Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels.

Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.

Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.

BACKGROUND: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa. RESULTS: We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses-performed with datasets differing on levels of missing data and taxa under distinct analytical methods-strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels. CONCLUSIONS: Complete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.

CERRADO SMALL MAMMALS: abundance and distribution of marsupials, lagomorphs, and rodents in a Neotropical savanna.

Patterns in distribution and local abundance of species within a biome are central concerns in ecology and allow the understanding of the effects of habitat loss on rates of species extinction; provide support for the creation and management of reserves; and contribute to the identification and quantification of the processes that allow niche partitioning by species. However, despite the importance in the conservation and management of the ecosystems, most systematized information on the abundance and distribution of small mammals is restricted to the northern hemisphere or forest ecosystems. For tropical biomes, an important part of this information remains dispersed and difficult to access in the form of theses, technical reports, or unpublished data sets. Here we present a comprehensive data set of abundance and richness of small mammals in the Cerrado, the largest Neotropical savanna. This data set includes 2,599 records of 446 sites from 96 studies. More than 50% of references in this data set are peer-reviewed journal articles, but 45.78% of communities were compiled from theses. The data set comprises 24,283 individuals of 55 genera and at least 118 species of small mammals including 29 marsupials, two lagomorphs (one exotic), and 87 rodents (three exotic). Local species richness ranged from 1 to 26 species (5.82 ± 3.55, average species richness ± SD). We observed hyperdominance of a few species; the 10 most abundant species in this data set represented 60.19% of all recorded individuals. The hairy-tailed bolo mouse (Necromys lasiurus) represented over than 20% of all individuals and occurred at more than 50% of sites. Furthermore, we identified 18 environments, 16 native vegetation types, and 2 anthropic environments. Typical savanna and gallery forest were the most frequently sampled vegetation types (comprising 46.94% of all sampled sites) and the most speciose ones (57 species for typical savanna and 53 species for gallery forest). The information contained in this data set can be used to analyze ecological questions such as the relationship between local abundance and regional distribution, the relevance of local and regional factors to community structuring, and the role of phylogenetic mechanisms in community assemblage. It can also be useful in conservation efforts in this biodiversity hotspot. No copyright, proprietary, or cost restrictions apply. Please cite this paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

ATLANTIC MAMMAL TRAITS: a data set of morphological traits of mammals in the Atlantic Forest of South America.

Measures of traits are the basis of functional biological diversity. Numerous works consider mean species-level measures of traits while ignoring individual variance within species. However, there is a large amount of variation within species and it is increasingly apparent that it is important to consider trait variation not only between species, but also within species. Mammals are an interesting group for investigating trait-based approaches because they play diverse and important ecological functions (e.g., pollination, seed dispersal, predation, grazing) that are correlated with functional traits. Here we compile a data set comprising morphological and life history information of 279 mammal species from 39,850 individuals of 388 populations ranging from -5.83 to -29.75 decimal degrees of latitude and -34.82 to -56.73 decimal degrees of longitude in the Atlantic forest of South America. We present trait information from 16,840 individuals of 181 species of non-volant mammals (Rodentia, Didelphimorphia, Carnivora, Primates, Cingulata, Artiodactyla, Pilosa, Lagomorpha, Perissodactyla) and from 23,010 individuals of 98 species of volant mammals (Chiroptera). The traits reported include body mass, age, sex, reproductive stage, as well as the geographic coordinates of sampling for all taxa. Moreover, we gathered information on forearm length for bats and body length and tail length for rodents and marsupials. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

Atlantic small-mammal: a dataset of communities of rodents and marsupials of the Atlantic forests of South America.

The contribution of small mammal ecology to the understanding of macroecological patterns of biodiversity, population dynamics, and community assembly has been hindered by the absence of large datasets of small mammal communities from tropical regions. Here we compile the largest dataset of inventories of small mammal communities for the Neotropical region. The dataset reviews small mammal communities from the Atlantic forest of South America, one of the regions with the highest diversity of small mammals and a global biodiversity hotspot, though currently covering less than 12% of its original area due to anthropogenic pressures. The dataset comprises 136 references from 300 locations covering seven vegetation types of tropical and subtropical Atlantic forests of South America, and presents data on species composition, richness, and relative abundance (captures/trap-nights). One paper was published more than 70 yr ago, but 80% of them were published after 2000. The dataset comprises 53,518 individuals of 124 species of small mammals, including 30 species of marsupials and 94 species of rodents. Species richness averaged 8.2 species (1-21) per site. Only two species occurred in more than 50% of the sites (the common opossum, Didelphis aurita and black-footed pigmy rice rat Oligoryzomys nigripes). Mean species abundance varied 430-fold, from 4.3 to 0.01 individuals/trap-night. The dataset also revealed a hyper-dominance of 22 species that comprised 78.29% of all individuals captured, with only seven species representing 44% of all captures. The information contained on this dataset can be applied in the study of macroecological patterns of biodiversity, communities, and populations, but also to evaluate the ecological consequences of fragmentation and defaunation, and predict disease outbreaks, trophic interactions and community dynamics in this biodiversity hotspot.

Ticks (Acari: Ixodidae) identified from prey-predator interactions via faecal analysis of Brazilian wild carnivores.

Between July 2008 and May 2010, we conducted a trophic study on 12 Brazilian wild carnivore species through their faecal analysis in a silvicultural landscape at Angatuba municipality, southern São Paulo state. Predator faeces was identified by morphology, predator hair, and surrounding tracks; prey remnants within faeces were used for morphological identification of the prey. Among the recovered ectoparasites, there were 89 specimens of six tick species in 21 (4.0%) out of 523 analysed samples. Ticks were identified to species level, based on external morphological characters, as following: adults of Amblyomma ovale and Amblyomma sculptum; nymphs of Amblyomma brasiliense, Amblyomma calcaratum, Amblyomma dubitatum, A. ovale, and Ixodes schulzei; and larvae of Amblyomma sp. and Ixodes sp. Generally, the recovered immature ticks were associated with consumed prey (small birds or small mammals), whereas adults were associated with the predator itself, ingested during its self-grooming. Our data show that faeces is an additional information source on ticks in Brazil and which may provide information on ectoparasite-predator-prey interactions.

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.

Small mammals, ticks and rickettsiae in natural and human-modified landscapes: Diversity and occurrence of Brazilian spotted fever in Brazil.

We studied communities of small mammals and their ticks in endemic (E) and non-endemic (NE) areas for Brazilian spotted fever (BSF), aiming to infer if diversity parameters of parasites and hosts could be related to occurrence and prevalence of rickettsial infection, especially Rickettsia rickettsii. We compared E and NE areas in human-modified landscapes (HMLs) and natural areas (BIO) with no report of BSF cases. Composition and equitability were important components of diversity explaining differences among areas. The marsupial Didelphis albiventris was dominant in HMLs, but not in natural areas, and this opossum was the main host for the tick Amblyomma sculptum, principal vector of R. rickettsii, especially in E areas. Communities of ticks were dominated by A. sculptum, followed by Amblyomma dubitatum in E areas. In NE areas, this dominance was inverted, with more A. dubitatum than A. sculptum infesting small mammals, but the numbers of ticks were much lower than in E areas. Composition and abundance of ticks in natural areas were very dissimilar from HMLs, with the lowest tick burdens. Didelphis albiventris in E areas presented higher seroprevalence and endpoint titres against R. rickettsii than in other areas. At least three Rickettsia species, non-pathogenic to humans, were detected in natural areas (Rickettsia bellii, Rickettsia amblyommatis and 'Candidatus Rickettsia andeanae'), and only one non-pathogenic species in HMLs (R. bellii). Our results suggest that higher diversity of ticks, hosts and rickettsiae could be relevant factors in buffering the effect in BSF occurrence. Particularly for D. albiventris, its importance has to be quantified in further studies considering the epidemiological scenario of BSF.

A new genus of oryzomyine rodents (Cricetidae, Sigmodontinae) with three new species from montane cloud forests, western Andean cordillera of Colombia and Ecuador.

The Andean cloud forests of western Colombia and Ecuador are home to several endemic mammals; members of the Oryzomyini, the largest Sigmodontinae tribe, are extensively represented in the region. However, our knowledge about this diversity is still incomplete, as evidenced by several new taxa that have been described in recent years. Extensive field work in two protected areas enclosing remnants of Chocó montane forest recovered a high diversity of small mammals. Among them, a medium-sized oryzomyine is here described as a new genus having at least three new species, two of them are named and diagnosed. Although externally similar to members of the genera Nephelomys and Tanyuromys, the new genus has a unique molar pattern within the tribe, being characterized by a noticeable degree of hypsodonty, simplification, lamination, and third molar compression. A phylogeny based on a combination of molecular markers, including nuclear and mitochondrial genes, and morphological data recovered the new genus as sister to Mindomys, and sequentially to Nephelomys. The new genus seems to be another example of a sigmodontine rodent unique to the Chocó biogeographic region. Its type species inhabits cloud forest between 1,600 and 2,300 m in northernmost Ecuador (Carchi Province); a second species is restricted to lower montane forest, 1,200 m, in northern Ecuador (Imbabura Province); a third putative species, here highlighted exclusively by molecular evidence from one immature specimen, is recorded in the montane forest of Reserva Otonga, northern Ecuador (Cotopaxi Province). Finally, the new genus is also recorded in southernmost Colombia (Nariño Department), probably represented there also by a new species. These species are spatially separated by deep river canyons through Andean forests, resulting in marked environmental discontinuities. Unfortunately, Colombian and Ecuadorian Pacific cloud forests are under rapid anthropic transformation. Although the populations of the type species are moderately abundant and occur in protected areas, the other two persist in threatened forest fragments.

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.

Mammals in São Paulo State: diversity, distribution, ecology, and conservation / Mamíferos do Estado de São Paulo: diversidade, distribuição, ecologia e conservação

Abstract Mammals are charismatic organisms that play a fundamental role in ecological functions and ecosystem services, such as pollination, seed dispersal, nutrient cycling, and pest control. The state of São Paulo represents only 3% of the Brazilian territory but holds 33% of its mammalian diversity. Most of its territory is dominated by agriculture, pastures, and urban areas which directly affect the diversity and persistence of mammals in the landscape. In addition, São Paulo has the largest port in Latin America and the largest offshore oil reservoir in Brazil, with a 600 km stretch of coastline with several marine mammal species. These human-made infrastructures affect the diversity, distribution, ecology, and the future of mammals in the state. Here, we answer five main questions: 1) What is the diversity of wild mammals in São Paulo state? 2) Where are they? 3) What is their positive and negative impact on human well-being? 4) How do mammals thrive in human-modified landscapes? 5) What is the future of mammals in the state? The state of São Paulo holds 255 species of native mammals, with four endemic species, two of them globally endangered. At least six species (two marsupials, Giant otter, Pampas deer, Brazilian dwarf brocket deer, and Giant armadillo) were extirpated from the state due to hunting and habitat loss. The intense human land use in the state forced many mammalian species to change their diet to cope with the intense fragmentation and agriculture. Large-scale monoculture has facilitated the invasion of exotic species such as wild boars (javali) and the European hare. Several "savanna-dwelling" species are expanding their ranges (Maned wolf, Brocket deer) over deforested areas and probably reflect changes towards a drier climate. Because the state has the largest road system, about 40,000 mammals from 33 species are killed per year in collisions causing an economic loss of 12 million dollars/year. The diversity of mammals is concentrated in the largest forest remnants of Serra do Mar and in the interior of the State, mainly in the regions of Ribeirão Preto and Jundiaí. Sampling gaps are concentrated throughout the interior of the state, particularly in the northwest region. Wild mammals play a fundamental role in many ecosystem services, but they can also be a concern in bringing new emergent diseases to humans. Although the taxonomy of mammals seems to be well known, we show that new species are continuously being discovered in the state. Therefore, continuous surveys using traditional and new technologies (eDNA, iDNA, drones), long-term population monitoring, investigation of the interface of human-wildlife conflict, and understanding of the unique ecosystem role played by mammals are future avenues for promoting sustainable green landscapes allied to human well-being in the state. The planting of forest or savanna corridors, particularly along with major river systems, in the plateau, controlling illegal hunting in the coastal areas, managing fire regimes in the Cerrado, and mitigating roadkill must be prioritized to protect this outstanding mammal diversity.

Resumo Os mamíferos são organismos carismáticos que desempenham um papel fundamental na função ecológica e nos serviços ecossistêmicos, como polinização, dispersão de sementes, ciclagem de nutrientes e controle de pragas. O Estado de São Paulo representa apenas 3% do território brasileiro, mas detém 33% da diversidade de mamíferos. A maior parte de seu território é dominado pela agricultura, pastagens e áreas urbanas que afetam diretamente a diversidade e a persistência dos mamíferos na paisagem. Além disso, São Paulo possui o maior porto da América Latina e o maior reservatório de petróleo costeiro do Brasil, com 600 km de extensão de litoral com diversas espécies de mamíferos marinhos. Essas infraestruturas afetam a diversidade, distribuição, ecologia e o futuro dos mamíferos no estado. Aqui, respondemos cinco perguntas principais: 1) Qual é a diversidade de mamíferos silvestres no Estado de São Paulo? 2) Onde eles ocorrem? 3) Qual é o seu impacto positivo e negativo no bem-estar humano? 4) Como os mamíferos persistem em paisagens modificadas pelo homem? 5) Qual é o futuro dos mamíferos no estado? O estado de São Paulo possui 255 espécies de mamíferos nativos, com quatro espécies endêmicas, duas delas globalmente ameaçadas de extinção. Pelo menos seis espécies (dois marsupiais, ariranha, veado-campeiro, veado-cambuta e tatu-canastra) foram extirpadas do estado devido à caça e perda de habitat. O intenso uso humano da terra no estado forçou muitas espécies de mamíferos a mudar sua dieta para lidar com a intensa fragmentação e agricultura. A monocultura em larga escala facilitou a invasão de espécies exóticas, como porcos selvagens (javaporco) e a lebre europeia. Várias espécies de áreas abertas estão expandindo suas áreas de distribuição (lobo-guará, veado-catingueiro) sobre áreas desmatadas e provavelmente refletem mudanças em direção a um clima mais seco. Como o estado possui o maior sistema rodoviário do Brasil, cerca de 40 mil mamíferos de 33 espécies são mortos por ano em colisões, causando um prejuízo econômico de 12 milhões de dólares/ano. A diversidade de mamíferos está concentrada nos maiores remanescentes florestais da Serra do Mar e no interior do Estado, principalmente nas regiões de Ribeirão Preto e Jundiaí. As lacunas amostrais estão concentradas em todo o interior do estado, principalmente na região noroeste. Os mamíferos silvestres desempenham um papel fundamental em muitos serviços ecossistêmicos, mas também podem ser uma preocupação em trazer novas doenças emergentes para as populações humanas. Embora a taxonomia de mamíferos pareça ser bem conhecida, mostramos que novas espécies estão sendo continuamente descobertas no estado. Portanto, pesquisas usando tecnologias tradicionais e novas (eDNA, iDNA, drones), monitoramento populacional de longo prazo, a investigação da interface do conflito homem-vida selvagem e a compreensão do papel único no ecossistema desempenhado pelos mamíferos são um caminho futuro para promover uma paisagem verde sustentável aliada ao bem-estar humano no estado. O plantio de corredores florestais ou de cerrado, principalmente junto aos principais sistemas fluviais, no planalto, o controle da caça ilegal nas áreas costeiras, o manejo dos regimes de fogo no Cerrado e a mitigação dos atropelamentos devem ser uma prioridade para proteger essa notável diversidade de mamíferos.