Abstract:
:Sequence alignments of multiple genes are routinely used to infer phylogenetic relationships among species. The analysis of their concatenation is more likely to give correct results under an assumption of homotachy (i.e., the evolutionary rates within lineages in each of the concatenated genes are constant during evolution). Here, we examine how the violation of homotachy (i.e., presence of within-site rate variation, called heterotachy) distorts species phylogenies. A theoretical examination has been conducted using a four taxon case and the neighbor joining (NJ) method, concluding that NJ recovers the incorrect tree when concatenated genes exhibit heterotachy. The application of average and weighted-average distance approaches, where gene boundaries are kept intact, overcomes the detrimental effect of heterotachy in multigene analysis using the NJ method.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Som A,Fuellen Gdoi
10.1016/j.ympev.2009.05.025subject
Has Abstractpub_date
2009-09-01 00:00:00pages
846-51issue
3eissn
1055-7903issn
1095-9513pii
S1055-7903(09)00207-3journal_volume
52pub_type
杂志文章abstract::We analyzed 2995 base pairs of nucleotide sequence data (nuclear beta-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2006.02.021
更新日期:2006-08-01 00:00:00
abstract::It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRN...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2005.12.016
更新日期:2006-06-01 00:00:00
abstract::The gene encoding the progesterone receptor (PGR) acts as a transcription factor, and participates in the regulation of reproductive processes including menstruation, implantation, pregnancy maintenance, parturition, mammary development, and lactation. Unlike other mammals, primates do not exhibit progesterone withdra...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.12.026
更新日期:2008-05-01 00:00:00
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
更新日期:2008-09-01 00:00:00
abstract::Viviparity has evolved from oviparity in many vertebrate lineages, and species that contain both oviparous and viviparous populations offer the best opportunity for a detailed examination of the processes involved in this major life-history transition. However, although several such species have been reported, none ha...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1997.0468
更新日期:1998-08-01 00:00:00
abstract::The longhorn bee tribe Eucerini (Hymenoptera: Apidae) is a diverse, widely distributed group of solitary bees that includes important pollinators of both wild and agricultural plants. About half of the species in the tribe are currently assigned to the genus Eucera and to a few other related genera. In this large genu...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.10.007
更新日期:2018-02-01 00:00:00
abstract::The pattern of genetic variation of the lizard Mabuya maculilabris from São Tomé Island (Gulf of Guinea) was investigated using a combination of three mitochondrial DNA gene fragments. Forty-eight haplotypes were recovered among 66 individuals covering the whole island. The genealogy inferred from the most parsimoniou...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2005.04.032
更新日期:2005-11-01 00:00:00
abstract::Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.05.009
更新日期:2018-10-01 00:00:00
abstract::Allopolyploid speciation is widespread in plants, yet the molecular requirements for successful orchestration of coordinated gene expression for two divergent and reunited genomes are poorly understood. Recent studies in several plant systems have revealed that allopolyploid genesis under both synthetic and natural co...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章,评审
doi:10.1016/s1055-7903(03)00213-6
更新日期:2003-12-01 00:00:00
abstract::The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another a...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2016.04.012
更新日期:2016-07-01 00:00:00
abstract::Eukaryotes encompass a remarkable variety of organisms and unresolved lineages. Different phylogenetic analyses have lead to conflicting conclusions as to the origin and associations between lineages and species. In this work, we investigated evolutionary relationship of a family of cation pumps exclusive for the secr...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.10.023
更新日期:2008-02-01 00:00:00
abstract::Model species often provide initial hypotheses and tools for studies of development, genetics and molecular evolution in closely related species. Flour beetles of the genus Tribolium Macleay (1825) are one group with potential for such comparative studies. Tribolium castaneum (Herbst 1797) is an increasingly useful de...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.08.017
更新日期:2008-01-01 00:00:00
abstract::The alpine genus Chionohebe is one of seven genera in the southern hemisphere Hebe complex. The main aims of this study were to infer the evolutionary relationships and assess phylogeographic patterns among the six species of Chionohebe, determine the origin of the two species with trans-Tasman distributions, and test...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.12.019
更新日期:2008-04-01 00:00:00
abstract::The Yellow-shouldered bats, Genus Sturnira, are widespread, diverse, and abundant throughout the Neotropical Region, but little is known of their phylogeny and biogeography. We collected 4409 bp of DNA from three mitochondrial (cyt-b, ND2, D-loop) and two nuclear (RAG1, RAG2) sequences from 138 individuals representin...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.04.016
更新日期:2013-09-01 00:00:00
abstract::The goal of the current study was to determine if cuticular hydrocarbons could be used to empirically delimit taxa within the Cryptocercus punctulatus species complex in the eastern United States. Cockroaches were collected from rotting logs in 22 locations across four states. Hydrocarbon phenotypes and two mitochondr...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.03.011
更新日期:2008-06-01 00:00:00
abstract::Snakes of the subfamily Boinae are found in Madagascar, the Papuan-Pacific Islands, and the Neotropics. It has been suggested that genera within each of these particular areas do not form monophyletic groups. Further, it was proposed that the New World Boa constrictor is more closely related to boine genera in Madagas...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2004.08.017
更新日期:2005-01-01 00:00:00
abstract::The catfish family Diplomystidae is one of the earliest branching lineages within the diverse order Siluriformes and shows a deep phylogenetic split from all other extant and extinct major catfish groups. Despite its relevance in the evolution of siluriforms, phylogenetic relationships within the Diplomystidae are poo...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.01.015
更新日期:2014-04-01 00:00:00
abstract::To better understand the underlying causes of rarity and extinction risk in Acropora (staghorn coral), we contrast the minimum divergence ages and nucleotide diversity of an array of species with different range sizes and levels of threat. Time-calibrated Bayesian analyses based upon concatenated nuclear and mitochond...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.06.020
更新日期:2013-12-01 00:00:00
abstract::The habit of mining within leaves has evolved convergently in numerous plant-feeding insect taxa. Many leaf-mining groups contain a large number of species with distinct feeding preferences, which makes them highly suitable for studies on the evolutionary history of host-plant use and on the role of niche shifts in sp...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2012.04.005
更新日期:2012-08-01 00:00:00
abstract::Within the southwestern Australian biodiversity hotspot, the Shark Bay region displays high levels of plant and animal endemism, particularly in the herpetofauna. The region has been subjected to dramatic climatic fluctuations and has been geologically active from the Late Miocene to the present. The myobatrachid frog...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.05.023
更新日期:2007-11-01 00:00:00
abstract::Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.07.012
更新日期:2018-11-01 00:00:00
abstract::We investigated mitochondrial COII gene sequences of Japanese wood-feeding cockroaches (Salganea spp. and Panesthia angustipennis) in detail to investigate their biogeography. The transition (TI) numbers between each genus north and south of the Tokara Strait, which is a border of the Oriental and the Palaearctic faun...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/s1055-7903(02)00399-8
更新日期:2003-04-01 00:00:00
abstract::The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolut...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.01.005
更新日期:2013-02-01 00:00:00
abstract::Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalell...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.03.004
更新日期:2018-08-01 00:00:00
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
更新日期:2018-12-01 00:00:00
abstract::Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore th...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.08.013
更新日期:2017-12-01 00:00:00
abstract::Recent generic rearrangement of the circumtropical distributed skink genus 'Mabuya' has raised a lot of debate. According to this molecular phylogeny based rearrangement, the tropical Asian members of this genus have been assigned to Eutropis. However, in these studies the Asian members of 'Mabuya' were largely sample...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2012.02.022
更新日期:2012-06-01 00:00:00
abstract::Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nu...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2006.11.029
更新日期:2007-08-01 00:00:00
abstract::Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the l...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.03.011
更新日期:2007-09-01 00:00:00
abstract::There is a huge data base of genetic information for the domestic artiodactyl species Bos taurus (cow), Ovis aries (sheep), and Capra hircus (goat). However, the phylogenetic relationships of these economically critical taxa and their close relatives, family Bovidae, remain for the most part unresolved. In this report...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1997.0402
更新日期:1997-06-01 00:00:00