So far away, yet so close: strong genetic structure in Homonota uruguayensis (Squamata, Phyllodactylidae), a species with restricted geographic distribution in the Brazilian and Uruguayan Pampas

Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction

Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406-0.134 and nucleotide diversity 0.0812-0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (Fis - 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.

Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae)

Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.

Phenotypic and genomic differences between biomes of the South America marsh rat, Holochilus brasiliensis

Abiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.

The lizard that never sleeps: activity of the pampa marked gecko Homonota uruguayensis

ABSTRACT It is generally assumed that lizards are active whenever climatic conditions are favorable. Homonota uruguayensis (Vaz-Ferreira & Sierra de Soriano, 1961) is the only native gecko - and nocturnal lizard - living in the northern Pampa biome, and its ecology is poorly known. This study aimed at describing this species’ pattern of daily and annual activity and its relation with environmental temperatures. The study was conducted in the extreme south of Brazil (Rosário do Sul, State of Rio Grande do Sul), between May 2010 and January 2011 at a rocky outcrop located in the Pampa biome. The study was carried out in a total of four seasonal field trips, totalizing 1185 hours of field work. The data were collected, both during the day and the night in 6-hour shifts (duration of the sampling period). The area was randomly covered at each shift to record activity and microhabitat use by the lizards. In total 1541 specimens were recorded throughout the study. Homonota uruguayensis showed diurnal and nocturnal activity in the four seasons, with periods of daily activity varying significantly between all seasons in a cyclic and multimodal pattern, with no significant relation with environmental temperatures. There was no difference in activity related to sex and age classes. Most active lizards were found when air temperatures ranged from 14 °C to 32.9 °C (82% of active lizards) and substrate temperatures ranged from 10 °C to 32.9 °C (87% of active lizards).

Population Genetic Structure of Cnesterodon decemmaculatus (Poeciliidae): A Freshwater Look at the Pampa Biome in Southern South America

The Pampas is a Neotropical biome formed primarily by low altitude grasslands and encompasses the southernmost portion of Brazil, Uruguay, and part of Argentina. Despite the high level of endemism, and its significant environmental heterogeneity, Pampean species are underrepresented in phylogeographic studies, especially aquatic organisms. The Pampean hydrological system resulted from a long history of tectonism, climate, and sea level changes since the Neogene. In this study, we examined the population genetic structure of Cnesterodon decemmaculatus, a freshwater fish species that occurs throughout most of the Pampa biome. We characterized mitochondrial and autosomal genetic lineages in populations sampled from Southern Brazil and Uruguay to investigate (1) the correspondence between current drainage systems and evolutionary lineages, (2) the demographic history for each genetic lineage, and (3) the temporal depth of these lineages. Overall, we found that the major evolutionary lineages in this species are strongly related to the main Pampean drainage systems, even though stream capture events may have affected the distribution of genetic lineages among drainages. There was evidence for recent population growth in the lineages occupying drainages closest to the shore, which may indicate the effect of quaternary sea-level changes. In general, divergence time estimates among evolutionary lineages were shallow, ranging from 20,000 to 800,000 years before present, indicating a geologically recent history for this group, as previously reported in other Pampean species. A Bayesian phylogeographical reconstruction suggested that an ancestral lineage probably colonized the Uruguay River Basin, and then expanded throughout the Pampas. This evolutionary scenario may represent useful starting models for other freshwater species having a similar distribution.

Pleistocene climatic oscillations in Neotropical open areas: Refuge isolation in the rodent Oxymycterus nasutus endemic to grasslands

Pleistocene climatic oscillations favoured the expansion of grassland ecosystems and open vegetation landscapes throughout the Neotropics, and influenced the evolutionary history of species adapted to such environments. In this study, we sampled populations of the rodent Oxymycterus nasutus endemic to open areas in the Pampas and Atlantic Forest biomes to assess the tempo and mode of population divergence using an integrative approach, including coalescence theory, ecological niche models, and morphometry. Our results indicated that these O. nasutus populations exhibited high levels of genetic structure. Six major mtDNA clades were found, structuring these biomes into distinct groups. Estimates of their divergence times was indicated to be 0.571 myr. The high degree of genetic structure is reflected in the analyses of geometric morphometric; skull differences between lineages in the two ecoregions were detected. During the last glacial maximum, there was a strong increase in suitable abiotic conditions for O. nasutus. Distinct molecular markers revealed a population expansion over time, with a possible demographic retraction during the post-glacial period. Considering that all clades coalesce with the last interglacial maximum, our results indicated that reduction in suitable conditions during this period may have resulted in a possible vicariance associated with refuge isolation.

High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America

Relative to South America's ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is a small-size species (<20mm) with extensive coloration and morphological variation, we suspected that it might represent a complex of cryptic species. In addition, we expected strong genetic and geographic structuring within Pseudopaludicola falcipes due to its large geographic distribution, potentially short dispersal distances, and multiple riverine barriers. We found that P. falcipes is a single evolutionary lineage with poor geographic structuring. Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow. We conclude that the demographic history of P. falcipes, combined with its ecological attributes and the landscape features of the Pampas, favored a unique combination among anurans of small body size, large population size, high genetic variability, but high cohesiveness of populations over a wide geographic distribution.