Species tree estimation using Neighbor Joining

Rusinko, Joseph; McPartlon, Matthew

doi:10.1016/j.jtbi.2016.11.005

Cited by 23 publications

(19 citation statements)

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“…These included three multispecies coalescent methods34,35: the Bayesian SNAPP36 (with a subset of 48,922 unlinked SNPs in 12 individuals representing the eco-morphological groups), the algebraic method SVDquartets37,38, which allows for site-specific rate variation and is robust to gene-flow between sister taxa39, and the summary method ASTRAL40,41, using the 2543 local ML trees that were described above as input. We also built a whole genome Neighbour-Joining (NJ) tree using the Dasarathy et al algorithm, which has been shown to be a statistically consistent and accurate species tree estimator under ILS42,43. The above methods have also been applied to datasets where the individuals that are genetically intermediate between eco-morphological groups ( C. trimaculatus , A. stuartgranti , and A. steveni ) have been removed, thus likely reducing the extent of violation of the multispecies coalescent model.…”

Section: Resultsmentioning

confidence: 99%

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

et al. 2018

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The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.

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Section: Resultsmentioning

confidence: 99%

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

et al. 2018

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“…These included three multispecies coalescent methods 36,37 : the Bayesian SNAPP 38 (with a subset of 48,922 unlinked SNPs in 12 individuals representing the eco-morphological groups), the algebraic method SVDquartets 39,40 , which allows for site-specific rate variation and is robust gene-flow between sister taxa 41 , and the summary method ASTRAL 42,43 , using the 2543 local ML trees that were described above as input. We also built whole genome Neighbour-Joining (NJ) tree using the Dasarathy et al algorithm, which has been shown to be a statistically consistent and accurate species tree estimator under ILS 44,45 It is also clear that the mtDNA phylogeny is an outlier, being substantially different from all the whole-genome phylogenies and also from the majority of the local ML trees (Fig. 2b,c and…”

Section: Phylogenetic Framework Relationshipsmentioning

confidence: 99%

Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Malinsky

Svardal

Tyers

et al. 2017

Preprint

100

172

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Abstract:The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/143859 doi: bioRxiv preprint first posted online May. 31, 2017; Main Text: The formation of every lake or island represents a fresh opportunity for colonization, proliferation and diversification of living forms. In some cases, the ecological opportunities presented by underutilized habitats facilitate adaptive radiation -rapid and extensive diversification of the descendants of the colonizing lineages (1-3). Adaptive radiations are thus exquisite examples of the power of natural selection, as recognized by Darwin in the case of Galapagos finches (4, 5), and seen for example in Anoles lizards of the Caribbean (6) and in East African cichlid fishes (7,8).Cichlids are the most species rich and diverse family of vertebrates, and nowhere are their radiations more spectacular than in the Great Lakes of East Africa: Malawi, Tanganyika, and Victoria (2), each of which contains several hundred endemic species, with the largest number in Lake Malawi. Molecular genetic studies have made major contributions to reconstructing the evolutionary histories of these adaptive radiations, especially in terms of the relationships between the lakes (9), between some major lineages in Lake Tanganyika (10), and in describing the role of hybridization in the origins of the Lake Victoria radiation (11). However, the task of reconstructing within-lake relationships and of identifying sister species in lakes Malawi and Victoria remains challenging due both to retention of large amounts of ancestral genetic polymorphism (i.e. incomplete lineage sorting) and to evidence suggesting gene flow between taxa (12, 13).Initial genome assemblies of cichlids from ...

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“…Summary coalescent-based methods have, however, been criticized for placing unrealistic confidence in gene tree estimation, and concerns have been raised regarding their performance when the accuracy of inferred gene trees varies (Springer and Gatesy 2016). In some circumstances, such as poor phylogenetic signal or low ILS and high gene tree estimation error, concatenation can provide as good or even better species-tree estimates Liu et al 2015a;Rusinko and McPartlon 2017;Molloy and Warnow 2018). Full coalescent methods on the other hand, can overcome these problems by simultaneously estimating gene and species trees and taking into account their uncertainty under a Bayesian framework (Knowles et al 2012).…”

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confidence: 99%

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting

et al. 2018

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Resolving patterns of ancient and rapid diversifications is one of the most challenging tasks in evolutionary biology. These difficulties arise from confusing phylogenetic signals that are associated with the interplay of incomplete lineage sorting and homoplasy. Phylogenomic analyses of hundreds, or even thousands, of loci offer the potential to resolve such contentious relationships. Yet, how much useful phylogenetic information these large data sets contain remains uncertain and often goes untested. Here, we assess the utility of different data filtering approaches to maximize phylogenetic information and minimize noise when reconstructing an ancient radiation of Neotropical electric knifefishes (Order Gymnotiformes) using ultraconserved elements. We found two contrasting hypotheses of gymnotiform evolutionary relationships depending on whether phylogenetic inferences were based on concatenation or coalescent methods. In the first case, all analyses inferred a previously-and commonly-proposed hypothesis, where the family Apteronotidae was found as the sister group to all other gymnotiform families. In contrast, coalescent-based analyses suggested a novel hypothesis where families producing pulse-type (viz., Gymnotidae, Hypopomidae and Rhamphichthyidae) and wave-type electric signals (viz., Apteronotidae, Sternopygidae) were reciprocally monophyletic.Nodal support for this second hypothesis increased when analyzing loci with the highest phylogenetic information content and further increased when data were pruned using targeted filtering methods that maximized phylogenetic informativeness at the deepest nodes of the Gymnotiformes. Bayesian concordance analyses and topology tests of individual gene genealogies demonstrated that the difficulty of resolving this radiation was likely due to high gene-tree incongruences that resulted from incomplete lineage sorting. We show that data filtering reduces gene tree heterogeneity and increases nodal support and consistency of species Downloaded from https://academic.oup.com/sysbio/advance-article-abstract/doi/10.1093/sysbio/syy085/5232148 by Bukkyo University user on 06 December 20183 trees using coalescent methods; however, we failed to observe the same effect when using concatenation methods. Furthermore, the targeted filtering strategies applied here support the use of "gene data interrogation" rather than "gene genealogy interrogation" approaches in phylogenomic analyses, to extract phylogenetic signal from intractable portions of the Tree of Life.

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Species tree estimation using Neighbor Joining

Cited by 23 publications

References 20 publications

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting

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