当前位置： SCI文献检索 > MOLECULAR PHYLOGENETICS AND EVOLUTION期刊下所有文献 > Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions.

Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions.

Abstract：

:Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes. We fully reconstruct phylogenetic relationships of AA- genome species with confidence. Oryza meridionalis, native to Australia, is found to be the earliest divergent lineage around 2.93 mya, whereas O. punctata, a BB- genome species, serves as the best outgroup to distinguish their phylogenetic relationships. They separated from O. punctata approximately 9.11 mya during the Miocene epoch, and subsequently radiated to generate the entire AA- genome lineage diversity. The success in resolving the phylogeny of AA- genome species highlights the potential of phylogenomics to determine their divergence and evolutionary histories.

journal_name

Mol Phylogenet Evol

journal_title

Molecular phylogenetics and evolution

authors

Zhu T,Xu PZ,Liu JP,Peng S,Mo XC,Gao LZ

doi

10.1016/j.ympev.2013.10.008

subject

Has Abstract

pub_date

2014-01-01 00:00:00

pages

348-61

eissn

1055-7903

issn

1095-9513

pii

S1055-7903(13)00394-1

journal_volume

70

pub_type

杂志文章

相关文献

MOLECULAR PHYLOGENETICS AND EVOLUTION文献大全
  • Structure and evolution of the mitochondrial genomes of Haematobia irritans and Stomoxys calcitrans: the Muscidae (Diptera: Calyptratae) perspective.

    abstract：:We present the first two mitochondrial genomes of Muscidae dipterans for the species Haematobia irritans (the horn fly) and Stomoxys calcitrans (the stable fly). Typical insect mtDNA features are described, such as a high A+T content (79.1% and 78.9%, respectively), the preference for A+T-rich codons, and the evidence...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2008.05.022

    authors： Oliveira MT,Barau JG,Junqueira AC,Feijão PC,Rosa AC,Abreu CF,Azeredo-Espin AM,Lessinger AC

    更新日期：2008-09-01 00:00:00

  • New insights into the phylogeny of Pleopeltis and related Neotropical genera (Polypodiaceae, Polypodiopsida).

    abstract：:The fern family Polypodiaceae plays an important role in Neotropical epiphyte diversity. Most of its American representatives are assembled in a monophyletic clade that, apart from the grammitids, nearly exclusively comprises species restricted to the New World. The phylogenetic relationships of these ferns are still ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2009.05.001

    authors： Otto EM,Janssen T,Kreier HP,Schneider H

    更新日期：2009-10-01 00:00:00

  • Molecular taxonomy and phylogenetic relationships among Australian Nasutitermes and Tumulitermes genera (Isoptera, Nasutitermitinae) inferred from mitochondrial COII and 16S sequences.

    abstract：:The subfamily Nasutitermitinae Hare (1937) is a tropical and subtropical group, generally considered as the most specialised subfamily of Termitidae. To highlight some taxonomic inconsistencies, the phylogenetic relationships among seven Australian species, morphologically ascribed to the genera Nasutitermes and Tumul...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2007.07.014

    authors： Bergamaschi S,Dawes-Gromadzki TZ,Luchetti A,Marini M,Mantovani B

    更新日期：2007-12-01 00:00:00

  • Reappraisal of the "Molecular phylogeny of Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora)": when poor science meets GenBank.

    abstract：:A paper on the 'Molecular phylogeny of Western Palaearctic Helicidae s.l.', published by Steinke et al. (2004) in this journal, is critically analysed. Several obvious errors are corrected and methodological weaknesses are revealed. BLAST searches on the sequences published in that paper and now in GenBank, showed hig...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2011.08.024

    authors： Groenenberg DS,Neubert E,Gittenberger E

    更新日期：2011-12-01 00:00:00

  • Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy.

    abstract：:With the proliferation of species-tree methods, empiricists now have to confront the daunting task of method choice. Such decisions might be made based on theoretical considerations alone. However, the messiness of real data means that theoretical ideals may not hold in practice (e.g., with convergence of complicated ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.07.004

    authors： Knowles LL,Lanier HC,Klimov PB,He Q

    更新日期：2012-11-01 00:00:00

  • The mitochondrial cytochrome oxidase II gene in Bacillus stick insects: ancestry of hybrids, androgenesis, and phylogenetic relationships.

    abstract：:Sequencing of a cytochrome oxidase II (COII) gene fragment in Bacillus taxa provided evidence that the bisexual B. rossius is the maternal ancestor of the hybridogenetic B. rossius-grandii strains and revealed the same ancestry for both parthenogenetic hybrids: the diploid B. whitei (B. rossius/grandii grandii) and th...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.2000.0850

    authors： Mantovani B,Passamonti M,Scali V

    更新日期：2001-04-01 00:00:00

  • Gene conversion generates hypervariability at the variable regions of kallikreins and their inhibitors.

    abstract：:The two mechanisms for generating hypervariability at the reactive center of serine proteases and their inhibitors are gene conversion followed by natural selection and natural selection for point mutation. One way to clarify the effects of these two mechanisms is to calculate separately the number of nonsynonymous su...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/1055-7903(92)90022-9

    authors： Ohta T,Basten CJ

    更新日期：1992-06-01 00:00:00

  • In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus).

    abstract：:The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic d...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2016.12.009

    authors： Domingos FMCB,Colli GR,Lemmon A,Lemmon EM,Beheregaray LB

    更新日期：2017-02-01 00:00:00

  • A molecular phylogenetic analysis of the vampire moths and their fruit-piercing relatives (Lepidoptera: Erebidae: Calpinae).

    abstract：:Within butterflies and moths, adult hematophagy is limited to species within the vampire moth genus Calyptra. These moths are placed within the subfamily Calpinae, whose other members are known to exhibit a broad range of feeding behaviors including those that can be considered 'piercers' of fruits or other hosts and ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.06.029

    authors： Zaspel JM,Zahiri R,Hoy MA,Janzen D,Weller SJ,Wahlberg N

    更新日期：2012-11-01 00:00:00

  • Phylogeny of the hillstream loach genus Mesonoemacheilus reveals widespread diversification through ancient drainage connections in the Western Ghats Biodiversity Hotspot.

    abstract：:Rivers draining the Western Ghats (WG) mountain ranges in peninsular India harbor an exceptionally diverse, unique and evolutionarily distinct assemblage of lower vertebrates with high levels of endemism, attributed to their evolution and potentially long history of isolation during the Late Cretaceous or Early Tertia...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.08.013

    authors： Anoop VK,Dahanukar N,Philip S,Thomas L,Raghavan R

    更新日期：2018-12-01 00:00:00

  • Molecular systematics and biogeography of aridland gnatcatchers (genus Polioptila) and evidence supporting species status of the California gnatcatcher (Polioptila california).

    abstract：:Over 2000 basepairs of mitochondrial DNA (mtDNA) sequences were compared to (1) examine evolution in protein coding versus noncoding [control region (CR)] segments, and (2) test the species-level distinctiveness of the California gnatcatcher (Polioptila californica) and clarify its phylogenetic and biogeographic relat...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.1997.0444

    authors： Zink RM,Blackwell RC

    更新日期：1998-02-01 00:00:00

  • Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy.

    abstract：:The cpDNA of Welwitschia mirabilis (the only species of Welwitschiales) was recently reported to be the most reduced and compact among photosynthetic land plants. However, cpDNAs of the other two gnetophyte lineages (viz. Ephedrales and Gnetales) have not yet been studied. It remains unclear what underlining mechanism...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2008.12.026

    authors： Wu CS,Lai YT,Lin CP,Wang YN,Chaw SM

    更新日期：2009-07-01 00:00:00

  • Species-level phylogeography and evolutionary history of the hyperdiverse marine gastropod genus Conus.

    abstract：:Phylogenetic and paleontological analyses are combined to reveal patterns of species origination and divergence and to define the significance of potential and actual barriers to dispersal in Conus, a species-rich genus of predatory gastropods distributed throughout the world's tropical oceans. Species-level phylogene...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2004.09.012

    authors： Duda TF Jr,Kohn AJ

    更新日期：2005-02-01 00:00:00

  • Total evidence, consensus, and bat phylogeny: A distance-based approach.

    abstract：:Resolution of the total evidence (i.e., character congruence) versus consensus (i.e., taxonomic congruence) debate has been impeded by (1) a failure to employ validation methods consistently across both tree-building and consensus analyses, (2) the incomparability of methods for constructing as opposed to those for co...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1006/mpev.1998.0561

    authors： Lapointe FJ,Kirsch JA,Hutcheon JM

    更新日期：1999-02-01 00:00:00

  • Phylogeography of a morphologically diverse Neotropical montane species, the Common Bush-Tanager (Chlorospingus ophthalmicus).

    abstract：:The Common Bush-Tanager (Chlorospingus ophthalmicus) is distributed in Neotropical cloud-forests from Mexico to Argentina and contains 25 subspecies divided into eight subspecies groups based on biogeography, eye coloration, presence of a postocular spot and chest band. All of Central America is occupied by a single s...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2008.02.004

    authors： Weir JT,Bermingham E,Miller MJ,Klicka J,González MA

    更新日期：2008-05-01 00:00:00

  • Shark tales: a molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes).

    abstract：:Sharks are a diverse and ecologically important group, including some of the ocean's largest predatory animals. Sharks are also commercially important, with many species suffering overexploitation and facing extinction. However, despite a long evolutionary history, commercial, and conservation importance, phylogenetic...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2010.11.018

    authors： Vélez-Zuazo X,Agnarsson I

    更新日期：2011-02-01 00:00:00

  • Ecological divergence in the yellow-bellied kingsnake (Lampropeltis calligaster) at two North American biodiversity hotspots.

    abstract：:Several biogeographic barriers in the Eastern Nearctic appear to reduce gene flow among populations of many species in predictable ways, however these patterns used to infer process of divergence may be deceiving if alternative modes of diversification are not considered. By using a multilocus statistical phylogeograp...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2016.09.006

    authors： McKelvy AD,Burbrink FT

    更新日期：2017-01-01 00:00:00

  • Molecular phylogeny and character evolution in the Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora).

    abstract：:In this study, we present a molecular phylogeny for the west Palaearctic Helicidae sensu lato based on sequence data from two mitochondrial (COI, 16S rDNA) and two nuclear (ITS-1, 18S rDNA) genes. Maximum likelihood analysis and Bayesian inference revealed well supported monophyletic clades partly conflicting traditio...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2004.03.004

    authors： Steinke D,Albrecht C,Pfenninger M

    更新日期：2004-09-01 00:00:00

  • Combined molecular and morphological phylogenetic analyses of the New Zealand wolf spider genus Anoteropsis (Araneae: Lycosidae).

    abstract：:Datasets from the mitochondrial gene regions NADH dehydrogenase subunit I (ND1) and cytochrome c oxidase subunit I (COI) of the 20 species in the New Zealand wolf spider (Lycosidae) genus Anoteropsis were generated. Sequence data were phylogenetically analysed using parsimony and maximum likelihood analyses. The phylo...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/s1055-7903(03)00219-7

    authors： Vink CJ,Paterson AM

    更新日期：2003-09-01 00:00:00

  • Towards a species level tree of the globally diverse genus Chenopodium (Chenopodiaceae).

    abstract：:Chenopodium is a large and morphologically variable genus of annual and perennial herbs with an almost global distribution. All subgenera and most sections of Chenopodium were sampled along with other genera of Chenopodieae, Atripliceae and Axyrideae across the subfamily Chenopodioideae (Chenopodiaceae), totalling to ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2011.10.006

    authors： Fuentes-Bazan S,Mansion G,Borsch T

    更新日期：2012-01-01 00:00:00

  • Cryptic diversity in a widespread North American songbird: phylogeography of the Brown Creeper (Certhia americana).

    abstract：:The identification of species via morphological characteristics has traditionally left cryptic species undescribed in taxa under selection for morphological conservation (or a lack of selection for morphological change). Treecreepers (Genus: Certhia) have a conserved morphological appearance, making it difficult to as...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2010.12.003

    authors： Manthey JD,Klicka J,Spellman GM

    更新日期：2011-03-01 00:00:00

  • Phylogenetic relationships, subdivision, and biogeography of the cyprinid tribe Labeonini (sensu) (Teleostei: Cypriniformes), with comments on the implications of lips and associated structures in the labeonin classification.

    abstract：:The Labeonini (sensu Rainboth, 1991) is a tribe of the subfamily Cyprininae, the largest subfamily of Cypriniformes. With around 400 species in 34 genera, this tribe is widely distributed in the freshwaters of tropical Africa and Asia. Most species are adapted to fast-flowing streams and rivers, and exhibit unique mor...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2009.09.027

    authors： Yang L,Mayden RL

    更新日期：2010-01-01 00:00:00

  • Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago.

    abstract：:The extant endemic katydids (Orthoptera: Tettigoniidae) of the Hawaiian Archipelago include one to three species per high island and a single species on Nihoa, all currently placed in the genus Banza. These acoustic insects provide an excellent opportunity for investigating the evolution of reproductive isolation and ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2006.04.006

    authors： Shapiro LH,Strazanac JS,Roderick GK

    更新日期：2006-10-01 00:00:00

  • Genetic structure, phylogeography, and migration routes of Bouteloua gracilis (Kunth) Lag. ex Griffiths (Poaceae:Chloridoideae).

    abstract：:Blue grama grass (Bouteloua gracilis) populations are found in widely variable environments, tolerating drought, alkaline soils and different levels of grazing. Many ploidy levels have been reported for this species that is also considered to be phenotypically plastic and morphologically variable. Recently a decline i...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2019.01.005

    authors： Avendaño-González M,Morales-Domínguez JF,Siqueiros-Delgado ME

    更新日期：2019-05-01 00:00:00

  • A time-calibrated phylogeny of the butterfly tribe Melitaeini.

    abstract：:The butterfly tribe Melitaeini [Nymphalidae] contains numerous species that have been the subjects of a wide range of biological studies. Despite numerous taxonomic revisions, many of the evolutionary relationships within the tribe remain unresolved. Utilizing mitochondrial and nuclear gene regions, we produced a time...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2014.06.010

    authors： Long EC,Thomson RC,Shapiro AM

    更新日期：2014-10-01 00:00:00

  • Biogeography and diversification dynamics of the African woodpeckers.

    abstract：:The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world's avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and t...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2017.01.007

    authors： Fuchs J,Pons JM,Bowie RC

    更新日期：2017-03-01 00:00:00

  • Phylogeography and species boundaries of the western North American Nightsnake (Hypsiglena torquata): revisiting the subspecies concept.

    abstract：:The subspecies concept has received considerable debate throughout the past century. Subspecies were originally used to delineate potential incipient species, but were later employed to simply capture geographical variation. There is a recent trend to eliminate the trinomial in light of new evidence. Discrete, diagnos...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2007.12.012

    authors： Mulcahy DG

    更新日期：2008-03-01 00:00:00

  • Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization.

    abstract：:Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life hi...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2020.107023

    authors： Sharanowski BJ,Ridenbaugh RD,Piekarski PK,Broad GR,Burke GR,Deans AR,Lemmon AR,Moriarty Lemmon EC,Diehl GJ,Whitfield JB,Hines HM

    更新日期：2021-03-01 00:00:00

  • Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae).

    abstract：:Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular p...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2012.05.011

    authors： Aliabadian M,Kaboli M,Förschler MI,Nijman V,Chamani A,Tillier A,Prodon R,Pasquet E,Ericson PG,Zuccon D

    更新日期：2012-10-01 00:00:00

  • Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America.

    abstract：:White-nosed coatis (Nasua narica) are widely distributed throughout North, Central, and South America, but the patterns of temporal and spatial diversification that have contributed to this distribution are unknown. In addition, the biogeographic history of procyonid species in the Americas remains contentious. Using ...

    journal_title：Molecular phylogenetics and evolution

    pub_type： 杂志文章

    doi：10.1016/j.ympev.2018.11.011

    authors： Nigenda-Morales SF,Gompper ME,Valenzuela-Galván D,Lay AR,Kapheim KM,Hass C,Booth-Binczik SD,Binczik GA,Hirsch BT,McColgin M,Koprowski JL,McFadden K,Wayne RK,Koepfli KP

    更新日期：2019-02-01 00:00:00