Population genomics indicates micro‐refuges and riverine barriers for a southern South American grassland nightshade

Abstract

Aim Pleistocene climate oscillations influenced the species distribution and genetic diversity in grasslands, and such climatic changes promoted expansion and contraction cycles, leading to fragmentation and isolation of evolutionary lineages in refuges. This study aimed to infer the evolutionary processes that most influenced the genetic diversity of a South American nightshade Petunia inhabiting subtropical grasslands under the Pleistocene influence. Location Pampa and Chaco. Taxon The widely distributed herb Petunia axillaris subsp. parodii (Solanaceae). Methods We obtained high‐density genome coverage throughout the geographical distribution of Petunia axillaris subsp. parodii. We estimated the genetic diversity and structure to evaluate population differentiation and applied a model‐based demographic analysis to investigate the scenarios that could have influenced the species' evolutionary history. We evaluated the association between neutral and outlier polymorphisms with environmental variables to distinguish the influence of the geographical distance and environmental differences between populations. Results There are three evolutionary lineages in P. axillaris subsp. parodii. The origin and differentiation of these lineages were related to the Pleistocene refuges and rivers acting as barriers to gene flow. We also identified 496 outlier loci related to adaptation to environmental conditions. Main conclusion The Pleistocene climate changes drove lineage diversification isolated in micro‐refugia. Rivers and changes in their courses may have also acted on the population divergence, serving as barriers to gene flow or even as corridors for species range expansion. These findings contribute to the knowledge of the evolutionary processes that influenced the lineage diversification of South American subtropical grassland species.

Shades of white: The Petunia long corolla tube clade evolutionary history

“…In the same way, ecological features pointed to the same P. axillaris subgroups and three groups in P. parodii (Chaco, Pampa-Brazil, and Pampa-Uruguay), which were not perceived based on morphologic analysis. The P. parodii subdivision was not confirmed here in the phylogenetic tree and SSR, but it was also identified using a sizeable genomic evaluation ( Giudicelli et al, 2022 ).…”

“…On the other hand, the present work is the first to include multiple samples and intraspecific lineages throughout their entire geographic distribution. In the Petunia genus, geographic isolation is often implicated in population structure and reproductive isolation (e.g., Giudicelli et al, 2022 ; Guzmán et al, 2022 ). Moreover, local adaptation and microenvironmental conditions keep species limits (e.g., Segatto et al, 2017 ; Caballero-Villalobos et al, 2021 ), contributing to differentiation ( Fregonezi et al, 2013 ; Pezzi et al, 2022 ).…”

“…Each taxon in LT shows different patterns of genetic structure throughout the geographic range ( Segatto et al, 2014 ; Turchetto et al, 2014a , b , 2016 ; Giudicelli et al, 2022 ) and a complex process of intraspecific diversification emerges: P. parodii shows three main lineages, geographically structured (Chaco, Pampa-Brazil, and Pampa-Uruguay; Giudicelli et al , 2022 ); P. exserta revealed two lineages with slight morphological variation and distribution ( P. exserta E1 and P. exserta E2), each one occurring in a different rock formation in Serra do Sudeste; and P. secreta that would have two main genetic lineages ( Turchetto et al , 2016 ), more distinct from each other than canonical P. secreta is from P. axillaris (here treated as P. secreta and P. sp1, respectively) . An unnamed taxon ( P. sp3) occurs close to P. secreta and P. exserta E1.…”

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

“…These findings are congruent with other studies about barriers as the Andes (see Hazzi et al., 2018 ; Luebert & Weigend, 2014 ; Musher et al., 2019 ; Quintana et al., 2017 ) and Amazonia (e.g., Dal Vechio et al., 2020 ; Del‐Rio et al., 2021 ; Naka & Brumfield, 2018 ; Nazareno et al., 2017 ; Pirani et al., 2019 ). Research on the importance of barriers to the diversification of non‐Amazonian taxa has increased in recent years, highlighting the importance of barriers in driving and maintaining population differentiation in South American biomes (Baranzelli et al., 2020 ; Cáceres, 2007 ; Giudicelli et al., 2022 ; Kopuchian et al., 2020 ; Nascimento et al., 2013 ).…”

“…Vechio Del-Rio et al, 2021;Naka & Brumfield, 2018;Nazareno et al, 2017;Pirani et al, 2019). Research on the importance of barriers to the diversification of non-Amazonian taxa has increased in recent years, highlighting the importance of barriers in driving and maintaining population differentiation in South American biomes (Baranzelli et al, 2020;Cáceres, 2007;Giudicelli et al, 2022;Kopuchian et al, 2020;Nascimento et al, 2013).…”