Plant migration under long‐lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth

Abstract

The post-Miocene climatic histories of arid environments have been identified as key drivers of dispersal and diversification. Here, we investigate how climatic history correlates with the historical biogeography of the Atacama Desert genus Cristaria (Malvaceae).We analyze phylogenetic relationships and historical biogeography by using nextgeneration sequencing (NGS), molecular clock dating, Dispersal Extinction Cladogenesis and Bayesian sampling approaches. We employ a novel way to identify biogeographically meaningful regions as well as a rarely utilized program permitting the use of dozens of ancestral areas.Partial incongruence between the established taxonomy and our phylogenetic data argue for a complex historical biogeography with repeated introgression and incomplete lineage sorting. Cristaria originated in the central southern part of the Atacama Desert, from there the genus colonized other areas from the late Miocene onwards. The more recently diverged lineages appear to have colonized different habitats in the Atacama Desert during pluvial phases of the Pliocene and early Pleistocene.We show that NGS combined with near-comprehensive sampling can provide an unprecedented degree of phylogenetic resolution and help to correlate the historical biogeography of plant communities with cycles of arid and pluvial phases.

Two Sides of the Same Desert: Floristic Connectivity and Isolation Along the Hyperarid Coast and Precordillera in Peru and Chile

“…More recently, a study of Schwarzer et al (2010) indicated that elements of typical loma vegetation and even presumed loma endemics may be found in certain habitats along the southern Peruvian precordillera reaching elevations of up to 2,600 m asl. Ruhm et al (2020) demonstrated a relative floristic coherence along the precordillera from Chile to southern Peru, confirming the presence of a "floristic corridor" along the Andean precordillera of Peru and Chile as previously suggested (Moreno et al, 1994) and shown by phylogenetic studies (e.g., Luebert et al, 2009;Luebert and Weigend, 2014;Böhnert et al, 2022). This is in stark contrast to the "floristic break" between the loma floras of Peru and Chile, respectively, as previously hypothesized in floristic (Rundel et al, 1991;Galán de Mera et al, 1997;Pinto and Luebert, 2009;Manrique et al, 2014) and phylogenetic studies (Gengler-Nowak, 2002;Merklinger et al, 2021).…”

“…We would find this hypothesis supported, if habitat suitability models indicated a pronounced gap for loma vegetation (Rundel et al, 1991;Pinto and Luebert, 2009). Conversely, we propose that (3) the precordillera floras of Peru and Chile show a closer connectivity (Luebert et al, 2009;Böhnert et al, 2022). We here expect a gradual latitudinal floristic change-over in a continuous belt of suitable habitat.…”

Phylogeny based generic reclassification of Muscari sensu lato (Asparagaceae) using plastid and genomic DNA

“…(2019). The restriction site‐associated DNA sequencing method provided a much higher degree of phylogenetic resolution, which is in line with an increasing number of systematic as well as taxonomic studies in recent years (e.g., Andrews & al., 2016; Merklinger & al., 2021; Yahara & al., 2021; Böhnert & al., 2022). This is the first study using a RADseq approach within Asparagaceae in a genus‐wide phylogenetic context and proves to be able to untangle the complex evolutionary processes of Mediterranean geophytes, which might be responsible for the cryptic taxonomic history of this group (Garbari & Greuter, 1970; Speta, 1982; Davis & Stuart, 1984; Grundmann & al., 2010).…”

Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae)

“…Our approach shows that quantitative evaluation of nonsequenced specimens that were identified based on morphological characters and using existing prephylogenetic treatments can be successful in evaluating the status of so‐called nested singletons that were found in phylogenetic analyses. Such singletons are frequent in published molecular phylogenetic trees based on multiple sequence alignments of few to multiple loci (Bengtson et al, 2021 ; Lu‐Irving et al, 2021 ; García‐Moro et al, 2022 ) and as well in phylogenomic analyses using RAD (Böhnert et al, 2022 ) or hyb seq data (Jones et al, 2019 ; Xu & Chen, 2021 ). Under normal circumstances, one would target several specimens of a species complex to address species delimitation, then also ideally combining molecular, morphological, ecological, and distributional data in an integrative taxonomy approach.…”