Abstract:
:Repeated sea-level fluctuations during and prior to the Pleistocene had a dramatic effect on the distribution of land and connection among islands between the Asian and Australian continents. These cycles of connection and isolation have long been recognized as an important factor determining the distribution and organization of biodiversity in the Philippines. However, surprisingly few studies have tested for predicted patterns of genetic diversity derived from a Pleistocene sea-level model of geography. Here, we examine evidence for fit to such a model in a widely distributed lineage of shrews (Crocidura). The topology of relationships among Crocidura from the Philippines is concordant with a Pleistocene sea-level model, but (1) AMOVAs reveal that genetic diversity is explained at least as well by modern islands as by Pleistocene islands; (2) Mantel tests reveal a significant influence of isolation by distance; and (3) the degree of genetic divergence between some populations connected by dry land during the last glacial maximum reveals isolation that almost certainly predates the most recent glacial activity. We further employ multiple strategies for inferring time-calibrated phylogenies, but these result in widely varying time estimates for the invasion of SE Asian islands by shrews. Overall, our results suggest Pleistocene sea-level fluctuations have been an important, but not dominant factor shaping shrew diversity.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Esselstyn JA,Brown RMdoi
10.1016/j.ympev.2009.05.034subject
Has Abstractpub_date
2009-10-01 00:00:00pages
171-81issue
1eissn
1055-7903issn
1095-9513pii
S1055-7903(09)00219-Xjournal_volume
53pub_type
杂志文章abstract::We developed a novel BLAST-Based Relative Distance (BBRD) method by Pearson's correlation coefficient to avoid the problems of tedious multiple sequence alignment and complicated outgroup selection. We showed its application on reconstructing reliable phylogeny for nucleotide and protein sequences as exemplified by th...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.12.002
更新日期:2015-03-01 00:00:00
abstract::Zambian rivers belong to two major drainages: the Luapula-Congo and the Zambezi River system. Tectonic activity repeatedly altered drainage systems in Africa, so that current fish faunas can only be understood in the context of historic drainage capture events. We use phylogenetic relationships of one widespread linea...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.02.011
更新日期:2007-10-01 00:00:00
abstract::Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconst...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2005.09.004
更新日期:2006-03-01 00:00:00
abstract::Phylogenetic analyses of Polytrichales were conducted using morphology and sequence data from the chloroplast genes rbcL and rps4 plus the trnL-F gene region, part of the mitochondrial nad5 and the nuclear-encoded 18S rDNA. Our analyses included 46 species representing all genera of Polytrichales. Phylogenetic trees w...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2003.11.003
更新日期:2004-06-01 00:00:00
abstract::Variation in the mitochondrial cytochrome b gene (1143 bp) was examined to estimate the phylogenetic relationships of taxa within the Peromyscus boylii species group. In addition, phylogenetic relationships among the aztecus, boylii, and truei species groups were addressed. Maximum-likelihood, neighbor-joining, and ma...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.2000.0806
更新日期:2000-09-01 00:00:00
abstract::This is the first phylogenetic study of the intraspecific variability within Paramecium multimicronucleatum with the application of two-loci analysis (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) carried out on numerous strains originated from different continents. The species has been shown to have a complex structure of...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2012.01.024
更新日期:2012-05-01 00:00:00
abstract::The genus Alcantarea comprises near 30 species endemic to rocky outcrops from eastern Brazil. Most species are ornamental and several are threatened due to habitat loss and over collection. In this paper we examine the phylogenetics of Alcantarea and its relationship with the Brazilian members of Vriesea, a genus of w...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2012.03.015
更新日期:2012-07-01 00:00:00
abstract::The superfamily Conoidea is one of the most speciose groups of marine mollusks, with estimates of about 340 recent valid genera and subgenera, and 4000 named living species. Previous classifications were based on shell and anatomical characters, and clades and phylogenetic relationships are far from well assessed. Bas...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.11.007
更新日期:2008-06-01 00:00:00
abstract::That homologies exist and can be recognized and discovered is of central importance to comparative and evolutionary biology. Traditionally, homology assessment for both molecular and morphological data has been treated as a two-step process involving the generation of a proposition of homology and then the evaluation ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2010.03.032
更新日期:2010-07-01 00:00:00
abstract::Platypodinae is a peculiar weevil subfamily of species that cultivate fungi in tunnels excavated in dead wood. Their geographical distribution is generally restricted, with genera confined to a single continent or large island, which provides a useful system for biogeographical research. This study establishes the fir...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.05.028
更新日期:2015-11-01 00:00:00
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
更新日期:2008-05-01 00:00:00
abstract::Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.06.022
更新日期:2013-12-01 00:00:00
abstract::Within the Gentianaceae-Exaceae, the most species-rich genus Sebaea has received very little attention in terms of phylogenetic or karyological investigations. As a result, the exact number of species remains vague and the relationships with the other members of the Exaceae poorly understood. In this paper, we provide...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2009.07.025
更新日期:2009-12-01 00:00:00
abstract::Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, s...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.05.027
更新日期:2015-11-01 00:00:00
abstract::While polyploidization is recognized as a major evolutionary driver for ferns and angiosperms, little is known about its impact in gymnosperms, where polyploidy is much less frequent. We explore Ephedra to evaluate (i) the extent of genome size diversity in the genus and the influence polyploidy has had on the evoluti...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2020.106786
更新日期:2020-06-01 00:00:00
abstract::Positive selection has been shown to be pervasive in sex-related proteins of many metazoan taxa. However, we are only beginning to understand molecular evolutionary processes on the lineage to humans. To elucidate the evolution of proteins involved in human reproduction, we studied the sequence evolution of MAM domain...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2005.04.001
更新日期:2005-10-01 00:00:00
abstract::Most ciliate phylogenetic analyses have largely relied on the nuclear small subunit ribosome DNA (nSSU-rDNA) locus. However, single locus or multi-loci from the same genome or chromosome may not be sufficient enough to elucidate phylogenetic relationships among ciliate taxa. Therefore, in addition to nSSU-rDNA, the mi...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.04.018
更新日期:2017-07-01 00:00:00
abstract::The species category is the fundamental unit in biology. In the last decades, several studies have been carried out, using sequence information and phylogenies to resolve issues in taxonomically problematic groups. The multispecies coalescent theory, and the species-delimitation methods developed in the last years bas...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.05.024
更新日期:2018-10-01 00:00:00
abstract::The Cape flora is compositionally biased, being dominated by a few fynbos clades (such as Iridaceae, Ericaceae, Proteaceae and Restionaceae) that make up major part of the distinct heathland vegetation in the Cape Floristic Region. Uncertainty exists concerning what excluded the subtropical to tropical palm-dominated ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2019.106645
更新日期:2020-01-01 00:00:00
abstract::Wrens of the genus Thryothorus comprise over a third of the species diversity in the family Troglodytidae. In addition to this species diversity, these wrens vary in a number of behavioral characteristics, in particular in the presence and structure of vocal duets, which makes them an interesting target for comparativ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2006.04.014
更新日期:2006-09-01 00:00:00
abstract::To elucidate the evolutionary history of snow voles, genus Chionomys, we studied the phylogeography of Chionomysnivalis across its range and investigated its relationships with two congeneric species, Chionomysgud and Chionomysroberti, using independent molecular markers. Analyses were based on mitochondrial (~940 bp ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2011.12.004
更新日期:2012-03-01 00:00:00
abstract::Phylogenetic analyses of new DNA sequence data from the mitochondrial 16S rRNA gene in xantusiid lizards support the intergeneric relationships obtained previously (S.B. Hedges, R.L. Bezy, and L.B. Maxson, 1991, Mol. Biol. Evol. 8:767-780) with data from the 12S rRNA and cytochrome b (cyt b) genes. The total data set ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1993.1008
更新日期:1993-03-01 00:00:00
abstract::Angiosperm mitochondrial horizontal gene transfer (HGT) has been widely reported during the past decades. With a few exceptions, foreign sequences are mitochondrial genes or intronic regions from other plants, indicating that HGT has played a major role in shaping mitochondrial genome evolution. Host-parasite relation...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.12.006
更新日期:2019-03-01 00:00:00
abstract::The data on the distribution and frequencies of private polymorphisms in the tribal populations of Central and South America are used to address the question of the extent to which such data can be used to address questions of phylogenetic history. It is shown that due to the great increases in population number that ...
journal_title:Molecular phylogenetics and evolution
pub_type: 历史文章,杂志文章
doi:10.1006/mpev.1996.0015
更新日期:1996-02-01 00:00:00
abstract::Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species. A robust phylogeny and taxonomy of snakes is crucial for us to know, study and protect them. For a large group such as snakes, broad-scale phylogenetic reconstructions largely rely on data integration. Increas...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2020.106807
更新日期:2020-07-01 00:00:00
abstract::Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are requi...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.07.018
更新日期:2016-01-01 00:00:00
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
更新日期:2008-03-01 00:00:00
abstract::The ring-necked pheasants (Phasianus colchicus) are widely distributed in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic changes in 139 ring-necked pheasants (P. colchicus) sampled from the species' distribution range. A total of 1078 nucleotides from the control re...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2009.03.015
更新日期:2009-07-01 00:00:00
abstract::Cleaner fishes remove and consume ectoparasites and are often categorized by whether they perform this behavior: (1) predominately as juveniles, (2) facultatively throughout ontogeny, or (3) obligately. Through a literature search, we confirmed that with at least 58 species exhibiting cleaning behavior, the Labridae (...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.09.006
更新日期:2016-01-01 00:00:00
abstract::Phylogenetic trees are a starting point for the study of further evolutionary and ecological questions. We show that for avian evolutionary relationships, improved taxon sampling, longer sequences and additional data sets are giving stability to the prediction of the grouping of pelecaniforms and ciconiiforms, thus al...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.03.021
更新日期:2013-08-01 00:00:00