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 mitochondrial small subunit ribosome DNA (mtSSU-rDNA) was applied in this study. We expanded the taxon sampling especially within the class Phyllopharyngea. Phylogenetic analyses based on nSSU-rDNA and mtSSU-rDNA, independently, as well as concatenated were performed and revealed the following: (1) mtSSU-rDNA is more variable than nSSU-rDNA, and is better at elucidating relationships at lower levels, e.g. intra-/inter-specific or generic relationships; (2) the validity of the two genera Mirodysteria and Spirodysteria is challenged based on their similar morphology with Dysteria and the analyses from both mtSSU-rDNA and nSSU-rDNA; (3) Brooklynella is confirmed to be an intermediate taxon between Dysteriidae and Hartmannulidae, and may represent a distinct family; (4) Trithigmostoma should remain in Chilodonellidae; (5) the separation of Paraspathidium from Litostomatea is supported and it groups with prostomateans and plagiopyleans. In summary, results from mtSSU-rDNA corroborated those of nSSU-rDNA for highly supported clades, and the mtSSU-rDNA tree with its secondary structure gave topologies that could be explained by the morphology; therefore it can be useful in some cases towards better resolution of robust phylogenies.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Wang P,Wang Y,Wang C,Zhang T,Al-Farraj SA,Gao Fdoi
10.1016/j.ympev.2017.04.018subject
Has Abstractpub_date
2017-07-01 00:00:00pages
96-106eissn
1055-7903issn
1095-9513pii
S1055-7903(16)30360-8journal_volume
112pub_type
杂志文章abstract：:Tree snails of the endemic subfamily Achatinellinae comprise a diverse and important component of the Hawaiian fauna. In recent decades anthropogenic impacts have resulted in devastating extinction rates in Hawaiian tree snails. To address long-standing biogeographic, systematic, and evolutionary questions we used cyt...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2004.01.003
更新日期：2004-08-01 00:00:00
abstract：:Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2006.10.009
更新日期：2007-03-01 00:00:00
abstract：:Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to inc...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1999.0657
更新日期：1999-11-01 00:00:00
abstract：:Based on nuclear and chloroplast sequences we resolve species relationships in Calycanthaceae and develop a biogeographic hypothesis that explains their intercontinental disjunctions and intra-continental diversification in eastern Asia. Fossil-calibrated penalized likelihood and Bayesian divergence time estimates ind...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2006.01.015
更新日期：2006-04-01 00:00:00
abstract：:Argonaute proteins (AGOs) are mediators of gene silencing via recruitment of small regulatory RNAs to induce translational regression or degradation of targeted molecules. Platyhelminths have been reported to express microRNAs but the diversity of AGOs in the phylum has not been explored. Phylogenetic relationships of...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2012.11.014
更新日期：2013-03-01 00:00:00
abstract：:Phylogeny of ants of the tribe Lasiini (Lasius, Acanthomyops, Prenolepis, Euprenolepis, Paratrechina, Pseudolasius, and Myrmecocystus) was analysed using 81 morphological, ecological, and behavioural characters (for 41 species) and mitochondrial DNA sequences (COI, COII, tRNA-Leu; for 19 species). The free-living subg...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2004.07.012
更新日期：2004-12-01 00:00:00
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 evo...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.05.025
更新日期：2009-09-01 00:00:00
abstract：:Since the Oligocene, regions adjacent to the Red Sea have experienced major environmental changes, from tectonic movements and continuous geological activity to shifting climatic conditions. The effect of these events on the distribution and diversity of the regional biota is still poorly understood. Agamid members of...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.12.021
更新日期：2016-04-01 00:00:00
abstract：:Dendroctonus mexicanus is polyphagous within the Pinus genus and has a wide geographical distribution in Mexico and Guatemala. We examined the pattern of genetic variation across the range of this species to explore its demographic history and its phylogeographic pattern. Analysis of the mtDNA sequences of 173 individ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.09.005
更新日期：2008-12-01 00:00:00
abstract：:All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identificat...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/s1055-7903(02)00039-8
更新日期：2002-06-01 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：:Cladogenesis is often driven by the interplay of dispersal and vicariance. The importance of long-distance dispersal in biogeography and speciation is increasingly recognised, but still ill-understood. Here, we study faunal interconnectivity between four large Brazilian floodplains, namely the Amazon, Araguaia, Pantan...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.12.019
更新日期：2018-04-01 00:00:00
abstract：:The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2016.11.005
更新日期：2017-02-01 00:00:00
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
更新日期：2011-12-01 00:00:00
abstract：:Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the ricef...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.05.018
更新日期：2018-10-01 00:00:00
abstract：:Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron gain and loss, changes in gene order) as these data become available from comparative studies...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.04.008
更新日期：2005-09-01 00:00:00
abstract：:The walnut family Juglandaceae was widely distributed in the Northern Hemisphere while several extant genera now exhibit intercontinental disjunctions. Recent progress in the systematics of Juglandaceae has greatly broadened our knowledge about its origin and evolution. However, there are still uncertainties about the...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2020.106802
更新日期：2020-06-01 00:00:00
abstract：:The phylogenetic pattern and timing of the radiation of Old World deer was determined based on the complete mitochondrial cytochrome b gene from 33 Cervinae taxa. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support was achieved for monophyly of the Old World deer with mun...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2004.07.013
更新日期：2004-12-01 00:00:00
abstract：:Long-branch attraction (LBA) is a well-known artifact in phylogenetic reconstruction. Sparse taxon sampling and extreme heterogeneity of evolutionary rates among lineages generate propitious situations for LBA, even defying probabilistic methods of phylogenetic inference. A clear example illustrating LBA challenges is...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2018.12.019
更新日期：2019-04-01 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：: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：:Galápagos hawks (Buteo galapagoensis) are one of the most inbred bird species in the world, living in small, isolated island populations. We used mitochondrial sequence and nuclear minisatellite data to describe relationships among Galápagos hawk populations and their colonization history. We sampled 10 populations (e...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.11.014
更新日期：2006-04-01 00:00:00
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
更新日期：2001-04-01 00:00:00
abstract：:To investigate phylogenetic relationships among Leuciscus species occurring in Portuguese inland waters, the cytochrome b gene was sequenced from representatives of the main rivers. This study supports the recognition of the species level for L. pyrenaicus, including populations from the southern Portuguese drainages ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1997.0429
更新日期：1997-12-01 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 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 nuclear-encoded small subunit ribosomal DNA gene of many lichen-forming green algae in the genus Trebouxia contains a group I intron at Escherichia coli genic position 1512. We studied the evolutionary history of the 1512 intron in Trebouxia spp. (Trebouxiophyceae) by analyzing intron and "host" cell phylogenies. ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1999.0711
更新日期：2000-03-01 00:00:00
abstract：:Mediterranean trout populations display a diversity of phenotypes, representing a valuable model for the study of adaptation and a puzzling dilemma for taxonomists and biogeographers, which is further entangled by the widespread introgression of allochthonous genes. In this paper we analysed DNA polymorphism at multip...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2014.06.022
更新日期：2014-10-01 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：:New world coralsnakes of the genus Micrurus are a diverse radiation of highly venomous and brightly colored snakes that range from North Carolina to Argentina. Species in this group have played central roles in developing and testing hypotheses about the evolution of mimicry and aposematism. Despite their diversity an...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2020.106770
更新日期：2020-06-01 00:00:00
