Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA
DNA data has been widely used in animal phylogenetic studies over the past 15 years. Here
we review how these studies have used advances in knowledge of molecular evolutionary …
we review how these studies have used advances in knowledge of molecular evolutionary …
Implications of large-effect loci for conservation: A review and case study with Pacific salmon
The increasing feasibility of assembling large genomic datasets for non-model species
presents both opportunities and challenges for applied conservation and management. A …
presents both opportunities and challenges for applied conservation and management. A …
Using PhyloSuite for molecular phylogeny and tree‐based analyses
CY Xiang, F Gao, I Jakovlić, HP Lei, Y Hu, H Zhang… - Imeta, 2023 - Wiley Online Library
Phylogenetic analysis has entered the genomics (multilocus) era. For less experienced
researchers, conquering the large number of software programs required for a multilocus …
researchers, conquering the large number of software programs required for a multilocus …
Renewing Felsenstein's phylogenetic bootstrap in the era of big data
F Lemoine, JB Domelevo Entfellner, E Wilkinson… - Nature, 2018 - nature.com
Felsenstein's application of the bootstrap method to evolutionary trees is one of the most
cited scientific papers of all time. The bootstrap method, which is based on resampling and …
cited scientific papers of all time. The bootstrap method, which is based on resampling and …
[HTML][HTML] Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes
Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major
role in nitrogen cycling. AOA have been studied intensively based on the amoA gene …
role in nitrogen cycling. AOA have been studied intensively based on the amoA gene …
[HTML][HTML] A species-level phylogeny of extant snakes with description of a new colubrid subfamily and genus
Background With over 3,500 species encompassing a diverse range of morphologies and
ecologies, snakes make up 36% of squamate diversity. Despite several attempts at …
ecologies, snakes make up 36% of squamate diversity. Despite several attempts at …
[HTML][HTML] Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation
Several evolutionary theories predict that rates of morphological change should be
positively associated with the rate at which new species arise. For example, the theory of …
positively associated with the rate at which new species arise. For example, the theory of …
[HTML][HTML] Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have
become increasingly controversial. Squamates include> 9000 species, making them the …
become increasingly controversial. Squamates include> 9000 species, making them the …
[HTML][HTML] A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
L Liu, L Yu, SV Edwards - BMC evolutionary biology, 2010 - Springer
Background Several phylogenetic approaches have been developed to estimate species
trees from collections of gene trees. However, maximum likelihood approaches for …
trees from collections of gene trees. However, maximum likelihood approaches for …
Genome-scale approaches to resolving incongruence in molecular phylogenies
One of the most pervasive challenges in molecular phylogenetics is the incongruence
between phylogenies obtained using different data sets, such as individual genes. To …
between phylogenies obtained using different data sets, such as individual genes. To …