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Caballero S, Jackson J, Mignucci-Giannoni AA, Barrios-Garrido H, Beltrán-Pedreros S, Montiel-Villalobos MAG, Robertson KM, Baker CS. Molecular systematics of South American dolphins Sotalia: sister taxa determination and phylogenetic relationships, with insights into a multi-locus phylogeny of the Delphinidae. Mol Phylogenet Evol 2007; 46:252-68. [PMID: 18053749 DOI: 10.1016/j.ympev.2007.10.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 09/19/2007] [Accepted: 10/17/2007] [Indexed: 11/16/2022]
Abstract
The evolutionary relationships among members of the cetacean family Delphinidae, the dolphins, pilot whales and killer whales, are still not well understood. The genus Sotalia (coastal and riverine South American dolphins) is currently considered a member of the Stenoninae subfamily, along with the genera Steno (rough toothed dolphin) and Sousa (humpbacked dolphin). In recent years, a revision of this classification was proposed based on phylogenetic analysis of the mitochondrial gene cytochrome b, wherein Sousa was included in the Delphininae subfamily, keeping only Steno and Sotalia as members of the Stenoninae subfamily. Here we investigate the phylogenetic placement of Sotalia using two mitochondrial genes, six autosomal introns and four Y chromosome introns, providing a total of 5,196 base pairs (bp) for each taxon in the combined dataset. Sequences from these genomic regions were obtained for 17 delphinid species, including at least one species from each of five or six currently recognized subfamilies plus five odontocete outgroup species. Maximum Parsimony, Maximum Likelihood and Bayesian phylogenetic analysis of independent (each fragment) and combined datasets (mtDNA, nuDNA or mtDNA+nuDNA) showed that Sotalia and Sousa fall within a clade containing other members of Delphininae, exclusive of Steno. Sousa was resolved as the sister taxon to Sotalia according to analysis of the nuDNA dataset but not analysis of the mtDNA or combined mtDNA+nuDNA datasets. Based on the results from our multi-locus analysis, we offer several novel changes to the classification of Delphinidae, some of which are supported by previous morphological and molecular studies.
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Affiliation(s)
- Susana Caballero
- Laboratory of Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
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202
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Jordal B, Gillespie JJ, Cognato AI. Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae). ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00306.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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203
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Buffington ML, Nylander JAA, Heraty JM. The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea). Cladistics 2007. [DOI: 10.1111/j.1096-0031.2007.00153.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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204
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Burton RS, Byrne RJ, Rawson PD. Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus. Gene 2007; 403:53-9. [PMID: 17855023 DOI: 10.1016/j.gene.2007.07.026] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 06/29/2007] [Accepted: 07/25/2007] [Indexed: 11/29/2022]
Abstract
Previous work on the harpacticoid copepod Tigriopus californicus has focused on the extensive population differentiation in three mtDNA protein coding genes (COXI, COXII, Cytb). In order to get a more complete understanding of mtDNA evolution in this species, we sequenced three complete mitochondrial genomes (one from each of three California populations) and compared them to two published mtDNA genomes from an Asian congener, Tigriopus japonicus. Several features of the mtDNA genome appear to be conserved within the genus: 1) the unique order of the protein coding genes, rRNA genes and most of the tRNA genes, 2) the genome is compact, varying between 14.3 and 14.6 kb, and 3) all genes are encoded on the same strand of the mtDNA. Within T. californicus, extremely high levels of nucleotide divergence (>20%) are observed across much of the mitochondrial genome. Inferred amino acid sequences of the proteins encoded in the mtDNAs also show high levels of divergence; at the extreme, the three ND3 variants in T. californicus showed >25% amino acid substitutions, compared with <3% amino acid divergence at the previously studied COXI locus. Unusual secondary structures make functional assignments of some tRNAs difficult. The only apparent tRNA(trp) in these genomes completely overlaps the 5' end of the 16S rRNA in all three T. californicus mtDNAs. Although not previously noted, this feature is also conserved in T. japonicus mtDNAs; whether this sequence is processed into a functional tRNA has not been determined. The putative control region contains a duplicated segment of different length (from 88 to 155 bp) in each of the T. californicus sequences. In each case, the duplicated segments are not tandem repeats; despite their different lengths, the distance between the start of the first and the start of the second repeat is conserved (520 bp). The functional significance, if any, of this repeat structure remains unknown.
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Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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205
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Lin CP, Cast MS, Wood TK, Chen MY. Phylogenetics and phylogeography of the oak treehopper Platycotis vittata indicate three distinct North American lineages and a neotropical origin. Mol Phylogenet Evol 2007; 45:750-6. [PMID: 17658274 DOI: 10.1016/j.ympev.2007.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 05/19/2007] [Accepted: 06/06/2007] [Indexed: 11/23/2022]
Affiliation(s)
- Chung-Ping Lin
- Department of Life Science, Center for Tropical Ecology and Biodiversity, Tunghai University, No. 181, Sec. 3, Taichung-Kan Road, Taichung 40704, Taiwan.
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206
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McLeish MJ, Crespi BJ, Chapman TW, Schwarz MP. Parallel diversification of Australian gall-thrips on Acacia. Mol Phylogenet Evol 2007; 43:714-25. [PMID: 17467300 DOI: 10.1016/j.ympev.2007.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 03/12/2007] [Accepted: 03/14/2007] [Indexed: 10/23/2022]
Abstract
The diversification of gall-inducing Australian Kladothrips (Insecta: Thysanoptera) on Acacia has produced a pair of sister-clades, each of which includes a suite of lineages that utilize virtually the same set of 15 closely related host plant species. This pattern of parallel insect-host plant radiation may be driven by cospeciation, host-shifting to the same set of host plants, or some combination of these processes. We used molecular-phylogenetic data on the two gall-thrips clades to analyze the degree of concordance between their phylogenies, which is indicative of parallel divergence. Analyses of phylogenetic concordance indicate statistically-significant similarity between the two clades. Their topologies also fit with a hypothesis of some degree of host-plant tracking. Based on phylogenetic and taxonomic information regarding the phylogeny of the Acacia host plants in each clade, one or more species has apparently shifted to more-divergent Acacia host-plant species, and in each case these shifts have resulted in notable divergence in aspects of the phenotype including morphology, life history and behaviour. Our analyses indicate that gall-thrips on Australian Acacia have undergone parallel diversification as a result of some combination of cospeciation, highly restricted host-plant shifting, or both processes, but that the evolution of novel phenotypic diversity in this group is a function of relatively few shifts to divergent host plants. This combination of ecologically restricted and divergent radiation may represent a microcosm for the macroevolution of host plant relationships and phenotypic diversity among other phytophagous insects.
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Affiliation(s)
- M J McLeish
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Claremont, Cape Town, South Africa.
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207
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Winterton SL, Wiegmann BM, Schlinger EI. Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera: Acroceridae) using multiple molecular markers. Mol Phylogenet Evol 2007; 43:808-32. [PMID: 17196837 DOI: 10.1016/j.ympev.2006.08.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 07/19/2006] [Accepted: 08/13/2006] [Indexed: 11/22/2022]
Abstract
The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered "primitive" based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.
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MESH Headings
- Animals
- Carbamoyl-Phosphate Synthase (Ammonia)/genetics
- Diptera/classification
- Diptera/genetics
- Electron Transport Complex IV/genetics
- Evolution, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Shaun L Winterton
- Department of Entomology, North Carolina State University, Raleigh, NC, USA.
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208
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Magnacca KN, Danforth BN. Low nuclear DNA variation supports a recent origin of Hawaiian Hylaeus bees (Hymenoptera: Colletidae). Mol Phylogenet Evol 2007; 43:908-15. [PMID: 17049277 DOI: 10.1016/j.ympev.2006.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Revised: 08/14/2006] [Accepted: 09/04/2006] [Indexed: 11/16/2022]
Abstract
Previous phylogenetic work on the Hawaiian bees of the genus Hylaeus, based on mitochondrial DNA and morphology, appeared to support a recent origin for the group, but support for the resulting tree was weak. Four nuclear genes with varying evolutionary rates -- arginine kinase, EF-1alpha, opsin, and wingless -- were sequenced for a reduced taxon set in an attempt to find one or more data set that would provide better support. All showed very low variation (<2%) in the ingroup. Comparison among genes revealed a much higher than expected rate of evolution in mtDNA, especially at first and second positions. While the data from the nuclear genes showed insufficient variation for phylogenetic analysis, the strong sequence similarity among the Hawaiian species supports the previous hypothesis of a recent origin for the group.
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Affiliation(s)
- Karl N Magnacca
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA.
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209
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Chaboo CS. BIOLOGY AND PHYLOGENY OF THE CASSIDINAE GYLLENHAL SENSU LATO (TORTOISE AND LEAF-MINING BEETLES) (COLEOPTERA: CHRYSOMELIDAE). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2007. [DOI: 10.1206/0003-0090(2007)305[1:bapotc]2.0.co;2] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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210
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Cardinal S, Packer L. Phylogenetic analysis of the corbiculate Apinae based on morphology of the sting apparatus (Hymenoptera: Apidae). Cladistics 2007; 23:99-118. [DOI: 10.1111/j.1096-0031.2006.00137.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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211
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Ayoub NA, Garb JE, Hedin M, Hayashi CY. Utility of the nuclear protein-coding gene, elongation factor-1 gamma (EF-1γ), for spider systematics, emphasizing family level relationships of tarantulas and their kin (Araneae: Mygalomorphae). Mol Phylogenet Evol 2007; 42:394-409. [PMID: 16971146 DOI: 10.1016/j.ympev.2006.07.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 07/21/2006] [Accepted: 07/24/2006] [Indexed: 10/24/2022]
Abstract
Spider systematics has overwhelmingly relied on morphological characters to resolve higher-level phylogenetic questions. Molecular phylogenetic studies of spiders above the genus level have been rare, partly because of a paucity of characterized genes available for amplification and sequencing. Here we show the phylogenetic utility of a new molecular marker, elongation factor-1 gamma (EF-1gamma) for discerning family level relationships in the spider infraorder, Mygalomorphae. We included genomic sequences from 26 mygalomorph genera in 14 families as well as cDNA sequences from 10 families in the infraorder Araneomorphae. We found strong support for the traditional split of mygalomorphs into atypoids (Antrodiaetidae, Atypidae, and Mecicobothriidae) and non-atypoids (all other families). Some families with multiple generic representatives were found to be polyphyletic or paraphyletic, such as the Nemesiidae, Ctenizidae, and Hexathelidae. A small portion of genomic EF-1gamma that could be amplified from araneomorphs contained a short intron, suggesting that longer genomic sequences could not be amplified due to the presence of introns. This intron may be useful for intra-familial araneomorph relationships. A tentative timeline for spider evolution is proposed using the evolutionary rate of EF-1gamma, estimated to be approximately 0.22% pairwise divergence per million years based on a non-parametric smoothing method (NPRS) and fossil constraints.
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Affiliation(s)
- Nadia A Ayoub
- Department of Biology, University of California, Riverside, CA 92521, USA.
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212
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Balke M, Pons J, Ribera I, Sagata K, Vogler AP. Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea. Mol Phylogenet Evol 2007; 42:505-16. [PMID: 16979911 DOI: 10.1016/j.ympev.2006.07.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 07/10/2006] [Accepted: 07/27/2006] [Indexed: 11/21/2022]
Abstract
We present a molecular phylogenetic analysis of 2808 aligned bp of rrnL, cox1, cob, H3 and 18S rRNA of all major morphological groups of Papuadytes diving beetles (Coleoptera: Dytiscidae) which are diverse in running water habitats throughout the Australian region. We focus on the origin of the fauna of the megadiverse islands of New Guinea and New Caledonia. Parsimony as well as Bayesian analyses suggest a basal position of Australian species in a paraphyletic series, with more recent nested radiations in New Caledonia and New Guinea. According to molecular clock analyses, both landmasses were colonized during the Miocene, which matches geological data and corroborates similar findings in other taxonomic groups. Our analyses suggest that dispersal played an important role in the formation of these large insular faunas, although successful colonization appears to be a rare event, and, in this case, is unidirectional. Whether or not a lineage is present on an island is due to chance: Papuadytes are absent from Fiji, where related Copelatus have radiated extensively in the same habitats occupied by Papuadytes in New Caledonia and New Guinea, while Copelatus are absent from New Caledonia. Lineages of Papuadytes apparently colonized New Caledonia twice, around 14 and 9 MYA according to the molecular calibration, and both lineages are derived from an Australian ancestor. The older clade is represented only by two apparently relictual mountain species (one morphologically strongly adapted to highly ephemeral habitats), while the younger clade contains at least 18 species exhibiting a great morphological diversity. The 150+ species in New Guinea are monophyletic, apparently derived from an Australian ancestor, and constitute a morphologically rather homogenous group. The tree backbone remains insufficiently supported under parsimony and Bayesian analyses, where shorter branches suggest a rapid sequence of major branching events.
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Affiliation(s)
- Michael Balke
- Department of Entomology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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213
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Arnedo MA, Ferrández MA. Mitochondrial markers reveal deep population subdivision in the European protected spider Macrothele calpeiana (Walckenaer, 1805) (Araneae, Hexathelidae). CONSERV GENET 2007. [DOI: 10.1007/s10592-006-9270-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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214
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McLeish MJ, Chapman TW, Schwarz MP. Host-driven diversification of gall-inducing Acacia thrips and the aridification of Australia. BMC Biol 2007; 5:3. [PMID: 17257412 PMCID: PMC1796849 DOI: 10.1186/1741-7007-5-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 01/26/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insects that feed on plants contribute greatly to the generation of biodiversity. Hypotheses explaining rate increases in phytophagous insect diversification and mechanisms driving speciation in such specialists remain vexing despite considerable attention. The proliferation of plant-feeding insects and their hosts are expected to broadly parallel one another where climate change over geological timescales imposes consequences for the diversification of flora and fauna via habitat modification. This work uses a phylogenetic approach to investigate the premise that the aridification of Australia, and subsequent expansion and modification of arid-adapted host flora, has implications for the diversification of insects that specialise on them. RESULTS Likelihood ratio tests indicated the possibility of hard molecular polytomies within two co-radiating gall-inducing species complexes specialising on the same set of host species. Significant tree asymmetry is indicated at a branch adjacent to an inferred transition to a Plurinerves ancestral host species. Lineage by time diversification plots indicate gall-thrips that specialise on Plurinerves hosts differentially experienced an explosive period of speciation contemporaneous with climatic cycling during the Quaternary period. Chronological analyses indicated that the approximate age of origin of gall-inducing thrips on Acacia might be as recent as 10 million years ago during the Miocene, as truly arid landscapes first developed in Australia. CONCLUSION Host-plant diversification and spatial heterogeneity of hosts have increased the potential for specialisation, resource partitioning, and unoccupied ecological niche availability for gall-thrips on Australian Acacia.
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Affiliation(s)
- Michael J McLeish
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Claremont, Cape Town, 7735, Republic of South Africa
| | - Thomas W Chapman
- Department of Biology, Memorial University, St. John's, Newfoundland, A1B 3X9, Canada
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215
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Tello JG, Bates JM. Molecular Phylogenetics of The Tody-Tyrant and Flatbill Assemblage of Tyrant Flycatchers (Tyrannidae). ACTA ACUST UNITED AC 2007. [DOI: 10.1093/auk/124.1.134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The tody-tyrant and flatbill assemblage, sensuLanyon (1988a), includes 12 genera of tyrant flycatchers known variously as “tody-tyrants” and “flatbills.” Lanyon supported the monophyly of the group based on similar skull morphology and nest form, and built intergeneric relationships based on syringeal characters. However, these comparisons were made without a phylogenetic framework. A more recent study assessing relationships in the tyrant flycatchers using published morphological and behavioral data failed to recover monophyly of this assemblage (Birdsley 2002). Using DNA sequence data, we test for the monophyly of the tody-tyrant and flatbill assemblage and compare and contrast phylogenetic signals from mitochondrial and nuclear DNA character systems. We discuss our results in light of results from previous studies. We include representatives of the other major tyrant flycatcher assemblages for a total of 42 individuals (representing 27 tyrannid genera and 36 species). We sequenced 3,022 base pairs (bp) of three mitochondrial genes (ND2, ND3, and cytochrome b) and one nuclear intron (FIB5). Our results resolve many of the basal relationships of the tody-tyrant and flatbill phylogeny, but separate and combined analyses of data partitions are necessary to understand the nature of conflict among data sets. The tody-tyrants constitute a monophyletic clade, but the genera Hemitriccus and Lophotriccus are not monophyletic, and the limits of Oncostoma-Lophotriccus need to be revised with more complete sampling at the species level. The flatbills as defined by Lanyon are not monophyletic (Onychorhynchus and Platyrinchus are not true flatbills). Pseudotriccus and Corythopis are sister taxa and, together with Leptopogon and Mionectes, are allied to the tody-tyrant and flatbill clade.
Filogenia Molecular del Grupo de los Picochatos y Mosquiteros de la Familia Tyrannidae
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Affiliation(s)
- Jose G. Tello
- Department of Zoology, Field Museum of Natural History, Chicago, Illinois 60605, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - John M. Bates
- Department of Zoology, Field Museum of Natural History, Chicago, Illinois 60605, USA
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216
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Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implications for DNA barcoding. Mol Phylogenet Evol 2006; 44:325-45. [PMID: 17270468 DOI: 10.1016/j.ympev.2006.12.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 11/27/2006] [Accepted: 12/07/2006] [Indexed: 11/17/2022]
Abstract
DNA barcoding has focused increasing attention on the use of specific regions of mitochondrial cytochrome c oxidase I and II genes (COI-COII) to diagnose and delimit species. However, our understanding of patterns of molecular evolution within these genes is limited. Here we examine patterns of nucleotide divergence in COI-COII within species and between species pairs of Lepidoptera and Diptera using a sliding window analysis. We found that: (1) locations of maximum divergence within COI-COII were highly variable among taxa surveyed in this study; (2) there was major overlap in divergence within versus between species, including within individual COI-COII profiles; (3) graphical DNA saturation analysis showed variation in percent nucleotide transitions throughout COI-COII and only limited association with levels of DNA divergence. Ultimately, no single optimally informative 600 bp location was found within the 2.3 kb of COI-COII, and the DNA barcoding region was no better than other regions downstream in COI. Consequently, we recommend that researchers should maximize sequence length to increase the probability of sampling regions of high phylogenetic informativeness, and to minimize stochastic variation in estimating total divergence.
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217
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Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2006. [DOI: 10.1146/annurev.ecolsys.37.091305.110018] [Citation(s) in RCA: 429] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chris Simon
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
- School of Biological Sciences, Victoria University of Wellington, Wellington 6014, New Zealand
| | | | - Francesco Frati
- Department of Evolutionary Biology, University of Siena, 53100 Siena, Italy;
| | - James B. Stewart
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; ,
- Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Norvum 141 86, Stockholm, Sweden
| | - Andrew T. Beckenbach
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; ,
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218
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Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics. BMC Evol Biol 2006; 6:97. [PMID: 17107620 PMCID: PMC1664589 DOI: 10.1186/1471-2148-6-97] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 11/15/2006] [Indexed: 11/23/2022] Open
Abstract
Background Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. Results Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. Conclusion Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction.
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219
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Galewski T, Tilak MK, Sanchez S, Chevret P, Paradis E, Douzery EJP. The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies. BMC Evol Biol 2006; 6:80. [PMID: 17029633 PMCID: PMC1618403 DOI: 10.1186/1471-2148-6-80] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 10/09/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial and nuclear genes have generally been employed for different purposes in molecular systematics, the former to resolve relationships within recently evolved groups and the latter to investigate phylogenies at a deeper level. In the case of rapid and recent evolutionary radiations, mitochondrial genes like cytochrome b (CYB) are often inefficient for resolving phylogenetic relationships. One of the best examples is illustrated by Arvicolinae rodents (Rodentia; Muridae), the most impressive mammalian radiation of the Northern Hemisphere which produced voles, lemmings and muskrats. Here, we compare the relative contribution of a nuclear marker--the exon 10 of the growth hormone receptor (GHR) gene--to the one of the mitochondrial CYB for inferring phylogenetic relationships among the major lineages of arvicoline rodents. RESULTS The analysis of GHR sequences improves the overall resolution of the Arvicolinae phylogeny. Our results show that the Caucasian long-clawed vole (Prometheomys schaposnikowi) is one of the basalmost arvicolines, and confirm that true lemmings (Lemmus) and collared lemmings (Dicrostonyx) are not closely related as suggested by morphology. Red-backed voles (Myodini) are found as the sister-group of a clade encompassing water vole (Arvicola), snow vole (Chionomys), and meadow voles (Microtus and allies). Within the latter, no support is recovered for the generic recognition of Blanfordimys, Lasiopodomys, Neodon, and Phaiomys as suggested by morphology. Comparisons of parameter estimates for branch lengths, base composition, among sites rate heterogeneity, and GTR relative substitution rates indicate that CYB sequences consistently exhibit more heterogeneity among codon positions than GHR. By analyzing the contribution of each codon position to node resolution, we show that the apparent higher efficiency of GHR is due to their third positions. Although we focus on speciation events spanning the last 10 million years (Myr), CYB sequences display highly saturated codon positions contrary to the nuclear exon. Lastly, variable length bootstrap predicts a significant increase in resolution of arvicoline phylogeny through the sequencing of nuclear data in an order of magnitude three to five times greater than the size of GHR exon 10. CONCLUSION Our survey provides a first resolved gene tree for Arvicolinae. The comparison of CYB and GHR phylogenetic efficiency supports recent assertions that nuclear genes are useful for resolving relationships of recently evolved animals. The superiority of nuclear exons may reside both in (i) less heterogeneity among sites, and (ii) the presence of highly informative sites in third codon positions, that evolve rapidly enough to accumulate synapomorphies, but slow enough to avoid substitutional saturation.
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Affiliation(s)
- Thomas Galewski
- Laboratoire de Paléontologie, Phylogénie et Paléobiologie--CC064, Institut des Sciences de l'Evolution UMR 5554/CNRS, Université Montpellier II, France.
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Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. INSECT MOLECULAR BIOLOGY 2006; 15:657-86. [PMID: 17069639 PMCID: PMC2048585 DOI: 10.1111/j.1365-2583.2006.00689.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/28/2006] [Indexed: 05/12/2023]
Abstract
As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.
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Affiliation(s)
- J J Gillespie
- Department of Entomology, Texas A & M University, College Station, TX, USA.
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221
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Kourti A. Mitochondrial DNA Restriction Map and Cytochrome c Oxidase Subunits I and II Sequence Divergence of Corn Stalk Borer Sesamia nonagrioides (Lepidoptera: Noctuidae). Biochem Genet 2006; 44:321-32. [PMID: 16977511 DOI: 10.1007/s10528-006-9032-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 11/17/2005] [Indexed: 10/24/2022]
Abstract
Corn stalk borer Sesamia nonagrioides (Lefebvre) (Lepidoptera: Noctuidae) is among the most important insect pests of corn in the Mediterranean basin. The mitochondrial DNA of this insect was purified and a restriction map was constructed. The size of the mtDNA genome is 16.3 kb. Genetic analysis of four corn stalk borer populations, collected from Greece (three populations) and Spain (one population), was undertaken using DNA sequences of the mtDNA cytochrome oxidase (CO) I and II genes. Sequencing of a 2079 bp region of these genes revealed 25 polymorphic sites among the populations. Five molecular RFLP markers, located in the mtDNA COI and COII genes, were surveyed, and two different haplotypes were detected. Phylogenetic analysis based on COI/COII nucleotide sequences revealed genetic differentiation between samples, and the results are discussed in relation to the geographic distribution of the corn stalk borer in two Mediterranean countries.
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Affiliation(s)
- Anna Kourti
- Department of Agricultural Biotechnology, Agricultural University of Athens, Iera Odos 75, Athens 11855, Greece.
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222
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Kawakita A, Kato M. Assessment of the diversity and species specificity of the mutualistic association between Epicephala moths and Glochidion trees. Mol Ecol 2006; 15:3567-81. [PMID: 17032258 DOI: 10.1111/j.1365-294x.2006.03037.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The obligate mutualisms between flowering plants and their seed-parasitic pollinators constitute fascinating examples of interspecific mutualisms, which are often characterized by high levels of species diversity and reciprocal species specificity. The diversification in these mutualisms has been thought to occur through simultaneous speciation of the partners, mediated by tight reciprocal adaptation; however, recent studies cast doubt over this general view. In this study, we examine the diversity and species specificity of Epicephala moths (Gracillariidae) that pollinate Glochidion trees (Phyllanthaceae), using analysis of mitochondrial and nuclear gene sequences. Phylogenetic analysis of Epicephala moths associated with five Glochidion species in Japan and Taiwan reveal six genetically isolated species that are also distinguishable by male genital morphology: (i) two species specific to single host species (G. acuminatum and G. zeylanicum, respectively); (ii) two species that coexist on G. lanceolatum; and (iii) two species that share two, closely-related parapatric hosts (G. obovatum and G. rubrum). Statistical analysis shows that the two species associated with G. lanceolatum are not sister species, indicating the colonization of novel Glochidion host in at least one lineage. Behavioural observations suggest that all six species possess the actively-pollinating habit, thus none of the studied species has become a nonmutualistic 'cheater' that exploits the benefit resulting from pollination by other species. Our results parallel recent findings in ecologically similar associations, namely the fig-fig wasp and yucca-yucca moth mutualisms, and contribute to a more general understanding of the factors that determine ecological and evolutionary outcomes in these mutualisms.
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Affiliation(s)
- Atsushi Kawakita
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo, Kyoto 606-8501, Japan.
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223
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Buckley TR, Cordeiro M, Marshall DC, Simon C. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst Biol 2006; 55:411-25. [PMID: 16684720 DOI: 10.1080/10635150600697283] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these issues with the radiation of New Zealand alpine cicadas of the genus Maoricicada Dugdale. Gene trees were estimated from four putative independent loci: mitochondrial DNA (2274 nucleotides), elongation factor 1-alpha (1275 nucleotides), period (1709 nucleotides), and calmodulin (678 nucleotides). We reconstructed phylogenies using maximum likelihood and Bayesian methods from 44 individuals representing the 19 species and subspecies of Maoricicada and two outgroups. Species-level relationships were reconstructed using a novel extension of gene tree parsimony, whereby gene trees were weighted by their Bayesian posterior probabilities. The inferred gene trees show marked incongruence in the placement of some taxa, especially the enigmatic forest and scrub dwelling species, M. iolanthe. Using the species tree estimated by gene tree parsimony, we simulated coalescent gene trees in order to test the null hypothesis that the nonrandom placement of M. iolanthe among gene trees has arisen by chance. Under the assumptions of constant population size, known generation time, and panmixia, we were able to reject this null hypothesis. Furthermore, because the two alternative placements of M. iolanthe are in each case with species that share a similar song structure, we conclude that it is more likely that an ancient introgression event rather than lineage sorting has caused this incongruence.
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224
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MCLEISH MICHAELJ, CHAPMAN THOMASW, MOUND LAURENCEA. Gall morpho-type corresponds to separate species of gall-inducing thrips (Thysanoptera: Phlaeothripidae). Biol J Linn Soc Lond 2006. [DOI: 10.1111/j.1095-8312.2006.00641.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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225
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Steiner FM, Schlick-Steiner BC, Konrad H, Moder K, Christian E, Seifert B, Crozier RH, Stauffer C, Buschinger A. No sympatric speciation here: multiple data sources show that the ant Myrmica microrubra is not a separate species but an alternate reproductive morph of Myrmica rubra. J Evol Biol 2006; 19:777-87. [PMID: 16674574 DOI: 10.1111/j.1420-9101.2005.01053.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
No aspect of speciation is as controversial as the view that new species can evolve sympatrically, among populations in close physical contact. Social parasitism has been suggested to yield necessary disruptive selection for sympatric speciation. Recently, mitochondrial DNA phylogeography has shown that the ant Myrmica microrubra is closely related to its host, Myrmica rubra, leading to the suggestion that sympatric speciation has occurred. We investigated the relationships between the two ant forms using mitochondrial and nuclear DNA sequences, microsatellite genotyping and morphometrics. Molecular phylogenetic and population structure analyses showed that M. microrubra does not evolve separately to its host but rather shares a gene pool with it. Probability analysis showed that mitochondrial DNA data previously adduced in favour of sympatric speciation do not in fact do so. Morphometrically, M. microrubra is most readily interpreted as a miniature queen form of M. rubra, not a separate species. Myrmica microrubra is not an example of speciation. The large (typical M. rubra) and small (M. microrubra) queen forms are alternative reproductive strategies of the same species. Myrmica microrubraSeifert 1993 is consequently synonymized here with M. rubra Linnaeus, 1758.
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Affiliation(s)
- F M Steiner
- Department of Integrative Biology, Institute of Zoology, Boku, University of Natural Resources and Applied Life Sciences Vienna, Vienna, Austria.
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226
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Jansa SA, Barker FK, Heaney LR. The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences. Syst Biol 2006; 55:73-88. [PMID: 16507525 DOI: 10.1080/10635150500431254] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].
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Affiliation(s)
- Sharon A Jansa
- Bell Museum of Natural History, University of Minnesota, 1987 Upper Buford Circle, (S.A.J.), St. Paul, Minnesota 55108, USA.
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227
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Wang BC, Park J, Watabe HA, Gao JJ, Xiangyu JG, Aotsuka T, Chen HW, Zhang YP. Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences. Mol Phylogenet Evol 2006; 40:484-500. [PMID: 16678448 DOI: 10.1016/j.ympev.2006.03.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 03/17/2006] [Accepted: 03/18/2006] [Indexed: 11/23/2022]
Abstract
Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.
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Affiliation(s)
- Bao-cheng Wang
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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228
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Phillips MJ, McLenachan PA, Down C, Gibb GC, Penny D. Combined Mitochondrial and Nuclear DNA Sequences Resolve the Interrelations of the Major Australasian Marsupial Radiations. Syst Biol 2006; 55:122-37. [PMID: 16507529 DOI: 10.1080/10635150500481614] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the "reduced-bias" mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.].
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Affiliation(s)
- Matthew J Phillips
- Henry Wellcome Ancient Biomolecules Center, Department of Zoology, Oxford University, South Parks Road, Oxford OX1 3PS, United Kingdom.
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229
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Jansa SA, Forsman JF, Voss RS. Different patterns of selection on the nuclear genes IRBP and DMP-1 affect the efficiency but not the outcome of phylogeny estimation for didelphid marsupials. Mol Phylogenet Evol 2006; 38:363-80. [PMID: 16054401 DOI: 10.1016/j.ympev.2005.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/03/2005] [Accepted: 06/07/2005] [Indexed: 11/29/2022]
Abstract
Selection at the protein-level can influence nucleotide substitution patterns for protein-coding genes, which in turn can affect their performance as phylogenetic characters. In this study, we compare two protein-coding nuclear genes that appear to have evolved under markedly different selective constraints and evaluate how selection has shaped their phylogenetic signal. We sequenced 1,100+ bp of exon 6 of the gene encoding dentin matrix protein 1 (DMP1) from most of the currently recognized genera of New World opossums (family: Didelphidae) and compared these data to an existing matrix of sequences from the interphotoreceptor retinoid-binding protein gene (IRBP) and morphological characters. In comparison to IRBP, DMP1 has far fewer sites under strong purifying selection and exhibits a number of sites under positive directional selection. Furthermore, selection on the DMP1 protein appears to conserve short, acidic, serine-rich domains rather than primary amino acid sequence; as a result, DMP1 has significantly different nucleotide substitution patterns from IRBP. Using Bayesian methods, we determined that DMP1 evolves almost 30% faster than IRBP, has 2.5 times more variable sites, has less among-site rate heterogeneity, is skewed toward A and away from CT (IRBP has relatively even base frequencies), and has a significantly lower rate of change between adenine and any other nucleotide. Despite these different nucleotide substitution patterns, estimates of didelphid relationships based on separate phylogenetic analyses of these genes are remarkably congruent whether patterns of nucleotide substitution are explicitly modeled or not. Nonetheless, DMP1 contains more phylogenetically informative characters per unit sequence and resolves more nodes with higher support than does IRBP. Thus, for these two genes, relaxed functional constraints and positive selection appear to improve the efficiency of phylogenetic estimation without compromising its accuracy.
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Affiliation(s)
- Sharon A Jansa
- Bell Museum of Natural History and Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, 55108, USA.
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230
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Larkin LL, Neff JL, Simpson BB. Phylogeny of the Callandrena subgenus of Andrena (Hymenoptera: Andrenidae) based on mitochondrial and nuclear DNA data: Polyphyly and convergent evolution. Mol Phylogenet Evol 2006; 38:330-43. [PMID: 16343953 DOI: 10.1016/j.ympev.2005.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 08/30/2005] [Accepted: 10/03/2005] [Indexed: 11/29/2022]
Abstract
We propose a phylogenetic hypothesis of relationships within Callandrena, a North American subgenus of the bee genus Andrena, based on both mitochondrial and nuclear DNA sequences. Our data included 695 aligned base pairs comprising parts of the mitochondrial genes cytochrome oxidase subunits I and II and the intervening tRNA-leucine and 767 aligned base pairs of the F2 copy of the nuclear gene elongation factor-1alpha. We also suggest a preliminary hypothesis of relationships of the North American subgenera in the genus. Our analyses included 54 species of Callandrena, 42 species of Andrena representing 24 additional subgenera, and 11 outgroup species in the family Andrenidae. Parsimony analyses of each marker separately suggested that Callandrena was polyphyletic, with a combined analysis suggesting that there were at least two phylogenetically independent clades of bees with similar morphological features. Maximum likelihood and Bayesian analyses supported this conclusion, as did the non-parametric bootstrapping SOWH test. Convergence in morphological characters was likely due to their common use of members of Asteraceae as pollen hosts.
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Affiliation(s)
- Leah L Larkin
- Section of Integrative Biology, The University of Texas at Austin, USA.
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231
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Zaldivar-Riverón A, Mori M, Quicke DLJ. Systematics of the cyclostome subfamilies of braconid parasitic wasps (Hymenoptera: Ichneumonoidea): A simultaneous molecular and morphological Bayesian approach. Mol Phylogenet Evol 2006; 38:130-45. [PMID: 16213168 DOI: 10.1016/j.ympev.2005.08.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Revised: 08/11/2005] [Accepted: 08/18/2005] [Indexed: 11/27/2022]
Abstract
Phylogenetic relationships among 95 genera collectively representing 17 of the 18 currently recognized cyclostome braconid wasp subfamilies were investigated based on DNA sequence fragments of the mitochondrial COI and the nuclear 28S rDNA genes, in addition to morphological data. The treatment of sequence length variation of the 28S partition was explored by either excluding ambiguously aligned regions and indel information (28SN) or recoding them (28SA) using the 'fragment-level' alignment method with a modified coding approach. Bayesian MCMC analyses were performed for the separate and combined data sets and a maximum parsimony analysis was also carried out for the simultaneous molecular and morphological data sets. There was a significant incongruence between the two genes and between 28S and morphology, but not for morphology and COI. Different analyses with the 28SA data matrix resulted in topologies that were generally similar to the ones from the 28SN matrix; however, the former topologies recovered a higher number of significantly supported clades and had a higher mean Bayesian posterior probability, thus supporting the inclusion of information from ambiguously aligned regions and indel events in phylogenetic analyses where possible. Based on the significantly supported clades obtained from the simultaneous molecular and morphological analyses, we propose that a total of 17 subfamilies should be recognized within the cyclostome group. The subfamilial placements of several problematic cyclostome genera were also established.
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232
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Cameron SA, Hines HM, Williams PH. Molecular phylogeny of the bumble bee subgenus Pyrobombus (Hymenoptera:Apidae:Bombus) with insights into gene utility for lower-level analysis. INVERTEBR SYST 2006. [DOI: 10.1071/is05028] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Comprising nearly 20% of all bumble bees, the subgenus Pyrobombus is distributed across diverse habitats in the Northern Hemisphere and exhibits considerable morphological and behavioural variation relative to other subgenera. Its size and variation have led to questions concerning its monophyly and intrasubgeneric relationships, but too few known morphological synapomorphies and insufficient taxon sampling have precluded robust answers to these questions. To obtain a robust phylogeny of the group, we obtained DNA sequences for 36 of the 43 species from four genes (mitochondrial 16S rRNA and three nuclear genes: elongation factor – 1α (EF-1α), long wavelength rhodopsin (LW Rh or opsin) and arginine kinase (ArgK)). Both Bayesian and parsimony phylogenies are well resolved and indicate a monophyletic Pyrobombus when assessed against representatives of 20 additional subgenera. The more conserved nuclear genes, especially EF-1α and ArgK, provided good support across all of the taxonomic levels examined, whereas support of the more rapidly evolving mt16S was restricted mostly to close relationships at the tips of the tree. The exon regions of ArgK were the most conserved and may be promising for higher-level phylogenetics. We discuss species relationships within Pyrobombus and its sister-group, Bombus s.s. + Alpinobombus, in relation to previous taxonomic studies.
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233
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Jiang ZF, Huang DW, Zhu CD, Zhen WQ. New insights into the phylogeny of fig pollinators using Bayesian analyses. Mol Phylogenet Evol 2005; 38:306-15. [PMID: 16364663 DOI: 10.1016/j.ympev.2005.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 08/31/2005] [Accepted: 11/07/2005] [Indexed: 11/25/2022]
Abstract
The interaction between figs and fig pollinators is one of the most species-specific mutualisms. Recently, phylogenies of both partners based on molecular data provided insights into a wide spectrum of co-evolutionary questions. However, for the phylogeny of fig pollinators, there are some discrepancies between different studies and left some relationships unresolved, especially for deep nodes. The phylogenetic uncertainties of pollinators prohibit our further understanding of the history of the mutualism. Here, we present phylogenetic analyses of a larger COI sequence dataset that includes previously published datasets and our sequences from 20 species using Bayesian method and maximum parsimony. The analyses using different methods share similar topologies. Bayesian analyses provide high level of confidence for most internal nodes in terms of posterior probability. This study also clarifies some discrepancies between previous studies. After rooting with Tetrapus, other pollinators split into two clades. Wiebesia and Blastophaga are at basal positions in respective clade. Ceratosolen is not monophyletic because Kradibia and Liporrhopalum fall inside this group. Three subgenera of Ceratosolen: subgen. Ceratosolen, subgen. Rothropus, and subgen. Strepitus are not supported. Therefore, Ceratosolen is suggested to be re-divided into three groups. Urostigma pollinators (including Dolichoris and Blastophaga psenes) are clustered together. The monophylies of Wiebesia, Blastophaga, Dolichoris are not supported in this analysis. This study also provides a new framework for re-evaluating character evolution and re-inspecting the definition of some genera.
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Affiliation(s)
- Zi-Feng Jiang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
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Rubinoff D, Holland BS. Between Two Extremes: Mitochondrial DNA is neither the Panacea nor the Nemesis of Phylogenetic and Taxonomic Inference. Syst Biol 2005; 54:952-61. [PMID: 16385775 DOI: 10.1080/10635150500234674] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Daniel Rubinoff
- Department of Plant and Environmental Protection Sciences, University of Hawaii, 3050 Maile Way, 310 Gilmore Hall, Honolulu, 96822, USA.
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Silva-Brandão KL, Lucci Freitas AV, Brower AVZ, Solferini VN. Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1α genes. Mol Phylogenet Evol 2005; 36:468-83. [PMID: 15953737 DOI: 10.1016/j.ympev.2005.04.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 12/06/2004] [Accepted: 04/05/2005] [Indexed: 11/15/2022]
Abstract
A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1alpha). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.
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Affiliation(s)
- Karina Lucas Silva-Brandão
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, CEP 13083-970, Campinas, SP, Brazil
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236
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Robe LJ, Valente VLS, Budnik M, Loreto ELS. Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: A nuclear versus mitochondrial gene approach. Mol Phylogenet Evol 2005; 36:623-40. [PMID: 15970444 DOI: 10.1016/j.ympev.2005.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Revised: 04/26/2005] [Accepted: 05/10/2005] [Indexed: 11/23/2022]
Abstract
The genus Drosophila has played an essential role in many biological studies during the last 100 years but much controversy and many incompletely addressed issues still remain to be elucidated regarding the phylogeny of this genus. Because information on the Neotropical species contained in the subgenus Drosophila is particularly incomplete, with this taxonomic group being underrepresented in many studies, we designed a study to answer some evolutionary questions related to these species. We subjected at least 41 Drosophilidae taxa to a phylogenetic analysis using a 516-base pair (bp) fragment of the alpha-methyldopa (Amd) nuclear gene and a 672 bp fragment of the mitochondrial cytochrome oxidase subunit II (COII) gene both individually and in combination. We found that the subgenus Drosophila is paraphyletic and subdivided into two main clusters: the first containing species traditionally placed in the virilis-repleta radiation and the second assembling species of the immigrans-Hirtodrosophila radiation. Inside the first of these clusters we could detect the monophyly of both the flavopilosa (the sister-clade of the annulimana group) and the mesophragmatica (closely related to the repleta group) species groups. Concerning the immigrans-Hirtodrosophila lineage, Zaprionus, Liodrosophila, Samoaia, and Hirtodrosophila were the early offshoots, followed by the immigrans, quinaria, testacea, and funebris species groups. The tripunctata radiation appears to be a derived clade, composed of a paraphyletic tripunctata group, intimately interposed with members of the cardini, guarani, and guaramunu species groups. Overall, the COII gene yielded a poor phylogenetic performance when compared to the Amd gene, the evolutionary hypothesis of which agreed with the total evidence tree. This phenomenon can be explained by the fast saturation of transitional substitutions in COII, due to strong biases in both base composition and substitution patterns, as also by its great among-site rate variation heterogeneity.
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Affiliation(s)
- Lizandra J Robe
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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237
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Lin CP, Danforth BN, Wood TK. Molecular phylogenetics and evolution of maternal care in Membracine treehoppers. Syst Biol 2004; 53:400-21. [PMID: 15503670 DOI: 10.1080/10635150490445869] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The treehopper subfamily Membracinae (Insecta: Hemiptera: Membracidae) comprises the majority of genera and species diversity in the New World tropics. These treehoppers exhibit a wide range of social behaviors, making them an excellent group for studying patterns of social evolution in insects. However, to date the tribal and generic relationships have remained unclear. We reconstructed the phylogeny of the Membracinae using a combined mitochondrial (COI, COII, tRNA-Leu, and 12S) and nuclear (Wg) gene data set. A total of 2608 aligned nucleotide sites were obtained for 112 species, representing 25 of 38 currently recognized genera and all four tribes. A strict consensus of five equally parsimonious trees recovered the subfamily and three of its four tribes. The majority rule consensus tree derived from the Bayesian analyses based on the GTR+I+G and mixed-models recovered many clades shared with the parsimony trees and is identical to the single best tree inferred from maximum likelihood analysis, aside from the rearrangement of one node. A comparison of mitochondrial and nuclear genes indicated that Wg provided higher consistency index (CI), data decisiveness (DD), partitioned Bremer support (PBS) than any of the mitochondrial genes analyzed. The combined mitochondrial and nuclear DNA provide strong support for the monophyly of the subfamily and three of its four tribes (Aconophorini, Hoplophorionini, and Hypsoprorini). Membracini is paraphyletic with respect to Hoplophorionini and contains two lineages, the Membracini sensu strictu and the newly resurrected tribe Bolbonotini. Our analyses show that there is a strong phylogenetic component to the evolution of maternal care. Given the widespread occurrence of maternal care within the subfamily, this trait is estimated to have < or = 3 origins, two reversals, and one loss. Our results suggest that the evolution of maternal care in insects may not be as evolutionarily labile as previously thought.
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Affiliation(s)
- Chung-Ping Lin
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY 14853-0901, USA.
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