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Molecular Phylogenetics (molecular + phylogenetic)
Terms modified by Molecular Phylogenetics Selected AbstractsFloristics and Plant Biogeography in ChinaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 7 2008De-Zhu Li Abstract In 1998, a revolutionary system of angiosperm classification, the Angiosperm Phylogeny Group system was published. Meanwhile, another new system of classification of angiosperms, the eight-class system was proposed by C. Y. Wu and colleagues based on long term work on the flora of China. The Flora Reipublicae Popularis Sinicae project was initiated in 1959 and completed by 2004. It is the largest Flora so far completed in the world, including 31 228 species of vascular plants, or one-eighth of the global plant diversity. The English-language and updated Flora of China (FOC) is an international joint effort initiated in 1988 and accelerated in 1998. Up to now, 15 of the 24 volumes of the FOC have been published. Based on the floristic data, the composition, characteristics, floristic divisions and affinities of the flora of China have been studied by Wu and colleagues since 1965. In the past 10 years, analyses of the available floristic data have been very productive. The East Asiatic Floristic Kingdom was proposed in 1998. All 346 families of angiosperms in China, according to the eight-class system of classification, were comprehensively discussed by using knowledge of current and historical distribution of seed plants in the world, together with some morphological and molecular data. A scheme of distribution patterns or areal-types of families and genera of seed plants in China was modified and elucidated, together with a proposed scheme of areal-types of the world. Molecular phylogenetic and biogeographical studies of angiosperms in China in the past 10 years also witnessed a progressive development. Integration of morphological and molecular data and fossil evidence revealed some significant results. Eastern Asia, which used to be regarded as an important center of survival during the ice age, is likely an important center of diversification of angiosperms. [source] Molecular phylogenetics of soricid shrews (Mammalia) based on mitochondrial cytochrome b gene sequences: with special reference to the SoricinaeJOURNAL OF ZOOLOGY, Issue 1 2006S. D. Ohdachi No abstract is available for this article. [source] Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizationsMOLECULAR ECOLOGY, Issue 4 2005JENNIFER L. TRUSTY Abstract A molecular phylogenetic study of Bystropogon L'Hèr. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution. [source] The minimum evolution problem: Overview and classificationNETWORKS: AN INTERNATIONAL JOURNAL, Issue 2 2009Daniele Catanzaro Abstract Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means of molecular data. These relationships are typically described by means of weighted trees, or phylogenies, whose leaves represent the observed organisms, internal vertices the intermediate ancestors, and edges the evolutionary relationships between pairs of organisms. Molecular phylogenetics provides several criteria for selecting one phylogeny from among plausible alternatives. Usually, such criteria can be expressed in terms of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important criteria is the minimum evolution (ME) criterion, which states that the optimal phylogeny for a given set of organisms is the one whose sum of edge weights is minimal. Finding the phylogeny that satisfies the ME criterion involves solving an optimization problem, called the minimum evolution problem (MEP), which is notoriously -Hard. This article offers an overview of the MEP and discusses the different versions of it that occur in the literature. © 2008 Wiley Periodicals, Inc. NETWORKS, 2009 [source] Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga, Dasoclema and Australian species of MelodorumBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010LINLIN ZHOU An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA-trnH spacer, rbcL and trnL-F). The additional taxa include the monotypic West African genus Balonga, the monotypic South-East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well-supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re-evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163, 33,43. [source] Molecular phylogenetics of tribe Synandreae, a North American lineage of lamioid mints (Lamiaceae)CLADISTICS, Issue 3 2008Anne-Cathrine Scheen The five mint genera Brazoria, Macbridea, Physostegia, Synandra and Warnockia (Lamioideae: Lamiaceae) are all North American endemics. Together with the monotypic European genus Melittis and the Asian genus Chelonopsis, these taxa have been classified as subtribe Melittidinae. Previous morphological studies have failed to uncover synapomorphic characters for this group. We sequenced the plastid trnL-trnF region and trnS-trnG spacer and the nuclear ribosomal 5S non-transcribed spacer (5S-NTS) to assess phylogenetic relationships within Melittidinae. Standard parsimony and direct optimization (POY) analyses show Melittis, the type genus of the subtribe, as sister to Stachys. Thus, the monophyly of subtribe Melittidinae is not supported either by molecular or morphological data. However, the North American endemics form a monophyletic group that can be recognized as the recircumscribed tribe Synandreae. The molecular relationships among these genera are corroborated by both morphological and cytological data. The expected close relationship between the south-central endemics Warnockia and Brazoria and their sister relationship to the widespread genus Physostegia is confirmed. Nevertheless, most of the North American endemics are restricted to the south-east of the continent. Dispersal westwards and northwards is correlated with an increase in chromosome numbers. No specific Eurasian origin (i.e., transatlantic or transpacific) can be determined, but Synandreae are clearly distinct from the large Stachys clade, and therefore represent a separate migration into North America. © The Willi Hennig Society 2007. [source] Use of a PCR-based approach for sequencing whole mitochondrial genomes of insects: two examples (cockroach and dragonfly) based on the method developed for decapod crustaceansINSECT MOLECULAR BIOLOGY, Issue 4 2004M. M. Yamauchi Abstract Recent development of a PCR-based approach for sequencing vertebrate mitochondrial genomes has attracted much attention as being more rapid and economical than traditional methods using cloned mtDNA and primer walking. Such a method has not been available for insect mitochondrial genomes, despite widespread use of them for the molecular phylogenetic, biogeographical and population genetic markers. A recently developed PCR-based approach for sequencing whole mitochondrial genomes of decapod crustaceans, which included the design of many versatile PCR primers for the latter, was applied with the same primers sets to mitochondrial genomes of two insects, smokybrown cockroach Periplaneta fuliginosa (Serville, 1839) and skimmer dragonfly Orthetrum triangulare melania (Selys, 1883). Almost the entire region of the two mitochondrial genomes was successfully sequenced. Features of the two mitochondrial genomes are described and the usefulness of this PCR-based approach for sequencing insect mitochondrial genomes demonstrated. [source] TESTING THE ROLE OF INTERSPECIFIC COMPETITION IN THE EVOLUTIONARY ORIGIN OF ELEVATIONAL ZONATION: AN EXAMPLE WITH BUARREMON BRUSH-FINCHES (AVES, EMBERIZIDAE) IN THE NEOTROPICAL MOUNTAINSEVOLUTION, Issue 5 2007Carlos Daniel Cadena Interspecific competition might drive the evolution of ecological niches and result in pairs of formerly competing species segregating along ecological gradients following a process of character displacement. This mechanism has been proposed to account for replacement of related species along gradients of elevation in many areas of the world, but the fundamental issue of whether competition is responsible for the origin of elevational replacements has not been tested. To test hypotheses about the role of interspecific competition in the origin of complementary elevational ranges, I combined molecular phylogenetics, phylogeography, and population genetic analyses on Buarremon torquatus and B. brunneinucha (Aves, Emberizidae), whose patterns of elevational distribution suggest character displacement or ecological release. The hypothesis that elevational distributions in these species changed in opposite directions as a result of competition is untenable because: (1) a historical expansion of the range of B. brunneinucha into areas occupied by B. torquatus was not accompanied by a shift in the elevational range of the former species; (2) when B. brunneinucha colonized the range of B. torquatus, lineages of the latter distributions had already diverged; and (3) historical trends in effective population size do not suggest populations with elevational ranges abutting those of putative competitors have declined as would be expected if competition caused range contractions. However, owing to uncertainty in coalescent estimates of historical population sizes, the hypothesis that some populations of B. torquatus have declined cannot be confidently rejected, which suggests asymmetric character displacement might have occurred. I suggest that the main role of competition in elevational zonation may be to act as a sorting mechanism that allows the coexistence along mountain slopes only of ecologically similar species that differ in elevational distributions prior to attaining sympatry. The contrasting biogeographic histories of B. brunneinucha and B. torquatus illustrate how present-day ecological interactions can have recent origins, and highlights important challenges for testing the hypothesis of character displacement in the absence of data on population history and robust reconstructions of the evolution of traits and geographic ranges. [source] CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIESEVOLUTION, Issue 4 2006Michael J. Wade Abstract We report the findings of our theoretical investigation of the effect of random genetic drift on the covariance of identity-by-descent (ibd) of nuclear and cytoplasmic genes. The covariance in ibd measures of the degree to which cyto-nuclear gene combinations are heritable, that is, transmitted together from parents to offspring. We show how the mating system affects the covariance of ibd, a potentially important aspect of host-pathogen or host-symbiont coevolution. The magnitude of this covariance influences the degree to which the evolution of apparently neutral cytoplasmic genes, often used in molecular phylogenetics, might be influenced by selection acting on unlinked nuclear genes. To the extent that cyto-nuclear gene combinations are inherited together, genomic conflict is mitigated and intergenomic transfer it facilitated, because genes in both organelle and nuclear genomes share the same evolutionary fate. The covariance of ibd also affects the rate at which cyto-nuclear epistatic variance is converted to additive variance necessary for a response to selection. We find that conversion is biased in species with separate sexes, so that the increment of additive variance added to the nuclear genome exceeds that added to the cytoplasmic genome. As a result, the host might have an adaptive advantage in a coevolutionary arms race with vertically (maternally) transmitted pathogens. Similarly, the nuclear genome could be a source of compensatory mutations for its organellar genomes, as occurs in cytoplasmic male sterility in some plant species. We also discuss the possibility that adaptive cytoplasmic elements, such as favorable mitochondrial mutations or endosymbionts (e.g., Wolbachia), have the potential to release heritable nuclear variation as they sweep through a host population, supporting the view that cytoplasmic introgression plays an important role in adaptation and speciation. [source] Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed HalimedaGLOBAL ECOLOGY, Issue 4 2009Heroen Verbruggen ABSTRACT Aim Because of their broad distribution in geographical and ecological dimensions, seaweeds (marine macroalgae) offer great potential as models for marine biogeographical inquiry and exploration of the interface between macroecology and macroevolution. This study aims to characterize evolutionary niche dynamics in the common green seaweed genus Halimeda, use the observed insights to gain understanding of the biogeographical history of the genus and predict habitats that can be targeted for the discovery of species of special biogeographical interest. Location Tropical and subtropical coastal waters. Methods The evolutionary history of the genus is characterized using molecular phylogenetics and relaxed molecular clock analysis. Niche modelling is carried out with maximum entropy techniques and uses macroecological data derived from global satellite imagery. Evolutionary niche dynamics are inferred through application of ancestral character state estimation. Results A nearly comprehensive molecular phylogeny of the genus was inferred from a six-locus dataset. Macroecological niche models showed that species distribution ranges are considerably smaller than their potential ranges. We show strong phylogenetic signal in various macroecological niche features. Main conclusions The evolution of Halimeda is characterized by conservatism for tropical, nutrient-depleted habitats, yet one section of the genus managed to invade colder habitats multiple times independently. Niche models indicate that the restricted geographical ranges of Halimeda species are not due to habitat unsuitability, strengthening the case for dispersal limitation. Niche models identified hotspots of habitat suitability of Caribbean species in the eastern Pacific Ocean. We propose that these hotspots be targeted for discovery of new species separated from their Caribbean siblings since the Pliocene rise of the Central American Isthmus. [source] Adaptive radiation in Lesser Antillean lizards: molecular phylogenetics and species recognition in the Lesser Antillean dwarf gecko complex, Sphaerodactylus fantasticusMOLECULAR ECOLOGY, Issue 6 2008R. S. THORPE Abstract The time associated with speciation varies dramatically among lower vertebrates. The nature and timing of divergence is investigated in the fantastic dwarf gecko Sphaerodactylus fantasticus complex, a nominal species that occurs on the central Lesser Antillean island of Guadeloupe and adjacent islands and islets. This is compared to the divergence in the sympatric anole clade from the Anolis bimaculatus group. A molecular phylogenetic analysis of numerous gecko populations from across these islands, based on three mitochondrial DNA genes, reveals several monophyletic groups occupying distinct geographical areas, these being Les Saintes, western Basse Terre plus Dominica, eastern Basse Terre, Grand Terre, and the northern and eastern islands (Montserrat, Marie Galante, Petite Terre, Desirade). Although part of the same nominal species, the molecular divergence within this species complex is extraordinarily high (27% patristic distance between the most divergent lineages) and is compatible with this group occupying the region long before the origin of the younger island arc. Tests show that several quantitative morphological traits are correlated with the phylogeny, but in general the lineages are not uniquely defined by these traits. The dwarf geckos show notably less nominal species-level adaptive radiation than that found in the sympatric southern clade of Anolis bimculatus, although both appear to have occupied the region for a broadly similar period of time. Nevertheless, the dwarf gecko populations on Les Saintes islets are the most morphologically distinct and are recognized as a full species (Sphaerodactylus phyzacinus), as are anoles on Les Saintes (Anolis terraealtae). [source] Interspecific hybridization in plant-associated fungi and oomycetes: a reviewMOLECULAR ECOLOGY, Issue 11 2003C. L. Schardl Abstract Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants. [source] Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and processMOLECULAR ECOLOGY, Issue 6 2002B. C. Emerson Abstract By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands. [source] Their Day in the Sun: molecular phylogenetics and origin of photosymbiosis in the ,other' group of photosymbiotic marine bivalves (Cardiidae: Fraginae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009LISA KIRKENDALE The subfamily Fraginae (Cardiidae) is a morphologically diverse group of small-bodied marine clams inhabiting shallow seas worldwide. Like the exclusively photosymbiotic giant clams (Cardiidae: Tridacninae), some fragines are known to host zooxanthellae photosymbionts. However, surveys to widely determine photosymbiotic status and the lack of a comprehensive phylogeny have hindered attempts to track the evolution of photosymbiosis in the group. Worldwide sampling of all fragine genera and subgenera with phylogenetic reconstructions based on four gene regions [nuclear (28S) and mtDNA (16S, cytochrome oxidase I, cytochrome b)] does not support a monophyletic Fraginae. Sampled taxa form four restructured clades: (1) the ,Fragum' group, (2) the ,Trigoniocardia' and ,Ctenocardia' groups, (3) the ,Parvicardium' group and (4) the ,Papillicardium' group. Maximum likelihood analyses strongly support a clade of European cardiids uniting species from three subfamilies. Live examination of > 50% of species reveals that less than half of derived genera and subgenera host photosymbionts, supporting a single and relatively late origin of photosymbiosis in the Fraginae. The evolutionary implications for a small and little modified earliest diverging photosymbiotic lineage are discussed. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 448,465. [source] | |||||||||||||||||||||||||