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Home > Communication > Scientific newsletter > Scientific publications

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25 June 2018

Reannotation of eight Drosophila genomes [BioRxiv]

The sequenced genomes in the Drosophila phylogeny is a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated studying the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on Drosophila melanogaster to develop a pipeline that best matched the extensively curated annotation. We then applied this to the other species to add tens of thousands of new gene models per species.(...)

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25 June 2018

Cultural conformity generates extremely stable traditions in bird song [Nature Communications]

Cultural traditions have been observed in a wide variety of animal species. It remains unclear, however, what is required for social learning to give rise to stable traditions: what level of precision and what learning strategies are required. We address these questions by fitting models of cultural evolution to learned bird song. We recorded 615 swamp sparrow (Melospiza georgiana) song repertoires, and compared syllable frequency distributions to the output of individual-based simulations. We find that syllables are learned with an estimated error rate of 1.85% and with a conformist bias in learning. This bias is consistent with a simple mechanism of overproduction and selective attrition. Finally, we estimate that syllable types could frequently persist for more than 500 years. Our results demonstrate conformist bias in natural animal behaviour and show that this, along with moderately precise learning, may support traditions whose stability rivals those of humans.

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25 June 2018

Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis [BioRxiv]

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. Previous studies have been limited to a small number of model species, mostly mammals, and no studies have investigated genomic variation in non-avian reptiles. Here we present the first population genomics survey using whole genome re-sequencing in the green anole (Anolis carolinensis). This species has emerged as a model for the study of genomic evolution in squamates. 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.(...)

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25 June 2018

Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon [BioRxiv]

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) from the western and eastern Atlantic range diverged >600K YBP, with each clade isolated in independent southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic differences. Here, we investigate genomic consequences of glacial isolation and trans-Atlantic secondary contact using a 220K single nucleotide polymorphism (SNP) array genotyped in 80 North American and European populations.(...)

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22 June 2018

Tempo and timing of ecological trait divergence in bird speciation [Nature Ecology & Evolution]

Organismal traits may evolve either gradually or in rapid pulses, but the relative importance of these modes in the generation of species differences is unclear. Additionally, while pulsed evolution is frequently assumed to be associated with speciation events, few studies have explicitly examined how the tempo of trait divergence varies with respect to different geographical phases of speciation, starting with geographic isolation and ending, in many cases, with spatial overlap (sympatry). Here we address these issues by combining divergence time estimates, trait measurements and geographic range data for 952 avian sister species pairs worldwide to examine the tempo and timing of trait divergence in recent speciation events. (...)

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