Yuri Luiz Reis Leite

Universidade Federal do Espírito Santo | UFES · Departamento de Ciências Biológicas

Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as...

South America's complex geological and environmental dynamics contributed to the origin of Neotropical biodiversity and shaped the pattern of species distribution on the continent. Massartella Lestage (Ephemeroptera, Leptophlebiidae, Atalophlebiinae) is a genus currently composed of five species endemic to South America, with a disjunct distributio...

Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroeco...

Brazil is South America's largest country and economy, represented mainly by agricultural commodities. Its vast rainforest and biodiversity are at constant risk from human actions that are seen by scientists contributing to climate change. This article dissects how Brazil influences and is directly and indirectly affected by climate change and poss...

The Neotropics have high levels of species diversity across multiple taxonomic groups. Despite this, studies about the diversity of certain taxonomic groups are scarce. Among these taxa, the genus Nectomys Peters, 1861 (Cricetidae: Sigmodontinae), a widespread group of semi-aquatic rats that occupies forested phyto-physiognomies along rivers and st...

The limited temporal completeness and taxonomic accuracy of species lists, made available in a traditional manner in scientific publications, has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent up-to-date knowledge of all species and classification. In this context, the B Brazilian meg...

Delimiting species and quantifying their underlying variation is imperative for documenting diversity in highly speciose regions like the Neotropics. To aid with proper delimitation and avoid the perils of inflating or underestimating taxonomic units, approaches combining environmental, genetic, and phenotypic data are essential to provide a holist...

Current climate change represents the unprecedented change in weather patterns across global and regional scales over a short period due to human activity. It is expected to drive changes in species distributions across the globe. Our goal here was to analyse (i) how climate change can impact the future distribution of species in two Neotropical ho...

The great loss of biodiversity and population declines include mammals as one of the most vulnerable groups worldwide. It is therefore important to monitor species populations, and several methodologies have been designed and improved to obtain information indirectly, with non-invasive or minimally invasive approaches. Our objective was to evaluate...

Biological collections are the basis of the Earth’s biodiversity knowledge and most of them are regional collections. Here we present two collections from the Federal University of Espírito Santo—Mammal Collection (UFES-MAM) and the associated Animal Tissue Collection (UFES-CTA)—which have been the main repository for mammal specimens collected in...

The Atlantic Forest, a hotspot for biodiversity conservation, harbours five forest deer species (Mazama spp.). Due to their elusiveness, there is a severe scarcity of occurrence data to support ecological studies and conservation planning. Thus, we assembled an occurrence dataset of Atlantic Forest deer with reliable taxonomic information aggregati...

Atalophlebiinae (Ephemeroptera, Leptophlebiidae) is a mayfly subfamily present in temperate and mountainous areas of South America and Australia. We tested the hypothesis that both vicariance and dispersal related to the second phase of Gondwana breakup—which began in the Early Cretaceous and resulted in the separation between Madagascar and India...

RESUMO Definir qualidade no ensino superior não é algo trivial, já que o próprio conceito de qualidade pode ter diferentes significados em diferentes contextos. A despeito das falhas conceituais e metodológicas que envolvem os rankings universitários, eles são uma realidade que veio para ficar. Eles necessitam de dados sobre as mais diversas dimens...

Pterygodermatites are parasitic nematodes found in mammals worldwide, except Australia. There are 38 described species, which are found parasitizing bats, rodents, marsupials, carnivores and primates. We present taxonomic notes on nematodes collected from the digestive tract of bats from the Atlantic Forest in southeast Brazil. Two species previous...

The Atlantic Forest biodiversity hotspot in eastern South America has been the focus of several phylogeographic studies concerning relationships between populations and areas and how taxa respond to environmental changes. We infer and compare the demographic and biogeographic histories of two didelphid marsupial species, Gracilinanus microtarsus an...

Mammals from the Pontões Capixabas Natural Monument: species inventory and new occurrences for Espírito Santo, southeastern Brazil. Pontões Capixabas National Monument is a region in northeastern Espírito Santo, dominated by large granitic inselbergs separated by valleys covered by Atlantic Forest remnants. It is one of the poorest known regions in...

O Brasil possui uma das maiores riquezas de mamíferos do mundo, com mais de 700 espécies reconhecidas, pertencentes a 12 ordens. O processo de avaliação do estado de conservação dos mamíferos brasileiros contou com a participação de quatro Centros de Pesquisa e Conservação do Instituto Chico Mendes: Centro Nacional de Pesquisa e Conservação de Mamí...

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 D...

Cyt b sequences used in this article

Amplification profiles, locality data, GenBank accession numbers, microsatellite data, genetic distances, divergence dates, heterozygote rates for microsatellite data, FST/ RST values, and validation indices

List of genetic samples of Nectomys

Phylogenies for Cyt b, D-loop, and concatenated data; main SDM variables; historical connections

D-loop sequences used in this article

Arboreal spiny rats of the genus Phyllomys are the most diverse group of echimyid rodents in the Atlantic Forest. Many species of Phyllomys have small geographic ranges and are rare in scientific collections. One of them is Phyllomys kerri known from only three specimens collected in a single locality almost 80 year s ago. The identity and the taxo...

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 lon- gitude in the Atlantic forest of South America. We present trait information from 16,840 individ- uals of...

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,...

Oecomys tapajinus (Tapajós Oecomys) is currently a junior synonym of Oecomys roberti (Robert's Oecomys), a widely distributed Amazonian mouse, which probably represents a complex of cryptic species. We investigated the taxonomic status of O. tapajinus by integrating phylogenetic analyses of DNA sequences and morphological analyses of museum specime...

The Atlantic Forest faces a critical fragmentation process, and is now reduced to just 12.5% of its historical coverage. The state of Espírito Santo is completely inserted within the Atlantic Forest and has a high mammal richness, despite the severe habitat reduction and fragmentation. The Mestre Álvaro Environmental Protection Area is located in t...

The aim of this study was to reevaluate the ecology of an area in the Atlantic Forest, southeast Brazil, where Chagas disease (CD) has been found to occur. In a previous study, immediately after the occurrence of a CD case, we did not observe any sylvatic small mammals or dogs with Trypanosoma cruzi cruzi infections, but Triatoma vitticeps presente...

SSU rRNA and gGAPDH GenBank reference sequences used in the phylogenetic analyses of Trypanosoma spp. (DOCX)

Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae)...

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...

This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).

The family Sciuridae is one of the most widespread and ecologically diverse lineage of rodents and represents an ideal model for investigating the evolution of locomotion modes and the historical biogeography of terrestrial mammals. We used a comprehensive database on locomotion modes, an updated phylogeny and novel biogeographic comparative method...

Against all odds, rodents won the sweepstakes and crossed the Atlantic Ocean from Africa to enter South America for the first time in the Eocene, ca. 40 million years ago. These gnawing pilgrims gave rise to one of the most spectacular monophyletic groups of mammals: the caviomorphs. This name is an allusion to one of its prominent members, the gui...

One or two diversification models alone cannot explain biodiversity evolution in the Atlantic Forest, or any other megadiverse biome, as we (1, 2) pointed out long before Raposo do Amaral et al. (3). In our recent paper (4), we present the Atlantis Forest hypothesis (AFH), which is an additional perspective to the Atlantic Forest evolution, beyond...

Significance The tropical forests of South America are among the most diverse and unique habitats in the world in terms of plant and animal species. One of the most popular explanations for this diversity and endemism is the idea that forests retracted and fragmented during glacial periods, forming ecological refuges, surrounded by dry lands or sav...

Abstract Research on the biology of Neotropical small mammals has increased in recent decades, and many studies have emphasized ecological and population attributes, but information on reproduction is still scarce. Reproduction is one of the most important natural history attributes because it is related to almost every structural, physiological an...

We present herein the first record of Euryzygomatomys spinosus (G. Fischer, 1814) in the Brazilian Cerrado, based on two adult male specimens collected in a " campo limpo " (dry grassland) area at Sempre Vivas National Park, state of Minas Gerais, southeastern Brazil, in June and August 2014. This taxon was previously known only from the Brazilian...

Owl pellets are a useful tool for inventorying small mammals and a robust complement to traditional trapping methods. Here we assessed if bone samples recovered from Barn owl pellets in the Neotropics represent a viable source of modern DNA. We used the upper incisor of rodents and jaws of marsupials of pellet material for DNA extraction and amplif...

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...

AimTo investigate the biogeographical history of the Pantepui region based on the phylogenetic relationships and divergence dates of a tepui-endemic small mammal: the Roraima mouse, Podoxymys roraimae. This mouse is one of the rarest and most restricted mammals in terms of geographical distribution, and its evolutionary position has never been eval...

Although codistributed species are affected by the same abiotic factors, such as rivers and seasonal flooding regimes, ecological traits, such as locomotion habits and habitat preferences, may also influence differences in levels of genetic diversity and differentiation. We examined population genetic structure and diversity of Hylaeamys megacephal...

Callistomys pictus is an arboreal echimyid rodent, and the only living species in this genus. It is endemic to a very small Atlantic Forest region in the state of Bahia, east Brazil. Here we used DNA sequences from 4 genes to infer the phylogenetic position of Callistomys within Echimyidae. The results show that Callistomys forms a clade with the s...

Phyllomys (Echimyidae, Rodentia) is a genus of Neotropical rodents with available cytogenetic data restricted to six out of 13 species, mainly based on simple staining methods, without detailed analyses. In this work, we present new karyotypes for Phyllomys lamarum (diploid number 2n = 56, fundamental number or number of autosomal arms FN = 102) an...

Background: The phylogenetic position of the sigmodontine genus Abrawayaomys, historically assigned to the tribe Thomasomyini or considered a sigmodontine incertae sedis, was assessed on the basis of nuclear and mitochondrial DNA sequences obtained from four individuals from different localities in the Atlantic forest of Brazil. Sequences of Abrawa...

Oryzomyini is the richest tribe among the Sigmodontine rodents, encompassing 32 living and extinct genera and including an increasing number of recently described species and genera. Some Oryzomyini are tetralophodont showing a reduction in the number of molar folds to four, while most taxa in this tribe retain the plesiomorphic pentalophodont stat...

We report the discovery of a new species of Coendou (Rodentia, Erethizontidae), here designated Coendou speratus sp. nov. This small porcupine, locally known as coandu-mirim, is found in the Pernambuco Endemism Centre in the Atlantic coast of northeastern Brazil north of the São Francisco river, one of the most important known biodiversity hotspots...

We report the discovery of a new species of Coendou (Rodentia, Erethizontidae), here designated Coendou speratus sp. nov. This small porcupine, locally known as coandu-mirim, is found in the Pernambuco Endemism Centre in the Atlantic coast of northeastern Brazil north of the São Francisco river, one of the most important known biodiversity hotspots...

The arboreal mouse Oecomys cleberi was described in 1981 based on just one specimen from Distrito Federal in central Brazil, and it has not been recorded ever since. Its taxonomic status as a valid species has been questioned and it is currently listed as Data Deficient in terms of conservation status. Here we used ancient DNA methods to obtain a p...

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses base...

We evaluated geographic variation in New World porcupines of Coendou (Erethizontidae) from eastern Brazil by analyzing morphological data from museum specimens we identified as Coendou insidiosus and C. spinosus. Coendou insidiosus ranges from the states of Bahia to Espirito Santo, reaching the state of Minas Gerais in Brazil; C. spinosus extends f...