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1.
Taxonomic relationships within the corals and anemones (Phylum Cnidaria: Class Anthozoa) are based upon few morphological characters. The significance of any given character is debatable, and there is little fossil record available for deriving evolutionary relationships. We analyzed complete 18S ribosomal sequences to examine subclass-level and ordinal-level organization within the Anthozoa. We suggest that the Subclass Ceriantipatharia is not an evolutionarily relevant grouping. The Order Corallimorpharia appears paraphyletic and closely related to the Order Scleractinia. The 18S rRNA gene may be insufficient for establishing robust phylogenetic hypotheses concerning the specific relationships of the Corallimorpharia and the Ceriantharia and the branching sequence for the orders within the Hexacorallia. The 18S rRNA gene has sufficient phylogenetic signal, however, to distinguish among the major groupings within the Class Anthozoa, and we use this information to suggest relationships for the enigmatic taxa Dactylanthus and Dendrobrachia.  相似文献   

2.
Pseudobulweria is one of the least known and most endangered of all seabird genera. It comprises six taxa, of which two are extinct, three are critically endangered and one is near threatened. Phylogenetic relationships between these taxa and position of the genus in the Order Procellariiformes have never been studied, and the taxonomic status of several taxa remains unsettled. Conservation management of Pseudobulweria taxa will be enhanced if these uncertainties are resolved. We used a multilocus gene tree approach with two mitochondrial DNA markers (cytochrome oxidase subunit 1 and cytochrome b gene) and one nuclear intron (β Fibrinogen intron 7) to investigate phylogenetic relationships within the genus using sequences from all taxa. We combined gene trees to estimate a phylogeny of the genus using a multispecies coalescent methodology. We confirmed the link between Pseudobulweria and a clade comprising Puffinus and Bulweria genera. The Fiji petrel’s status, as belonging to the genus, is confirmed, as is the specific status of newly rediscovered Beck’s petrel. Maintenance of the two sub-species of Tahiti petrel as currently described is not supported. Discovering the breeding grounds of all taxa is the key for their conservation, which is vital to both the marine and fragile insular tropical ecosystems where Pseudobulweria are apical predators.  相似文献   

3.
Abstract The phylogenetic relationships within the largest subfamily of Tachinidae, Exoristinae, were explored using nucleotide sequences of two genes (EF-1α and 28S rDNA). A total of fifty-five and forty-three taxa were represented in the analyses for each gene, respectively, representing forty-three genera. Neighbour joining, parsimony and maximum likelihood inference methods were employed to reconstruct phylogenetic relationships in separate analyses of each gene, and parsimony was used to analyse the combined dataset. Although certain taxa were highly mobile, phylogenetic reconstructions generally supported recent classification schemes based on reproductive habits and genitalia. Generally, the monophyly of Tachinidae and Exoristinae was supported. Tribes Winthemiini, Exoristini and Blondeliini were repeatedly constructed as monophyletic groups, with the former two clades often occupying a basal position among Exoristinae. Goniini and Eryciini generally clustered together as a derived clade within Exoristinae; however, they were never reconstructed as two distinct clades. These results suggest that the possession of unembryonated eggs is plesiomorphic within the subfamily and that there may have been multiple transitions between microtype and macrotype egg forms.  相似文献   

4.
The macaques, genus Macaca, represent one of the most successful radiations within the Order Primates, with a geographical distribution that ranks second in size only to that of humans among extant primates. Although the number of macaque species recognized depends on the classification scheme used, most authors currently follow the classifications of either Fooden or Delson, both of whom recognize 19 extant macaque species. These two classifications differ in their placement of macaque species into more inclusive taxa (i.e., species groups). While researchers have attempted to use mitochondrial DNA (mtDNA) to resolve these phylogenetic relationships, different studies have generated conflicting conclusions. Consequently, we screened nuclear DNA sequences of a large number of macaques to determine if such data provide greater insight into the phylogenetic relationships among macaques. The data generated from the comparison of two (noncoding) introns within the natural resistance-associated macrophage protein 1 (NRAMP1) gene generally agree with the classification scheme of Delson. However, the data also support several novel observations. Specifically, the NRAMP1 data demonstrate that M. silenus and M. nemestrina lack nuclear genetic variation, while M. assamensis and M. radiata exhibit the greatest amount of genetic variation. In addition, these data suggest that M. fascicularis may not be as "primitive" (with respect to other members of the fascicularis group) as the mtDNA based data suggest.  相似文献   

5.
The complete mitochondrial cytochrome oxidase II gene was sequenced from 17 black flies, representing 13 putative species, and used to infer phylogenetic relationships. A midge (Paratanytarsus sp.) and three mosquitoes (Aedes aegypti, Anopheles quadrimaculatus, and Culex quinquefasciatus) were used as outgroup taxa. All outgroup taxa were highly divergent from black flies. Phylogenetic trees based on weighted parsimony (a priori and a posteriori), maximum likelihood, and neighbor-joining (log-determinant distances) differed topologically, with deeper nodes being the least well-supported. All analyses supported current classification into species groups but relationships among those groups were poorly resolved. The majority of phylogenetic signal came from closely related sister taxa. The CO-II gene may be useful for exploring relationships at or below the subgeneric level, but is of questionable value at higher taxonomic levels. The weighting method employed gave phylogenetic results similar to those reported by other authors for other insect CO-II data sets. A best estimate of phylogenetic relationships based on the CO-II gene is presented and discussed in relation to current black fly classification.  相似文献   

6.
Evolutionary biologists have long commented on a seemingly universal "rule" of nature-that in large taxonomic assemblages from groups as diverse as bacteria, plants, insects, marine invertebrates, fish, reptiles, amphibians, birds, and mammals, there exists a frequency distribution of body sizes among species that is highly skewed to the right (positive skewness). This distribution reflects the strong inverse, or negative, relationship often noted between mean body size of taxa and the number of species they contain--i.e., the observation that small body size is often associated with high species diversity (speciosity). This is sometimes "explained" by recourse to the idea that smaller-bodied taxa are able to subdivide their environments more finely than larger-bodied taxa. With but few exceptions, the applicability of this "rule" to the Order Primates has not been studied in any detail. In this study I address the following questions of (paleo)anthropological interest: (1) How speciose is the Order Primates? (2) Does this biological "rule" characterize the Order Primates (at any taxonomic level) in any meaningful way? (3) Does the association between speciosity and body mass within the Order Primates provide any useful models for interpreting and/or predicting speciosity in the fossil primate record? Using phylogenetically independent contrasts methods, I conclude that the answers to those three questions are: (1) not very; (2) no; and (3) not particularly (with the possible exception of larger-bodied taxa).  相似文献   

7.
《Comptes Rendus Palevol》2016,15(8):950-957
Late Pleistocene palaeontological sites without human intervention are limited in the Cantabrian region, and even more so those with a good state of preservation and rich biodiversity. A new vertebrate fossiliferous locality discovered at Kobate Quarry (Arrasate, northern Iberian Peninsula) is presented in this article. This site, in which remains of 40 different vertebrate taxa were accumulated, acted as a natural trap. The preliminary vertebrate faunal list includes five amphibian taxa, four reptiles, seven species of birds and 24 mammalian taxa. While small mammals are represented by 13 small mammal taxa (seven in the Order Rodentia, five in the Order Eulipotyphla, and one in the Order Chiroptera), the large mammal fauna comprises eleven species, including ungulates and carnivores. The palaeoecology inferred from this faunal assemblage suggests the existence of large forested areas with some grassland and a watercourse nearby, within a notably warm and humid climate. These palaeoenvironmental conditions, combined with AMS and AAR results carried out in macrofaunal bone samples, suggest that the deposit from Artazu VII would be located in the first half of the Late Pleistocene, in the Marine Isotope Stage (MIS) 5c.  相似文献   

8.
This is the first study to use both molecular and fossil data to date the divergence of taxa within the coleoid cephalopods (octopus, squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to investigate the evolutionary divergences within the group. Divergence time analyses were performed using the Thorne/Kishino method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders Vampyromorpha, Octopoda and the majority of the extant higher level decapodiform taxa. These estimated divergence times are considerably older than paleontological estimates. The major lineages within the Order Octopoda were estimated to have diverged in the Mesozoic, with a radiation of many taxa around the Cretaceous/Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been obscured due to an ancient diversification of this group. © The Willi Hennig Society 2006.  相似文献   

9.
Brachyuran crabs of the family Bythograeidae are endemic to deep-sea hydrothermal vents and represent one of the most successful groups of macroinvertebrates that have colonized this extreme environment. Occurring worldwide, the family includes six genera (Allograea, Austinograea, Bythograea, Cyanagraea, Gandalfus, and Segonzacia) and fourteen formally described species. To investigate their evolutionary relationships, we conducted Maximum Likelihood and Bayesian molecular phylogenetic analyses, based on DNA sequences from fragments of three mitochondrial genes (16S rDNA, Cytochrome oxidase I, and Cytochrome b) and three nuclear genes (28S rDNA, the sodium-potassium ATPase a-subunit 'NaK', and Histone H3A). We employed traditional concatenated (i.e., supermatrix) phylogenetic methods, as well as three recently developed Bayesian multilocus methods aimed at inferring species trees from potentially discordant gene trees. We found strong support for two main clades within Bythograeidae: one comprising the members of the genus Bythograea; and the other comprising the remaining genera. Relationships within each of these two clades were partially resolved. We compare our results with an earlier hypothesis on the phylogenetic relationships among bythograeid genera based on morphology. We also discuss the biogeography of the family in the light of our results. Our species tree analyses reveal differences in how each of the three methods weighs conflicting phylogenetic signal from different gene partitions and how limits on the number of outgroup taxa may affect the results.  相似文献   

10.
The nuclear gene X-src is a member of the tyrosine-kinase class of proto-oncogenes whose normal product is localized within the cytoplasm of the cell. The X-src gene has been used in only a few phylogenetic studies, each focusing on systematics of killifishes (Cyprinodontiformes). The present study is an attempt to examine the phylogenetic utility of X-src for uncovering relationships of representative cichlid fishes, especially the cichlids of Middle America. The family Cichlidae is a species-rich group of tropical freshwater fish made up of more than 1000 species which show a Gondwanan pattern of distribution. Cichlid fish have been the focus of numerous studies ranging from behavioral to biogeographical to systematic in nature. Particular emphasis has focused on the cichlids of the African Great Lakes and the explosive adaptive radiation of this group. However, Neotropical cichlids have received considerably less attention than their African counterparts. Our findings regarding the utility of X-src concur with those of previous phylogenetic analyses showing the exons of X-src to be highly conserved and useful mostly for revealing deep relationships among taxa. Like previous X-src studies, we also found the intron sequences of the gene to be variable in length and difficult to align across distantly related taxa but they provided useful information for resolving relationships among more closely related taxa. The X-src phylogeny supports the monophyly of Neotropical cichlids and cichlasomines groups A (=heroines) + B (=cichlasomines). A highly resolved tree is obtained within the heroines but little support is evident for most nodes based on the low number of unambiguous substitutions. The X-src gene is likely to be quite useful for resolving deep phylogenetic relationships such as those among major groups of actinopterygian fishes.  相似文献   

11.
Comparative ontogeny of the perianth is reported for representative genera and species among mimosoid legumes in order to elucidate intertribal relationships and also relationships to the other two subfamilies of legumes. Initiation of the perianth is acropetal in two whorls. The calyx arises first followed by the corolla. Order of initiation of both calyx and corolla is determined during early ontogeny. Four different types of order of initiation have been found in the calyx: helical, simultaneous within one whorl, bidirectional, and ring meristem. Helical initiation is considered primitive; simultaneous within one whorl, bidirectional, and ring meristem are considered derived. Differences during early organogeny in the calyx among mimosoids result in similar morphologies of the mature calyx which indicates that parallel evolution may have played a major role in evolution of radial symmetry within the group. Order of initiation of the corolla is uniformly simultaneous whorled with one exception. Position of organs is a significant feature which separates mimosoids from caesalpinioids and papilionoids. In mimosoids the median sepal is located abaxially and the median petal adaxially in relation to the subtending bract. In both caesalpinioids and papilionoids the median sepal is located abaxially and the median petal adaxially in relation to the subtending bract. Fusion of the calyx in some taxa can be interpreted as an example of acceleration.  相似文献   

12.
Ultrastructural studies of tetrasporalean green algae have suggested the order is polyphyletic. These features, including the absolute orientation of the flagellar apparatus and the bi- versus quadriflagellated motile cell morphology, suggest that Chaetopeltis as well as a number of others, may be ancestral to a group that includes Tetraspora. In this study, we examine the phylogenetic relationships of selected tetrasporalean taxa based on analysis of 18S ribosomal RNA gene sequences. Results show that the tetrasporalean taxa are polyphyletic. Biflagellated genera group with biflagellated volvocalean taxa, whereas the quadriflagellated species compose a distinct monophyletic clade not closely related to the biflagellated taxa. In addition, tetrasporalean taxa group with other chlorophycean algal species with similar flagellar apparatus absolute orientation, but the quadriflagellated Tetrasporales do not appear to be ancestral to the entire Chlorophyceae. These results are concordant with previous conclusions drawn from ultrastructural data and further confirm the utility of (small-subunit) ribosomal RNA gene sequences to discern green algal evolutionary relationships.  相似文献   

13.
The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rodent species (representing seven families) were analyzed using phenetic, parsimony, and maximum-likelihood methods of phylogenetic inference; the rabbit, Oryctolagus cuniculus (Order Lagomorpha), and cow, Bos taurus (Order Artiodactyla), were used as outgroups. Investigation of 714 base pairs of the protein-coding cytochrome b gene indicate strong base bias at the third codon position with significant rate heterogeneity evident between the three structural domains of this gene. Similar analyses conducted on 816 base pairs of the 12S rRNA gene revealed a transversion bias in the loop sections of all taxa. The cytochrome b gene sequences proved useful in resolving associations between closely related species but failed to produce consistent tree topologies at the family level. In contrast, phylogenetic analysis of the 12S rRNA gene resulted in strong support for the clustering of Pedetidae/Heteromyidae/Geomyidae and Muridae in one clade to the exclusion of the Hystricidae/Thryonomyidae and Sciuridae, a finding which is concordant with studies of rodent fetal membranes as well as reproductive and other anatomical features.   相似文献   

14.
In the present study, relationships among three genera Acontias, Acontophiops, and Typhlosaurus, that comprise the South African limbless lizard subfamily Acontinae, were assessed with partial sequences of the 16S rRNA mitochondrial DNA gene. In addition, relationships within Acontias were further investigated using sequence data from the cytochrome oxidase I gene (COI). Maximum likelihood and maximum parsimony analyses of the 16S rRNA mtDNA data revealed that within this subfamily, Typhlosaurus is basal while Acontophiops and Acontias are sister taxa. Based on the 16S rRNA mtDNA data, the relationships within Acontias placed A. meleagris orientalis as the sister taxon of A. percivali tasmani, with A. m. orientalis lineacauda morph and A. m. meleagrus being the sister taxa to this group. The small-bodied skinks A. lineatus lineatus and A. l. tristis formed a monophyletic group, with the medium-bodied species A. gracilicauda gracilicauda being their sister taxon. Analyses of the COI gene for Acontias place A. m. orientalis as the sister taxon of A. p. tasmani with both A. meleagris meleagris and A. m. orientalis lineacauda being distinct. In contrast to the 16S rRNA mtDNA data, the COI data placed A. g. gracilicauda as the sister taxon to these medium-bodied species; while the subspecies status of the small-bodied taxa A. l. lineatus and A. l. tristis is reaffirmed. Combined analysis of both gene fragments for Acontias taxa recovered the same clades as found using only COI data. Systematic affinities in Acontias are discussed. These results indicate that Acontias is more species rich than previously thought.  相似文献   

15.
Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.  相似文献   

16.
As a first attempt to use molecular data to resolve the relationships between the four suborders of lice and within the suborder Ischnocera, we sequenced a 347-bp fragment of the elongation factor 1alpha gene of 127 lice (Insecta: Phthiraptera) as well as outgroup taxa from the order Psocoptera. A number of well-supported monophyletic groups were found but the relationships among many of these groups could not be resolved. While it is probable that multiple substitutions at high divergences and ancient radiation over a short period of time have contributed to the problem, we attribute most of this lack of resolution to the high ratio of taxa to characters. Nevertheless, the sequence data unequivocally support a number of important relationships that are at variance with the conclusions of morphological taxonomy. These include the sister group relationship of Chelopistes and Oxylipeurus, two lice occupying different ecological niches on the same host, which have previously been assigned to different families. These results provide evidence in support of the hypothesis that lice have speciated in situ on the host in response to niche specialization and that this has given rise to convergent morphologies in the lice of different host groups which share similar ecological niches. We discuss our attempts to overcome the limitations of this large data set, including the use of leaf stability analysis, a new method for analyzing the stability of taxa in a phylogenetic tree, and examine a number of hypotheses of relationships based on both traditional taxonomy and host associations.  相似文献   

17.
Lahr DJ  Grant J  Nguyen T  Lin JH  Katz LA 《PloS one》2011,6(7):e22780
Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.  相似文献   

18.
Partial DNA and amino acid sequences translated from the mitochondrial cytochrome subunit I gene (408 bp) of 17 mite species have been used for analyzing the phylogenetic relationships within the terrestrial Parasitengona (Trombidia). Due to mutational saturation of the third codon position, only first and second codon positions and amino acid sequences were analyzed, applying neighbor-joining, maximum-parsimony, and maximum-likelihood tree-building methods. The reconstructed trees revealed similar topologies of taxa; however, the phylogenetic relationships could be convincingly resolved only within several trombidioid taxa. The proposed basic relationships within the Parasitengona, in particular those of Calyptostomatoidea, Smarididae, and Erythraeidae, were poorly supported in bootstrap tests. A comparison of the presented gene tree with a phylogenetic tree based upon traditional characters revealed only few contradictions in nodes only weakly supported by morphological data. The most astonishing result is the proposed early derivative position of Microtrombidiidae within the terrestrial Parasitengona.  相似文献   

19.
Partial sequences (1032 bp) of the nuclear-encoded large ribosomal RNA gene (LSU) were determined for 16 gelidialean species, and analyzed separately and in combination with plastid rbcL and nuclear SSU gene sequences. The number of informative characters and levels of sequence divergence among taxa are intermediate in LSU sequences as compared to that for rbcL and SSU. Analyses of the separate LSU, and a combined LSU, SSU, and rbcL data sets have identified early-diverging lineages within the Gelidiales including Gelidiella, Pterocladia, Pterocladiella, and a lineage including Gelidium and species classified in other genera. The relationships among most gelidialean taxa are well-resolved and well-supported by analyses of the combined data; however, the relationships of Ptilophora and Capreolia remain unclear. It is speculated that these two lineages have diverged from a common ancestor over an evolutionarily short period of time. This revised version was published online in June 2006 with corrections to the Cover Date.  相似文献   

20.
Phylogenetic relationships in the Mesostigmata are assessed using DNA sequence data for a segment of the elongation factor-1alpha gene. This is the first application of this nuclear protein coding gene to problems of higher relationships in Parasitiformes. Initial testing revealed extensive variability in nucleotide and corresponding amino acid sequences, both among and within mesostigmatid infraorders. However, accuracy, as assessed by the ability of these data to recover well-supported taxa, was inconsistent for all analyses using unweighted data. None of these analyses consistently recovered Mesostigmata, although less inclusive taxa, such as Uropodina and Trigynaspida, were often recovered. Accuracy was highest for an analysis using applied weighting on the nucleotide sequence data. The overall results provide support for monophyly of Uropodina, Trigynaspida, and a grouping of Zerconina, Parasitina, and Dermanyssina, and suggest close relationships between Heterozerconina and Sejina.  相似文献   

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