Dataset Information

Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats.

ABSTRACT: Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here, we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological, and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that divergent ecological strategies are reflected in genomic features, for example a generalist species shows historically larger effective population size and higher heterozygosity than habitat specialists. The demographic history of these cats seems to have been jointly driven by climate fluctuations and habitat specialization, with different ecological adaptations leading to distinct trajectories. Finally, a gene involved in vertebrate retinal neurogenesis (POU4F2) was found to be under positive selection in the margay, a cat with notoriously large eyes that are likely associated with its nocturnal and arboreal specializations.

SUBMITTER: Ramirez JL

PROVIDER: S-EPMC9189605 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats.

Ramirez Jorge L JL Lescroart Jonas J Figueiró Henrique V HV Torres-Florez Juan Pablo JP Villela Priscilla M S PMS Coutinho Luiz L LL Freitas Patricia D PD Johnson Warren E WE Antunes Agostinho A Galetti Pedro M PM Eizirik Eduardo E

Molecular biology and evolution 20220601 6

Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here, we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological, and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that div ...[more]

PMID: 35639983

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Project description:Background and aimsIn eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata, one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest-Cerrado.MethodsThe ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double-digest restriction site-associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated.Key resultsHigh divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction.ConclusionsThe high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics.

Project description:Much debate has focused on how transitions in life history have influenced the proliferation of some clades. Rodents of the subfamily Sigmodontinae (family Cricetidae) comprise one of the most diverse clades of Neotropical mammals (~400 living species in 86 genera). These rodents occupy a wide range of habitats and lifestyles so that ecological context seems relevant to understand the evolution of this group. Several changes in the landscape of South America through the Neogene might have provided vast resources and opportunity to diversify. The aim of this study was to examine whether transitions between i) lowland and montane habitats, ii) open vegetation and forest, and iii) distinct molar architectures are correlated with shifts in diversification rates and to characterize the general pattern of diversification.Based on a dense taxon sampling of 269 species, we recovered a new phylogeny of Sigmodontinae that is topologically consistent with those of previous studies. It indicates that the subfamily and its major lineages appeared during the Late Miocene. Analyses suggest that vegetation type and elevational range are correlated with diversification rates, but not molar architecture. Tropical lowlands accumulated more lineage diversity than other areas and also supported high speciation rates. Across the radiation the subfamily Sigmodontinae appear to have experienced a decline in diversification rate through time. We detected mixed evidence for lineage-specific diversification rate shifts (e.g., leading to the clades of Akodon, Bibimys, Calomys and Thomasomys).We report that the evolution of habitat preference (considering vegetation type and elevational range) was associated with diversification rates among sigmodontine rodents. We propose that the observed diversification slowdown might be the result of ecological or geographical constraints. Our results also highlight the influence of the tropical lowlands -which might have acted as both "a cradle and a museum of species." The tropical lowlands accumulated greater diversity than the remainder of the group's range.

Project description:Background and aimsTrait-based frameworks assess plant survival strategies using different approaches. Some frameworks use functional traits to assign species to a priori defined ecological strategies. Others use functional traits as the central element of a species ecophysiological strategy. We compared these two approaches by asking: (1) what is the primary ecological strategy of three dominant co-occurring shrub species from inselbergs based on the CSR scheme, and (2) what main functional traits characterize the ecophysiological strategy of the species based on their use of carbon, water and light?MethodsWe conducted our study on a Colombian inselberg. In this extreme environment with multiple stressors (high temperatures and low resource availability), we expected all species to be stress tolerant (S in the CSR scheme) and have similar ecophysiological strategies. We measured 22 anatomical, morphological and physiological leaf traits.Key resultsThe three species have convergent ecological strategies as measured by CSR (S, Acanthella sprucei; and S/CS, Mandevilla lancifolia and Tabebuia orinocensis) yet divergent resource-use strategies as measured by their functional traits. A. sprucei has the most conservative carbon use, risky water use and a shade-tolerant strategy. M. lancifolia has acquisitive carbon use, safe water use and a shade-tolerant strategy. T. orinocensis has intermediate carbon use, safe water use and a light-demanding strategy. Additionally, stomatal traits that are easy to measure are valuable to describe resource-use strategies because they are highly correlated with two physiological functions that are hard to measure: stomatal conductance and maximum photosynthesis per unit mass.ConclusionsThe two approaches provide complementary information on species strategies. Plant species can co-occur in extreme environments, such as inselbergs, because they exhibit convergent primary ecological strategies but divergent ecophysiological strategies, allowing them to use limiting resources differently.

Dataset Information

Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats.

Publications

Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats.

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