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1.
2.
The only bees native to the Hawaiian Islands form a single clade of 60 species in the genus Hylaeus. The group is understudied and relatively poorly known. A data set consisting of 1201 base pairs of the mitochondrial genes cytochrome oxidase I and II and tRNA‐Leucine, and 14 morphological characters was used to construct a phylogenetic tree for 48 of the 60 known species. Genetic variation was high, including amino acid changes, and a number of species showed evidence of heteroplasmy. Tree support was low due to high levels of homoplasy. Biogeographical analysis using DIVA indicates that early radiation took place on the island of Hawaii. This places an upper age limit of only 0.4–0.7 Myr for the group, an unusually short time for such a large radiation. Moreover, it is an unusual biogeographical pattern among the Hawaiian biota. © The Willi Hennig Society 2006.  相似文献   

3.
Recent studies of the phylogeny of several groups of native Hawaiian vascular plants have led to significant insights into the origin and evolution of important elements of the Hawaiian flora. No groups of Hawaiian pteridophytes have been subjected previously to rigorous phylogenetic analysis. We conducted a molecular phylogenetic analysis of the endemic Hawaiian fern genus Adenophorus employing DNA sequence variation from three cpDNA fragments: rbcL, atpbeta, and the trnL-trnF intergenic spacer (IGS). In the phylogenetic analyses we employed maximum parsimony and Bayesian inference. Bayesian phylogenetic inference often provided stronger support for hypothetical relationships than did nonparametric bootstrap analyses. Although phylogenetic analyses of individual DNA fragments resulted in different patterns of relationships among species and varying levels of support for various clades, a combined analysis of all three sets of sequences produced one, strongly supported phylogenetic hypothesis. The primary features of that hypothesis are: (1) Adenophorus is monophyletic; (2) subgenus Oligadenus is paraphyletic; (3) the enigmatic endemic Hawaiian species Grammitis tenella is strongly supported as the sister taxon to Adenophorus; (4) highly divided leaf blades are evolutionarily derived in the group and simple leaves are ancestral; and, (5) the biogeographical origin of the common ancestor of the Adenophorus-G. tenella clade remains unresolved, although a neotropical origin seems most likely.  相似文献   

4.
The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.  相似文献   

5.
Phylogenetic relationships within the flowering plant genus Styrax were investigated with DNA sequence data from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) and with chloroplast DNA restriction site data from the genes trnK, rpoC1, and rpoC2. The data sets from each genome were analyzed separately and in combination with parsimony methods. The results strongly support the monophyly of each of the four series of the genus but provide little phylogenetic resolution among them. Reticulate evolution may at least partly explain discordance between the molecular phylogenetic estimates and a prior morphological estimate within series Cyrta. The historical biogeography of the genus was inferred with unweighted parsimony character optimization of trees recovered from a combined ITS and morphological data set, after a series of combinability tests for data set congruence was conducted. The results are consistent with the fossil record in supporting a Eurasian origin of Styrax. The nested phylogenetic position of the South American members of the genus within those from southern North America and Eurasia suggests that the boreotropics hypothesis best explains the amphi-Pacific tropical disjunct distribution occurring within section Valvatae. The pattern of relationship recovered among the species of section Styrax ((western North America + western Eurasia) (eastern North America + eastern Eurasia)) is rare among north-temperate Tertiary forest relicts. The monophyly of the group of species from western North America and western Eurasia provides qualified support for the Madrean-Tethyan hypothesis, which posits a Tertiary floristic connection among the semiarid regions in which these taxa occur. A single vicariance event between eastern Asia and eastern North America accounts for the pattern of relationship among intercontinental disjuncts in series Cyrta.  相似文献   

6.
The internal transcribed spacer (ITS) region of 18-26S nuclear ribosomal DNA was sequenced in 12 representatives of the Compositae subtribe Madiinae and two outgroup species to assess its utility for phylogeny reconstruction. High sequence alignability and minimal length variation among ITS 1, 5.8S, and ITS 2 sequences facilitated determination of positional homology of nucleotide sites. In pairwise comparisons among Madiinae DNAs, sequence divergence at unambiguously aligned sites ranged from 0.4 to 19.2% of nucleotides in ITS 1 and from 0 to 12.9% of nucleotides in ITS 2. Phylogenetic relationships among ITS sequences of Hawaiian silversword alliance species (Argyroxiphium, Dubautia, and Wilkesia) and California tarweed taxa in Adenothamnus, Madia, Raillardella, and Raillardiopsis are highly concordant with a chloroplast DNA-based phylogeny of this group. Maximally parsimonious trees from ITS and chloroplast DNA data all suggest (a) origin of the monophyletic Hawaiian silversword alliance from a California tarweed ancestor, (b) closer relationship of the Hawaiian species to Madia and Raillardiopsis than to Adenothamnus or Raillardella, (c) paraphyly of Raillardiopsis, a segregate of Raillardella, and (d) closer relationship of Raillardiopsis to Madia and the silversword alliance than to Raillardella. These findings indicate that the ITS region in plants should be further explored as a promising source of nuclear phylogenetic markers.  相似文献   

7.
We investigated genetic variation in asexual polyploid members of the water flea Daphnia pulex complex from a set of 12 Bolivian high-altitude lakes. We used nuclear microsatellite markers to study genetic relationships among all encountered multilocus genotypes, and combined this with a phylogenetic approach using DNA sequence data of three mitochondrial genes. Analyses of mitochondrial gene sequence divergence showed the presence of three very distinct clades that likely represent cryptic undescribed species. Our phylogenetic results suggest that the Daphnia pulicaria group, a complex of predominantly North American species that has diversified rapidly since the Pleistocene, has its origin in South America, as specific tests of topology indicated that all three South American lineages are ancestral to the North American members of this species group. A comparison between variation of nuclear and mitochondrial markers revealed that closely related polyploid nuclear genotypes sometimes belonged to very divergent mitochondrial lineages, while distantly related nuclear genotypes often belonged to the same mitochondrial lineage. This discrepancy suggests that these South American water fleas originated through reciprocal hybridization between different endemic, sexually reproducing parental lineages. It is also likely that polyploidy of the investigated lineages resulted from this hybridization. Nevertheless, no putative diploid parental lineages were found in the studied region.  相似文献   

8.
In this study, we present phylogenetic data to characterize the relationships among sironids centered in the Balkan region, and use these results to discuss biogeographical aspects of sironid evolution. Analysis of ca. 4.5 kb of sequence data from three nuclear and two mitochondrial genes reveals monophyly of a Balkan clade for which we resurrect the name Cyphophthalmus, considered a junior synonym of Siro for over a century. This clade diversified into several groups, and at least three of them--the duricorius group, the serbicus group, and the minutus group--are well corroborated by the data as monophyletic lineages. The members of the different groups, mostly living in troglobitic environments, have diversified in overlapping geographic regions, with evidence of an eastern origin for the group. Our data also suggest that mitochondrial and nuclear genes are all contributing towards the final resolution of the combined analysis of the data.  相似文献   

9.
Specialists studying the genus Viola have consistently allied the Hawaiian violets comprising section Nosphinium--most of which are subshrubs or treelets--with putatively primitive subshrubs in certain South American violet groups. Hawaiian violets also possess inflorescences, a floral disposition otherwise found only in other genera of the Violaceae, thus strengthening the hypothesis of a very ancient origin for the Hawaiian species. A survey of phylogenetic relationships among infrageneric groups of Viola worldwide using nuclear rDNA internal transcribed spacer (ITS) sequences revealed a dramatically different biogeographic origin for the Hawaiian violets: A monophyletic Hawaiian clade was placed in a close sister relationship with the amphi-Beringian tundra violet, V. langsdorffii s. 1., in a highly derived position. This remarkable and unforeseen relationship received strong clade support values across analyses, and monophyly of the Hawaiian lineage was further indicated by a unique 26-base-pair deletion in section Nosphinium. The high polyploid base chromosome number (n approximately equal to 40) in the Hawaiian violets relates them to Alaskan and eastern Siberian populations in the polyploid V. langsdorffii complex. More than 50 species of the 260 allochthonous birds wintering in the Hawaiian Islands are found to breed in the Arctic, occupying habitats in which individual birds might have encountered ancestral V. langsdorffii populations and served as dispersers to the central Pacific region. Acquisition of derived morphological traits (e.g., arborescence and inflorescences), significance of a confirmed Arctic origin for a component of the Hawaiian flora, and the likelihood of other "cryptic" Arctic elements in the Hawaiian flora deserving independent molecular phylogenetic corroboration are discussed.  相似文献   

10.
A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprising three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most-parsimonious cladogram with relatively strong support at the majority of nodes. The phylogenetic utility of different classes of molecular data was also examined. In particular, using a number of different measures of utility in both a combined and separate analysis framework, we focused on the distinction between mitochondrial and nuclear genes and between faster-evolving characters and slower-evolving characters. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationships than are the mitochondrial genes. The nuclear genes exhibit less homoplasy, are less incongruent with one another and with the combined data, and contribute more support to the combined analysis topology than do the mitochondrial genes. Results from the second comparison, however, provide little evidence of a clear difference in utility. Despite indications of rapid divergence and saturation, faster-evolving characters in both the nuclear and mitochondrial data sets still provide substantial phylogenetic signal. In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions.  相似文献   

11.
Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create complex signals of phylogenetic relationships, especially among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian duck (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (Anas platyrhynchos) and Laysan duck (Anas laysanensis). Whereas mtDNA clearly shows a sister relationship between Hawaiian duck and mallard, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan duck and mallard. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the predefined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene–Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian subfossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin and support the hypothesis that the Hawaiian duck may represent a young hybrid species.  相似文献   

12.
Results of the first genus-wide phylogenetic analysis for Santalum (Santalaceae), using a combination of 18S-26S nuclear ribosomal (ITS, ETS) and chloroplast (3' trnK intron) DNA sequences, provide new perspectives on relationships and biogeographic patterns among the widespread and economically important sandalwoods. Congruent trees based on maximum parsimony, maximum likelihood, and Bayesian methods support an origin of Santalum in Australia and at least five putatively bird-mediated, long-distance dispersal events out of Australia, with two colonizations of Melanesia, two of the Hawaiian Islands, and one of the Juan Fernandez Islands. The phylogenetic data also provide the best available evidence for plant dispersal out of the Hawaiian Islands to the Bonin Islands and eastern Polynesia. Inability to reject rate constancy of Santalum ITS evolution and use of fossil-based calibrations yielded estimates for timing of speciation and colonization events in the Pacific, with dates of 1.0-1.5 million yr ago (Ma) and 0.4-0.6 Ma for onset of diversification of the two Hawaiian lineages. The results indicate that the previously recognized sections Polynesica, Santalum, and Solenantha, the widespread Australian species S. lanceolatum, and the Hawaiian species S. freycinetianum are not monophyletic and need taxonomic revision, which is currently being pursued.  相似文献   

13.
Determining the mode, or geographical context, of speciation is a critical first step to understanding the evolutionary mechanisms that cause new species to arise. In this study, we estimated phylogenetic relationships in the cerasina species group of the Hawaiian cricket genus Laupala (Orthoptera: Gryllidae) to test competing phylogeographical hypotheses and thus infer the mode of speciation. A previous phylogenetic result based on nuclear sequence data suggested that populations of L. cerasina on the Big Island of Hawaii are the result of two independent colonizations from Maui, implying parallel speciation and convergent song evolution, and contradicting systematic hypotheses based on behavioural and morphological data. We used amplified fragment length polymorphisms to investigate further the relationships among species and populations in the cerasina species group. Results of these analyses provide a robust estimate of phylogenetic relationships and support the phylogeographical history indicated by behavioural and morphological data.  相似文献   

14.
From a phylogenetic perspective, the genus Manihot can be considered as an orphan group of plants, and the scientific knowledge acquired has been mainly related to cassava, one of the most important crops in poor tropical countries. The goal of the majority of evolutionary studies in the genus has been to decipher the domestication process and identify the closest relatives of cassava. Few investigations have focused on wild Manihot species, and the phylogeny of the genus is still unclear. In this study the DNA sequence variation from two chloroplast regions, the nuclear DNA gene G3pdh and two nuclear sequences derived from the 3'-end of two cassava ESTs, were used in order to infer the phylogenetic relationships among a subset of wild Manihot species, including two species from Cnidoscolus as out-groups. Maximum parsimony and Bayesian analyses were conducted for each data set and for a combined matrix due to the low variation of each region when analyzed independently. A penalized likelihood analysis of the chloroplast region trnL-trnF, calibrated with various age estimates for genera in the Euphorbiaceae extracted from the literature was used to determine the ages of origin and diversification of the genus. The two Mesoamerican species sampled form a well-defined clade. The South American species can be grouped into clades of varying size, but the relationships amongst them cannot be established with the data available. The age of the crown node of Manihot was estimated at 6.6 million years ago. Manihot esculenta varieties do not form a monophyletic group that is consistent with the possibility of multiple introgressions of genes from other wild species. The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates.  相似文献   

15.
A recent phylogenetic study based only on chloroplast DNA (cpDNA) variation revealed that populations of an Isodon species are frequently embedded paraphyletically among other Isodon species. This phylogenetic discrepancy between species taxonomy and molecular phylogeny was considered to have resulted from chloroplast DNA captures and/or incomplete lineage sorting. To elucidate which of these factors was mainly responsible for the observed phylogenetic pattern, we performed phylogenetic analyses of multiple populations of Isodon species in Japan using cpDNA variation, three single-copy nuclear genes, and double-digest restriction-site-associated DNA sequencing (ddRAD-seq). Although a species often shared chlorotypes with other species, our phylogenetical analyses based on variation in the three single-copy nuclear genes and the ddRAD-seq data showed that most populations belonging to the same species were monophyletic at the species level, suggesting that chloroplast capture may have frequently occurred between Isodon species. Some populations of an intraspecific taxon were embedded paraphyletically within the species, regardless of the large amount of phylogenetic information in nuclear DNA; this incongruity may have resulted from incomplete lineage sorting.  相似文献   

16.
Scaptomyza is a highly diversified genus in the family Drosophilidae, having undergone an explosive radiation, along with the Hawaiian‐endemic genus Idiomyia in the Hawaiian Islands: about 60% of 269 Scaptomyza species so far described are endemic to the Hawaiian Islands. Two hypotheses have been proposed for the origin and diversification of Hawaiian drosophilids. One is the “single Hawaiian origin” hypothesis: Scaptomyza and Idiomyia diverged from a single common ancestor that had once colonized the Hawaiian Islands, and then non‐Hawaiian Scaptomyza migrated back to continents. The other is the “multiple origins” hypothesis: Hawaiian Scaptomyza and Idiomyia derived from different ancestors that independently colonized the Hawaiian Islands. A key issue for testing these two hypotheses is to clarify the phylogenetic relationships between Hawaiian and non‐Hawaiian species in Scaptomyza. Toward this goal, we sampled additional non‐Hawaiian Scaptomyza species, particularly in the Old World, and determined the nucleotide sequences of four mitochondrial and seven nuclear genes for these species. Combining these sequence data with published data for 79 species, we reconstructed the phylogeny and estimated ancestral distributions and divergence times. In the resulting phylogenetic trees, non‐Hawaiian Scaptomyza species were interspersed in two Hawaiian clades. From a reconstruction of ancestral biogeography, we inferred that Idiomyia and Scaptomyza diverged outside the Hawaiian Islands and then independently colonized the Hawaiian Islands, twice in Scaptomyza, thus supporting the “multiple origins” hypothesis.  相似文献   

17.
Tree snails of the endemic subfamily Achatinellinae comprise a diverse and important component of the Hawaiian fauna. In recent decades anthropogenic impacts have resulted in devastating extinction rates in Hawaiian tree snails. To address long-standing biogeographic, systematic, and evolutionary questions we used cytochrome c oxidase subunit I (COI) gene sequences to reconstruct the phylogeny of 23 extant species spanning the range of the subfamily from five Hawaiian Islands. To investigate family-level relationships, data were analyzed from 11 terrestrial pulmonate families. Although nodal support for monophyly of the endemic Pacific family Achatinellidae and endemic Hawaiian subfamily Achatinellinae was strong, bifurcation order among deeper ingroup nodes was not well-supported by bootstrap resampling. We hypothesize that lineage extinction and rapidity of lineage formation may have rendered evolutionary reconstruction difficult using a standard phylogenetic approach. Use of an optimized evolutionary model, however, improved resolution and recovered three main clades. The diversification pattern inferred contradicts the traditional biogeographic hypothesis of a Maui origin of the achatinelline lineage. Taxa comprising the basal ingroup clade (Achatinella spp.) and seeding lineages for subsequent clades originated on O'ahu. Therefore it appears that the ancestral colonizing species of achatinellines arrived first on O'ahu from an unknown source, and that O'ahu is the Hawaiian origin of the subfamily. Species previously defined by morphological criteria were generally found to be phylogenetically distinct, and the overall colonization pattern follows the island-age progression rule with several instances of generic polyphyly and back-colonization.  相似文献   

18.
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.  相似文献   

19.
Smith EJ  Shi L  Tu Z 《Genetica》2005,124(1):23-32
Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGC1) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1 among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39–48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.  相似文献   

20.
A genus-wide molecular phylogeny for Polystichum and allied genera (Dryopteridaceae) was reconstructed to address the biogeographic origin and evolution of the three Hawaiian Polystichum species, all endemic there. The analysis was based on the cpDNA sequences rbcL and the trnL-F spacer from a taxonomically and geographically diverse sample. Parsimony and Bayesian phylogenetic analyses of the combined data support a monophyletic Polystichum and corroborate recent hypotheses as to membership and sequence of origin of the major groups within the genus. The Hawaiian Polystichum species are polyphyletic; two separate lineages appear to have arrived independently from the Old World. The provenance of the diploid Polystichum hillebrandii is continental eastern Asia, while the source of the polyploid lineage comprising tetraploid P. haleakalense and octoploid P. bonseyi is likely continental Asia. From our results, the origin of the Hawaiian species of Polystichum, like many Hawaiian fern genera with several species, is the result of multiple migrations to the islands, rather than single migrations yielding nearly all the local diversity as in the angiosperms. This emerging pattern provides a modern test of the premise that propagule vagility has a central role in determining pattern of evolution.  相似文献   

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