Phylogeny of the tribe Abrotrichini (Cricetidae, Sigmodontinae): integrating morphological and molecular evidence into a new classification

An ecomorphological approach to the relationship between craniomandibular morphology and diet in sigmodontine rodents from central-eastern Argentina

The key role of the skull in food intake and processing implicates its morphology should be to some extent adapted to the functional demands present in different diets, while also showing similarities between those which are closely related. Sigmodontine rodents, with a generalist body plan and broad dietary habits, are an interesting case study to explore these relationships. We used linear morphometrics to assess craniomandibular morphology, and explored its relationship with dietary composition and phylogeny in a sample of sigmodontines from central-eastern Argentina, representative of this subfamily's morphological and ecological diversity. We took 26 measurements performed on 558 specimens belonging to 22 species, and resorted to bibliographic information for proportion of food items in their diets, dietary categories, and phylogeny. Multivariate statistical analyses revealed a strong evolutionary integration between morphological traits of crania and mandibles, and a conspicuous relationship between them and dietary composition in our study group, independent of phylogeny. Species of larger sizes exhibited more robust skulls and a tendency towards folivorous diets, whereas smaller species had more gracile craniomandibular apparatuses and diets richer in seeds and invertebrates. Additionally, we used the observed patterns to made predictions of dietary categories for the three species of this region with unknown diets, completing the map of feeding ecology of one of the most researched group of sigmodontines and enabling future studies to further explore this topic. The present work contributes to understanding the link between morphology, ecology and phylogeny in small mammals.

TE, Solari S, Colmenares-Pinzon J, Nivelo C, Rodríguez Herrera B, Merino W, Medina CE, Murillo-García O, Pardiñas UF. Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches

Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.

Activity patterns and interactions of rodents in an assemblage composed by native species and the introduced black rat: implications for pathogen transmission

Background

The degree of temporal overlap between sympatric wild hosts species and their behavioral interactions can be highly relevant to the transmission of pathogens. However, this topic has been scantly addressed. Furthermore, temporal overlap and interactions within an assemblage of wild rodents composed of native and introduced species have been rarely discussed worldwide. We assessed the nocturnal activity patterns and interactions between rodent taxa of an assemblage consisting of native species (Oligoryzomys longicaudatus, Abrothrix hirta, and Abrothrix olivaceus) and the introduced black rat (Rattus rattus) in a temperate forest from southern Chile. All rodent species in this study are known hosts for various zoonotic pathogens.

Results

We found a high nocturnal temporal overlap within the rodent assemblage. However, pairwise comparisons of temporal activity patterns indicated significant differences among all taxa. Rattus rattus showed aggressive behaviors against all native rodents more frequently than against their conspecifics. As for native rodents, agonistic behaviors were the most common interactions between individuals of the same taxon and between individuals of different taxa (O. longicaudatus vs Abrothrix spp.).

Conclusions

Our findings reveal several interactions among rodent taxa that may have implications for pathogens such as hantaviruses, Leptospira spp., and vector-borne pathogens. Furthermore, their transmission may be facilitated by the temporal overlap observed between rodent taxa.

Unlocking Andean sigmodontine diversity: five new species of Chilomys (Rodentia: Cricetidae) from the montane forests of Ecuador

The Andean cloud forests of Ecuador are home to several endemic mammals. Members of the Thomasomyini rodents are well represented in the Andes, with Thomasomys being the largest genus (47 species) of the subfamily Sigmodontinae. Within this tribe, however, there are genera that have escaped a taxonomic revision, and Chilomys Thomas, 1897, constitutes a paradigmatic example of these "forgotten" Andean cricetids. Described more than a century ago, current knowledge of this externally unmistakable montane rodent is very limited, and doubts persist as to whether or not it is monotypic. After several years of field efforts in Ecuador, a considerable quantity of specimens of Chilomys were collected from various localities representing both Andean chains. Based on an extensive genetic survey of the obtained material, we can demonstrate that what is currently treated as C. instans in Ecuador is a complex comprising at least five new species which are described in this paper. In addition, based on these noteworthy new evidence, we amend the generic diagnosis in detail, adding several key craniodental traits such as incisor procumbency and microdonty. These results indicate that Chilomys probably has a hidden additional diversity in large parts of the Colombian and Peruvian territories, inviting a necessary revision of the entire genus.

DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and andean areas in argentina

Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. We apply DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analyzed 335 COI barcodes in 34 morphologically determined species from 39 localities along central Andes and arid lands of Argentina. Neighbor Joining and Maximum Likelihood reconstruction provided clear separation between species. The Barcode Index Number and Bayesian Poisson Tree Processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A.oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) vs. a minimum nearest-neighbor distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A. oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.

Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

A new species of Cynomops (Chiroptera: Molossidae) from the northwestern slope of the Andes

The systematics and taxonomy of the broadly distributed bats of the genus Cynomops has changed considerably in the last few years. Among the major changes, Cynomops abrasus was split into two species of large-bodied forms (Cynomops mastivus and C. abrasus) distributed east of the Andes. However, large Colombian specimens identified as C. abrasus from the western side of the Andes had yet to be included in any revisionary work. Phylogenetic analysis performed in this study, using mtDNA sequences (Cytochrome-b), revealed that these Colombian individuals are more closely related to Cynomops greenhalli. Morphological and molecular data allowed us to recognize populations from western Colombia, western Ecuador and northwestern Peru, as members of a new species of Cynomops. Characters that allow for its differentiation from C. greenhalli include a larger forearm, paler but more uniform ventral pelage, more globular braincase, and well-developed zygomatic processes of the maxilla (almost reaching the postorbital constriction). This study serves as another example of the importance of including multiple lines of evidence in the recognition of a new species. Given its rarity and the advanced transformation of its habitat, this new species is particularly important from a conservation perspective.

Morphological similarity and dental homologies in two sigmodontine rodents (Mammalia, Cricetidae) from different tribes: A topological analysis to explore convergence

We present a topological analysis of the third upper molars (M3) using the recently developed ICAMER nomenclatural system as a way to understand the dental morphological similarity in sigmodontine rodents, the most speciose subfamily of cricetids. The method is explored in Scapteromys aquaticus and Abrothrix olivacea, taxa belonging to two diverse tribes, Akodontini and Abrotrichini, respectively, which exhibit high similarity regarding several craniodental traits as well as external anatomy. Both species show morphologically similar M3 in adults characterized by cylindrification and the isolation of a large central fossette arising from the marginal fusion of the anterior and posterior lobes. The results indicate that, before the wear, these rodents have a strongly different topological pattern at the cuspal level, mostly involving production of the connection between the main cusps. The central fossette derives from the isolation of part of the metaflexus in Scapteromys, while in Abrothrix it originates from the hypoflexus. The topological analysis provides a new approach to sigmodontine systematics, including the ability to detect diagnostic characters of both tribes. More important, it constitutes a new step toward an integrative phylogeny of fossil and living cricetids.

Gross stomach morphology in akodontine rodents (Cricetidae: Sigmodontinae: Akodontini): a reappraisal of its significance in a phylogenetic context

Akodontini, the second largest tribe within sigmodontine rodents, encompasses several stomach morphologies. This is striking because most sigmodontine groups of comparable taxonomic rank are very conservative in this respect. Based on extensive sampling of newly dissected specimens (213 stomachs representing 36 species), as well as published examples, covering almost all akodontine living genera (15 of 16), we undertook a reappraisal of the gross morphology of this organ. We then mapped this information, together with gallbladder occurrence, in a refined multilocus molecular phylogeny of the tribe. We surveyed three different configurations of stomachs in akodontines, according to the degree of development and location of the glandular epithelium; in addition, two minor variations of one of these types were described. Of the five major clades that integrate Akodontini, four are characterized by a single stomach morphology, while one clade exhibits two morphologies. Mapping stomach type on the phylogeny recovered two configurations for the most recent ancestor of Akodontini. A revised survey of gallbladder evidence also revealed overlooked congruencies. The observed stomach diversity and its arrangement in the phylogeny, along with additional morphological characters and the genetic diversity among the main clades, supports the necessity of changes in the current classification of the tribe. Recognition of subtribes or partitioning of Akodontini into several additional tribes of equal rank could be suitable options.

Molecular phylogenetics of slit-faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South-East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species-ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well-resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male-biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species-rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.

The usage of subgenera in mammalian taxonomy

In this note, I discuss the advantages of the usage of subgenera as a practical taxonomic rank in mammalian taxonomy. Use of this category preserves traditional usage, reduces nomenclatural instability and avoids unnecessary change of names. Subgenera are useful to label diagnosable clades of closely related species, especially in morphologically and ecologically diverse monophyletic genera, without alteration of traditional binomial usage. Contrary to informal names such as “divisions” or “groups”, subgenera are governed by the rules of the International Commission on Zoological Nomenclature (ICZN), having usage constrained (and stability promoted) by typification and priority.

A gene-tree test of the traditional taxonomy of American deer: the importance of voucher specimens, geographic data, and dense sampling

The taxonomy of American deer has been established almost entirely on the basis of morphological data and without the use of explicit phylogenetic methods; hence, phylogenetic analyses including data for all of the currently recognized species, even if based on a single gene, might improve current understanding of their taxonomy. We tested the monophyly of the morphology-defined genera and species of New World deer (Odocoileini) with phylogenetic analyses of mitochondrial DNA sequences. This is the first such test conducted using extensive geographic and taxonomic sampling. Our results do not support the monophyly of Mazama, Odocoileus, Pudu, M. americana, M. nemorivaga, Od. hemionus, and Od. virginianus. Mazama contains species that belong to other genera. We found a novel sister-taxon relationship between "Mazama" pandora and a clade formed by Od. hemionus columbianus and Od. h. sitkensis, and transfer pandora to Odocoileus. The clade formed by Od. h. columbianus and Od. h. sitkensis may represent a valid species, whereas the remaining subspecies of Od. hemionus appear closer to Od. virginianus. Pudu (Pudu) puda was not found sister to Pudu (Pudella) mephistophiles. If confirmed, this result will prompt the recognition of the monotypic Pudella as a distinct genus. We provide evidence for the existence of an undescribed species now confused with Mazama americana, and identify other instances of cryptic, taxonomically unrecognized species-level diversity among populations here regarded as Mazama temama, "Mazama" nemorivaga, and Hippocamelus antisensis. Noteworthy records that substantially extend the known distributions of M. temama and "M." gouazoubira are provided, and we unveil a surprising ambiguity regarding the distribution of "M." nemorivaga, as it is described in the literature. The study of deer of the tribe Odocoileini has been hampered by the paucity of information regarding voucher specimens and the provenance of sequences deposited in GenBank. We pinpoint priorities for future systematic research on the tribe Odocoileini.

The mammalian faunas endemic to the Cerrado and the Caatinga

We undertook a comprehensive, critical review of literature concerning the distribution, conservation status, and taxonomy of species of mammals endemic to the Cerrado and the Caatinga, the two largest biomes of the South American Dry-Diagonal. We present species accounts and lists of species, which we built with criteria that, in our opinion, yielded results with increased scientific rigor relative to previously published lists - e.g., excluding nominal taxa whose statuses as species have been claimed only on the basis of unpublished data, incomplete taxonomic work, or weak evidence. For various taxa, we provided arguments regarding species distributions, conservation and taxonomic statuses previously lacking in the literature. Two major findings are worth highlighting. First, we unveil the existence of a group of species endemic to both the Cerrado and the Caatinga (i.e., present in both biomes and absent in all other biomes). From the biogeographic point of view, this group, herein referred to as Caatinga-Cerrado endemics, deserves attention as a unit - just as in case of the Caatinga-only and the Cerrado-only endemics. We present preliminary hypotheses on the origin of these three endemic faunas (Cerrado-only, Caatinga-only, and Caatinga-Cerrado endemics). Secondly, we discovered that a substantial portion of the endemic mammalian faunas of the Caatinga and the Cerrado faces risks of extinction that are unrecognized in the highly influential Red List of Threatened Species published by the International Union for Conservation of Nature (IUCN). "Data deficient" is a category that misrepresents the real risks of extinction of these species considering that (a) some of these species are known only from a handful of specimens collected in a single or a few localities long ago; (b) the Cerrado and the Caatinga have been sufficiently sampled to guarantee collection of additional specimens of these species if they were abundant; (c) natural habitats of the Cerrado and the Caatinga have been substantially altered or lost in recent decades. Failures either in the design of the IUCN criteria or in their application to assign categories of extinction risks represent an additional important threat to these endemic faunas because their real risks of extinctions become hidden. It is imperative to correct this situation, particularly considering that these species are associated to habitats that are experiencing fast transformation into areas for agriculture, at an unbearable cost for biodiversity.