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 the difficulty of reconstructing the deep gastropod phylogeny, particularly using mitochondrial (mt) genomes. Previous studies consistently obtained unorthodox phylogenetic relationships due to the LBA between the mitogenomes of patellogastropods (true limpets, represented only by Lottia digitalis), heterobranchs, and outgroup taxa. Here, we use the reconstruction of the gastropod mitogenomic phylogeny as a case exercise to test the effect of key methodological approaches proposed to counteract LBA, including the selection of slow-evolving representatives, the use of different outgroups, the application of site-heterogeneous evolutionary models, and the removal of fast-evolving sites. In this regard, we sequenced three new patellogastropod mt genomes, which displayed shorter branches than the one of Lottia as well as gene organizations more similar to that of the hypothetical gastropod ancestor. Phylogenetic analyses incorporating the mt genomes of Patella ferruginea, Patella vulgata, and Cellana radiata allowed eliminating the artificial clustering of Patellogastropoda and Heterobranchia that had prevailed in previous studies. Furthermore, the use of site-heterogeneous models with certain combinations of lineages within the outgroup allowed eliminating also the LBA between Heterobranchia and the outgroup, and recovering Apogastropoda (i.e., Caenogastropoda + Heterobranchia). Hence, for the first time, we were able to obtain a mitogenomic phylogeny of gastropods that is congruent with both morphological and nuclear datasets.
journal_name
Mol Phylogenet Evoljournal_title
Molecular phylogenetics and evolutionauthors
Uribe JE,Irisarri I,Templado J,Zardoya Rdoi
10.1016/j.ympev.2018.12.019subject
Has Abstractpub_date
2019-04-01 00:00:00pages
12-23eissn
1055-7903issn
1095-9513pii
S1055-7903(18)30408-1journal_volume
133pub_type
杂志文章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::Polycyclic triterpenoids, such as sterols and hopanoids, are essential components of plasmatic membrane in eukaryotic organisms. Although it is generally assumed that ciliates do not synthesize sterols, and many of them are indeed auxotrophic, a large set of annotated genomic sequences and experimental data from recen...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章,评审
doi:10.1016/j.ympev.2014.01.026
更新日期:2014-05-01 00:00:00
abstract::The purpose of this study was to determine the higher-level phylogenetic relationships among Carnivora, using a conditional data combination (CDC) approach to analyzing multiple data sets. New nucleotide sequences (851 base pairs from intron I of the transthyretin gene) among 22 representatives of the 11 families of C...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.1998.0504
更新日期:1998-06-01 00:00:00
abstract::The neogastropod family Fasciolariidae Gray, 1853 - tulips, horse-conchs, spindles, etc., comprises important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae Gray, 1853, Fusininae Wrigley, 1927 and Peristerniinae Tryon, 1880. Fasciolariids have...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2016.03.025
更新日期:2016-06-01 00:00:00
abstract::The phylogenetic relationships within the family Syllidae have been analyzed previous to this study and a new subfamily (Anoplosyllinae) defined. However, the monophyly of the family Syllidae was not well-supported. A conflict between the different molecular data sets combined in previous preceding molecular analyses ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2010.01.012
更新日期:2010-06-01 00:00:00
abstract::Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.10.008
更新日期:2014-01-01 00:00:00
abstract::Next-generation genomic sequencing promises to quickly and cheaply resolve remaining contentious nodes in the Tree of Life, and facilitates species-tree estimation while taking into account stochastic genealogical discordance among loci. Recent methods for estimating species trees bypass full likelihood-based estimate...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.08.023
更新日期:2014-12-01 00:00:00
abstract::Reconstructing species trees by incorporating information from many independent gene trees reduces the confounding influence of stochastic lineage sorting. Such analyses are particularly important for taxa that share polymorphisms due to incomplete lineage sorting or introgressive hybridization. We investigated phylog...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2013.08.008
更新日期:2014-01-01 00:00:00
abstract::The nucleotide sequences of the rDNA second internal transcribed spacer (ITS-2) of 31 populations of 12 and 3 species of the two main Triatominae tribes Triatomini and Rhodniini, including the most important Chagas disease vectors, were obtained. Sequence comparisons and parsimony, distance, and maximum-likelihood ana...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1006/mpev.2000.0864
更新日期:2001-01-01 00:00:00
abstract::The Australian mesic biome spans c. 33° of latitude along Australia's east coast and ranges and is dissected by historical and contemporary biogeographical barriers. To investigate the impact of these barriers on evolutionary diversification and to predict the impact of future climate change on the distribution of spe...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.09.004
更新日期:2018-01-01 00:00:00
abstract::The phylogeny of Nolana (Solanaceae), a genus primarily distributed in the coastal Atacama and Peruvian deserts with a few species in the Andes and one species endemic to the Galápagos Islands, was reconstructed using sequences of four plastid regions (ndhF, psbA-trnH, rps16-trnK and trnC-psbM) and the nuclear LEAFY s...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.07.018
更新日期:2008-11-01 00:00:00
abstract::The family Macrobiotidae is one of the most speciose and diverse groups among tardigrades. Although there have been attempts to reconstruct the phylogeny of this family, the evolutionary relationships within Macrobiotidae are only superficially determined as available genetic data cover only a small fraction of this v...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2020.106987
更新日期:2020-10-12 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::The description of cryptic gecko species worldwide has revealed both that many putative species are, in fact, conformed by a complex of morphologically conserved species that are genetically distinct and highly divergent, and that gecko species diversity could be underestimated. The taxonomy and species delimitation o...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2017.07.008
更新日期:2017-10-01 00:00:00
abstract::A phylogenetic analysis of all 17 extant species of the clawed lobster genus Metanephrops based on mitochondrial 12S rRNA, 16S rRNA and cytochrome c oxidase I, and nuclear histone H3 gene sequences supports the morphological groupings of two of the traditional groups of the genus (the binghami and japonicus groups) bu...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2008.11.020
更新日期:2009-03-01 00:00:00
abstract::Owing to its peculiar paleogeographic history, Crete island is one of the most interesting biodiversity hotspots within the Aegean area. We here analyze the lineage diversity of Cretan Reticulitermes termites obtained on mitochondrial genes (COII and 16S) and nuclear Inter-SINE loci. The evolutionary pattern here dete...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2010.04.037
更新日期:2010-09-01 00:00:00
abstract::Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2011.01.001
更新日期:2011-03-01 00:00:00
abstract::Bryozoa is one of the most puzzling phyla in the animal kingdom and little is known about their evolutionary history. Its phylogenetic position among the Metazoa remains unsettled, as well as its intra-phylum relationships. Here, we present the first comprehensive molecular phylogeny of Bryozoa based on the mitochondr...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2009.01.021
更新日期:2009-07-01 00:00:00
abstract::Members of the AP1/SQUA subfamily of plant MADS-box genes play broad roles in the regulation of reproductive meristems, the specification of sepal and petal identities, and the development of leaves and fruits. It has been shown that AP1/SQUA-like genes are angiosperm-specific, and have experienced several major dupli...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2007.02.016
更新日期:2007-07-01 00:00:00
abstract::Astyanax fasciatus has become a model organism for the study of regressive and adaptive evolution in cave animals. To fully understand these processes, it is important to have background information on the systematics and phylogeography of surface and cave populations of this species. Here we investigate the phylogeog...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2004.07.001
更新日期:2004-11-01 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::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::Cryptic mitochondrial (mt) lineages are known to exist in the earthworm morphospecies Lumbricus rubellus and L. terrestris. The latter was recently split into two species, L. terrestris and L. herculeus, based on large genetic distances and a statistical difference in body size. There is support for the separation of ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2016.09.011
更新日期:2017-01-01 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
abstract::Lake Tanganyika (LT) is a biodiversity hotspot supporting many endemic radiations that provide comparative systems in which to investigate if there are common factors leading to the build-up of its considerable diversity. Despite LT containing the highest diversity of lacustrine catfishes on Earth, the evolutionary re...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2014.01.013
更新日期:2014-04-01 00:00:00
abstract::Chiroxiphia and Antilophia manakins are recognized as closely related genera. Nonetheless, Chiroxiphia has been recovered as paraphyletic in some studies with limited taxonomic coverage. This genus currently comprises five species, although this arrangement is still unsettled. Chiroxiphia pareola is the most widesprea...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2018.06.016
更新日期:2018-10-01 00:00:00
abstract::We studied phylogenetic relationships of the Eleutherodactylus auriculatus species group to infer colonization and diversification patterns in this endemic radiation of terrestrial frogs of the genus Eleutherodactylus in the largest of the Greater Antilles, Cuba. An initial screening of genetic diversity based on part...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2009.08.023
更新日期:2010-01-01 00:00:00
abstract::Comparative phylogeography of widespread species that span the same geographic areas can elucidate the influence of historical events on current patterns of biodiversity, identify patterns of co-vicariance, and therefore aid the understanding of general evolutionary processes. Soil-dwelling animals present characteris...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.07.017
更新日期:2016-01-01 00:00:00
abstract::The main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2019.106712
更新日期:2020-03-01 00:00:00
abstract::The precise boundary delineations between taxa in symbiotic associations are very important for evolutionary and ecophysiological studies. Growing evidence indicates that in many cases, the use of either morphological characters or molecular markers results in diversity underestimation. In lichen symbioses, Trebouxia ...
journal_title:Molecular phylogenetics and evolution
pub_type: 杂志文章
doi:10.1016/j.ympev.2015.10.021
更新日期:2016-01-01 00:00:00