Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations

Huang, Huateng; Tran, Lucy A. P.; Knowles, L. Lacey

doi:10.1016/j.ympev.2014.05.010

Cited by 9 publications

(10 citation statements)

References 76 publications

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“…Filardi & Moyle 2005;DaCosta & Klicka 2008;DaCosta et al 2009;Barker et al 2013;Klicka et al 2014). Although it represents a single matrilineal locus whose history may not necessarily be fully congruent with the species tree (Huang et al 2014), mitochondrial genes are believed to have a high probability of correctly tracking branching patterns of recent events of the species trees (Moore 1995;Avise 2009). The gene was amplified in two overlapping sections, by means of PCR, using the primers described in Table S2.…”

Section: Methodsmentioning

confidence: 99%

Diversification in the Andes: the Atlapetes brush‐finches

et al. 2014

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With nearly 30 species, the Atlapetes brush‐finches are one of the most species‐rich genera in the New World sparrows (Passerellidae). Atlapetes is mainly distributed in highland forests from Mexico to north‐western Argentina, with a few taxa in the foothills (<1000 m). Species diversity is highest in South America, because of high rates of local replacement but few cases of local co‐occurrence, creating a mosaic of forms with different plumage colours. With the purpose of understanding phylogenetic and environmental determinants of trait evolution, we reconstructed a molecular phylogeny based on full ND2 mtDNA sequences, with focus on the core group of Andean Atlapetes species and related outgroups. Phylogenetic relationships revealed that most Andean species are closely related to a geographical neighbour, although these neighbours may often be phenotypically quite different, with yellow‐plumaged species sister to grey‐plumaged taxa. Biogeographic analyses suggest Mesoamerica as the area of origin for Atlapetes, which dispersed through the Panama Isthmus to the eastern Andean slope, then the western Andes and finally the southern Andes. Diversification in the genus was apparently influenced by the glacial cycles that affected the distribution of montane forests in the Neotropics, particularly during the last million years. Phenotypic plumage changes may be associated with ecological conditions, with black dorsum in the wettest areas and a pale dorsum in a group of closely related species in dry environments on the Pacific slope. Local sympatry and ecological segregation presumably does not lead to increased divergence in plumage signals or song.

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Section: Methodsmentioning

confidence: 99%

Diversification in the Andes: the Atlapetes brush‐finches

et al. 2014

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“…Lake Tanganyika cichlids have been subject to numerous phylogenetic studies. Most of these studies were based on mitochondrial phylogenies, which in many lineages do not approximate the true species tree due to ancient incomplete lineage sorting (Takahashi, Terai, Nishida, & Okada, 2001) and hybridization/introgression, particularly in lamprologine cichlids (Huang, Tran, & Knowles, 2014;Koblmüller et al, 2007;McGee et al, 2016;Sturmbauer, Salzburger, Duftner, Schelly, & Koblmüller, 2010;Takahashi & Koblmüller, 2011). Hence, for trustable reconstruction of species trees in these cichlids, nuclear multilocus or genome-wide phylogenies are required.…”

Section: Quality Of Phylogenetic Informationmentioning

confidence: 99%

“…information content and a large proportion of missing data in the nuclear dataset. Consequently, the tree is heavily influenced by the mitochondrial data, which handicaps the approximation of the lamprologini species tree due to incomplete lineage sorting and prevalent hybridization/introgression (Huang et al, 2014;Koblmüller et al, 2007;McGee et al, 2016;Sturmbauer et al, 2010;Takahashi & Koblmüller, 2011;Takahashi & Sota, 2016). Measures taken to resolve these issues (topological constraints and omission of particular sequence data) unfortunately created further problems.…”

Section: Acknowledg Ementsmentioning

confidence: 99%

Evolutionary transitions to cooperative societies in fishes revisited

et al. 2018

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Unravelling the evolution of complex social organization in animals is an important aim, not least because it helps to understand the evolutionary roots of human sociality. Recent advances in comparative methods allow to approach this question in a phylogenetic context. The validity of such comparative approaches depends strongly on the quality of information regarding the behaviour, sociality, and reproduction of animals in natural systems, and on the quality of the phylogenetic reconstruction. Applying a novel comparative approach, a recent study of Dey et al. (, Nature Ecology & Evolution, 1, 137) concluded that evolutionary transitions to cooperative breeding in cichlid fishes were not associated with the social mating pattern. Here we argue that this result was adversely affected by equivocal classifications of mating patterns, and inadequate phylogenetic data. In order to illustrate the impact of the mating system misclassifications, we scored mating patterns as reported in the original literature and re‐analysed the dataset based on Dey et al.’s tree topology. The result suggests that the mating system does in fact significantly explain the evolutionary transition to cooperative breeding in lamprologine cichlids, but we submit that a reliable conclusion cannot be reached before improving the behavioural information and the underlying phylogenetic reconstruction. The problems identified in this case study are not unique and we urge caution in the interpretation of results from comparative phylogenetic studies in general. We do agree with Dey et al. () though that the lamprologine cichlids of Lake Tanganyika may constitute a fundamental test case for the theory of social evolution, but better information on their behaviour and phylogenetic relationships is needed to allow meaningful analyses.

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“…When carrying out phylogenetic analyses for species that are substantially divergent, ignoring gene flow following speciation may not bias the resulting estimates. However, with the advent of large-scale genomic data sets that allow study of evolutionary relationships among closely related populations or species, the necessity of simultaneously examining these factors is becoming increasingly apparent (Eckert and Carstens, 2008; Leaché et al, 2013; Huang et al, 2014). In particular, since gene flow may easily occur between sister taxa following speciation, even in the presence of incomplete lineage sorting (Yu et al, 2011), it is necessary to incorporate these processes simultaneously into models used to analyze data for closely related species or populations.…”

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confidence: 99%

Distribution of gene tree histories under the coalescent model with gene flow

Tian

Kubatko²

2015

Preprint

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We propose a coalescent model for three species that allows gene flow be-23 tween both pairs of sister populations. The model is designed to analyze multilocus genomic 24 sequence alignments, with one sequence sampled from each of the three species. The model 25 is formulated using a Markov chain representation, which allows use of matrix exponentia-26 tion to compute analytical expressions for the probability density of gene tree genealogies. 27 The gene tree history distribution as well as the gene tree topology distribution under this 28 coalescent model with gene flow are then calculated via numerical integration. We analyze 29 the model to compare the distributions of gene tree topologies and gene tree histories for 30 species trees with differing effective population sizes and gene flow rates. Our results suggest 31 conditions under which the species tree and associated parameters are not identifiable from 32 the gene tree topology distribution when gene flow is present, but indicate that the gene 33 tree history distribution may identify the species tree and associated parameters. Thus, the 34 gene tree history distribution can be used to infer parameters such as the ancestral effective 35 population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We 36 conduct computer simulations to evaluate the performance of our method in estimating these 37 parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 38 2015) to demonstrate the usefulness of our method for the analysis of empirical data. 39 40 maximum likelihood, speciation. 41 42 gruence between a gene tree and the species tree for the same set of species (Maddison, 43 1997). Incomplete lineage sorting (also called deep coalescence) has long been recognized to 44 be one of the major causes of variation in gene trees across a genome (Pamilo and Nei, 1988; 45 Takahata, 1989). Another important factor leading to discord between gene trees and the 46 species tree is gene flow between populations following speciation (Maddison, 1997; Leaché 47 et al., 2013; Degnan et al., 2012). With some exceptions (noted below), these two pro-48 cesses have been studied in isolation. When carrying out phylogenetic analyses for species 49 that are substantially divergent, ignoring gene flow following speciation may not bias the 50 resulting estimates. However, with the advent of large-scale genomic data sets that allow 51 study of evolutionary relationships among closely related populations or species, the neces-52 sity of simultaneously examining these factors is becoming increasingly apparent (Eckert 53 and Carstens, 2008; Leaché et al., 2013; Huang et al., 2014). In particular, since gene flow 54 may easily occur between sister taxa following speciation, even in the presence of incomplete 55 lineage sorting (Yu et al., 2011), it is necessary to incorporate these processes simultaneously 56 into models used to analyze data for closely related species or populations. 57Degnan and Sal...

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Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations

Cited by 9 publications

References 76 publications

Diversification in the Andes: the Atlapetes brush‐finches

Diversification in the Andes: the Atlapetes brush‐finches

Evolutionary transitions to cooperative societies in fishes revisited

Distribution of gene tree histories under the coalescent model with gene flow

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