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Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake
TLDR
It is shown that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing.
The genome of the green anole lizard and a comparative analysis with birds and mammals
TLDR
Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins, and an anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
TLDR
Estimates are obtained from three approaches that the most likely divergence date of SARS-CoV-2 from its most closely related available bat sequences ranges from 1948 to 1982, indicating that there are high levels of co-infection in horseshoe bats and that the viral pool can generate novel allele combinations and substantial genetic diversity.
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome
TLDR
It is shown here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%–69% of the human chromosome is repetitive or repeat-derived, and that the human genomes consists of substantially more repetitive sequence than previously believed.
Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography
Aim  We used inferences of phylogenetic relationships and divergence times for three lineages of highland pitvipers to identify broad‐scale historical events that have shaped the evolutionary history
Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards.
TLDR
This work partitions among-site rate variation separately among the c-mos, ND4, and 12S + 16S gene regions, and uses this three-way gamma partitioning in Bayesian analyses to reconstruct a robust phylogenetic hypothesis for the relationships of genera within the lizard family Gymnophthalmidae.
Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America
TLDR
It is highlighted how phylogeographic transition zones between Middle and South America and the Nicaragua Depression appear to have undergone multiple episodes of diversification in different lineages, in contrast to other examples where apparently a single vicariant period is shared across multiple lineages.
Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
TLDR
Results using high‐throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead were rapid, cost‐effective and identified thousands of useful micros satellite loci in a previously unstudied species.
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
TLDR
It is shown that regulatory components of the venom secretory system may have evolved from a pancreatic origin and that venom toxin genes were co-opted by distinct genomic mechanisms, which provides insight into mechanisms of protein evolution under strong selection.
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