A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical savannas

Abstract

The main objective of this study was to evaluate biogeographical hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve this, we used genomic markers (genotyping‐by‐sequencing) to evaluate the genetic structure, population phylogenetic relationships and historical range shifts of four Neotropical passerines with peri‐Atlantic distributions: the narrow‐billed woodcreeper (Lepidocolaptes angustirostris), the plain‐crested elaenia (Elaenia cristata), the grassland sparrow (Ammodramus humeralis) and the white‐banded tanager (Neothraupis fasciata). Population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations in Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri‐Atlantic distribution. Our results reveal that the biogeographical history of the region is complex and cannot be explained by simple vicariant models.

The role of biogeographical barriers on the historical dynamics of passerine birds with a circum‐Amazonian distribution

“…The South American avifauna is widely known as the richest and most diverse in the world (Stotz et al., 1996 ), and extensive research has been devoted to explaining the mechanisms underlying its outstanding diversity (Burney & Brumfield, 2009 ; Haffer, 1969 ; Harvey et al., 2020 ; Ribas et al., 2012 ; Sick, 1967 ; Silva et al., 2019 ; Smith et al., 2014 ). Comparative analyses of genetic variation in co‐distributed taxa have featured prominently among those studies, and they have generated important insights into the diversification and biogeographical history of the South American biota (Bocalini et al., 2021 ; Carnaval et al., 2009 ; Harvey et al., 2017 ; Johnson et al., 2023 ; Lima‐Rezende et al., 2022 ; Musher et al., 2022 ; Naka & Brumfield, 2018 ; Silva et al., 2019 ; Thom et al., 2021 ; Thom, Xue, et al., 2020 ). However, whereas ample research has focused on the mechanisms generating and maintaining diversity in species‐rich areas, such as the Amazonian and the Andean realms (Carvalho et al., 2021 ; Gergonne et al., 2022 ; Hazzi et al., 2018 ; Miranda et al., 2021 , among others), the mechanisms responsible for the diversity of regions with less homogeneous habitats remain poorly understood.…”

Historical demography of Trichothraupis melanops (Aves: Thraupidae) and the Pleistocene Atlantic Forest biogeography

“…The climatic oscillations that occurred during the late Pleistocene affected the demography, population diversification and distribution of the organisms that inhabit the AF, and thus have driven the evolution of the high biological diversity of the biome. Up to now, most studies on the impacts of climatic fluctuations on AF organisms focused on species that are specialists in well-preserved forests (Cabanne et al 2008), while there are few studies on organisms that are generalists or less sensitive to environmental disturbance (Batalha-Filho et al 2012, Lima-Rezende et al 2022, Bukowski et al 2023.…”