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Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers.
The polymerase chain reaction is used to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates, and the unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset and can consistently estimate the topology and branch lengths of the species tree.
Whole-genome analyses resolve early branches in the tree of life of modern birds
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Estimating species phylogenies using coalescence times among sequences.
- Liang Liu, Lili Yu, D. Pearl, S. Edwards
- Biology, Environmental ScienceSystematic Biology
- 1 October 2009
It can be shown that the 2 methods are statistically consistent under the multispecies coalescent model, and it is suggested that STAR consistently outperforms STEAC, SC, and GLASS when the substitution rates among lineages are highly variable.
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
- S. Edwards
- BiologyEvolution; international journal of organic…
- 1 January 2009
It is argued that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, the primacy of species trees should be embraced.
High-resolution species trees without concatenation
A Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process is analyzed.
The genome of a songbird
This work shows that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets and shows evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience.
Comparative genomics reveals insights into avian genome evolution and adaptation
This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales
A review of recent advances in estimating divergence times from molecular data, emphasizing the continuum between processes at the phylogenetic and population genetic scales, and the importance of model testing during the process of divergence time estimation.
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
- Sen Song, Liang Liu, S. Edwards, Shaoyuan Wu
- BiologyProceedings of the National Academy of Sciences
- 28 August 2012
It is demonstrated that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades and the analyses suggest that such incONGruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.