Abstract：
:A well-resolved phylogeny would facilitate study of adaptation to nocturnality in the avian superorder Strisores, a group that includes both nocturnal and diurnal lineages. Based on previous estimates, it could be hypothesized that there were multiple independent origins of nocturnality in this group. In order to refine the Strisores phylogeny, we generated genome-scale datasets of 2289-4243 ultraconserved elements for 23 taxa representing all major living lineages in the group. Among the considerations for using genome-scale, molecular sequence data in phylogenomic analyses are issues related to GC content, GC variance and their effects on model selection. In this study, we employed a variety of analytical techniques to empirically investigate those issues in our data, as well as biases and errors resulting from alignment trimming, taxon selection, matrix completeness and evolutionary rate variation among sites and across lineages. Extensive analyses revealed conflict within the data, especially in regard to variation in GC content, that would not have been detected by more cursory study. Our results indicate that readily available models of molecular evolution are insufficient to encapsulate all phenomena present in genome-scale matrices, and that this problem may be at the root of many current issues in phylogenomic analysis. The analytical methods employed in this study are relevant to phylogenomic analysis of any large, heterogeneous matrix. In conclusion, we present a strongly supported estimate of the Strisores tree, and discuss visual adaptations for, and potential evolutionary pathways to, nocturnality in this clade.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
White ND,Braun MJdoi
10.1016/j.ympev.2019.106611subject
Has Abstractpub_date
2019-12-01 00:00:00pages
106611eissn
1055-7903issn
1095-9513pii
S1055-7903(19)30351-3journal_volume
141pub_type
杂志文章abstract：:Phylogenetic relationships among the trichomycterid catfishes are investigated for the first time using molecular sequence data. Data derived from mitochondrial and nuclear DNA sequences for representatives of 17 genera were analyzed to test previous hypotheses of relationships among trichomycterid subfamilies, the mo...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2009.02.016
更新日期：2009-08-01 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：:Bigeye (Thunnus obesus) is a large, pelagic, and migratory species of tuna that inhabits tropical and temperate marine waters worldwide. Previous studies based on mitochondrial RFLP data have shown that bigeye tunas from the Atlantic Ocean are the most interesting from a genetic point of view. Two highly divergent mit...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2005.07.022
更新日期：2006-05-01 00:00:00
abstract：:Chicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Recent CR1 retrotranspositions in waterfowl suggested that, unlike chicken at least one subfamily remains active. Based on sequence information from 143 CR1 loci, six distinct groups of CR1 within the waterfowl coscoroba each with unique 3' ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.09.020
更新日期：2008-12-01 00:00:00
abstract：:Influenza A virus infects a wide range of hosts including birds, humans, pigs, horses, and other mammals. Because hosts differ in immune system structure and demography, it is therefore expected that host populations leave different imprints on the viral genome. In this study, we investigated the evolutionary trajecto...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.04.039
更新日期：2010-08-01 00:00:00
abstract：:Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2019.106688
更新日期：2020-02-01 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：: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：:The majority of the approximately 80-90 species in subtribe Arctotidinae occur in southern Africa with the centre of diversity in the winter-rainfall region. Three species are restricted to afromontane eastern Africa and three species are endemic to Australia. To investigate biogeographic and phylogenetic relationship...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.07.007
更新日期：2008-10-01 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 Ciminalis section of Gentiana comprises seven species, two of them growing on siliceous substrates (G. alpina and G. acaulis), the other ones being calcareous taxa (G. clusii, G. angustifolia, G. ligustica, G. occidentalis and G. dinarica). A total of 515 individuals from 183 populations over the entire Ciminalis ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2013.09.022
更新日期：2014-01-01 00:00:00
abstract：:We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unres...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.10.001
更新日期：2016-02-01 00:00:00
abstract：:Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondr...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.10.010
更新日期：2009-01-01 00:00:00
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
更新日期：2004-09-01 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：:The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant w...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2012.10.012
更新日期：2013-02-01 00:00:00
abstract：:Montane barriers influence the evolutionary history of lineages by promoting isolation of populations. The effects of these historical processes are evident in patterns of differentiation among extant populations, which are often expressed as genetic and behavioral variation between populations. We investigated the ef...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2015.08.017
更新日期：2016-01-01 00:00:00
abstract：:Molecular studies have enlightened our understanding of freshwater zooplankton biogeography, yet questions remain regarding the scale and commonality of geographic speciation. Here, we present a mtDNA-based phylogenetic hypothesis for 92 Daphnia species from all seven continents, with a focus on North and South Americ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2008.11.026
更新日期：2009-03-01 00:00:00
abstract：:Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and ha...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.10.018
更新日期：2018-02-01 00:00:00
abstract：:Sika deer (Cervus nippon Temminck) are endemic to mainland and insular Asia. Numerous subspecies have been named, but they are not quantitatively well defined. Portions of the mitochondrial cytochrome b gene (450 bp) and control region (512 bp) were sequenced from 28 individuals belonging to five sika subspecies and t...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1998.0593
更新日期：1999-06-01 00:00:00
abstract：:A species-level phylogeny is presented for Triglochin, the largest genus of Juncaginaceae (Alismatales) comprising about 30 species of annual and perennial herbs. Triglochin has an almost cosmopolitan distribution with Australia as centre of species diversity. Trans-Atlantic and trans-African disjunctions exist in the...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2014.10.014
更新日期：2015-02-01 00:00:00
abstract：:Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lin...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.05.005
更新日期：2017-07-01 00:00:00
abstract：:Phylogenetic relationships between Trogoniformes and several other putative closely related groups of birds, based on complete cytochrome b and nearly complete 12S ribosomal RNA sequences, were studied. The taxa included trogons, owls, cuckoos, parrots, nightjars, hummingbirds, kingfishers, motmots, rollers, mousebird...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1999.0683
更新日期：2000-01-01 00:00:00
abstract：:The Hawaiian Drosophilidae contains approximately 1000 species, placed in species groups and subgroups based largely on secondary sexual modifications to wings, forelegs and mouthparts. Members of the spoon tarsus subgroup possess a cup-shaped structure on the foretarsi of males. Eight of the twelve species in this su...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2010.12.015
更新日期：2011-03-01 00:00:00
abstract：:Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an ...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2017.04.022
更新日期：2017-07-01 00:00:00
abstract：:In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degre...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2019.106670
更新日期：2020-02-01 00:00:00
abstract：:Phylogenetic hypotheses generated from cladistic analysis of organismal and molecular data are shown to be generally congruent and/or complementary for comparisons of unicellular and colonial green algae in the Chlorophyceae. Cladistic analysis of organismal character data corroborates the alliance of colonial Stephan...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1006/mpev.1994.1039
更新日期：1994-12-01 00:00:00
abstract：:Classical Sanger sequencing is still frequently used to generate sequence data for phylogenetic and phylogeographic inference. In this contribution we present a novel approach to genotype whole mitogenomic haplotypes using Illumina MiSeq reads from indexed amplicons. Our new approach reduces preparation time by multip...
journal_title：Molecular phylogenetics and evolution
pub_type： 杂志文章
doi：10.1016/j.ympev.2016.05.023
更新日期：2016-09-01 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：:The hypothesis that endemic species could have originated by the isolation and divergence of peripheral populations of widespread species can be tested through the use of ecological niche models (ENMs) and statistical phylogeography. The joint use of these tools provides complementary perspectives on historical dynami...
journal_title：Molecular phylogenetics and evolution
pub_type： 历史文章,杂志文章
doi：10.1016/j.ympev.2015.08.027
更新日期：2016-01-01 00:00:00
