Guillermo D’Elía

Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography.

With about 400 living species and 82 genera, rodents of the subfamily Sigmodontinae comprise one of the most diverse and more broadly distributed Neotropical mammalian clades. There has been much debate on the origin of the lineage or the lineages of sigmodontines that entered South America, the timing of entrance and different aspects of further diversification within South America. The ages of divergence of the main lineages and the crown age of the subfamily were estimated by using sequences of the interphotoreceptor retinoid binding protein and cytochrome b genes for a dense sigmodontine and muroid sampling. Bayesian inference using three fossil calibration points and a relaxed molecular clock estimated a middle Miocene origin for Sigmodontinae (∼12Ma), with most tribes diversifying throughout the Late Miocene (6.9-9.4Ma). These estimates together results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution for the most recent common ancestor of Oryzomyalia.

The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

BackgroundMuch debate has focused on how transitions in life history have influenced the proliferation of some clades. Rodents of the subfamily Sigmodontinae (family Cricetidae) comprise one of the most diverse clades of Neotropical mammals (~400 living species in 86 genera). These rodents occupy a wide range of habitats and lifestyles so that ecological context seems relevant to understand the evolution of this group. Several changes in the landscape of South America through the Neogene might have provided vast resources and opportunity to diversify. The aim of this study was to examine whether transitions between i) lowland and montane habitats, ii) open vegetation and forest, and iii) distinct molar architectures are correlated with shifts in diversification rates and to characterize the general pattern of diversification.ResultsBased on a dense taxon sampling of 269 species, we recovered a new phylogeny of Sigmodontinae that is topologically consistent with those of previous studies. It indicates that the subfamily and its major lineages appeared during the Late Miocene. Analyses suggest that vegetation type and elevational range are correlated with diversification rates, but not molar architecture. Tropical lowlands accumulated more lineage diversity than other areas and also supported high speciation rates. Across the radiation the subfamily Sigmodontinae appear to have experienced a decline in diversification rate through time. We detected mixed evidence for lineage-specific diversification rate shifts (e.g., leading to the clades of Akodon, Bibimys, Calomys and Thomasomys).ConclusionWe report that the evolution of habitat preference (considering vegetation type and elevational range) was associated with diversification rates among sigmodontine rodents. We propose that the observed diversification slowdown might be the result of ecological or geographical constraints. Our results also highlight the influence of the tropical lowlands -which might have acted as both “a cradle and a museum of species.” The tropical lowlands accumulated greater diversity than the remainder of the groups range.

Alpha taxonomy of Dromiciops (Microbiotheriidae) with the description of 2 new species of monito del monte

A previous study showed that Dromiciops gliroides has deep phylogeographic structure, with 3 allopatric and highly differentiated groups. Here, we constructed on that study by assessing the morphologic variation of D. gliroides. Our results show that along its distribution Dromiciops is morphologically highly variable and that the geographic pattern of morphologic variation matches the phylogeographic pattern. Taken together, morphological and molecular data indicate the existence of 2 unrecognized and unnamed species of monito del monte, which are here named and described. Cranial and dental features can easily distinguish species of Dromiciops. One of the new species is endemic of Chile, and the other new species occurs in Argentina and Chile. D. gliroides s.s. is restricted to the southern part of the genus distribution including Chiloé Island. We comment on the conservation significance of our findings and on the need of continuing with field- and collection-based research in order to characterize the richness of the Chilean mammal assemblage.

Austrogena: a new genus of chemosymbiotic bivalves (Bivalvia; Vesicomyidae; Pliocardiinae) from the oxygen minimum zone off central Chile described through morphological and molecular analyses

A new genus, Austrogena, is established for a new species of vesicomyid bivalve (A. nerudai sp. nov.) described from sediments within the oxygen minimum zone off El Quisco, Chilean margin (∼33°S) from ∼340 m depth. The new genus is distinguished by a unique combination of conchological and anatomical features for vesicomyids, including the presence of an escutcheon, a lunular incision, an elongated 4-b tooth in the left valve, a subumbonal pit, both inner and outer pairs of demibranchs and the absence of pallial sinus and processes on the inner vulva of the inhalant siphon. In comparison with the majority of highly specialized pliocardiins, the alimentary gut of Austrogena is not straight and its middle gut changes direction twice. Molecular analysis, based on COI sequences, confirms that A. nerudai sp. nov. is not related to any other pliocardiin. So far, Austrogena gen. nov. is the only endemic vesicomyid genus in the south-eastern Pacific area and A. nerudai sp. nov. is the fourth species of vesicomyids reported from chemosynthetic communities of the Chilean margin. The description of the new genus further contributes to knowledge of biodiversity of chemosymbiotic assemblages in the south-eastern Pacific. http://zoobank.org/urn:lsid:zoobank.org:pub:476A9734-B510-4954-A623-2C0E1F254F9A.

Molecular Systematics of South American Marsh Rats of the Genus Holochilus (Muroidea, Cricetidae, Sigmodontinae)

We present a comprehensive systematic study of Holochilus, a sigmodontine genus of large, herbivorous, and semiaquatic rodents widely distributed in South America. Remarkably, given its complex taxonomic history and large economic as well as epidemiological importance, the alpha taxonomy of Holochilus has not benefited from a molecular-based approach. The study is based on sequences of 1 mitochondrial and 3 nuclear loci that were analyzed by maximum likelihood and Bayesian inference. Analyses include sequences of specimens from localities from Argentina, Bolivia, Brazil, Colombia, Paraguay, Peru, Suriname, and Uruguay, representing all but 2 of the species currently recognized in the genus. Of the 4 data matrices, the mitochondrial data set contains the largest geographic coverage and recovered 6 species-level lineages that form 2 well-supported species groups: the brasiliensis species group formed by H. brasiliensis and H. vulpinus and the sciureus species group composed by H. chacarius, H. sciureus, and 2 currently unnamed forms. Surprisingly, in the cytochrome b gene analyses, the 2 species groups are not sister to each other; i.e., Holochilus is not monophyletic, although these topologies lack significant support. However, the monophyly of Holochilus was supported by the 3 nuclear loci as well as by the combined analysis of all 4 loci. These genealogical results are the basis of taxonomic and biogeographic considerations. Presentamos un estudio sistemático comprensivo sobre Holochilus, un género sigmodontino de grandes roedores herbívoros y semi-acuáticos ampliamente distribuido en América del Sur. Llamativamente, dada su compleja historia taxonómica y el gran impacto económico y epidemiológico, la taxonomía alfa de Holochilus no se ha beneficiado de un abordaje basado en evidencia molecular. El estudio se basa en secuencias de 1 gen mitocondrial y de 3 nucleares que fueron analizadas con máxima verosimilitud e inferencia Bayesiana. Los análisis incluyen secuencias de especímenes colectados en localidades de Argentina, Bolivia, Brasil, Colombia, Paraguay, Perú, Surinam y Uruguay, representando todas, con excepción de 2, las especies actualmente reconocidas en el género. La genealogía mitocondrial, que es la que tiene la mayor cobertura geográfica de Holochilus, recobra 6 linajes de nivel de especie que forman 2 grupos de especies bien apoyados: el grupo de especies brasiliensis integrado por H. brasiliensis y H. vulpinus y el grupo de especies sciureus que está compuesto por H. chacarius, H. sciureus y 2 formas aparentemente sin nominar. Llamativamente, en los análisis basados en el gen mitocondrial los 2 grupos de especies no son hermanos; i.e., Holochilus no es monofilético, aunque esta topología no tiene apoyo significativo. Sin embargo la monofilia de Holochilus es apoyada por los análisis de los 3 genes nucleares y por el análisis combinado de los 4 genes. Estos resultados genealógicos son la base de consideraciones taxonómicas y biogeográficas.

Additions to the Paraguayan mammal fauna: the first records of two marsupials (Didelphimorphia, Didelphidae) with comments on the alpha taxonomy of Cryptonanus and Philander

Abstract Even though Paraguay has had a long history of Mammalogy, since 2007, several new rodent, bat, marsupial, and armadillo species have been added to the list of known species for the country. Herein, we add two new species of marsupials to the fauna of Paraguay, Philander opossum and Cryptonanus unduaviensis. These records improve the understanding of both species in South America. The Paraguayan records of P. opossum, corresponding to the subspecies Philander opossum canus, fill in a major gap in its known distribution between Bolivia and Argentina, while the record of C. unduaviensis accounts for an extension of at least 290 km toward the southeast and is the first record reported outside of Bolivia. These two new species increase the known Paraguayan marsupial fauna to 18 species.

Description of a new soft-haired mouse, genus Abrothrix (Sigmodontinae), from the temperate Valdivian rainforest

Analyses of morphological and molecular data indicate the existence of an unrecognized and unnamed species of soft-haired mouse, genus Abrothrix. Here, we name and describe this new species, which inhabits the Valdivian ecoregion, from the north of Chiloé Island onto the mainland in the Chilean regions of Los Lagos and Los Ríos; it also occurs at a single locality in the Argentinean province of Neuquén. Long confused with A. sanborni, the new species presents a unique combination of characters that differentiate it in external, cranial, phallic, and dental terms from its congeners. Phylogenetic analysis, based on cytochrome-b gene sequences, indicates that the new species is sister to a clade formed by the austral species A. lanosa and A. sanborni and differs on average from them by 5.7% and 5.2%, respectively. Results based on the nuclear Fgb-I7 locus are less conclusive regarding the phylogenetic position of the new species but also show its distinction. We comment on the conservation significance of our findings, considering that forests of the Valdivian ecoregion are suffering substantial human disturbance through intensive logging.

Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data

The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.

Integration of morphological, ecological, and genetic evidence suggests that the genus Andinomys (Rodentia, Cricetidae) is monospecific

Two subspecies of Andinomys edax are currently recognized. Andinomys e. edax ranges from southern Perú to northernmost northwestern Argentina and A. e. lineicaudatus is mainly distributed in southern northwestern Argentina. However, some workers have recognized both taxa as distinct species, stating that A. edax is restricted to Puna and Prepuna habitats between 2,000 and 4,800 m elevation, whereas A. lineicaudatus occurs in Yungas forest below 2,500 m. We assessed the taxonomic status of both forms through an integrative approach including morphological (discrete skin and skull characters), morphometric (univariate and multivariate), geographicenvironmental niche modeling (Mahalanobis Typicalities), and molecular (Bayesian analysis of cytochrome-b gene sequences) analyses. We did not find characters that consistently differentiated skins and skulls of the 2 forms. The morphometric analysis indicated that lineicaudatus is, on average, larger than edax for some measurements, but only 2 (alveolar width and occipital condyle width) differed significantly between forms. No group of specimens was clearly segregated in the PCA morphospace. Distribution models obtained separately for each taxon do not offer a better fit to the known distribution than models based on the combined data sets. We documented coincident environmental variables as relevant in the model building of edax and lineicaudatus, noting some segregation in elevation, but similar habitat suitability for the remainder of the environmental variables. The geographic continuity between niche models of edax and lineicaudatus was clear but specimens morphologically assignable to each of the nominal forms were not found in areas of overlap. The phylogenetic analyses recovered a polytomy of 4 allopatric and genetically divergent clades, which also failed to support the taxonomic hypothesis of 2 species. Based on all available evidence, we conclude that Andinomys consists of a single species. Nevertheless, observed genetic divergences among clades and their geographic distribution indicate that past events probably fragmented populations of A. edax.

Taxonomy of the Phyllotis osilae species group in Argentina; the status of the “Rata de los nogales” ( Phyllotis nogalaris Thomas, 1921; Rodentia: Cricetidae)

The taxonomic status of populations of the genus Phyllotis from northwestern Argentina (NWA) has undergone recent changes, with the addition of two species (P. alisosiensis and P. anitae) to the traditionally recognized forms (P. caprinus, P. xanthopygus, and P. osilae). Three of these species (P. anitae, P. osilae, and P. alisosiensis) were included within the Phyllotis osilae species group. Most authors recognized three subspecies of P. osilae for NWA: P. osilae osilae, P. o. nogalaris, and P. o. tucumanus. Morphological, morphometric, and molecular studies based on recently collected specimens suggest that current classification does not reflect the diversity of this group in NWA, revealing the need of some taxonomic reallocations and new distributional delimitations. Here we propose that P. nogalaris must be recognized as a valid species and the restriction of P. osilae to southern Peru and central Bolivia. Following our results, we expect an outstanding improvement in the taxonomic knowledge of the Phyllotis osilae species group in the coming years.