Phylogénie et évolution des pigeons et tourterelles (Columbidae) à différentes échelles de temps et d’espace

Pigeons and doves (Columbidae) belong to a species-rich worldwide-distributed family and are of major historical and ecological importance. We generated phylogenetic hypotheses from museum samples to clarify the diversification of the family, which probably took place between mid-Eocene and mid-Miocene, where all extant clades were already established. Almost 60% of species are present on islands, and these entities probably played a role in the dispersal through stepping-stones movement between continents. On the other side, speciation rates vary following a normal distribution and islands do not seem to have played an important role in diversification. Nevertheless, the highest Columbidae species-richness is reached in South-East Asia and Australasia, regions especially rich in islands. New Guinea, in particular, hosts an impressive diversity. The biggest Columbidae, belonging to the genus Goura (crowned pigeons), are endemic to this island. Our analyses suggest that their diversification probably started within New Guinea around 5.73 Ma. Geological events such as the cordillera orogeny probably played a major role by splitting ancestral distribution, while more recent dispersals over barriers may have also led to the settlement of isolated populations that promoted diversification. This work allowed the generation of phylogenetic hypotheses, which will allow answering numerous questions regarding Columbidae biogeography and diversification.Les pigeons et tourterelles (Columbidae) appartiennent à une famille riche en espèces et mondialement distribuée, d’importance majeur sur le plan historique et écologique. Nous avons généré des hypothèses phylogénétiques à partir d’échantillons de musées pour clarifier le processus de diversification de la famille, qui s’est probablement déroulé entre le milieu de l’Eocène et du Miocène. Près de 60% des espèces de columbidés sont présentes sur des îles, et ces entités ont probablement joué un rôle dans la dispersion entre continents. A l’inverse, les taux de spéciation varient selon une distribution normale et l’insularité ne semble pas avoir joué un rôle important dans la diversification. Malgré tout, la diversité maximale est atteinte en Asie du Sud-Est et en Australasie, régions particulièrement riches en îles. La Nouvelle-Guinée, en particulier, héberge une diversité impressionnante. Les columbidés les plus gros, appartenant au genre Goura (pigeons couronnés), sont endémiques de cette île. Nos analyses suggèrent que leur diversification a probablement démarré au sein de la Nouvelle-Guinée il y a environ 5.73 millions d’années. Des événements géologiques tels que l’orogénèse de la cordillère centrale ont probablement joué un rôle important en partageant la distribution de l’aire ancestrale. Des dispersions par-delà des barrières géographiques établies peuvent ensuite avoir permis l’établissement de populations isolées et entrainé leur diversification

Effets environnementaux des antiparasitaires endectocides dans le cadre des parcs nationaux et du pastoralisme (exemple de l'ivermectine)

LYON1-BU Santé (693882101) / SudocTOULOUSE-EN Vétérinaire (315552301) / SudocSudocFranceF

A new, undescribed species of Melanocharis berrypecker from western New Guinea and the evolutionary history of the family Melanocharitidae

Western New Guinea remains one of the last biologically underexplored regions of the world, and much remains to be learned regarding the diversity and evolutionary history of its fauna and flora. During a recent ornithological expedition to the Kumawa Mountains in West Papua, we encountered an undescribed species of Melanocharis berrypecker (Melanocharitidae) in cloud forest at an elevation of 1200 m asl. Its main characteristics are iridescent blue-black upperparts, satin-white underparts washed lemon yellow, and white outer edges to the external rectrices. Initially thought to represent a close relative of the Mid-mountain Berrypecker Melanocharis longicauda based on elevation and plumage colour traits, a complete phylogenetic analysis of the genus based on full mitogenomes and genome-wide nuclear data revealed that the new species, which we name Satin Berrypecker Melanocharis citreola sp. nov., is in fact sister to the phenotypically dissimilar Streaked Berrypecker Melanocharis striativentris. Phylogenetic relationships within the family Melanocharitidae, including all presently recognized genera (Toxorhamphus, Oedistoma, Rhamphocharis and Melanocharis), reveal that this family endemic to the island of New Guinea diversified during the main uplift of New Guinea in the Middle and Late Miocene (14.6 Mya), and represents an evolutionary radiation with high disparity in bill morphology and signalling traits across species. Rhamphocharis berrypeckers fall within the Melanocharis clade despite their larger beaks and should be included in the latter genus. Interspecific genetic distances in Melanocharis are pronounced (average interspecific distance: 8.8% in COI, 12.4% in ND2), suggesting a long history of independent evolution of all lineages corresponding to currently recognized species, including the Satin Berrypecker, which shares a most recent common ancestor with its sister species in the early Pleistocene (~ 2.0 Mya)

Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with (Formula presented.) 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages

Data for microsatellites, spectrophotometry and melanins dosage

This file contains 1) microsatellites data in GENPOP format, 2) morphometric data for birds included in the pedigree analysis, 3) Spectrophotometry measurements and 4) Results from the dosage of melanins for 12 individuals. Localities coordinates are also provided

Unfiltered VCF file for 42 individuals

SNPs calls for individual GBS data from the same three localities as in Pooled RAD-seq. Colors and localities for each individuals are provided in a separate excel file

Domestication in dry-cured meat Penicillium fungi: convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision

Abstract Many fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers. We studied the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense , the most common species in the dry-cured meat food industry, and P. salamii , used locally by farms. Both species displayed low genetic diversity, with no differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild-type conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed evidence of multiple horizontal gene transfers, particularly between P. nalgiovense and P. salamii . Some horizontal gene transfers involving P. biforme , also found in dry-cured meat products, were also detected. We also detected positive and purifying selection based on amino-acid changes. Our genetic and phenotypic findings suggest that human selection has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii , P. nalgiovense, and P. biforme , providing an interesting case of convergent adaptation to the same human-made environment

A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colourmorphs are always found inmixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection

Information about individuals included in the GBS VCF file

Morph and localities for each individual included in the GBS study

Supplementary Methods and TablesThis file includes details about methods and parameters used, as well as supplementary results on analyses ofphenotype and whole genome analyses. from A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the <i>Zosterops borbonicus</i> white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex <i>cis</i>-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection