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MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
TLDR
The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons).
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The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?
TLDR
It is shown that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950-1,259 million years ago (Mya), animals diverged from choanoflagellates 761-957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642-761 Mya.
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The tribal radiation of the family Bovidae (Artiodactyla) and the evolution of the mitochondrial cytochrome b gene.
TLDR
The nucleotide sequence of the complete mitochondrial cytochrome b gene has been determined and compared for 51 species of the family Bovidae and 10 potential pecoran and tragulid outgroups and depicts a major split within Bovids.
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Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability.
TLDR
The nonparametric bootstrap resampling procedure is applied to the Bayesian approach and shows that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated onbootstrapped character matrices.
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Molecular and morphological phylogenies of ruminantia and the alternative position of the moschidae.
TLDR
A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches was applied to estimate the divergence ages between the major clades of ruminants, confirming the traditional view that separates Tragulina and Pecora.
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Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans
TLDR
The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans, and these findings open ways to test this hypothesis further in other South American mammalian endemics.
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Arrival and diversification of caviomorph rodents and platyrrhine primates in South America.
TLDR
Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene.
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Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences.
TLDR
The combined analysis of the two genes suggests a monophyletic Cetacea +Artiodactyla clade, whereas PerissodactylA, Carnivora, and Tethytheria fall outside this clade.
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Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.
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From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents.
TLDR
The phylogenetic relationships among 23 Hystricognathi species are reconstructed using a nuclear marker, and it is suggested that Chinchillidae and Dinomyidae are sister clades, Abrocomidae is a true Octodontoidea, and Capromyidae, Echimyidae, and Myocastoridae cluster together.
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