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This Week in PLoS: Dec 28, 2010

As they report in PLoS Biology, the University of York's Michael Hofreiter and colleagues used a combination of multiplex PCR and next-gen sequencing to compare the nuclear genomes of the African savanna elephant, African forest elephant, Asian elephant, the American mastodon, and the woolly mammoth. From this, they found that the savanna and forest elephants, which some have thought to be the same species, are as divergent as Asian elephants and mammoths, which belong to different genera. This, they add, resolves "a long-standing debate about the appropriate taxonomic classification of the African elephants."

Researchers in Israel studied divergence and polymorphisms in yeast intergenic sequences and report in PLoS Computational Biology that "yeast low nucleosome occupancy sequences have maintained a high A+T content throughout the evolution of the Saccharomyces cerevisiae lineage." This, they say, was possible due to a "compensatory coupling of decreased rates of A/T-losing substitutions and increased rates of corrective A/T-gaining substitutions."

Danish researchers compared the genome of the fungal wheat pathogen Mycosphaerella graminicola to its closest known endemic relative, which infects wild grasses including wheat — the wild pathogen has a broader range than the domesticated one. The comparison found that the specialization of M. graminicola is associated with genomic changes on the smallest chromosome. "Although we found a high degree of nucleotide similarity between the two genomes, our findings suggest that the divergence of these pathogens has been accompanied by structural rearrangements in their genomes and strong positive selection on a small set of genes with unknown function," they say.

Linda Vigilant and her colleagues sequenced the mitochondrial genomes of 51 gibbons from three genera and 11 species to study their evolutionary history. From this they found that "splitting events in the Hylobatidae family occurred from the late Miocene to the Pliocene" at around the same time as many speciation events in other mammalian families. "These data produce a reliable phylogeny featuring strong support values and most notably contribute to resolution of the phylogeny of Hylobates species and the timings of molecular divergence events," Vigilant et al. say.

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.