Selecting optimal partitioning schemes for phylogenomic datasets

Published on Jan 1, 2014in BMC Evolutionary Biology3.045
· DOI :10.1186/1471-2148-14-82
Robert Lanfear29
Estimated H-index: 29
(National Evolutionary Synthesis Center),
Brett Calcott12
Estimated H-index: 12
(ANU: Australian National University)
+ 2 AuthorsAlexandros Stamatakis50
Estimated H-index: 50
(Heidelberg Institute for Theoretical Studies)
Background Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fewer than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics.
  • References (48)
  • Citations (283)
📖 Papers frequently viewed together
2,965 Citations
6,868 Citations
9,297 Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
#1Robert LanfearH-Index: 1
1 CitationsSource
126k Citations
#1Nicolas Lartillot (UdeM: Université de Montréal)H-Index: 36
#2Nicolas Rodrigue (AAFC: Agriculture and Agri-Food Canada)H-Index: 20
Last. J. Richer (UdeM: Université de Montréal)H-Index: 21
view all 4 authors...
Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity. However, they are computationally more challenging. This has resulted in practical compromises in the design of infi...
331 CitationsSource
#1James R. Leavitt (BYU: Brigham Young University)H-Index: 1
#2Kevin D. Hiatt (BYU: Brigham Young University)H-Index: 4
Last. Hojun Song (BYU: Brigham Young University)H-Index: 19
view all 4 authors...
One of the main challenges in analyzing multi-locus phylogenomic data is to find an optimal data partitioning strategy to account for variable evolutionary histories of different loci for any given dataset. Although a number of studies have addressed the issue of data partitioning in a Bayesian phylogenetic framework, such studies in a maximum likelihood framework are comparatively lacking. Furthermore, a rigorous statistical exploration of possible data partitioning schemes has not been applied...
55 CitationsSource
#1Philippe Gayral (University of Montpellier)H-Index: 16
#2José Melo-Ferreira (University of Porto)H-Index: 20
Last. Nicolas Galtier (University of Montpellier)H-Index: 49
view all 15 authors...
In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis from wild samples in five non-model animal species, based on next-generation sequencing transcriptome da...
107 CitationsSource
#1Chieh-Hsi Wu (University of Auckland)H-Index: 13
#2Marc A. Suchard (UCLA: University of California, Los Angeles)H-Index: 64
Last. Alexei J. Drummond (University of Auckland)H-Index: 58
view all 3 authors...
Probabilistic inference of a phylogenetic tree from molecular sequence data is predicated on a substitution model describing the relative rates of change between character states along the tree for each site in the multiple sequence alignment. Commonly, one assumes that the substitution model is homogeneous across sites within large partitions of the alignment, assigns these partitions a priori, and then fixes their underlying substitution model to the best-fitting model from a hierarchy of name...
29 CitationsSource
#1Alexis F. L. A. Powell (AMNH: American Museum of Natural History)H-Index: 5
#2F. Keith Barker (AMNH: American Museum of Natural History)H-Index: 24
Last. Scott M. Lanyon (AMNH: American Museum of Natural History)H-Index: 29
view all 3 authors...
Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate he...
45 CitationsSource
#1Peter C. Wainwright (UC Davis: University of California, Davis)H-Index: 63
#2W. Leo Smith (FMNH: Field Museum of Natural History)H-Index: 14
Last. Thomas J. Near (Yale University)H-Index: 48
view all 9 authors...
The perciform group Labroidei includes approximately 2600 species and comprises some of the most diverse and successful lineages of teleost fishes. Composed of four major clades, Cichlidae, Labridae (wrasses, parrotfishes, and weed whitings), Pomacentridae (damselfishes), and Embiotocidae (surfperches); labroids have been an icon for studies of biodiversity, adaptive radiation, and sexual selection. The success and diversification of labroids have been largely attributed to the presence of a maj...
152 CitationsSource
#1Iker Irisarri (CSIC: Spanish National Research Council)H-Index: 13
#2Diego San Mauro (University of Barcelona)H-Index: 18
Last. Rafael Zardoya (CSIC: Spanish National Research Council)H-Index: 55
view all 6 authors...
Background Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genome...
34 CitationsSource
#1Jonathan J. Fong (UPR-RP: UPRRP College of Natural Sciences)H-Index: 14
#2Jeremy M. Brown (University of California, Berkeley)H-Index: 15
Last. Bastien Boussau (University of California, Berkeley)H-Index: 29
view all 4 authors...
In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa...
44 CitationsSource
Cited By283
#1Yanghui Cao (UIUC: University of Illinois at Urbana–Champaign)
#1Yanghui Cao (UIUC: University of Illinois at Urbana–Champaign)H-Index: 1
Last. Christopher H. Dietrich (UIUC: University of Illinois at Urbana–Champaign)H-Index: 21
view all 3 authors...
The first comprehensive timetree is presented for phytoplasmas, a diverse group of obligate intracellular bacteria restricted to phloem sieve elements of vascular plants and tissues of their hemipteran insect vectors. Maximum likelihood-based phylogenetic analysis of DNA sequence data from the 16S rRNA and methionine aminopeptidase (map) genes yielded well resolved estimates of phylogenetic relationships among major phytoplasma lineages, 16Sr groups and known strains of phytoplasmas. Age estimat...
#1Grey T. Gustafson (KU: University of Kansas)H-Index: 5
#2Stephen M. Baca (KU: University of Kansas)H-Index: 3
Last. Andrew E. Z. Short (KU: University of Kansas)H-Index: 15
view all 4 authors...
2 CitationsSource
#1Vera Opatova (UC Davis: University of California, Davis)H-Index: 2
#1Vera Opatova (UC Davis: University of California, Davis)H-Index: 6
Last. Jason E. Bond (UC Davis: University of California, Davis)H-Index: 2
view all 6 authors...
The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-m...
3 CitationsSource
#1Christopher S. Lobban (U.O.G.: University of Guam)H-Index: 19
#2Claire O. Perez (U.O.G.: University of Guam)
Last. Matt P. Ashworth (University of Texas at Austin)H-Index: 10
view all 3 authors...
#1Rodolpho S. T. Menezes (USP: University of São Paulo)H-Index: 4
#2Michael W. Lloyd (National Museum of Natural History)H-Index: 11
Last. Seán G. Brady (National Museum of Natural History)H-Index: 30
view all 3 authors...
The Neotropical realm harbours unparalleled species richness and hence has challenged biologists to explain the cause of its high biotic diversity. Empirical studies to shed light on the processes ...
#1Jong Seok Kim (Chonnam National University)H-Index: 4
#2Min Jee Kim (Chonnam National University)H-Index: 17
Last. Iksoo Kim (Chonnam National University)H-Index: 29
view all 4 authors...
The complete mitochondrial genome (mitogenome) of Amorophaga japonica Robinson, 1986 (Lepidoptera: Tineidae), comprises 15,027 base pairs (bp) and contains a typical set of genes (13 protein-coding...
#1Bin‐Bin Liu (CAS: Chinese Academy of Sciences)H-Index: 1
#1Bin-Bin Liu (CAS: Chinese Academy of Sciences)H-Index: 2
Last. Jun Wen (National Museum of Natural History)H-Index: 42
view all 4 authors...
Abstract The Amelanchier-Malacomeles-Peraphyllum (AMP) clade consists of ca. 26 species distributed in North and Central America, Europe, Asia, and northwestern Africa. While molecular and morphological data strongly support this clade, relationships of its genera are uncertain. Support for the monophyly of Amelanchier and for the phylogenetic positions of Malacomeles and Peraphyllum has varied between studies. Our goals were to reconstruct a robust phylogeny of the AMP clade in the framework of...
2 CitationsSource
#1James P. TownsendH-Index: 1
#2Michael G. TassiaH-Index: 3
Last. Alison M. SweeneyH-Index: 14
view all 6 authors...
#1Martín Miguel Montes (UNLP: National University of La Plata)H-Index: 4
#2J. Barneche (UNLP: National University of La Plata)
Last. Sergio Roberto Martorelli (UNLP: National University of La Plata)H-Index: 6
view all 8 authors...
Adult forms of members of the Callodistomidae always parasitize the gallbladder of freshwater fishes and occur in Africa and America. This study provides a description of a new South American species belonging in Prosthenhystera from the gallbladder of a characid fish (Bryconamericus ikaa), and ribosomal gene sequences (28S rDNA and ITS1-5.8S-ITS2) are used to demonstrate molecular differences between the new species and congeners as well as explore interrelationships among congeners. Additional...