Cichla, Astronotus, geophagines (including crenicichlines) + chaetobranchines, and cichlasomines + heroines. Relative rate tests applied to mitochondrial DNA suggest significantly higher rates of genetic variation in Neotropical than in African taxa, and both mitochondrial and nuclear sequences show that rate heterogeneity among Neotropical lineages is confined to the geophagine cichlids.  相似文献   

6.
A phylogenetic and systematic study of Orius species (Heteroptera: Anthocoridae) from Korea has been conducted using both morphological and molecular characters. Thirty morphological character states were coded for 10 strains of 9 species. Five molecular markers, partial cytochrome c oxidase I (COI), cytochrome b (CytB), 16S rRNA (16S), 18S rRNA (18S), and 28S rRNA (28S), from mitochondrial and nuclear genes, were tested. Phylogenetic analyses based on molecular data were conducted by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic (BP) analyses. Analysis of morphological data was performed using the parsimony programs NONA, and the combined dataset of morphological and molecular data was analyzed using BP analyses. The results of this study indicate that use of COI and CytB enabled relatively effective identification of species, whereas the sequences of 16S, 18S and 28S did not enable identification of closely related species such as Orius minutus and O. strigicollis. We discuss the usefulness of the five molecular markers for determining phylogenetic relationships and identifying the species.  相似文献   

7.
Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5 kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most‐parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species‐rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non‐monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter‐sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total‐evidence tree unambiguously optimizes trunk segmentation: a 23‐segmented trunk has a single origin in the blind clade. © The Willi Hennig Society 2011.  相似文献   

8.
We studied the phylogeny and systematics of the tribe Paragini (Diptera: Syrphidae) using morphological and molecular data. The paper presents separate parsimony analyses of both adult morphological characters and partial DNA sequence data from mitochondrial cytochrome c oxidase I and nuclear ribosomal 28S rRNA gene, as well as a combined analysis of all the data. The data set of morphological characters included some features of the male terminalia (i.e. shape of the ejaculatory apodeme; relative position of elements of the aedeagal complex; shape of surstylar apodeme; shape of the aedeagal apodeme) not previously used in the systematics of the Paragini. The trees obtained from separate parsimony analyses of molecular and morphological data produced almost identical topologies. Four lineages are supported by the combined data set, and we establish two new subgenera, i.e. Serratoparagus Vujić et Radenković subgen. nov., and Afroparagus Vujić et Radenković subgen. nov., and redefine Pandasyopthalmus Stuckenberg, 1954 stat. rev. and Paragus Latreille, 1804, stat. rev. The monophyly of the Pandasyopthalmus clade, including the species fitting neither of the current species groups ( jozanus -group) of Paragini, is established. Diagnoses of all known species groups are presented, including a new arrangement of almost all valid species of Paragini.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 507–536.  相似文献   

9.
时敏  陈学新  马云  何俊华 《昆虫学报》2007,50(2):153-164
本研究选取矛茧蜂亚科Doryctinae(昆虫纲Insecta:膜翅目Hymenoptera:茧蜂科Braconidae)的6族15属18种做内群,茧蜂科其它7亚科11属11种做外群,首次结合同源核糖体28S rDNA D2基因序列片段和100个形态学和解剖学特征对该亚科进行了系统发育学研究。利用“非圆口类"的小腹茧蜂亚科Microgastrinae为根,以PAUP*4.0和MrBayes 3.0B4软件分别应用最大简约法(MP)和贝叶斯法对矛茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了运算分析;并以PAUP*4.0对矛茧蜂亚科的28S rDNA D2基因序列片段的碱基组成与碱基替代情况进行了分析。结果表明:矛茧蜂亚科的28S rDNA D2基因序列片段的GC含量在39.33%~48.28%之间变动,而对于碱基替代情况来讲,矛茧蜂亚科各成员间序列变异位点上颠换(transversion)大于转换(transition)。不同的分析算法所产生的系统发育树都表明矛茧蜂亚科是一个界限分明的单系群;在矛茧蜂亚科内,除了吉丁茧蜂族Siragrini为单系群外,其他族(矛茧蜂族Doryctini和方头茧蜂族Hecabolini)都是并系群。对于矛茧蜂亚科内各属之间的相互亲缘关系,不同算法所得的系统发育树的拓扑结构不完全一致,表明矛茧蜂亚科内(属及族)的系统发育关系还有待于进一步研究。  相似文献   

10.
The phylogenetic relationships within the fungus gnat subfamily Mycetophilinae (Diptera) are addressed using a combined morphological and molecular approach. Twenty-four species, representing nine genera of the tribe Mycetophilini and 15 genera of the tribe Exechiini, were included in the study. Analyses include nucleotide sequences of mitochondrial (cytochrome oxidase I and 16S), and nuclear (18S and 28S rDNA) genes, in addition to 65 morphological characters. A combined parsimony analysis, including all characters, supports the monophyly of the subfamily Mycetophilinae and two of its tribes, Exechiini and Mycetophilini. There is also statistical support for a Mycetophila- group and a Phronia- group within the tribe Mycetophilini. The Phronia- group includes the genera Phronia , Macrobrachius and Trichonta . The Mycetophila- group includes the genera Mycetophila , Epicypta , Platurocypta , Sceptonia and Zygomyia . A Bayesian analysis based on the nucleotide sequences alone also support these clades within Mycetophilini except for the position of Dynatosoma which is recovered as the sister taxon to the Phronia- group. A somewhat different pattern, however, is observed for the tribe Exechiini – neither molecular data nor the combined data set support unambiguously any intergeneric relationships within Exechiini.  相似文献   

11.
Molecular and biochemical genetic analyses have revealed that many marine invertebrate taxa, including some well-studied and presumably cosmopolitan species, are actually complexes of sibling species. When morphological differences are slight and estimated divergence times are old, data suggest either unusually high rates of sequence evolution or long-term morphological stasis. Here, five gene regions (mitochondrial cytochrome oxidase subunit I and large-subunit ribosomal 16S rDNA and nuclear ITS1, 5.8S rDNA, and ITS2) were analyzed in four geographic samples of the meiobenthic harpacticoid copepod Cletocamptus deitersi. Molecular sequences revealed four extremely differentiated molecular lineages with unalignable nuclear intergenic spacers and mitochondrial uncorrected divergences reaching 25% (cytochrome oxidase) and 36% (16S rDNA). These levels of divergence are greater than those reported previously for congeneric species in diverse invertebrate taxa, including crustaceans. The nominally intraspecific divergence matches or exceeds the corresponding divergence from a known congener (Cletocamptus helobius). A molecular clock applied to the cytochrome oxidase subunit I data suggests that these lineages split in the Miocene, consistent with the fossil record of a North American Cletocamptus from the same period. Morphological differences among the major lineages are subtle but congruent with the patterns of genetic differentiation. Our conclusion, based on concordant patterns of variation in two mitochondrial and three nuclear gene regions, as well as morphological observations, is that C. deitersi in North America is composed of at least four separate species by the genealogical concordance, phylogenetic, and morphological-species criteria. Alternative explanations for the deep phylogenetic nodes and apparent morphological stasis, including high rates of sequence evolution, balancing selection, and genetic signatures of historical events, are considered unlikely.  相似文献   

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

13.
Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.  相似文献   

14.
The tribe Lythriini is a small group of diurnally active geometrid moths consisting of a single Palaearctic genus Lythria with five species. The systematic placement of Lythriini has remained controversial: though traditionally it has been placed into the subfamily Larentiinae, a number of morphological characters link this tribe with the subfamily Sterrhinae. A molecular phylogenetic study was conducted to verify the systematic position of Lythriini, using sequences of both mitochondrial and nuclear genes: elongation factor 1α ( EF-1α ), wingless ( wgl ), 28S rRNA expansion segment D2 ( 28S D2 ), cytochrome oxidase subunit 1 ( COI ) and NADH dehydrogenase subunit 1 ( ND1 ) (a total of 3784 bp). Phylogenetic analysis reliably demonstrated that Lythriini belong to the subfamily Sterrhinae. Therefore, we propose to remove tribe Lythriini from Larentiinae and unite it with Sterrhinae. Moreover, our analysis supports the monophyly of both Sterrhinae and Larentiinae. However, although both morphological data and interspecific genetic distances insinuated that Lythria cruentaria and L. sanguinaria are sister species, the latter formed a clade of sister taxa together with L. purpuraria .  相似文献   

15.
DNA sequences were gathered from mitochondrial COII and nuclear ribosomal 18S and 28S genes for 21 moth species in the tribe Josiini (Notodontidae: Dioptinae) and two outgroup genera. These data complement a previously published morphological character set for the same taxa. We examine whether relationships in the Josiini are best reflected by a single phylogenetic analysis of all the data, or by a consensus of separate trees generated from DNA and morphology. Even in cases where analyses of partitioned data produce incongruent cladograms, the underlying disagreement between partitions is relatively small. While both molecular and morphological data provide useful character information by themselves, we conclude that the best supported phylogenetic hypothesis is the one derived from combined analysis.  相似文献   

16.
The leaf beetle genus Trirhabda contains 26 described species from the United States and Canada, feeding on host plants from the families Asteraceae and Hydrophyllaceae. In this study, we present a phylogeny for the genus that was reconstructed from mitochondrial COI and 12S rRNA fragments, nuclear ITS2 rRNA, and morphological characters. Both parsimony and mixed-model Bayesian likelihood analyses were performed. Under both methods, the mitochondrial and nuclear partitions support the same backbone phylogeny, as do the combined data. The utility of the molecular data is contrasted with the low phylogenetic signal among morphological characters. The phylogeny was used to trace the evolution of the host-plant association in Trirhabda. The recovered phylogeny shows that although the host-plant association is phylogenetically conservative, Trirhabda experienced one shift to a distantly related host-plant family, 6 shifts between host-plant tribes, and 6 between genera within tribes. The phylogeny reveals that Trirhabda were plesiomorphically adapted to tolerate complex secondary compounds of its host plants and this adaptation is retained in Trirhabda species, as evidenced by multiple shifts from chemically simpler host plants back to the more complex host plants.  相似文献   

17.
The phylogeny of spider flies is presented based on an analysis of DNA sequence data combined with morphological characters for both living and fossil species. We sampled 40 extant and extinct genera across all major lineages of Acroceridae, which were compared with outgroup taxa from various lower brachyceran families. In all, 81 morphological characters of 60 extant and 10 extinct ingroup species were combined with 7.1 kb of DNA sequences of two nuclear (CAD and 28S rDNA) and two mitochondrial genes (COI and 16S rDNA). Results strongly support the monophyly of Acroceridae, with major clades contained within classified here in five extant subfamilies (Acrocerinae, Cyrtinae stat. rev. , Ogcodinae stat. rev. , Panopinae and Philopotinae) and one extinct subfamily, Archocyrtinae. The evolution of important spider fly traits is discussed, including genitalia and wing venation. The status of the enigmatic Psilodera Gray and Pterodontia Gray as members of the Panopinae is confirmed based on both molecular and morphological data.  相似文献   

18.
The identification and phylogeny of muricids have been in a state of confusion for a long time due to the morphological convergence and plasticity. DNA-based identification and phylogeny methods often offer an analytically powerful addition or even an alternative. In this study, we employ a DNA barcoding method to identify 17 known and easily confused muricid species (120 individuals) from the whole China coast based on mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA sequences, and nuclear ITS-1 and 28S rRNA sequences. The phylogeny of muricid subfamilies is also analysed based on all mitochondrial and nuclear sequences. The universal COI and 16S rRNA primers did not work broadly across the study group, necessitating the redesign of muricid specific COI and 16S rRNA primers in this paper. Our study demonstrates that COI gene is a suitable marker for barcoding muricids, which can distinguish all muricid species studied. Phylogenetic analysis of 16S rRNA, ITS-1 and 28S rRNA data also provide good support for the species resolution observed in COI data. The relationships of muricid subfamilies are resolved based on the separate and combined gene data that showed the monophyly of each the subfamilies Ergalataxinae, Rapaninae, Ocenebrinae and Muricinae, especially that Ergalataxinae did not fall within Rapaninae.  相似文献   

19.
The phylogenetic relationships among major evolutionary lineages of the sea spiders (subphylum Pycnogonida) were investigated using partial sequences of nuclear DNA, 18S, and 28S ribosomal genes. Topological differences were obtained with separate analyses of 18S and 28S, and estimates of phylogeny were found to be significantly different between a combined molecular data set (18S and 28S) and a subset of a morphological data matrix analyzed elsewhere. Colossendeidae played a major role in the conflicts; it was closely related to Callipallenidae or Nymphonidae with 18S or 28S, respectively, but related to Ammotheidae according to morphological characters. Austrodecidae was defined as a basal taxon for Pycnogonida by these molecular data. The 18S sequences were surprisingly conserved among pycnogonid taxa, suggesting either an unusual case of slow evolution of the gene, or an unexpected recent divergence of pycnogonid lineages. Notwithstanding difficulties such as non-optimal taxon sampling, this is the first attempt to reconstruct the pycnogonid phylogeny based on DNA. Continued studies of sequences and other characters should increase the reliability of the analyses and our understanding of the phylogenetics of sea spiders.  相似文献   

20.
Weevils in the tribe Amorphocerini have been implicated in pollination of Encephalartos species in southern Africa. The services they render these plants and the unique attributes of the cycad-weevil interaction make them important from both conservation and evolutionary standpoints. Oberprieler [Oberprieler, R.G., 1996. Systematics and evolution of the tribe Amorphocerini, with a review of the cycad weevils of the world. Ph.D. dissertation, University of the Free State, Bloemfontein, South Africa], using morphological characters, proposed a tentative hypothesis of relationships among the Amorphocerini which is tested here using DNA sequence data. Sequences from one mitochondrial and three nuclear genes were used to infer phylogenetic relationships, levels of sequence divergence, evolution of host associations, and patterns of speciation in this tribe. The results are reasonably consistent with the morphological hypothesis of relationships and species concepts, though important differences are observed, particularly in relationships among a Porthetes hispidus Boheman species group, which is indicated to have experienced recent divergences. In general, low levels of sequence divergence among species within two of the three genera indicate a recent radiation of this tribe onto African cycads, thus while cycad-insect interactions have often been considered ancient this may not be the case for some extant interactions. A complex pattern of host shifts onto both closely related and more distantly related hosts is suggested.  相似文献   

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