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 evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Zimmer EA,Wen Jdoi
10.1016/j.ympev.2013.01.005subject
Has Abstractpub_date
2013-02-01 00:00:00pages
539-50issue
2eissn
1055-7903issn
1095-9513pii
S1055-7903(13)00024-9journal_volume
66pub_type
杂志文章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
更新日期：1999-02-01 00:00:00
abstract：:Afrocanarian blue tits (Cyanistes teneriffae) have a scattered distribution on the Canary Islands and on the North African continent. To date, the Canary Islands have been considered the species' main Pleistocene evolutionary center, but their colonization pathways remain uncertain. We set out to reconstruct a dated m...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2013.02.010
更新日期：2013-05-01 00:00:00
abstract：:A continuous 10.1kb fragment of the Cephalothrix rufifrons (Nemertea, Palaeonemertea) mitochondrial genome was sequenced and characterized to further assess organization of protostome mitochondrial genomes and evaluate the phylogenetic potential of gene arrangement and amino acid characters. The genome is A-T rich (72...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2006.10.025
更新日期：2007-06-01 00:00:00
abstract：:Comparative multispecies studies allow contrasting the effect of past and present oceanographic processes on phylogeographic patterns. In the present study, a fragment of the COI gene was analyzed in seven decapod crustacean species from five families and with different bathymetric distributions. A total of 769 indivi...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2011.11.009
更新日期：2012-02-01 00:00:00
abstract：:Climatic oscillations, heterogeneity in elevation, topographical position, and isolation time in southwestern Patagonia have been important in promoting diversification of the biota. Geological studies have shown that this region had wide ice-free areas during periods of the last glacial maximum and provided forested ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.11.026
更新日期：2011-02-01 00:00:00
abstract：:Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyr...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/s1055-7903(02)00215-4
更新日期：2002-10-01 00:00:00
abstract：:Phylogenetic relationships among members of the New World searobin genera Bellator and Prionotus (Family Triglidae, Subfamily Prionotinae) and among other searobins in the families Triglidae and Peristediidae were investigated using both mitochondrial and nuclear DNA sequences. Phylogenetic hypotheses derived from max...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2016.11.017
更新日期：2017-02-01 00:00:00
abstract：:Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but r...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2013.07.007
更新日期：2013-12-01 00:00:00
abstract：:Horizontal gene transfer (HGT) has been shown to widely spread in organisms by comparative genomic studies. However, its effect on the phylogenetic relationship of organisms, especially at a system level of different cellular functions, is still not well understood. In this work, we have constructed phylogenetic trees...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2003.08.011
更新日期：2004-04-01 00:00:00
abstract：:Manta rays have been taxonomically revised as two species, Manta alfredi and M. birostris, on the basis of morphological and meristic data, yet the two species occur in extensive mosaic sympatry. We analysed the genetic signatures of the species boundary using a portion of the nuclear RAG1 (681 base pairs), mitochondr...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2012.03.020
更新日期：2012-07-01 00:00:00
abstract：:The bootstrap is an important tool for estimating the confidence interval of monophyletic groups within phylogenies. Although bootstrap analyses are used in most evolutionary studies, there is no clear consensus as how best to interpret bootstrap probability values. To study further the bootstrap method, nine small su...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1996.0084
更新日期：1996-12-01 00:00:00
abstract：:Despite huge fossil, morphological and molecular data, bivalves' early evolutionary history is still a matter of debate: recently, established phylogeny has been mostly challenged by DNA studies, and little agreement has been reached in literature, because of a substantial lack of widely-accepted methodological approa...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.08.032
更新日期：2010-11-01 00:00:00
abstract：:Pleistocene climatic fluctuations played a principal role for range formation and population history of many biota, including regions not directly affected by glaciations, such as the arid habitats of the southwestern United States and adjacent Mexico. Specifically, drought-adapted species are expected to have persist...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.10.010
更新日期：2010-02-01 00:00:00
abstract：:Brittlestars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.10.003
更新日期：2019-01-01 00:00:00
abstract：:A species flock of the freshwater isopod genus Eophreatoicus Nicholls lives in seeps, springs and perched aquifers at the base of the Arnhem Plateau and associated sandstone outliers in Australia's Northern Territory. These species have been found to have surprisingly high levels of genetic divergence and narrow range...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.02.001
更新日期：2009-05-01 00:00:00
abstract：:We analyzed the phylogenetic relationships of echimyid genera based on sequences of the cytochrome b, 12S, and 16S mitochondrial genes. Our results corroborate the monophyly of Octodontoidea and the rapid diversification of echimyid rodents as previously proposed. The analyses indicate that the family Echimyidae, incl...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/s1055-7903(02)00279-8
更新日期：2002-12-01 00:00:00
abstract：:The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai'i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographi...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2004.11.001
更新日期：2005-02-01 00:00:00
abstract：:A phylogenetic analysis of the family Lemuridae was accomplished using multiple gene partitions and morphological characters. The results of the study suggest that several nodes in the lemurid phylogeny can be robustly resolved; however, the relationships of the species within the genus Eulemur are problematically non...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1999.0723
更新日期：2000-04-01 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 complete nucleotide sequence (15,719 nucleotides) of the mitochondrial DNA (mtDNA) from the sea urchin Arbacia lixula is presented. The comparison of gene arrangement between different echinoderm orders of the same class provides evidence that the gene organization is conserved within the same echinoderm class. Th...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1996.0027
更新日期：1996-04-01 00:00:00
abstract：:Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region's numerous archipelagos and well-characterized avian comm...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2020.107034
更新日期：2021-03-01 00:00:00
abstract：:Although the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiations despite some members, such as the oreochromine cichlid...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2019.04.008
更新日期：2019-07-01 00:00:00
abstract：:Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and hence are ubiquitous and present in high copy number. Ribosomal rDNA repeats often undergo rapid concerted evolution within and between arrays. Interspecific hybridization merges divergent repeat ty...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.10.023
更新日期：2010-04-01 00:00:00
abstract：:As circumscribed by Drude, the umbellifer subfamily Hydrocotyloideae posed a major hindrance to resolving the phylogeny of order Apiales. Previous studies have suggested its polyphyly, but have not had sufficient sampling to address the issue fully. To put an end to the out-dated concept of Hydrocotyloideae, we invest...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.06.010
更新日期：2009-10-01 00:00:00
abstract：:The North Atlantic red alga Mastocarpus stellatus is characterized by two life histories (sexual-type and direct-type), which correspond to two geographically isolated breeding groups. These features enable M. stellatus to be an interesting model to investigate how environmental shift and apomictic propagation have in...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.10.029
更新日期：2016-01-01 00:00:00
abstract：:We assayed the mtDNA phylogeography [196 base pairs (bp) of the cytochrome b] and population structure (n = 680) in the estuarine fish, Ethmalosa fimbriata, from its whole distribution range: 14 locations along the West African coasts were sampled. Specifically, we considered Pleistocene glaciations as well as the hyd...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.01.019
更新日期：2005-08-01 00:00:00
abstract：:The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2019.106579
更新日期：2019-11-01 00:00:00
abstract：:Malacosporeans are a poorly known myxozoan clade that uniquely demonstrates a tissue level of organisation. Thus, when exploiting their invertebrate hosts (freshwater bryozoans) they occur as non-motile sacs or vermiform stages capable of active swimming. We combine phylogenetic analyses of SSU and LSU rDNA with morph...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2014.03.010
更新日期：2014-07-01 00:00:00
abstract：:Mammalian G protein-coupled receptor (GPCR) genes are characterised by a large proportion of intronless genes or a lower density of introns when compared with GPCRs of invertebrates. It is unclear which mechanisms have influenced intron density in this protein family, which is one of the largest in the mammalian genom...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2006.11.007
更新日期：2007-06-01 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
