An assessment of species limits of the South American mouse genus Oligoryzomys (Rodentia, Cricetidae) using unilocus delimitation methods

Abstract

Oligoryzomys, as currently understood is formed by 25 living species, is the most diverse genus of the tribe Oryzomyini of the New World subfamily Sigmodontinae of cricetid rodents. Nonetheless, the species richness of Oligoryzomys seems to be an underestimate, given some species complex has been proposed in previous studies, at the time that large geographic areas remain to be sampled, and several taxonomic forms have not been assessed with contemporary approaches. In this study, we present a new assessment of the species diversity of Oligoryzomys based on multiple unilocus species delimitation methods (ABGD, BPP, PTP, GMYC and b GMYC), using 665 cytb gene sequences as evidence (532 gathered from Genbank and 133 obtained in this study). We sampled representatives of almost all currently known species of Oligoryzomys, at the time that extending the geographic coverage to the Central Andes, a large area that was largely unrepresented in previous studies. Phylogenetic relationships, based on a non‐redundant alignment, were inferred via maximum likelihood and Bayesian inference; an ultrametric tree, used in species delimitation analyses, was obtained using multiple secondary calibration points. Results of species delimitation methods are discussed at the light of previous knowledge (e.g., taxonomic history and geographic provenance of samples in relation to type localities) and the morphological assessments of some specimens. Results of the distinct delimitation methods are mostly congruent, being BPP and PTP the most sensible to estimate species delimitation, allowing us to suggest that Oligoryzomys is composed of 30 lineages of species level. Of these, 22 correspond to forms currently considered species; some of these include in their synonymy some forms currently considered valid species (e.g., yatesi would be a synonym of longicaudatus). The remaining eight lineages are candidate species that need to be further evaluated. This study, by advancing taxonomic hypothesis that should be further tested in future studies, constitutes a stepping‐stone for upcoming taxonomic and biogeographic studies centred on Oligoryzomys.

Historical biogeography of a rapid and geographically wide diversification in Neotropical mammals

“…In a period of ~2.64 Mya, Oligoryzomys diversified reaching approximately 32 living species and colonized almost all Neotropical biomes. There are two sigmodontine genera, Akodon and Thomasomys , which have more species than Oligoryzomys (see Hurtado and D'Elía, 2019a; for Akodon and Thomasomys , see Mammal Diversity Database, 2020; Brandão et al, 2021; Brito et al, 2021; Ruelas & Pacheco, 2021) but have smaller distributions than Oligoryzomys (Patton et al, 2015). Akodon , which is absent from Central America and most of northern South America, southern Patagonia and most of Chile, has 41 recognized living species and a crown age of ~3.80 Mya (Parada et al, 2015).…”

“…Distribution polygons of the species of Oligoryzomys were retrieved from Weksler and Bonvicino (2015) and the Red List of endangered species (http://www.redlist.org). We updated the distribution of O. andinus , O. arenalis , O. destructor , O. flavescens and O. occidentalis , according to the results of Hurtado and D'Elía (2019a, 2019b). Additionally, we retrieved the distribution of O. pachecoi from Hurtado and D'Elía (2018), while the distribution of O .…”

“…A lineage through time (LTT) analysis was completed by plotting the MCC tree with 95% confidence interval, using the package ‘ape’ (Paradis et al, 2004) in R 3.5.3 (R Core Team, 2019). As a method of comparing the speciation rate of Oligoryzomys with that of Akodon and Thomasomys , the only two sigmodontine genera that are more diverse than Oligoryzomys (Brito et al, 2021; Hurtado & D'Elía, 2019a; Mammal Diversity Database, 2020; Ruelas & Pacheco, 2021), and considering that no dating analysis has included the entire species richness of the three genera (e.g. Maestri et al, 2017; Parada et al, 2015; Steppan & Schenk, 2017), we followed Magallon and Sanderson (2001) as a first approximation to estimate speciation rates of these three genera.…”

“…Taxonomic coverage is wide, spanning representatives of 22 of 24 recognized living species (except O. magellanicus and O. griseolus ) and eight candidate species, which were identified using species delimitation methods by Hurtado and D'Elía (2019a). As such, sampling included 30 species of Oligoryzomys (Table S1).…”

“…We updated the distribution of O. andinus, O. arenalis, O. destructor, O. flavescens and O. occidentalis, according to the results of D'Elía (2019a, 2019b). Additionally, we retrieved the distribution of O. pachecoi from Hurtado and D'Elía (2018) Hurtado and D'Elía (2019a). A presence-absence matrix was built by overlaying species distributional polygons on the biogeographical units, allowing multiple units per species; positive presence was recorded if at least the 10% of the distribution of a given species fell within a particular geographical unit (see Figure S1).…”