Effects of missing data on species tree estimation under the coalescent

Hovmöller, Rasmus; Knowles, L. Lacey; Kubatko, Laura

doi:10.1016/j.ympev.2013.06.004

Cited by 73 publications

(37 citation statements)

References 37 publications

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“…The percentage of gene occupancy in the remaining eight species ranged from 60.5% (746/1233) to 78.6% (969/1233). Two recent studies showed that nonrandom bias in missing data might be potentially problematic for phylogenetic inference (Hosner et al 2016; Xi et al 2016), particularly for coalescence-based phylogenetic inference (Hovmöller et al 2013). Interestingly, the placements for the eight low gene-coverage species in our study were robust in both concatenation and coalescent analyses, as well as in the two data matrices and subsampling analyses (see results below), suggesting that the impact of missing data in this study is negligible.…”

Section: Resultsmentioning

confidence: 99%

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Shen

Zhou

Kominek

et al. 2016

G3 Genes|Genomes|Genetics

202

159

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Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

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Section: Resultsmentioning

confidence: 99%

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Shen

Zhou

Kominek

et al. 2016

G3 Genes|Genomes|Genetics

202

159

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“…The Iberian and Moroccan clades are sister groups (BPP = 1.0), while the Anatolian worm lizard B. strauchi is sister to all other congeners. Although mc1r sequences of B. strauchi were not available for the species-tree analysis, this small degree of missing data (4%) is unlikely to have affected the tree estimate as (1) the analyses achieved convergence and (2) *BEAST species-tree estimates are remarkably resilient to the effects of missing data (Hovm€ oller et al 2013). The phylogenetic relationships among the five Blanus species inferred through the concatenation approach are fully congruent with those recovered by the species-tree analysis ( Figure S1).…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic and diversity patterns ofBlanusworm lizards (Squamata: Amphisbaenia): insights from mitochondrial and nuclear gene genealogies and species tree

Sampaio

Harris

Perera

et al. 2014

J Zoolog Syst Evol Res

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Phylogenetic and phylogeographic patterns of amphisbaenians are poorly known. Molecular data from mitochondrial and nuclear loci are particularly needed for amphisbaenian phylogeny and taxonomy because their specializations to subterranean habits make morphology poorly informative and the occurrence of cryptic species probable. The Mediterranean genus Blanus includes five species – three of them have been recently studied mainly at the mitochondrial level. In this study, we collected mitochondrial (16S and nd4) and nuclear (mc1r and pomc) sequences from 49 specimens, including multiple individuals for each of the five species. We used multilocus coalescent‐based species‐tree inference and single‐gene analyses to estimate phylogenetic relationships among Blanus and to assess patterns of intraspecific differentiation within all the five species. Species‐tree and single‐gene phylogenies provided strong support for the Anatolian worm lizard B. strauchi lying outside a clade comprising all other congeners, with a sister relationship between the Iberian clade (B. cinereus and B. mariae) and the North African clade (B. tingitanus and B. mettetali). Mitochondrial and nuclear data supported the genetic distinctiveness of the recently described B. mariae and also indicated that the distribution of this species is wider than previously known and overlaps with B. cinereus in central Portugal. Blanus tingitanus showed two phylogeographic groups, from the northern and the southern portion of the range, respectively, having high mitochondrial and nuclear divergence and a possible contact zone in northwestern Morrocco. Finally, high genetic variation was found within B. mettetali and B. strauchi, suggesting in the latter case, the occurrence of cryptic taxa to be tested by further research.

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“…2). These processes, known as the coalescent (Hovmoeller et al, 2013), can have three important effects.…”

Section: Gene Genealogies and Species Phylogeniesmentioning

confidence: 99%

DNA-based species delimitation in algae

Leliaert

Verbruggen

Vanormelingen

et al. 2014

European Journal of Phycology

313

285

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Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming the standard for delimiting species and testing their traditional boundaries. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation. We review these recent developments in DNA-based species delimitation methods, and discuss how they have changed and continue to change our understanding of algal species boundaries. Although single-locus approaches have proven effective for a first rapid and large-scale assessment of species diversity, species delimitation based on single gene trees falls short due to gene tree-species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization and introgression. Data from unlinked loci and multi-species coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors. Several of these methods also provide statistical support regarding species boundaries, which is important because speciation is a process and therefore uncertainty about precise species boundaries is inevitable in recently diverged lineages.

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Effects of missing data on species tree estimation under the coalescent

Cited by 73 publications

References 37 publications

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Phylogenetic and diversity patterns ofBlanusworm lizards (Squamata: Amphisbaenia): insights from mitochondrial and nuclear gene genealogies and species tree

DNA-based species delimitation in algae

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