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Studies of biotic radiations following geographic invasions often overlook the potential role of subsequent climatic, biotic, and geologic triggers, instead focusing largely on the earliest stage of an invasion. For example, studies of the rodent subfamily Sigmodontinae, a clade of over 500 species that radiated throughout South America as an early participant in the Great American Biotic Interchange, have historically focused more on invasion than post-invasion opportunities or subsequent environmental change. Here, we place the timing and transitions of this radiation in context of changing climatic, biotic, and geologic factors by reconstructing the biogeography of the radiation. To accomplish this, we generated the largest genomic phylogeny of Sigmodontinae to date, one that includes over 80% of the genera and 40% of the known species (including all incertae sedis taxa), and we produced a fossil-calibrated chronogram. Our results indicate a single invasion of South America at the base of Sigmodontinae (~ 10.46 million years ago [mya]) with two waves of increased lineage generation and biogeographic transition rates, the first of which occurred following a four-million-year lag after the invasion. The timing and location of this initial radiation (6.61–5.78 mya, Oryzomyalia) coincided with the spread of montane cloud forest along the Andean cordillera during the Late Miocene Cooling. We propose a scenario where sigmodontines did not spread throughout the continent until the Mid-Pliocene Faunal Turnover (4.5–3.0 mya), a period of high extinction of South American mammals. A comprehensive classification for the subfamily (including two new Linnaean tribes) is provided that incorporates these new results.

Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.

The until recently monotypic cricetid genus Oreoryzomys inhabits piedmont and cloud forests, primarily in eastern Ecuador and northwestern Peru. Erected following the taxonomic revision of a polytypic Oryzomys complex two decades ago, Oreoryzomys has remained poorly understood, with most references limited to the original descriptions of its type species ( O. balneator ) and a subspecies ( O. b. hesperus ). Here, we present an integrative taxonomic revision of the genus, based on new field collections and comprehensive museum-based analyses. Phylogenetic reconstructions from mitochondrial and nuclear gene sequences, combined with morphometric and qualitative morphological data, support the recognition of three species: (1) a redescribed O. balneator from central-eastern Ecuador; (2) O. hesperus , elevated to full species rank based on topotypic material; and (3) a new species from populations of the Quijos River Valley, northeastern Ecuador. This revision triples the known species diversity of Oreoryzomys and highlights the genus as a notable radiation of small-bodied oryzomyines adapted to Andean environments. Our findings emphasize the need for systematic revisions of other poorly known Andean rodents to better reveal the hidden diversity of cricetids and the role of the Andes in shaping Neotropical biodiversity.

The genus Oecomys (Rodentia, Sigmodontinae) is distributed from southern Central America to southeastern Brazil in South America. It currently comprises 18 species, but multidisciplinary approaches such as karyotypic, morphological and molecular studies have shown that there is a greater diversity within some lineages than others. In particular, it has been proposed that O. paricola constitutes a species complex with three evolutionary units, which have been called the northern, eastern and western clades. Aiming to clarify the taxonomic status of O. paricola and determine the relevant chromosomal rearrangements, we investigated the karyotypes of samples from eastern Amazonia by chromosomal banding and FISH with Hylaeamys megacephalus (HME) whole-chromosome probes. We detected three cytotypes for O. paricola: A (OPA-A; 2n = 72, FN = 75), B (OPA-B; 2n = 70, FN = 75) and C (OPA-C; 2n = 70, FN = 72). Comparative chromosome painting showed that fusions/fissions, translocations and pericentric inversions or centromeric repositioning were responsible for the karyotypic divergence. We also detected exclusive chromosomal signatures that can be used as phylogenetic markers. Our analysis of karyotypic and distribution information indicates that OPA-A, OPA-B and OPA-C are three distinct species that belong to the eastern clade, with sympatry occurring between two of them, and that the \"paricola group\" is more diverse than was previously thought.

Studies of biotic radiations following geographic invasions often overlook the potential role of subsequent climatic, biotic, and geologic triggers, instead focusing largely on the earliest stage of an invasion. For example, studies of the rodent subfamily Sigmodontinae, a clade of over 500 species that radiated throughout South America as an early participant in the Great American Biotic Interchange, have historically focused more on invasion than post-invasion opportunities or subsequent environmental change. Here, we place the timing and transitions of this radiation in context of changing climatic, biotic, and geologic factors by reconstructing the biogeography of the radiation. To accomplish this, we generated the largest genomic phylogeny of Sigmodontinae to date, one that includes over 80% of the genera and 40% of the known species (including all incertae sedis taxa), and we produced a fossil-calibrated chronogram. Our results indicate a single invasion of South America at the base of Sigmodontinae (~ 10.46 million years ago [mya]) with two waves of increased lineage generation and biogeographic transition rates, the first of which occurred following a four-million-year lag after the invasion. The timing and location of this initial radiation (6.61-5.78 mya, Oryzomyalia) coincided with the spread of montane cloud forest along the Andean cordillera during the Late Miocene Cooling. We propose a scenario where sigmodontines did not spread throughout the continent until the Mid-Pliocene Faunal Turnover (4.5-3.0 mya), a period of high extinction of South American mammals. A comprehensive classification for the subfamily (including two new Linnaean tribes) is provided that incorporates these new results.

Microbial detoxification of plant toxins influences the use of plants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.

Rhipidomys (Sigmodontinae, Thomasomyini) has 25 recognized species, with a wide distribution ranging from eastern Panama to northern Argentina. Cytogenetic data has been described for 13 species with 12 of them having 2n = 44 with a high level of autosomal fundamental number (FN) variation, ranging from 46 to 80, assigned to pericentric inversions. The species are grouped in groups with low FN (46-52) and high FN (72-80). In this work the karyotypes of Rhipidomys emiliae (2n = 44, FN = 50) and Rhipidomys mastacalis (2n = 44, FN = 74), were studied by classical cytogenetics and by fluorescence in situ hybridization using telomeric and whole chromosome probes (chromosome painting) of Hylaeamys megacephalus (HME). Chromosome painting revealed homology between 36 segments of REM and 37 of RMA. We tested the hypothesis that pericentric inversions are the predominant chromosomal rearrangements responsible for karyotypic divergence between these species, as proposed in literature. Our results show that the genomic diversification between the karyotypes of the two species resulted from translocations, centromeric repositioning and pericentric inversions. The chromosomal evolution in Rhipidomys was associated with karyotypical orthoselection. The HME probes revealed that seven syntenic probably ancestral blocks for Sigmodontinae are present in Rhipidomys. An additional syntenic block described here is suggested as part of the subfamily ancestral karyotype. We also define five synapomorphies that can be used as chromosomal signatures for Rhipidomys.

The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genus Neotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.

The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.

Fil: Suarez, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina