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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.
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.
Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis.
It is proposed that natural selection tends to decrease the mitochondrial mutation rate in long-lived species, in agreement with the mitochondrial theory of aging.
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics
- Rémi Allio, Alex Schomaker-Bastos, J. Romiguier, F. Prosdocimi, B. Nabholz, F. Delsuc
- BiologyMolecular ecology resources
- 3 April 2020
MitoFinder, a user‐friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries, and shows that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA.
Mitochondrial DNA as a marker of molecular diversity: a reappraisal
It is argued that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock‐like, questioning its relevance as a witness of recent species and population history and the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome.
Comparative population genomics in animals uncovers the determinants of genetic diversity
It is shown that the diversity of a species is predictable, and is determined in the first place by its ecological strategy, and demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations.
The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals
Mitochondrial DNA diversity patterns in birds are strongly influenced by the wide, unexpected variation of mutation rate across species, strongly consistent with a relationship between species maximal longevity and mitochondrial mutation rate, in agreement with the mitochondrial theory of ageing.
Body mass‐corrected molecular rate for bird mitochondrial DNA
Using complete or nearly complete mitochondrial genomes of 475 species, it is shown that there are strong relationships between body mass and substitution rates across birds, and this information is used to build models that use bird species’ body mass to estimate their substitution ratesAcross a wide range of common mitochondrial markers.
Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker
It is demonstrated that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa, and the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection.
Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap
The population genomic profile of a hare, a turtle, an oyster, a tunicate, and a termite were found to be intermediate between those of human and Drosophila, indicating that the discordant genomic diversity patterns that have been reported between these two species do not reflect a generalized vertebrate versus invertebrate gap.