Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes

Matschiner, Michael; Musilová, Zuzana; Barth, Julia Maria Isis; Starostová, Zuzana; Salzburger, Walter; Steel, Mike; Bouckaert, Remco R.

doi:10.1093/sysbio/syw076

Cited by 78 publications

(108 citation statements)

References 111 publications

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“…Our trees include 71% of the New Zealand species, over 89% of families and 98% of orders. Overall, the phylogenetic relationships and the time‐line retrieved were in close general agreement with accepted relationships for fishes within the tree of life (Alfaro et al, ; Betancur‐R, Broughton et al, ; Betancur‐R et al, , ; Hughes et al, ; Matschiner et al, ; Near et al, , ; for more detailed comparisons of time lines from these studies, see Supporting Information Appendix S7). Our new phylogenies dramatically improve our ability to rigorously incorporate phylogenetic relationships into regional studies of ecological biodiversity for New Zealand's marine fish fauna.…”

Section: Results: the Most Comprehensive Phylogeny To Date For New Zesupporting

confidence: 78%

“…This function identifies the most widely shared gene regions across all taxa, removes microsatellites and sequences that are not assigned to any genomic region, extracts the gene name and/or abbreviation, and attempts to correct typographical errors and alternative spellings to synonymize gene region names. The function draws on the HUGO nomenclature database (http://www.genenames.org/) and focuses on 36 gene regions recognized as phylogenetically informative, including for fishes (Betancur‐R, Broughton, et al, , Betancur‐R, Li, et al, ; Betancur‐R, Ortí, & Pyron, ; Matschiner et al, ; Near et al, , ; Rabosky et al, , ; Santini et al, ). This function also enables removal of any known problematic sequences (i.e.…”

Section: Package Description and Methodsmentioning

confidence: 99%

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An integrated pathway for building regional phylogenies for ecological studies

Eme

Anderson

Struthers

et al. 2019

Global Ecol Biogeogr

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Aim Phylogenies are increasingly used in community ecology, biogeography and macroecology. However, sourcing a phylogeny comprising the entire species pool for a focal region can be difficult. Typically, a bespoke phylogeny must be created requiring considerable data manipulation and the use of many standalone software packages. Here we present a suite of methodological tools within the popular R environment that help to build molecular phylogenies appropriate for ecological studies with a regional focus. Innovation Our R package regPhylo provides a pipeline to construct a Bayesian posterior distribution of time‐calibrated trees suitable to address ecological questions. The novel contributions of regPhylo include options to: use prior phylogenetic knowledge through flexible topological constraints; include spatial metadata in sourcing DNA sequences; and include taxa without DNA sequences and then infer consequent phylogenetic uncertainty. Specifically, regPhylo helps researchers: retrieve DNA sequences; enhance available metadata; select DNA sequences based on their length or spatial proximity to the region of study; align sequences; and perform quality control. Output from the pipeline is a file ready to run in the Bayesian tree reconstruction software beast2, appropriate for estimating time‐calibrated trees and including phylogenetic uncertainty for downstream analyses. Main conclusions Overall, regPhylo improves the integration of popular standalone phylogenetic software into the flexible R environment. It provides a novel approach to include topological constraints based on prior knowledge, include taxa without DNA sequences, and select spatially appropriate DNA sequences. When coupled with a Bayesian tree‐building process, our approach provides estimates of uncertainty in both topology and branch lengths. We demonstrate the utility of the package by constructing a posterior distribution of time‐calibrated phylogenies for the New Zealand marine ray‐finned fishes (Actinopterygii) providing the unprecedented opportunity to include phylogenetic information in downstream ecological analyses for marine fishes in this region.

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Section: Results: the Most Comprehensive Phylogeny To Date For New Zesupporting

confidence: 78%

Section: Package Description and Methodsmentioning

confidence: 99%

An integrated pathway for building regional phylogenies for ecological studies

Eme

Anderson

Struthers

et al. 2019

Global Ecol Biogeogr

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“…Furthermore, three orders (Tetraodontiformes, Beloniformes, and Lophiiformes) appeared non-monophyletic, however, in all of these cases only weakly supported nodes separated two subgroups of the order. Thus, our results do not contradict the monophyly of these orders, which has been strongly supported in previous studies 10,32,33 . Most importantly, despite the not unexpected lower support values of basal nodes, our mitochondrial phylogeny corroborates the correct species identification and the absence of DNA contamination in the 66 new assemblies.…”

Section: Technical Validationsupporting

confidence: 92%

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

et al. 2017

Self Cite

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Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts.

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“…The fossil‐based time estimate for Cyprinodontiformes rejects the vicariant hypothesis for this group, as South America, Africa and the Indo‐Malagasy block were already separated from each other by seaways during the Campanian–Maastrichtian (Ali & Aitchison, ; Granot & Dyment, ). This timescale agrees with recent molecular studies that put the origin of killifishes in the Late Cretaceous (Near et al ., ; Matschiner et al ., ). However, this result should be treated with caution for two reasons.…”

Section: Resultsmentioning

confidence: 97%

Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective

Capobianco

Friedman

2018

Biological Reviews

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Widespread fish clades that occur mainly or exclusively in fresh water represent a key target of biogeographical investigation due to limited potential for crossing marine barriers. Timescales for the origin and diversification of these groups are crucial tests of vicariant scenarios in which continental break‐ups shaped modern geographic distributions. Evolutionary chronologies are commonly estimated through node‐based palaeontological calibration of molecular phylogenies, but this approach ignores most of the temporal information encoded in the known fossil record of a given taxon. Here, we review the fossil record of freshwater fish clades with a distribution encompassing disjunct landmasses in the southern hemisphere. Palaeontologically derived temporal and geographic data were used to infer the plausible biogeographic processes that shaped the distribution of these clades. For seven extant clades with a relatively well‐known fossil record, we used the stratigraphic distribution of their fossils to estimate confidence intervals on their times of origin. To do this, we employed a Bayesian framework that considers non‐uniform preservation potential of freshwater fish fossils through time, as well as uncertainty in the absolute age of fossil horizons. We provide the following estimates for the origin times of these clades: Lepidosireniformes [125–95 million years ago (Ma)]; total‐group Osteoglossomorpha (207–167 Ma); Characiformes (120–95 Ma; a younger estimate of 97–75 Ma when controversial Cenomanian fossils are excluded); Galaxiidae (235–21 Ma); Cyprinodontiformes (80–67 Ma); Channidae (79–43 Ma); Percichthyidae (127–69 Ma). These dates are mostly congruent with published molecular timetree estimates, despite the use of semi‐independent data. Our reassessment of the biogeographic history of southern hemisphere freshwater fishes shows that long‐distance dispersals and regional extinctions can confound and erode pre‐existing vicariance‐driven patterns. It is probable that disjunct distributions in many extant groups result from complex biogeographic processes that took place during the Late Cretaceous and Cenozoic. Although long‐distance dispersals likely shaped the distributions of several freshwater fish clades, their exact mechanisms and their impact on broader macroevolutionary and ecological dynamics are still unclear and require further investigation.

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Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes

Abstract: Abstract.-Divergence-time estimation based on molecular phylogenies and the fossil 18 record has provided insights into fundamental questions of evolutionary biology. In

Cited by 78 publications

References 111 publications

An integrated pathway for building regional phylogenies for ecological studies

An integrated pathway for building regional phylogenies for ecological studies

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective

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