Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab, Siavash; Bayzid, Md. Shamsuzzoha; Boussau, Bastien; Warnow, Tandy

doi:10.1126/science.1250463

Cited by 247 publications

(254 citation statements)

References 83 publications

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“…Recent statistical advances in coalescent-based methods have indicated that statistically grouping genes into subsets can improve the accuracy of species tree estimation (Mirarab et al 2014). Our analyses also benefited from this approach.…”

Section: Phylogenetics and Taxonomymentioning

confidence: 67%

North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade

Remedios

Lee

Burke

et al. 2015

Molecular Phylogenetics and Evolution

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Establishing phylogenetic relationships within a clade can help to infer ancestral origins and indicate how widespread species reached their current biogeographic distributions. The small plovers, genus Charadrius, are cosmopolitan shorebirds, distributed across all continents except Antarctica. Here we present a global, species-level molecular phylogeny of this group based on four nuclear (ADH5, FIB7, MYO2 and RAG1) and two mitochondrial (COI and ND3) genes, and use the phylogeny to examine the biogeographic origin of the genus. A Bayesian multispecies coalescent approach identified two major clades (CRD I and CRD II) within the genus. Clade CRD I contains three species (Thinornis novaeseelandiae, Thinornis rubricollis and Eudromias morinellus), and CRD II one species (Anarhynchus frontalis), that were previously placed outside the Charadrius genus. In contrast to earlier work, ancestral area analyses using parsimony and Bayesian methods supported an origin of the Charadrius plovers in the Northern hemisphere.We propose that major radiations in this group were associated with shifts in the range of these ancestral plover species, leading to colonisation of the Southern hemisphere.

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Section: Phylogenetics and Taxonomymentioning

confidence: 67%

North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade

Remedios

Lee

Burke

et al. 2015

Molecular Phylogenetics and Evolution

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“…We further used coalescent-based species tree estimation to test for potentially misleading phylogenetic signal due to incomplete lineage sorting. This analysis was conducted both with individual gene trees and with trees based on alignments binned according to the binning approach of Mirarab et al 55 .…”

Section: Methodsmentioning

confidence: 99%

Evolution of the immune system influences speciation rates in teleost fishes

et al. 2016

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With over 32,000 extant species 1 , teleost fishes comprise the majority of vertebrate species. Their taxonomic diversity is matched by extensive genetic and phenotypic variation, including novel immunological strategies. Although the functionality of the adaptive immune system has been considered to be conserved since its emergence in the ancestor of all jawed vertebrates 2,3 , fundamental modifications of the immune gene repertoire have recently been reported in teleosts [4][5][6][7] . One of the most dramatic changes has occurred in Atlantic cod (Gadus morhua), involving complete loss of the MHC II pathway that is otherwise responsible for the detection of bacterial pathogens in vertebrates 4 . Moreover, this loss is accompanied by a substantially enlarged repertoire of MHC I genes, which normally encode molecules for protection against viral pathogens. It has thus been hypothesized that the expanded MHC I repertoire of cod evolved as a compensatory mechanism, whereby broader MHC I functionality makes up for the initial loss of MHC II (refs. 4,6). However, the questions of how and when MHC II was lost relative to the MHC I expansion, and whether these genomic modifications are causally related, have so far remained unresolved.As key components of the vertebrate adaptive immune system, the complex MHC pathways and their functionality are now well characterized 8-10 , but less is known about the causes of MHC copy number variation, which poses an immunological tradeoff 11,12 . Although an increase in the number of MHC genes facilitates pathogen detection, it will also decrease the number of circulating T cells [13][14][15][16] , resulting in an immune system that can detect a large number of pathogens at the expense of being less efficient in removing them. The evolution of MHC copy numbers is therefore likely driven toward intermediate optima determined by a tradeoff between detection and elimination of pathogens-as suggested by selection for 5-10 copies inferred in case studies of fish 17,18 and birds 19 . Because pathogen load and the associated selective pressures vary between habitats, the optimal number of MHC copies depends on the environment [20][21][22] . As a result, interbreeding between different locally adapted populations is expected to produce hybrids with excess (above optimal) MHC diversity that are characterized by T cell deprivation and low fitness. This process would introduce postzygotic reproductive isolation and promote reinforcement of premating isolation between the populations. Consequently, MHC genes have been suggested to have an important role in speciation 22,23 , but, to our knowledge, this role has never been tested comparatively in a macroevolutionary context.Here we report comparative analyses of 76 teleost species, of which 66 were sequenced to produce partial draft genome assemblies, including 27 representatives of cod-like fishes within the order Gadiformes. First, we use phylogenomic analysis to resolve standing controversy regarding early-teleost divergences and to firmly ...

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“…Further, these simulations [86] did not compare the performance of coalescence methods to concatenation in their study of the effects of recombination on coalescence methods. More recently, the idea of concatalescence has been reimagined as statistical binning, in which gene trees and alignments are assigned to a bin based on 'combinability' before creating supergene trees for downstream coalescence analysis [87]. Accurate gene tree reconstructions are also central to the coalescent approach as each tree is given equal weight in the analysis; however, accurate reconstructions become increasingly difficult with decreasing c-gene sizes as more taxa are added to the analysis [19].…”

Section: Morphology Moleculesmentioning

confidence: 99%

Mammal madness: is the mammal tree of life not yet resolved?

Foley

Springer

Teeling

2016

Phil. Trans. R. Soc. B

215

195

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One contribution of 15 to a discussion meeting issue 'Dating species divergences using rocks and clocks'. Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90-110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain 'hard nodes' such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

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Statistical binning enables an accurate coalescent-based estimation of the avian tree

Cited by 247 publications

References 83 publications

North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade

North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade

Evolution of the immune system influences speciation rates in teleost fishes

Mammal madness: is the mammal tree of life not yet resolved?

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