Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation

• Published in: PloS one 2022-12, Vol.17 (12), p.e0276475
• Main Authors: Miranda, Cleuton Lima, Farias, Izeni Pires, Da Silva, Maria Nazareth F, Antonelli, Alexandre, Machado, Arielli Fabrício, Leite, Rafael N, Nunes, Mario Da Silva, De Oliveira, Tadeu Gomes, Pieczarka, Julio Cesar
• Format: Article
• Language: English
• Subjects: Analysis; andean uplift; Animals; area-relationships; Biodiversity; Biogeography; Biological diversity; Biological Sciences; Biologiska vetenskaper; Biology and Life Sciences; Birds; climate-change; Cytochrome; Cytochrome b; Cytochromes; Dispersal; Dispersion; Divergence; DNA, Mitochondrial - genetics; Earth Sciences; Ecology and Environmental Sciences; Evolution; Genetic Speciation; Guiana Shield; historical diversification; Hypotheses; landscape evolution; Makalata; Mammals; Miocene; Mitochondria; Phylogenetics; Phylogeny; Phylogeography; Pleistocene; pleistocene refugia; Pliocene; Rats; raw distributions; river; River basins; Rivers; Rodentia - genetics; Rodents; Science & Technology - Other Topics; sigmodontine rodents; Speciation; Taxonomy; Tributaries; Watercourses; Zoology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0276475

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.