The gene tree delusion (Q38978053)

8 September 2017

The gene tree delusion (English)

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8 September 2017

1

Mark S Springer

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8 September 2017

John Gatesy

2

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8 September 2017

31 July 2015

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Molecular Phylogenetics and Evolution

8 September 2017

33

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based on heuristic

inferred from page(s)

published in

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8 September 2017

94

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8 September 2017

Pt A

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8 September 2017

1-33

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Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis

8 September 2017

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Mammalian mitogenomic relationships and the root of the eutherian tree

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Mitogenomic relationships of placental mammals and molecular estimates of their divergences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Relationships of Endemic African Mammals and Their Fossil Relatives Based on Morphological and Molecular Evidence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Naive binning improves phylogenomic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

A review of long-branch attraction

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

The delayed rise of present-day mammals

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

The guinea-pig is not a rodent

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Discordance of species trees with their most likely gene trees.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

The supermatrix approach to systematics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Trees within trees: genes and species, molecules and morphology

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Is a new and general theory of molecular systematics emerging?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Concatenation versus coalescence versus "concatalescence".

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Mammalian evolution may not be strictly bifurcating

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

A genomic approach to examine the complex evolution of laurasiatherian mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

What is the danger of the anomaly zone for empirical phylogenetics?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Molecular and genomic data identify the closest living relative of primates

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Retroposed elements as archives for the evolutionary history of placental mammals

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Inconsistency of phylogenetic estimates from concatenated data under coalescence

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Is recombination a problem for species-tree analyses?

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

The accuracy of species tree estimation under simulation: a comparison of methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylogenetic analysis in the anomaly zone

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Coalescent methods for estimating phylogenetic trees

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Estimating species phylogenies using coalescence times among sequences.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Gene Trees in Species Trees

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Parallel adaptive radiations in two major clades of placental mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Widespread genomic signatures of natural selection in hominid evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Creating the CIPRES Science Gateway for inference of large phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

ASTRAL: genome-scale coalescent-based species tree estimation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Heterogeneous models place the root of the placental mammal phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Molecular phylogenetics and the origins of placental mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Resolution of the early placental mammal radiation using Bayesian phylogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Using genomic data to unravel the root of the placental mammal phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Resolution of the laurasiatherian phylogeny: evidence from genomic data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

The placental mammal ancestor and the post-K-Pg radiation of placentals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Error in Phylogenetic Estimation for Bushes in the Tree of Life

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

A molecular phylogeny of living primates

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

A two-stage pruning algorithm for likelihood computation for a population tree

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Insights into hominid evolution from the gorilla genome sequence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

STRAW: Species TRee Analysis Web server

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Higher taxonomic relationships among extant mammals based on morphology, with selected comparisons of results from molecular data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Land plant origins and coalescence confusion

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Mammalian evolution and biomedicine: new views from phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Placental mammal diversification and the Cretaceous-Tertiary boundary

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Molecules consolidate the placental mammal tree

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

DendroPy: a Python library for phylogenetic computing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylogenomic analyses elucidate the evolutionary relationships of bats

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylotranscriptomic analysis of the origin and early diversification of land plants

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Genomics, biogeography, and the diversification of placental mammals

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Phylogenomics and coalescent analyses resolve extant seed plant relationships

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Evaluating the phylogenetic position of Chinese tree shrew (Tupaia belangeri chinensis) based on complete mitochondrial genome: implication for using tree shrew as an alternative experimental animal to primates in biomedical research

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

Origin of land plants using the multispecies coalescent model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

BBCA: Improving the scalability of *BEAST using random binning

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.07.018

10.1016/J.YMPEV.2015.07.018

7 January 2021

Identifiers

DOI

1 reference

8 September 2017

1 reference

PubMed ID

26238460