Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary.

The "Amazon tipping point" is a global change scenario resulting in replacement of upland terra-firme forests by large-scale "savannization" of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM) has been proposed to have acted as such a tipping point in the past, with the prediction that terra-firme inhabiting species should have experienced reductions in population size as drier habitats expanded. Here, we use whole-genomes of an Amazonian endemic organism (Scale-backed antbirds - Willisornis spp.) sampled from nine populations across the region to test this historical demography scenario. Populations from southeastern Amazonia and close to the Amazon-Cerrado ecotone exhibited a wide range of demographic patterns, while most of those from northern and western Amazonia experienced uniform expansions between 400 kya and 80-60 kya, with gradual declines toward 20 kya. Southeastern populations of Willisornis were the last to diversify and showed smaller heterozygosity and higher runs of homozygosity values than western and northern populations. These patterns support historical population declines throughout the Amazon that affected more strongly lineages in the southern and eastern areas, where historical "tipping point" conditions existed due to the widespread replacement of humid forest by drier and open vegetation during the LGM.

Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat.

Species delimitation studies based on integrating different datasets such as genomic, morphometric, and cytogenetics data are rare in studies focused on Neotropical rodents. As a consequence, the evolutionary history of most of these genera remains poorly understood. Proechimys is a highly diverse and widely distributed genus of Neotropical spiny rats with unique traits like multiple sympatry, micro-habitat segregation, and fuzzy species limits. Here, we applied RAD-Seq to infer the phylogenetic relationships, estimate the species boundaries, and estimate the divergence times for Proechimys, one of the most common and least studied small mammals in the Amazon. We tested whether inferred lineages in the phylogenetic trees could be considered distinct species based on the genomic dataset and morphometric data. Analyses revealed the genus is not monophyletic, with Proechimys hoplomyoides sister to a group of Hoplomys gymnurus + all other Proechimys species, contesting the generic status of Hoplomys. There are five main clades in Proechimys stricto sensu (excluding H. gymnurus and P. hoplomyoides). Species delimitation analyses supported 25 species within the genus Proechimys. The five main clades in Proechimys stricto sensu also showed similar ages for their origins, and two rapid diversification events were identified in the Early Pliocene and in the Early Pleistocene. Most cases of sympatry in Proechimys occur among species from the different main clades, and although Proechimys is an inhabitant of the Amazon, three species occupied the Cerrado biome during the Pleistocene. We could associate available nominal taxon, cytogenetics information, and DNA sequences in Genbank to most of the 25 species we hypothesized from our delimitation analyses. Based on our analyses, we estimate that eight forms represent putative new species that need a taxonomic revision.

Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon.

The quillwort Isoëtes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N e) are expected for narrow endemic species (NES). Conservation biology studies centered in a single species show some limitations, but they are still useful considering the limited time and resources available for protection of species at risk of extinction. Here, we evaluated the genetic diversity, population structure, N e, and minimum viable population (MVP) of I. cangae to provide information for effective conservation programs. Our analyses were based on 55 individuals collected from the Amendoim Lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and N e in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential and that all individuals should be treated as one demographic unit. These results provide essential information to optimize ex situ conservation efforts and genetic diversity monitoring, which are currently applied to guide I. cangae conservation plans.

Tempo and mode of evolution of oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): A phylogenomic approach.

The tribe Oryzomyini is an impressive group of rodents, comprising 30 extant genera and an estimated 147 species. Recent remarkable advances in the understanding of the diversity, taxonomy and systematics of the tribe have mostly derived from analyses of single or few genetic markers. However, the evolutionary history and biogeography of Oryzomyini, its origin and diversification across the Neotropics, remain unrevealed. Here we use a multi-locus dataset (over 400 loci) obtained through anchored phylogenomics to provide a genome-wide phylogenetic hypothesis for Oryzomyini and to investigate the tempo and mode of its evolution. Species tree and supermatrix analyses produced topologies with strong support for most branches, with all genera confirmed as monophyletic, a result that previous studies failed to obtain. Our analyses also corroborated the monophyly and phylogenetic relationship of three main clades of Oryzomyini (B, C and D). The origin of the tribe is estimated to be in the Miocene (8.93-5.38 million years ago). The cladogenetic events leading to the four main clades occurred during the late Miocene and early Pliocene and most speciation events in the Pleistocene. Geographic range estimates suggested an east of Andes origin for the ancestor of oryzomyines, most likely in the Boreal Brazilian region, which includes the north bank of Rio Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous South America radiation, that colonized areas and dominions of this continent mainly by dispersal events. The evolutionary history of the tribe is deeply associated with the Andean cordillera and the landscape history of Amazon basin.

Historical connections among river basins and climatic changes explain the biogeographic history of a water rat.

BACKGROUND: The water rat Nectomys squamipes (Cricetidae: Sigmodontinae) is a semiaquatic rodent from eastern South America that shows shallow genetic structure across space, according to some studies. We tested the influence of hydrography and climatic changes on the genetic and phylogeographic structure of this semiaquatic small mammal. METHODS: DNA sequences of two mitochondrial genetic markers (Cyt b and D-loop) and six microsatellite loci from water rats were collected at 50 localities in five river basins in the Atlantic Forest along the eastern coast of South America. We evaluated the genetic structure within and among river basins, and we estimated divergence dates. Species distribution models for the present and past were built to identify possible gene flow paths. RESULTS: Mitochondrial data and species distribution models showed coherent results. Microsatellite loci showed a more complex pattern of genetic differentiation. The diversification of N. squamipes haplotypes occurred during the Pleistocene and the river basin cannot explain most of the genetic structure. We found evidence of population expansion during the last glacial maximum, and gene flow paths indicate historical connections among rivers in the Atlantic Forest. DISCUSSION: Historical connections among rivers in the Atlantic Forest may have allowed N. squamipes to disperse farther across and within basins, leading to shallow genetic structure. Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, thus challenging the forest refuge hypothesis.

How many species of mammals are there in Brazil? New records of rare rodents (Rodentia: Cricetidae: Sigmodontinae) from Amazonia raise the current known diversity.

BACKGROUND: Since 1996, when Vivo questioned how many species of mammals occur in Brazil, there has been a huge effort to assess this biodiversity. In this contribution, we present new records for rare species of the sigmodontine rodent genera Rhagomys and Neusticomys previously unknown to Brazilian Amazon. We provided detailed information on the morphologic variation to allow the proper identification of these species. We also furnished updated information on their collection, aiming to establish hypothesis of their geographic distribution, based on SDM's, aiming to hypothesize potential occurrence areas for these species. METHODS: Rodent specimens were sampled in separate inventories in two sites of Rondônia State (Hydroelectric Dam Jirau and Parque Nacional de Pacaás Novos) and one site in Pará State (Pacajá), Brazil, and were compared to specimens from museum collections to apply appropriate names. The SDM were conducted using two algorithms for rare species, MaxEnt and randomForest (RF), and were based on seven localities for Rhagomys, and 10 for Neusticomys. RESULTS: All specimens were collected with pitfall traps. One specimen of genus Rhagomys was trapped in the Hydroelectric Dam Jirau. We identified this specimen as R. longilingua, and the SDM species indicates suitable areas for its occurrence at high elevations near on the Andes and lowlands of Amazon Basin to the South of the Rio Amazonas. Two specimens of Neusticomys were recorded, and we identified the specimen from Pacaás Novos as N. peruviensis, with SDM suggesting main areas of occurrence on Western Amazon. We applied the name N. ferreirai to the specimen from Pacajá, with SDM recovering suitable areas in Eastern Amazon. DISCUSSION: We reinforced the importance of pitfall traps on the study of Neotropical rodents. We described morphologic variation within and among all species that do not invalidate their specific status, but in the near future a re-evaluation will be mandatory. The new records extended the species distribution considerably. SDM was successful to predict their distributions, as the two algorithms presented important differences in range size recovered by the models that can be explained by differences in the thresholds used for the construction of the models. Most suitable areas coincide with the areas facing most of the deforestation in Amazon. We added two rare species of sigmodontine rodents to the list of Brazilian Mammals, which now comprises 722 species (or 775 valid nominal taxa). Although more information is available than in 1996, it is essential that mammal experts maintain inventory and revisionary programs to update and revise this information. This is even more important, as changes in Brazilian environmental legislation are being discussed, suggesting reduced need for environmental impact reports prior to beginning commercial enterprises, resulting in the loss of information about native biodiversity in the affected areas.

Taxonomic implications of morphological variation in three species of Trinomys (Rodentia: Echimyidae) from eastern Brazil.

Trinomys is a genus of terrestrial spiny rats from the Atlantic Forest, and three species occur in the state of Espírito Santo, eastern Brazil: T. gratiosus, T. paratus, and T. setosus. The levels of morphological variation within and among these species are virtually unknown, and their geographic ranges have not been properly assessed. These three species are externally very similar, hampering their identification in surveys and ecological studies that are not based on voucher specimens. We evaluated 162 specimens of Trinomys spp. from eastern Brazil, especially from the state of Espírito Santo, and used data from skulls, skins, and bacula to examine morphological variation and its taxonomic implications. We found extensive morphological variation in the skins and skulls even when diagnostic characters were examined, such as the number of dental lophs and bones contributing to the postorbital process. We also found variation in bacular shape among and within species, including polymorphism among individuals from the same population. The geographic range of each species in Espírito Santo was well defined: T. setosus occurred on the left (north) bank of the Doce River, and the other two species, T. gratiosus and T. paratus, occurred on the right (south) bank of this river; however, T. gratiosus was found at altitudes above 500 m, whereas T. paratus occurred below 580 m. Despite difficulties in species identification, the results of morphological and morphometric analyses are compatible with the current classification of these three species. In addition, the level of morphological variation found in specimens identified as T. g. panema--including types--falls within the range of T. g. gratiosus, confirming the taxonomic status of the former as a junior synonym of the latter.