Cryptic speciation associated with geographic and ecological divergence in two Amazonian Heliconius butterflies

International audienc

Adaptive Introgression across Species Boundaries in Heliconius Butterflies

It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially in animals. Here, we have examined the role of introgressive hybridisation in transferring adaptations between mimetic Heliconius butterflies, taking advantage of the recent identification of a gene regulating red wing patterns in this genus. By sequencing regions both linked and unlinked to the red colour locus, we found a region that displays an almost perfect genotype by phenotype association across four species, H. melpomene, H. cydno, H. timareta, and H. heurippa. This particular segment is located 70 kb downstream of the red colour specification gene optix, and coalescent analysis indicates repeated introgression of adaptive alleles from H. melpomene into the H. cydno species clade. Our analytical methods complement recent genome scale data for the same region and suggest adaptive introgression has a crucial role in generating adaptive wing colour diversity in this group of butterflies

A setback into a success: What can batch effects tell us about best practices in genomics?

International audienceThe increasing access to high-throughput sequencing is certainly one of the major changes that molecular ecology has gone through over the last decade. With the positive trend towards more open science, most sequencing data sets are now available on public databases, which holds amazing potential, but also risks of introducing batch effects in studies combining data sets. In this issue of Molecular Ecology Resources, Lou and Therkildsen (2022) offer a timely discussion on the matter by analyzing an imperfect low-coverage Whole Genome Sequencing data set, in which they test the effects of differences in sequencing choices, DNA degradation, and read depth on routine population genomics analyses. Through a series of diagnostic tools, they uncover multiple factors producing technical artefacts that can bias estimates of genetic diversity, inference of population structure, and selection scans. For each confounding factor, they demonstrate the effectiveness of mitigation approaches and suggest other avenues to deal with the issue. In this perspective, we highlight considerations regarding (1) effects that arise from differences between batches of sequencing; (2) unavoidable heterogeneity within data sets; and (3) more general concerns around the use of next-generation sequencing in population genomics. Altogether, by exploring what may have appeared at first glimpse as a "failed" sequencing project, Lou and Therkildsen (2022) end up setting a standard of best practices to make the most of heterogeneous whole-genome sequences, opening a promising avenue towards efficient reuse of published data sets

L'édenté total et son alimentation

L'édentement total est une infirmité physique, psychologique et sociale qui touche une grande partie des personnes âgées. Face aux conséquences fonctionnelles et esthétiques de la perte des dents, la personne âgée, vulnérable de par son âge et par le cortège de pathologies qui accompagnent le vieillissement, se trouve dans une réelle situation de handicap. Le repas, signe de convivialité, devient un moment angoissant et les apports journaliers recommandés ne sont pas satisfaits. Ainsi, la réhabilitation prothétique de la cavité buccale apparaît comme une évidence mécanique et sociale où la rééducation masticatoire a une place prépondérante. Il s'agit en effet d'une prise en charge globale du patient tant au niveau technique que psychologique.NANTES-BU Médecine pharmacie (441092101) / SudocNANTES-Bib.Odontologie (441092219) / SudocSudocFranceF

Summary of likelihood ratio test statistics for the IMa analysis.

<p>Likelihood ratio statistics (2LLR), degrees of freedom (df) and significance level (P-value) when comparing the full likelihood model (ABCDE) to four different nested models. The results indicate significant support for bi-directional asymmetric gene flow in both data sets.</p

Phylogenetic clustering of the red colour linked markers.

<p>Top panel represents the order and gene content in the <i>HmB</i> red locus, with vertical lines representing exons. Lines drawn from top panel indicate the location of the marker in the <i>HmB</i> locus. All of the topologies were inferred by Neighbour-Joining clustering. Numbers above branches are the values for bootstrap support. Species and colour codes are as specified in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002752#pgen-1002752-g001" target="_blank">Figure 1</a>, with (a) <i>H. melpomene</i> (circles) and (b) <i>H. cydno</i> (triangles), <i>H. timareta</i> (squares) and <i>H. heurippa</i> (diamonds). <i>H. numata</i> (black) was used as outgroup. Size of shapes represents haplotype frequency. Taxa with a rayed phenotype are coloured orange, red-banded phenotypes are red and those taxa lacking a dorsal red wing phenotype are yellow.</p

Generation of gene-edited rats by delivery of CRISPR/Cas9 protein and donor DNA into intact zygotes using electroporation

International audienceThe generation of gene-edited animals using the CRISPRs/Cas9 system is based on microinjection into zygotes which is inefficient, time consuming and demands high technical skills. We report the optimization of an electroporation method for intact rat zygotes using sgRNAs and Cas9 protein in combination or not with ssODNs (~100 nt). This resulted in high frequency of knockouts, between 15 and 50% of analyzed animals. Importantly, using ssODNs as donor template resulted in precise knock-in mutations in 25-100% of analyzed animals, comparable to microinjection. Electroporation of long ssDNA or dsDNA donors successfully used in microinjection in the past did not allow generation of genome-edited animals despite dsDNA visualization within zygotes. Thus, simultaneous electroporation of a large number of intact rat zygotes is a rapid, simple, and efficient method for the generation of a variety of genome-edited rats

Directional introgression at <i>HmB453k</i>.

<p>Bayesian posterior probability distributions for the introgression rate (m) at <i>HmB453k</i> between <i>H. melpomene</i> and <i>H. timerata</i> in the rayed phenotypes, between <i>H. melpomene</i>, <i>H. timerata</i> and <i>H. heurippa</i> in the red-banded phenotype. Blue corresponds to introgression from <i>H. melpomene</i> to <i>H. timareta</i> whereas green corresponds to introgression in the other direction.</p

Phylogenetic clustering of unlinked markers.

<p>Neighbour-Joining tree of mitochondrial COI haplotypes and alleles at the nuclear loci <i>GAPDH</i> and <i>Hsp90</i>. Numbers above branches are the values for bootstrap support. Species and colour codes are as specified in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002752#pgen-1002752-g001" target="_blank">Figure 1</a>, with <i>H. melpomene</i> (circles) and <i>H. cydno</i> (triangles), <i>H. timareta</i> (squares) and <i>H. heurippa</i> (diamonds). <i>H. numata</i> (black) was used as the outgroup. Size of shapes represents haplotype frequency. Taxa with a rayed phenotype are coloured orange, red-banded phenotypes are red and those taxa lacking a dorsal red wing phenotype are yellow.</p

Phylogenetic clustering at HmB453k inferred by Maximum Likelihood.

<p>A phenotypic association regardless of species relationships is observed. Three major monophyletic clades (red, rays and no-red) are formed. Representative phenotypes of each clade are shown at the right (for full array of phenotypes and species see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002752#pgen-1002752-g001" target="_blank">Figure 1</a>). (i) <i>H. m. malleti</i>, (ii) <i>H. m. plesseni</i>, (iii) <i>H. t. timareta</i>, (iv) <i>H. c. cydnides</i>, (v) <i>H. c. weymeri</i> f. <i>gustavi</i>, (vi) <i>H. timareta</i> subsp. nov, (vii) <i>H. c. weymeri</i> f. <i>weymeri</i>, (viii) <i>H. c. chioneus</i>, (ix) <i>H. c. cordula</i>, (x) <i>H. c. zelinde</i>, (xi) <i>H. c. warningery</i>, (xii) <i>H. c. lisethae</i>, (xiii) <i>H. m. cythera</i>, (xiv) <i>H. m. melpomene</i>, (xv) <i>H. m. rosina</i>, (xvi) <i>H. m. vulcanus</i>, (xvii) <i>H. heurippa</i>, (xix) <i>H. m. amandus</i>, (xx) <i>H. m. amaryllis</i>, (xxi) <i>H. timareta</i> subsp. nov, (xxii) <i>H. m. aglaope</i>, (xxiii) <i>H. t. florencia</i>, (xxiv) <i>H. t. contigua</i>, (xxv) <i>H. m. thelxiopeia</i>, (xxvi) <i>H. m. ecuadoriensis</i>. Numbers above branches are the values for bootstrap support. <i>H. m. plesseni</i> and some of <i>H. m. malleti</i> (rayed phenotype) do not cluster within the three major phenotypic clades.</p