[HTML][HTML] Implementing and testing the multispecies coalescent model: a valuable paradigm for phylogenomics
In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the …
GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
GC-biased gene conversion (gBGC) is a recently discovered, recombination-associated
segregation distortion, which influences GC-content dynamics in the mammalian genome …
segregation distortion, which influences GC-content dynamics in the mammalian genome …
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and
comparative genomics studies. However, from the same set of sequences different MSAs …
comparative genomics studies. However, from the same set of sequences different MSAs …
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons
Until now the most efficient solution to align nucleotide sequences containing open reading
frames was to use indirect procedures that align amino acid translation before reporting the …
frames was to use indirect procedures that align amino acid translation before reporting the …
Genome-wide signatures of convergent evolution in echolocating mammals
Evolution is typically thought to proceed through divergence of genes, proteins and
ultimately phenotypes,,. However, similar traits might also evolve convergently in unrelated …
ultimately phenotypes,,. However, similar traits might also evolve convergently in unrelated …
The gene tree delusion
Higher-level relationships among placental mammals are mostly resolved, but several
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …
Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat
ML Zepeda Mendoza, Z **ong… - Nature ecology & …, 2018 - nature.com
Adaptation to specialized diets often requires modifications at both genomic and microbiome
levels. We applied a hologenomic approach to the common vampire bat (Desmodus …
levels. We applied a hologenomic approach to the common vampire bat (Desmodus …
Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes
The origin, evolution, and functional relevance of genomic variations in GC content are a
long-debated topic, especially in mammals. Most of the existing literature, however, has …
long-debated topic, especially in mammals. Most of the existing literature, however, has …
Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences
Abstract Background Multiple Sequence Alignments (MSAs) are the starting point of
molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can …
molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can …