Molecular phylogenetics of mouse opossums: new findings on the phylogeny ofThylamys(Didelphimorphia, Didelphidae)

Evolution, divergence, and convergence in the mandibles of opossums (Didelphidae, Didelphimorphia)

Didelphid marsupials are considered a morphologically unspecialized group with a generalist diet that includes vertebrates, invertebrates, and plant matter. While cranium and scapula variation has already been examined within Didelphidae, variation in mandible shape, usually associated with diet or phylogeny in other mammalian groups, has not yet been properly assessed in the family. We evaluated the variation in mandible shape and size of didelphids (2470 specimens belonging to 94 species) using 2D geometric morphometrics. We classified the diet of the didelphids into four broad categories to assess whether morphospace ordination relates to dietary habits. We also provided the most comprehensive phylogeny for the family (123 out of the 126 living species) using 10 nuclear and mitochondrial genes. We then mapped mandible size and shape onto that phylogeny for 93 selected taxa and ancestral size and shapes were reconstructed by parsimony. We found phylogenetically structured variation in mandible morphology between didelphid groups, and our results indicate that they have a significant phylogenetic signal. The main axis of shape variation is poorly related to size, but the second is strongly allometric, indicating that allometry is not the main factor in shaping morphological diversity on their mandibles. Our results indicate that the shape and size of the ancestral mandible of didelphids would be similar to that of the current species of the genus Marmosa.

An updated biogeographic evaluation of endemism and conservation of small mammals from Chile

Ecological factors such as temperature, precipitation, and vegetation type have been reported to influence biogeographic patterns (e.g., species distribution, richness, and endemism) in mammals. In Chile, these patterns only had been explored in selected mammal groups from certain localities. In this study, we describe and analyze biogeographic patterns for all small mammals (marsupials, armadillos, bats, rodents), reported until 2020, in different climatic and ecological regions from continental Chile. Using a compiled database of 89 species, we estimated their distributional similarity, described and characterized richness and areas of endemism using Bayesian and Parsimony Analysis of Endemism, and linked species distribution with conservation status according to the IUCN Red List. We found three similarity units of species distribution based on climate: Arid, Temperate, and Polar; higher richness and endemism in north and south-central Chile; two areas of endemism, one in north and one in south; and a hotspot in south-central Chile. Finally, species of greater conservation concern showed a similar and small distribution range. The concordance in the distribution of the species with Chilean climatic regions (as determined by precipitation and temperature) suggest that the spatial distribution of Chilean small mammals is influenced strongly by those abiotic factors. This also could explain the patterns of richness and endemism and, therefore species hotspots. Variations of climatic factors therefore should be considered in explaining biogeographic patterns and conservation plans of Chilean small mammal species, because species of greater concern tend to be associated and having similar distributional characteristics.

Insularity and Aridity as Drivers of Mandibular Disparity in Thylamys elegans (Waterhouse, 1839) from Populations of the Atacama Desert, Chile

Island ecosystems differ in several elements from mainland ecosystems and may induce variations related to natural selection and patterns of adaptation in most aspects of the biology of an organism. Thylamys elegans (Waterhouse, 1839) is a marsupial endemic to Chile, distributed from Loa River to Concepción. Historically, three subspecies have been described: Thylamys elegans elegans, Thylamys elegans coquimbensis and Thylamys elegans soricinus. For this research, two morphometric approaches and a biomechanical model were used to compare the mandible shapes and biomechanics between two Chilean mouse opossum populations belonging to different subspecies: one from the coastal desert of Chile (T. e. coquimbensis) and the other from the central inland region (T. e. elegans). Additionally, mandibles of insular populations found in the Reserva Nacional Pinguino de Humboldt (RNPH)), from which the subspecies association is unknown, were also included. The results showed that insular populations have differences in mandibular shapes, sizes and biomechanical characteristics compared to continental populations, which may be related to environmental variables like aridity and vegetation cover, prey type, insularity effects and/or the founder effect on micromammals, apart from vicariance hypotheses and other selective pressures.

A comprehensive overview of the genetic diversity in Thylamys elegans (Didelphimorphia: Didelphidae): establishing the phylogeographic determinants

Background

For the genus Thylamys, the rivers have been reported as barriers to dispersal, limiting current and historical distribution of its lineages. We hypothesized that the Maipo river has affected the genetic structure of northern and southern lineages of Thylamys elegans, recovering a phylogenetic relationships with reciprocally monophyletic sister groups on opposite river banks. We evaluated the role of other rivers in the Mediterranean zone of Chile as historical and recent modulators of the biogeographic processes of this species.

Methods

We applied a phylogeographic approach, using the cytochrome-b mitochondrial gene for 93 individuals of T. elegans, from 37 localities in a latitudinal gradient between 21°25’ and 35˚56’S, encompassing a geographic area between the Atacama Desert and most of the Mediterranean Chilean zone.

Results

The phylogenetics results recovered six lineages within T. elegans: Thylamys elegans elegans, Thylamys elegans coquimbensis, the Loa lineage and three other lineages not described previously (Aconcagua, South 1 and South 2). We suggest that following rivers play a role like primary barrier: the Maipo river in the genetic differentiation of northern and southern ancestral lineages, and the Mataquito river and its tributary Teno river for the South 1 and South 2 lineages. On the other hand, the Quilimarí river preserve the genetic divergence in T. e. coquimbensis and Aconcagua lineage and the Aconcagua river in Aconcagua lineage and T. e. elegans acting like secondary barriers.

Conclusions

We concluded that the genetic diversity and biogeographic history of T. elegans was shaped by mountain glaciers, changes in river water levels during the Pleistocene glaciations and hyperaridity, promoting the differentiation and persistance of the T. elegans lineages.

Amazonia as the Origin and Diversification Area of Didelphidae (Mammalia: Metatheria), and a Review of the Fossil Record of the Clade

Didelphidae is the largest New World radiation of marsupials, and is mostly represented by arboreal, small- to medium-sized taxa that inhabit tropical and/or subtropical forests. The group originated and remained isolated in South America for millions of years, until the formation of the Isthmus of Panama. In this study, we present the first reconstruction of the biogeographic history of Didelphidae including all major clades, based on parametric models and stratified analyses over time. We also compiled all the pre-Quaternary fossil records of the group, and contrasted these data to our biogeographic inferences, as well as to major environmental events that occurred in the South American Cenozoic. Our results indicate the relevance of Amazonia in the early diversification of Didelphidae, including the divergence of the major clades traditionally ranked as subfamilies and tribes. Cladogeneses in other areas started in the late Miocene, an interval of intense shifts, especially in the northern portion of Andes and Amazon Basin. Occupation of other areas continued through the Pliocene, but few were only colonized in Quaternary times. The comparison between the biogeographic inference and the fossil records highlights some further steps towards better understanding the spatiotemporal evolution of the clade. Finally, our results stress that the early history of didelphids is obscured by the lack of Paleogene fossils, which are still to be unearthed from low-latitude deposits of South America.

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.

Genetic variation of the Chilean endemic long-haired mouse Abrothrix longipilis (Rodentia, Supramyomorpha, Cricetidae) in a geographical and environmental context

Quaternary climate and associated vegetational changes affected the fauna of the Chilean Mediterranean ecosystem. Here we studied the genetic variation of the long-haired mouse, Abrothrix longipilis, a sigmodontine rodent endemic to this area. Within an environmentally explicit context, we examined the geographic distribution of the genetic diversity and demographic history of the species based on sequences of the mitochondrial Cytochrome-b gene of 50 individuals from 13 localities and a large panel of single nucleotide polymorphisms of 17 individuals from 6 localities. The gene genealogy of A. longipilis revealed three intraspecific lineages that are allopatric and latitudinally segregated (northern, central, and southern lineages) with an estimated crown age for the whole species clade of 552.3 kyr B.P. A principal component analysis based on 336,596 SNP loci is in line with the information given by the the mitochondrial gene genealogy. Along its complete distributional range, A. longipilis showed patterns of isolation by distance and also isolation by environment. The general pattern of historical demography showed stability for most intraspecific lineages of A. longipilis. Northern and central lineages showed signals of historical demographic stability, while the southern lineage showed contrasting signals. In agreement with this, the niche models performed showed that in the northern range of A. longipilis, areas of high suitability for this species increased towards the present time; areas of central range would have remained relatively stable, while southern areas would have experienced more change through time. In summary, our study shows three distinct allopatric lineages of A. longipilis, each showing slightly different demographic history.

Phylogeny of Neotropical Sicarius sand spiders suggests frequent transitions from deserts to dry forests despite antique, broad-scale niche conservatism

Phylogenetic niche conservatism (PNC) shapes the distribution of organisms by constraining lineages to particular climatic conditions. Conversely, if areas with similar climates are geographically isolated, diversification may also be limited by dispersal. Neotropical xeric habitats provide an ideal system to test the relative roles of climate and geography on diversification, as they occur in disjunct areas with similar biotas. Sicariinae sand spiders are intimately associated with these xeric environments, particularly seasonally dry tropical forests (SDTFs) and subtropical deserts/scrublands in Africa (Hexophthalma) and the Neotropics (Sicarius). We explore the role of PNC, geography and biome shifts in their evolution and timing of diversification. We estimated a time-calibrated, total-evidence phylogeny of Sicariinae, and used published distribution records to estimate climatic niche and biome occupancy. Topologies were used for estimating ancestral niches and biome shifts. We used variation partitioning methods to test the relative importance of climate and spatially autocorrelated factors in explaining the spatial variation in phylogenetic structure of Sicarius across the Neotropics. Neotropical Sicarius are ancient and split from their African sister-group around 90 (57-131) million years ago. Most speciation events took place in the Miocene. Sicariinae records can be separated in two groups corresponding to temperate/dry and tropical/seasonally dry climates. The ancestral climatic niche of Sicariinae are temperate/dry areas, with 2-3 shifts to tropical/seasonally dry areas in Sicarius. Similarly, ancestral biomes occupied by the group are temperate and dry (deserts, Mediterranean scrub, temperate grasslands), with 2-3 shifts to tropical, seasonally dry forests and grasslands. Most of the variation in phylogenetic structure is explained by long-distance dispersal limitation that is independent of the measured climatic conditions. Sicariinae have an ancient association to arid lands, suggesting that PNC prevented them from colonizing mesic habitats. However, niches are labile at a smaller scale, with several shifts from deserts to SDTFs. This suggests that PNC and long-distance dispersal limitation played major roles in confining lineages to isolated areas of SDTF/desert over evolutionary history, although shifts between xeric biomes occurred whenever geographical opportunities were presented.