Inferring the Root of a Phylogenetic Tree

Huelsenbeck, John P.; Bollback, Jonathan P.; Levine, Amy M.

doi:10.1080/106351502753475862

Cited by 204 publications

(179 citation statements)

References 33 publications

(29 reference statements)

Supporting

Mentioning

177

Contrasting

Order By: Relevance

“…Due to the limited genetic divergence within Pentagramma and the relatively large phylogenetic distance to its nearest relative Pryer 2009), a midpoint rooting approach was employed. Midpoint rooting has been shown to perform well at lower taxonomic levels (Hess and De Moraes Russo 2007) and the alternative, outgroup rooting with a distantly related outgroup, can be problematic (Maddison et al 1984;Wheeler 1990;Huelsenbeck et al 2002;Sanderson and Shaffer 2002;Schuettpelz and Hoot 2006).…”

Section: Methodsmentioning

confidence: 99%

A Unified Approach to Taxonomic Delimitation in the Fern Genus <I>Pentagramma</I> (Pteridaceae)

Schuettpelz¹,

Pryer²,

Windham³

2015

Systematic Botany

View full text Add to dashboard Cite

Section: Methodsmentioning

confidence: 99%

A Unified Approach to Taxonomic Delimitation in the Fern Genus <I>Pentagramma</I> (Pteridaceae)

Schuettpelz¹,

Pryer²,

Windham³

2015

Systematic Botany

View full text Add to dashboard Cite

“…Molecular clocks can help infer the root of a clade when appropriate close outgroups are unavailable [35]. Given the distant relationship of Sphenodon (the closest living relatives of squamates) and the relatively basal placement of dibamids in the squamate phylogeny, we therefore performed a series of dibamids-only analyses using (i) all positions of all genes, (ii) the nuclear data as a whole, and (iii) the data from individual genes.…”

Section: Methodsmentioning

confidence: 99%

Intercontinental dispersal by a microendemic burrowing reptile (Dibamidae)

2011

View full text Add to dashboard Cite

Intercontinental dispersal via land bridge connections has been important in the biogeographic history of many Holarctic plant and animal groups. Likewise, some groups appear to have accomplished trans-oceanic dispersal via rafting. Dibamid lizards are a clade of poorly known fossorial, essentially limbless species traditionally split into two geographically disjunct genera: Dibamus comprises approximately 20 Southeast Asian species, many of which have very limited geographical distributions, and the monotypic genus Anelytropsis occupies a small area of northeastern Mexico. Although no formal phylogeny of the group exists, a sister -taxon relationship between the two genera has been assumed based on biogeographic considerations. We used DNA sequence data from one mitochondrial and six nuclear protein-coding genes to construct a phylogeny of Dibamidae and to estimate divergence times within the group. Surprisingly, sampled Dibamus species form two deeply divergent, morphologically conserved and geographically concordant clades, one of which is the sister taxon of Anelytropsis papillosus. Our analyses indicate Palaearctic to Nearctic Beringian dispersal in the Late Palaeocene to Eocene. Alternatively, a trans-Pacific rafting scenario would extend the upper limit on dispersal to the Late Cretaceous. Either scenario constitutes a remarkable long-distance dispersal in what would seem an unlikely candidate.

show abstract

“…Under the stationary models HKY and GTR, the root of the tree is unidentifiable as both models are time reversible. Under nonstationary models, the root of the tree is identifiable, but we expect the data to contain little information to root the tree in this way (Yang and Roberts 1995;Huelsenbeck et al 2002).…”

Section: Analysis Of the Simulated Datamentioning

confidence: 99%

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

2015

View full text Add to dashboard Cite

Inference of gene sequences in ancestral species has been widely used to test hypotheses concerning the process of molecular sequence evolution. However, the approach may produce spurious results, mainly because using the single best reconstruction while ignoring the suboptimal ones creates systematic biases. Here we implement methods to correct for such biases and use computer simulation to evaluate their performance when the substitution process is nonstationary. The methods we evaluated include parsimony and likelihood using the single best reconstruction (SBR), averaging over reconstructions weighted by the posterior probabilities (AWP), and a new method called expected Markov counting (EMC) that produces maximum-likelihood estimates of substitution counts for any branch under a nonstationary Markov model. We simulated base composition evolution on a phylogeny for six species, with different selective pressures on G+C content among lineages, and compared the counts of nucleotide substitutions recorded during simulation with the inference by different methods. We found that large systematic biases resulted from (i) the use of parsimony or likelihood with SBR, (ii) the use of a stationary model when the substitution process is nonstationary, and (iii) the use of the Hasegawa-Kishino-Yano (HKY) model, which is too simple to adequately describe the substitution process. The nonstationary general time reversible (GTR) model, used with AWP or EMC, accurately recovered the substitution counts, even in cases of complex parameter fluctuations. We discuss model complexity and the compromise between bias and variance and suggest that the new methods may be useful for studying complex patterns of nucleotide substitution in large genomic data sets.

show abstract

Inferring the Root of a Phylogenetic Tree

Cited by 204 publications

References 33 publications

A Unified Approach to Taxonomic Delimitation in the Fern Genus <I>Pentagramma</I> (Pteridaceae)

A Unified Approach to Taxonomic Delimitation in the Fern Genus <I>Pentagramma</I> (Pteridaceae)

Intercontinental dispersal by a microendemic burrowing reptile (Dibamidae)

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

Contact Info

Product

Resources

About