Genomic diversity of SNPs across Anolis carolinensis lizard populations

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A fun paper, lead by Yann Bourgeois, was just published in Genome Biology and Evolution. It describes the variation in nucleotide polymorphisms across five major populations of green anoles in the southern US, their likely demographic changes across time, and evolutionary dynamics that have likely shaped the mutation composition of their chromosomes. Congratulations, Yann!

Recent secondary contacts, linked selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis.

Y Bourgeois, RP Ruggiero, JD Manthey, & S Boissinot (2019) Genome Biology and Evolution

Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Here we present the first population genomics survey using whole genome re-sequencing in the green anole (Anolis carolinensis). Anoles have been intensively studied to understand mechanisms underlying adaptation and speciation. The green anole in particular is an important model to study genome evolution. We quantified how demography, recombination and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole’s populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the interaction between linked selection and recombination is the main contributor to the genomic landscape of differentiation in the anole genome.

Good news for a great group of researchers is bad news for parasitic worms

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Congratulations to Todd Castoe, David Pollock and Dr. Elizabeth Carlton--a very cool project to help with the fight against infectious disease!

“Schistosomiasis is an acute and chronic disease caused by parasitic worms and is second only to malaria as the most devastating parasitic disease. It affects more than 200 million people worldwide, mostly in tropical and subtropical areas and especially in poor communities without access to safe drinking water and adequate sanitation… Using genomic sequencing, this project will provide unprecedented insight into the detailed patterns of transmission across hosts, across geographic areas and through time. This will help us to understand how to prevent infections and advance efforts to achieve permanent reductions in schistosomiasis and other human helminthiases [worm infections].”

Here’s the University of Texas at Arlington press release:

https://www.uta.edu/news/releases/2019/02/Castoe-NIH-NSF2.php

Congratulations to Sandra, Jacobo and Stephane!

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A new species of puddle frog from an unexplored mountain in southwestern Ethiopia

Sandra Goutte, Jacobo Reyes-Velasco, Stephane Boissinot

Abstract

A new species of Phrynobatrachus is described from the unexplored and isolated Bibita Mountain, southwestern Ethiopia, based on morphological characters and sequences of the mitochondrial rRNA16s. The new species can be distinguished from all its congeners by a small size (SVL = 16.8 ± 0.1 mm for males, 20.3 ± 0.9 mm for females), a slender body with long legs and elongated fingers and toes, a golden coloration, a completely hidden tympanum, and a marked canthus rostralis. The phylogenetic hypothesis based on 16s sequences places the new species as sister to the species group that includes P. natalensis, although it is morphologically more similar to other dwarf Phrynobatrachus species, such as the Ethiopian P.minutus.

Phrynobatrachus bibita sp. n. A Live pictures of P. bibita sp. n. Male holotype (left; SB440) and female paratopotype (right; SB424) B Ventral and dorsal views of the same individuals, with male on the left and female on the right. Scale bar: 10 mm

Phrynobatrachus bibita sp. n. A Live pictures of P. bibita sp. n. Male holotype (left; SB440) and female paratopotype (right; SB424) B Ventral and dorsal views of the same individuals, with male on the left and female on the right. Scale bar: 10 mm

A Boissinot Lab review of the Mobilome of Reptiles

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Here’s a good summary and a great for introducing students and new researchers to transposable elements and genomics. Always fun working with the the Boissinot Lab!

The Mobilome of Reptiles: Evolution, Structure, and Function

Abstract

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

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Transposon Day 2018

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Barbara McClintock, widely recognized as the founder of transposable elements research, was born June 16, 1902. That is why we have designated this day as Transposon Day: to honor her legacy and draw attention to the important research that has, and is, continuing to change the way researchers think about evolution, disease, and genomics.  https://mobilednajournal.biomedcentral.com/transposonday2018

Differential Effect of Selection against LINE Retrotransposons Among Vertebrates Inferred From Whole-Genome Data and Demographic Modeling

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Here's a cool paper I worked on with Stephane and the Hickerson group. Xander implemented a novel and very powerful approach, and the conclusions are really thought provoking.

https://academic.oup.com//gbe/advance-article/doi/10.1093/gbe/evy083/4983240