The Molecular Ecologist

With the holiday season in full swing, I thought that I share a link to a recent post on weathering the rejection storm that almost invariably accompanies grant and publication reviews.

those of you getting rejections are in great company. We’re slogging through a historically lean time and this shit is just hard right now.

As a young academic I’ve received my fair share of rejection emails, so these “we’re all in the same boat” posts certainly ease my mind. On top of that, they also provide some valuable advice: The path to success is paved with grit and persistence.

The ONLY reason I’ve been semi-successful is because I got back up every. damn. time. I don’t have better ideas than my colleagues. I’m not smarter than they are. I don’t have the pedigree or awards many of them have. But it turns out I can take a punch pretty well.

I think the great Maury Ballstein said it best:

Happy Holidays.

Reduction in genomic diversity around a site has been attributed to one of two mechanisms – (1) sites linked to positively selected mutant alleles are often `swept’ to fixation, in a process often called genetic hitchhiking, and/or (2) background selection at sites linked to deleterious mutants are purged (or purified). Recent selective sweeps are thus characterized by long sequences of homozygous sites, and reduced linkage disequilibrium. Ancient sweeps on the other hand, are difficult to characterize – with several methods being proposed to detect them, often using scaled (with respect to a common ancestor) haplotype diversity, Tajima’s D, number of segregating sites, etc  – see Enard et al. (2014) for an excellent recap.
Two recent studies that analyzed human genomes for ancient and recent recurrent selective sweeps revealed some very interesting results.

Racimo et al. (2014) propose a method based on ABC (Approximate Bayesian Computation) to detect ancestral selective sweeps that occurred soon after the split of humans and Neanderthals, and apply it to 26 phased human genomes from the 1000 Genomes Project. Scaled diversity (and other statistics) estimated in 0.02 cM windows around non-synonymous mutations, splice sites, 5’ UTR’s, regulatory motif changes show (1) no significant differences in signatures of positive selection between synonymous and non-synonymous sites, 5’ UTR’s, or regulatory motifs, but (2) significantly reduced differences in diversity in splice sites, and (3) failure of sites in favor of positive selection to lie in regions introgressed from Neanderthals.
Dutheil et al. (2014) take a different approach – they analyze regions of the genome (here X chromosome) that show signatures of Incomplete Lineage Sorting (ILS) – i.e. lower divergence, while reconstructing population histories. Low ILS regions thus would be expected to be either under strong background selection, or have experienced strong selective sweeps. Their analyses of reduction in genomic diversity at low-ILS sites from the 1000 genomes data on the X chromosome reveal (1) greater reduction in genomic diversity in non-African X chromosomes, compared to African X chromosomes, and (2) sites with low-ILS, and reduced genomic diversity do not lie in regions introgressed from Neanderthals.
Two studies, similar conclusions, leading into more questions about complex speciation in great apes. A classic clash of brooms. Quidditch, anyone?
References:
Dutheil, Julien Y., et al. “Strong selection in the human-chimpanzee ancestor links the X chromosome to speciation.” bioRxiv (2014): 011601. http://dx.doi.org/10.1101/011601
Enard, David, Philipp W. Messer, and Dmitri A. Petrov. “Genome-wide signals of positive selection in human evolution.” Genome research (2014). http://dx.doi.org/10.1101/gr.164822.113
Racimo, Fernando, Martin Kuhlwilm, and Montgomery Slatkin. “A test for ancient selective sweeps and an application to candidate sites in modern humans.” Molecular biology and evolution 31.12 (2014): 3344-3358. http://dx.doi.org/10.1093/molbev/msu255
 
 

Note: this post was has been corrected to reflect the fact that Flamingoes and Pigeons are not sister species, but members of sister clades.
Darwin’s favorite bird, the pigeon, has a new sister (clade) that includes Flamingoes and Grebes. This somewhat surprising result came from a recent phylogenomic analysis of 48 bird species published last week in Science. This analysis and its 27 companion papers were the culmination of years of work conducted by the Avian Phylogenomics Project, which is led by Erich Jarvis, a Professor of Neurobiology at Duke University, Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, and M. Thomas P. Gilbert of Natural History Museum of Denmark.
In this post I take you on a supervised speed date with 12 of the 28 papers:
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2014 was an exciting year for describing new biodiversity for researchers at the Louisiana State University Museum of Natural Science (LSUMNS). Top ten lists are ubiquitous this time of year and two such lists documenting the top new species of 2014 include taxa described by LSU researchers.
A list compiled by Discover Magazine includes a new fish species described by Prosanta Chakrabarty and colleagues and a new rat species described by Jake Esselstyn and colleagues.
The Hoosier Cavefish Amblyopsis hoosieri, the first new cavefish species described from the United States in the last 40 years, is found in subterranean habitats of southern Indiana. Amblyopsis hoosieri is distinct from its congener A. spelaea based on morphological and molecular characters. The Ohio River appears to act as a barrier for these two species with A. hoosieri distributed to the north of the river and A. spelaea to the south.

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