scholarly journals Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

2017 ◽  
Author(s):  
Koichiro Tamura ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Relative Rate ◽  
Molecular Data ◽  
Evolutionary Rates ◽  
Divergence Times ◽  
Computationally Efficient ◽  
Molecular Sequence ◽  
Branch Lengths ◽  
Variable Evolutionary Rates ◽  
Relationship Of ◽  
The Relationship

AbstractRelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of datasets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between an evolutionary lineage and its descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be also useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.

Phylogeny of Echiura updated, with a revised taxonomy to reflect their placement in Annelida as sister group to Capitellidae

2020 ◽  
Vol 34 (1) ◽  
pp. 101 ◽  
Author(s):  
Ryutaro Goto ◽  
James Monnington ◽  
Marija Sciberras ◽  
Isao Hirabayashi ◽  
Greg W. Rouse
Keyword(s):  
Molecular Phylogeny ◽  
Deep Sea ◽  
Sister Group ◽  
Molecular Data ◽  
Monterey Bay ◽  
Phylogenetic Studies ◽  
Littoral Zones ◽  
Family Level ◽  
Relationship Of ◽  
The Relationship

Echiura (commonly called spoon worms) are derived annelids that have an unsegmented sausage-shaped body with a highly extensible anterior end (i.e. a proboscis). Echiura currently contains two superfamilies: Echiurioidea (with Echiuridae, Urechidae and Thalassematidae) and Bonellioidea (with Bonelliidae, and Ikedidae). Ikedidae contains only Ikeda, which is distinctive in having a huge trunk, a highly elongate proboscis with stripes or dots, and numerous gonoducts. A recent molecular phylogeny of Echiura recovered Ikedidae as the sister group to Bonelliidae. However, due to relatively low support values for the monophyly of Bonelliidae, this relationship remains problematic. In this study, we reinvestigated the relationship of Bonelliidae and Ikedidae using an expanded dataset with more taxa and genes. In contrast to the previous results, our analyses strongly support that Ikeda is nested within Bonelliidae due to the placement of Maxmuelleria. On the basis of this result, we synonymise Ikedidae with Bonelliidae and transfer Ikeda to the latter, the diagnosis of which is amended. In addition, we synonymise Urechidae with its sister group Echiuridae because they share the synapomorphy of having anal chaetae rings. Furthermore, considering that recent phylogenetic studies have consistently recovered Echiura as the sister group to Capitelliidae within Annelida, we drop the rank of the echiuran clade to family-level and propose a revised classification: Thalassematidae with two subfamilies, Thalassematinae (with two tribes Echiurini and Thalassematini) and Bonelliinae. In addition, we identified a sample collected from the deep sea (~1820 m) of Monterey Bay, California, based on its molecular data. This terminal unexpectedly formed the sister group to the eight genera of Thalassematini, most members of which are inhabitants of littoral zones.

scholarly journals A note on the systematic position of the Bathynellacea (Crustacea, Malacostraca) using molecular evidence

2002 ◽  
Vol 71 (4) ◽  
pp. 123-129 ◽  
Author(s):  
Ana Isabel Camacho ◽  
Isabel Rey ◽  
Beatriz A. Dorda ◽  
Annie Machordom ◽  
Antonio G. Valdecasas
Keyword(s):  
Molecular Data ◽  
Systematic Position ◽  
Molecular Evidence ◽  
Gene Fragment ◽  
16S Rdna Gene ◽  
Internal Morphology ◽  
Mt 16S Rdna ◽  
Relationship Of ◽  
First Time ◽  
The Relationship

Molecular data for the mt 16S rDNA gene fragment of a bathynellacean is here presented for the first time and used to analyze the relationship of the group within the crustacean class Malacostraca (Arthropoda, Bathynellacea). Two contrasting views have classified the bathynelids as being either within the order Syncarida or in a separate super-order Podophallocarida belonging to the infra-class Eonomostraca, a disagreement based mainly on debates over external and internal morphology. The preliminary analyses offered here in question the placement of this Bathynellacea within the Syncarida, and suggest the need for a further study of relationships among the malacostracan groups.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference. Results We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as  some intermediate nodes may show large time differences between these two types of data. Conclusions Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2021 ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background: Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.Results: We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur because some deeper nodes show a large time differences between these two types of data.Conclusions: Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of time structure in morphological and molecular data before any dating analysis using combined datasets.

scholarly journals Estimation of coalescence probabilities and population divergence times from SNP data

Heredity ◽  
2021 ◽  
Author(s):  
Kristy Mualim ◽  
Christoph Theunert ◽  
Montgomery Slatkin
Keyword(s):  
Demographic History ◽  
Population History ◽  
Divergence Times ◽  
Population Divergence ◽  
High Coverage ◽  
Snp Data ◽  
Population Sizes ◽  
History Of ◽  
Relationship Of ◽  
The Relationship

AbstractWe present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

Collastoma esotericum (Neodalyellida: Umagillidae), a new species of sipunculan-inhabiting rhabdocoel from Queensland, Australia

Zootaxa ◽  
2019 ◽  
Vol 4701 (6) ◽  
pp. 563-573
Author(s):  
DANIEL C. HUSTON
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Distinct Genus ◽  
De Man ◽  
Relationship Of ◽  
The Relationship ◽  
Southeast Queensland

The Umagillidae Wahl, represent a group of endosymbiotic Platyhelminthes which inhabit two disparate invertebrate host groups, the echinoderms and sipunculans. Sipunculan-inhabiting umagillids are morphologically distinct from those inhabiting echinoderms and have traditionally been placed in a distinct genus and subfamily, Collastoma Dörler, and the Collastominae Wahl, respectively. Although molecular data are available for umagillid species inhabiting echinoids and holothurians, species inhabiting sipunculans have yet to be evaluated with molecular data. Collastoma esotericum n. sp. from the sipunculan Phascolosoma scolops (Selenka & de Man) collected in Moreton Bay, southeast Queensland, Australia, is described. Phylogenetic analyses based on 18S rRNA gene sequences placed C. esotericum in a clade with species of the Umagillidae and the Provorticinae Luther, with strong support. However, within this clade the relationship of C. esotericum to the Umagillidae and Provorticinae was not resolved. 

scholarly journals A new method for detecting autocorrelation of evolutionary rates in large phylogenies

2018 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Fabia Battistuzzi ◽  
Sudhir Kumar
Keyword(s):  
Sequence Data ◽  
Tree Of Life ◽  
Evolutionary Rates ◽  
New Method ◽  
Sequence Evolution ◽  
Computationally Efficient ◽  
Evolutionary Patterns ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Evolution Of Mammals

AbstractNew species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of mutation rates and the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates within lineages in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack power to detect autocorrelated rates. Here we present a machine learning method to detect the presence evolutionary rate autocorrelation in large phylogenies. The new method is computationally efficient and performs better than the available state-of-the-art methods. Application of the new method reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and non-molecular evolutionary patterns and will foster unbiased and precise dating of the tree of life.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2021 ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background: Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.Results: We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur because some deeper nodes may show large time differences between these two types of data.Conclusions: Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

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