Systematics and biogeography of the Atlantic Forest endemic genus Juliomys (Rodentia: Cricetidae): a test of diversification hypothesis using mitochondrial data

The Atlantic Forest harbors a large species richness and high levels of endemism, but the processes that shaped its biodiversity are poorly studied, especially for mammals. Among them are the endemic mice Juliomys, which comprise forest dwellers distributed in southeastern and southern Brazil, northeastern Argentina, and eastern Paraguay. In this study, we investigate the phylogenetic relationships among species and perform phylogeographic analyses to evaluate the population structure and demographic scenarios through mitochondrial gene cytochrome b sequences. We investigate three hypotheses of diversification (forest refuges, montane isolate, and geomorphological events) to understand the evolution of the Juliomys species. Phylogenetic analyses recovered five clades/lineages, four of which are congruent with species currently recognized. The fifth lineage expands the range of the genus 659 km to the north and may represent a new species. The observed demographic and geographic structure of genetic diversity does not match the forest refuge hypothesis as mechanism to explain the diversification in Juliomys. Our results recovered J. rimofrons and J. ximenezi as sister species, supporting predictions of montane isolate hypothesis. We also detected a shallow genetic structure in J. pictipes and J. ossitenuis. Both phylogeographic breaks were congruent with limits of the São Paulo Basin, an area that has undergone Neogene reactivations of tectonic faults. It is suggested that geomorphological events led to a deformed landscape that influenced the dynamics of sedimentary basins and promoted an incipient population structure in J. pictipes and J. ossitenuis. Our findings demonstrate that the divergences whithin Juliomys species occurred during the Quaternary, too recently to have produced strong geographic structure.

Systematics and biogeography of the atlantic forest endemic genus Juliomys (Rodentia: Cricetidae): A test of diversification hypothesis using mitochondrial data

The Atlantic Forest harbors a large species richness and high levels of endemism, but the processes that shaped its biodiversity are poorly studied, especially for mammals. Among them are the endemic mice Juliomys, which comprise forest dwellers distributed in southeastern and southern Brazil, northeastern Argentina, and eastern Paraguay. In this study, we investigate the phylogenetic relationships among species and perform phylogeographic analyses to evaluate the population structure and demographic scenarios through mitochondrial gene cytochrome b sequences. We investigate three hypotheses of diversification (forest refuges, montane isolate, and geomorphological events) to understand the evolution of the Juliomys species. Phylogenetic analyses recovered five clades/lineages, four of which are congruent with species currently recognized. The fifth lineage expands the range of the genus 659 km to the north and may represent a new species. The observed demographic and geographic structure of genetic diversity does not match the forest refuge hypothesis as mechanism to explain the diversification in Juliomys. Our results recovered J. rimofrons and J. ximenezi as sister species, supporting predictions of montane isolate hypothesis. We also detected a shallow genetic structure in J. pictipes and J. ossitenuis. Both phylogeographic breaks were congruent with limits of the São Paulo Basin, an area that has undergone Neogene reactivations of tectonic faults. It is suggested that geomorphological events led to a deformed landscape that influenced the dynamics of sedimentary basins and promoted an incipient population structure in J. pictipes and J. ossitenuis. Our findings demonstrate that the divergences whithin Juliomys species occurred during the Quaternary, too recently to have produced strong geographic structure.

Karyotypical Confirmation of Natural Hybridization between Two Manatee Species, Trichechus manatus and Trichechus inunguis.

Two species of manatees are found in Northern Brazil-the Antillean manatee (Trichechus manatus), which is found along the coast from Florida to Northeastern Brazil, and the Amazonian manatee (Trichechus inunguis), endemic to the Amazon drainage basin. These species show a sympatric distribution in the region of the Marajó Archipelago, an estuarine area surrounding the Amazon River mouth. There is evidence of the occurrence of interspecific hybrids in this area, based on mitochondrial DNA analyses, although the use of nuclear markers has not corroborated this proposal. Considering that these species show very distinct karyotypes, despite being closely related (2n = 48 in T. manatus and 2n = 56 in T. inunguis), hybrids would present distinct chromosome numbers. Based on this, we conducted cytogenetic analyses using classic and molecular techniques in three calves found stranded in the Marajó Island and Amapá coast. The results showed that one of them, morphologically classified as T. inunguis, presented the correspondent karyotype, with 2n = 56. However, the other two, which were phenotypically similar to T. manatus, showed 2n = 49. Despite the same diploid number, their G-banding patterns revealed some differences. The results of the distribution of some microsatellite sequences have also confirmed the heterozygosity of some chromosomal pairs in these two individuals. These results are the first indubitable confirmation of the occurrence of natural hybrids between T. manatus and T. inunguis, and also brings about some issues concerning the viability of hybrids, considering that these two individuals do not correspond to an F1 hybrid, but instead, both presented a possible F2 karyotype.

SINE-B1 Distribution and Chromosome Rearrangements in the South American Proechimys gr. goeldii (Echimyidae, Rodentia).

Proechimys species are remarkable for their extensive chromosome rearrangements, representing a good model to understand genome evolution. Herein, we cytogenetically analyzed 3 different cytotypes of Proechimys gr. goeldii to assess their evolutionary relationship. We also mapped the transposable element SINE-B1 on the chromosomes of P. gr. goeldii in order to investigate its distribution among individuals and evaluate its possible contribution to karyotype remodeling in this species. SINE-B1 showed a dispersed distribution along chromosome arms and was also detected at the pericentromeric regions of some chromosomes, including pair 1 and the sex chromosomes, which are involved in chromosome rearrangements. In addition, we describe a new cytotype for P. gr. goeldii, reinforcing the significant role of gross chromosomal rearrangements during the evolution of the genus. The results of FISH with SINE-B1 suggest that this issue should be more deeply investigated for a better understanding of its role in the mechanisms involved in the wide variety of Proechimys karyotypes.

Checklist of mammals from Goiás, central Brazil / Lista de Mamíferos de Goiás, Brasil central

Abstract: The state of Goiás, in central Brazil, is covered mainly by the Cerrado domain, with the Alto Paraná Atlantic Forest occupying its central-southern portion. Goiás is one of the 20 Brazilian federative units without a mammal checklist. In this study, we provide the first checklist of mammals from Goiás state. We recorded mammal species based primarily on the analysis of specimens housed in scientific collections as well as on literature with associated voucher material. We listed 191 mammalian species belonging to 125 genera, 31 families and 10 orders, which represents 25.2% of the mammal species occurring in Brazil. The most speciose orders were Chiroptera (90 spp.), followed by Rodentia (43 spp.), Carnivora (19 spp.) and Didelphimorphia (17 spp.). The following orders accounted for a smaller portion of the state diversity: Cetartiodactyla (7 spp.), Cingulata (7 spp.), Primates (4 spp.), Pilosa (2 spp.), Lagomorpha (1 sp.), and Perissodactyla (1 sp.). A total of 28 species (14.7%), mainly represented by medium and large-sized mammals, are nationally threatened while 12 (6.3%) are globally threatened. Our results indicate great portions of the state lacking a proper survey of mammals, especially the northwestern portion. We discuss species richness, distribution and conservation status of the mammals of Goiás state in national and regional scenarios. We highlight the need for mammal inventories based on complementary survey techniques with the collection of vouchers in order to provide karyologic, molecular, morphologic, parasitologic, and ecological data. These informations are the basis for integrative studies that lead to the understanding of current mammalian richness and diversity. Indeed, knowledge on species richness distribution in the state will guide conservation strategies, especially in areas undergoing habitat loss and fragmentation, such as the central-southern portion of Goiás.

Resumo: O estado de Goiás, no Brasil central, é coberto principalmente pelo domínio do Cerrado, com a Mata Atlântica do Alto Paraná ocupando sua porção centro-sul. Goiás é uma das 20 unidades federativas brasileiras que ainda não possui uma lista de espécies de mamíferos. Neste estudo, apresentamos a primeira lista de mamíferos para o estado. Registramos as espécies de mamíferos com base principalmente na análise de espécimes depositados em coleções científicas, bem como na literatura apresentando material testemunho associado. Listamos 191 espécies pertencentes a 125 gêneros, 31 famílias e 10 ordens, as quais representam 25,2% das espécies de mamíferos que ocorrem no Brasil. As ordens mais especiosas foram Chiroptera (90 spp.), seguida pelas ordens Rodentia (43 spp.), Carnivora (19 spp.) e Didelphimorphia (17 spp.), com as demais ordens respondendo por uma porção menor da diversidade: Cetartiodactyla (7 spp.), Cingulata (7 spp.), Primates (4 spp.), Pilosa (2 spp.), Lagomorpha (1 sp.) e Perissodactyla (1 sp.). Um total de 28 espécies (14,7%), principalmente representadas por mamíferos de médio e grande porte, estão ameaçadas nacionalmente e 12 (6,3%) encontram-se globalmente ameaçadas. Nossos resultados indicaram grandes porções do estado ainda não devidamente pesquisadas em relação aos seus mamíferos, com informações escassas e fragmentadas, principalmente no que diz respeito à sua porção noroeste. Discutimos a riqueza de espécies, a distribuição e o estado de conservação dos mamíferos do estado de Goiás nos cenários nacional e regional. Ressaltamos a importância da realização de inventários que utilizem técnicas complementares de amostragem, incluindo a coleta de material testemunho, proporcionando a obtenção de dados cariotípicos, moleculares, morfológicos, parasitológicos e ecológicos. Estas informações são a base de estudos integrativos, os quais aumentam nossa compreensão a respeito da riqueza e diversidade atual dos mamíferos. O conhecimento a respeito da distribuição da riqueza de espécies em Goiás é essencial para embasar estratégias de conservação, tão necessárias em áreas que vem sofrendo com a perda e fragmentação de seus hábitats naturais, como a porção centro-sul do estado.

Morphological variation in the genus Juliomys (Rodentia: Cricetidae: Sigmodontinae) and taxonomic status of Juliomys anoblepas (Winge 1887) from the Quaternary of Southeast Brazil.

The region of Lagoa Santa, Minas Gerais, Brazil, is one of the most important karstic areas of the Brazilian Quaternary due to the faunistic diversity of living and extinct forms. Among them, some taxa remain poorly studied, as is the case of Calomys anoblepas Winge 1887. Despite the recent allocation of the taxon within Juliomys, its description and morphological analysis are condensed, based on comparative few specimens and on few informative characters. In this study, we investigate characters proposed to distinguish species of Juliomys, and reevaluate the taxonomic status of the fossil Juliomys anoblepas. We analyzed 80 cranio-dental morphological characters in 233 specimens represented by the four species currently recognized: J. pictipes (Osgood 1933), J. rimofrons Oliveira Bonvicino 2002, J. ossitenuis Costa, Pavan, Leite Fagundes 2007, and J. ximenezi Christoff, Vieira, Oliveira, Gonçalves, Valiati Tomasi 2016. We also performed principal component analysis on eight craniodental measurements available for the J. anoblepas hypodigm. The review of morphological systems and the evaluation of the characters used in the literature revealed that there are no diagnostic characters in the anterior portion of the skull and in the molar series of Juliomys, being difficult to differentiate the fossil from the other living species. Only six qualitative characters were variable and applicable to the hypodigm of J. anoblepas. Characters are polymorphic, invariable, or the fossil is not sufficiently complete to determinate its states. The taxon could not be morphometrically differentiated from J. pictipes and J. ossitenuis. Based on the results presented herein, we consider J. anoblepas as a nomen dubium and restrict its name to the taxon's hypodigm.

DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts).

DNA barcoding has become a standard method for species identification in taxonomically complex groups. An important step of the barcoding process is the construction of a library of voucher-based material that was properly identified by independent methods, free of inaccurate identification, and paralogs. We provide here a cytochrome oxidase I (mt-Co1) DNA barcode database for species of the genus Oligoryzomys, based on type material and karyotyped specimens, and anchored on the mitochondrial genome of one species of Oligoryzomys, O. stramineus. To evaluate the taxonomic determination of new COI sequences, we assessed species intra/interspecific genetic distances (barcode gap), performed the General Mixed Yule Coalescent method (GMYC) for lineages' delimitation, and identified diagnostic nucleotides for each species of Oligoryzomys. Phylogenetic analyses of Oligoryzomys were performed on 2 datasets including 14 of the 23 recognized species of this genus: a mt-Co1 only matrix, and a concatenated matrix including mt-Co1, cytochrome b (mt-Cytb), and intron 7 of the nuclear fibrinogen beta chain gene (i7Fgb). We recovered nuclear-mitochondrial translocated (Numts) pseudogenes on our samples and identified several published sequences that are cases of Numts. We analyzed the rate of non-synonymous and synonymous substitution, which were higher in Numts in comparison to mtDNA sequences. GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys.

Does the widely distributed rodent Calomys tener (Cricetidae: Sigmodontinae) constitute a single evolutionary unit?

The nominal species Calomys tener (Winge, 1887) ranges broadly in open lands of the Caatinga, Cerrado, Pantanal and Mata Atlântica of Brazil, and was recently reported from the Pampas of southern Brazil, and in the Selva Paranaense of eastern Paraguay and northeastern Argentina. This rodent can be infected with the pathogenic Araraquara hantavirus in Brazil. Given that most epidemiological studies have not taken into account updated taxonomic findings of their rodent hosts, in this study, we obtained sequence data of the Cyt-b and COI genes of specimens of C. tener from 22 different geographical localities from throughout the currently known distribution of the species (including individuals from Argentina, Paraguay, Bolivia, and Brazil) to test if it constitutes a single genetic unit or if it presents genetic discontinuities that may represent different evolutionary lineages. Phylogenetic analyses including several species of Calomys recovered several clades with strong support. Regarding C. tener, it is recovered as sister to the node that cluster C. laucha (Fischer, 1814) sensu lato, C. expulsus (Lund, 1841) and species in the C. callosus (Rengger, 1830) species complex. At the intraspecific level there are no genetic gaps among haplotypes of C. tener that could suggest more than one species. The recent captures in the Pampas of southern Brazil and in the Selva Paranaense suggest that the species may be colonizing new geographic areas.(AU)

Does the widely distributed rodent Calomys tener (Cricetidae: Sigmodontinae) constitute a single evolutionary unit?

The nominal species Calomys tener (Winge, 1887) ranges broadly in open lands of the Caatinga, Cerrado, Pantanal and Mata Atlântica of Brazil, and was recently reported from the Pampas of southern Brazil, and in the Selva Paranaense of eastern Paraguay and northeastern Argentina. This rodent can be infected with the pathogenic Araraquara hantavirus in Brazil. Given that most epidemiological studies have not taken into account updated taxonomic findings of their rodent hosts, in this study, we obtained sequence data of the Cyt-b and COI genes of specimens of C. tener from 22 different geographical localities from throughout the currently known distribution of the species (including individuals from Argentina, Paraguay, Bolivia, and Brazil) to test if it constitutes a single genetic unit or if it presents genetic discontinuities that may represent different evolutionary lineages. Phylogenetic analyses including several species of Calomys recovered several clades with strong support. Regarding C. tener, it is recovered as sister to the node that cluster C. laucha (Fischer, 1814) sensu lato, C. expulsus (Lund, 1841) and species in the C. callosus (Rengger, 1830) species complex. At the intraspecific level there are no genetic gaps among haplotypes of C. tener that could suggest more than one species. The recent captures in the Pampas of southern Brazil and in the Selva Paranaense suggest that the species may be colonizing new geographic areas.

Integrative taxonomy of the Amazonian red-sided opossum Monodelphis glirina (J.A. Wagner, 1842) (Didelphimorphia: Didelphidae).

New records for Monodelphis glirina, a short-tailed opossum distributed throughout the Amazon region, from Humaitá, Amazonas state, and Confresa, Mato Grosso state, prompted new insights into the geographic distribution and genetic diversity of this species. One of the records extends the species range circa 350 km beyond the previous southeastern limit. Voucher specimens had their identification confirmed by morphological comparison with the holotype and corroborated by molecular data (mitochondrial gene Cytochrome b). Our analyses revealed an east-west geographic structure into two clades that could represent distinct species, M. glirina and M. maraxina. Furthermore, examination of the holotype brought to light that it was never formally linked with the voucher specimen collected by Johann Natterer.

Morphological and genetic diversity in Callithrix hybrids in an anthropogenic area in southeastern Brazil (Primates: Cebidae: Callitrichinae)

Two species of Callithrix, C. jacchus (Linnaeus, 1758) and C. penicillata (É. Geoffroy, 1812), are considered invasive in Rio de Janeiro. This study determined the genetic and morphological diversity and verified the species involved in the hybridization of 10 individuals from the municipalities of Silva Jardim (N = 9) and Rio das Ostras (N = 1). We compared the external morphology and skull of C. jacchus (N = 15) and C. penicillata (N = 14) specimens deposited in the collection of the National Museum of Rio de Janeiro (MN- UFRJ). Phylogenetic (maximum likelihood and Bayesian inference) and phylogeographical analyses (network analysis) were performed based on cytochrome b sequences. These analyses included hybrids from the metropolitan region of Rio de Janeiro (N = 3), C. penicillata (N = 2), C. jacchus (N = 2), C. geoffroyi (N = 2), C. kuhlii (N = 2), C. aurita (N = 1), and as outgroups, Mico emiliae (N = 1) and Saguinus mystax (N = 1). The pelage and skull characters of most hybrids were more closely related to C. jacchus. Skull morphometric analysis revealed an intermediate state for the hybrids. Phylogenetic analyses revealed a high similarity between the hybrids and C. penicillata. Six haplotypes of hybrids were identified. Network analysis including them and C. penicillata recovered the topology generated by phylogenetic analysis. The results corroborate that C. jacchus and C. penicillata participate in the hybridization process. There was no geographic structure between hybrids from the coastal lowlands and from the metropolitan region of Rio de Janeiro.

Morphological and genetic diversity in Callithrix hybrids in an anthropogenic area in southeastern Brazil (Primates: Cebidae: Callitrichinae)

Two species of Callithrix, C. jacchus (Linnaeus, 1758) and C. penicillata (É. Geoffroy, 1812), are considered invasive in Rio de Janeiro. This study determined the genetic and morphological diversity and verified the species involved in the hybridization of 10 individuals from the municipalities of Silva Jardim (N = 9) and Rio das Ostras (N = 1). We compared the external morphology and skull of C. jacchus (N = 15) and C. penicillata (N = 14) specimens deposited in the collection of the National Museum of Rio de Janeiro (MN- UFRJ). Phylogenetic (maximum likelihood and Bayesian inference) and phylogeographical analyses (network analysis) were performed based on cytochrome b sequences. These analyses included hybrids from the metropolitan region of Rio de Janeiro (N = 3), C. penicillata (N = 2), C. jacchus (N = 2), C. geoffroyi (N = 2), C. kuhlii (N = 2), C. aurita (N = 1), and as outgroups, Mico emiliae (N = 1) and Saguinus mystax (N = 1). The pelage and skull characters of most hybrids were more closely related to C. jacchus. Skull morphometric analysis revealed an intermediate state for the hybrids. Phylogenetic analyses revealed a high similarity between the hybrids and C. penicillata. Six haplotypes of hybrids were identified. Network analysis including them and C. penicillata recovered the topology generated by phylogenetic analysis. The results corroborate that C. jacchus and C. penicillata participate in the hybridization process. There was no geographic structure between hybrids from the coastal lowlands and from the metropolitan region of Rio de Janeiro.(AU)

New record of the rare Atlantic Forest rodent Phyllomys lundi (Mammalia: Rodentia)

The arboreal echimyid rodent of the genus Phyllomys Lund, 1839 is found in the eastern Brazilian Atlantic forest, from the state of Ceará to the state of Rio Grande do Sul, reaching the São Francisco and Paraná river basins in the west. There are 13 species in the genus. Phyllomys lundi Leite, 2003, which until now was known from only two localities, is one of the four endemic Atlantic Forest species of Phyllomys with very restricted distribution. We provide additional data on the morphology, distribution and phylogeography (based on cytochrome b sequences) of the rare P. lundi . Our new record broadens the northern limit of the distribution P. lundi by approximately 250 km with respect to previous records.

New record of the rare Atlantic Forest rodent Phyllomys lundi (Mammalia: Rodentia)

The arboreal echimyid rodent of the genus Phyllomys Lund, 1839 is found in the eastern Brazilian Atlantic forest, from the state of Ceará to the state of Rio Grande do Sul, reaching the São Francisco and Paraná river basins in the west. There are 13 species in the genus. Phyllomys lundi Leite, 2003, which until now was known from only two localities, is one of the four endemic Atlantic Forest species of Phyllomys with very restricted distribution. We provide additional data on the morphology, distribution and phylogeography (based on cytochrome b sequences) of the rare P. lundi . Our new record broadens the northern limit of the distribution P. lundi by approximately 250 km with respect to previous records.(AU)

A Taxonomic Update of Small Mammal Plague Reservoirs in South America.

Plague is a disease of epidemic potential that may emerge with discontinuous outbreaks. In South America, 50 wild rodent species have been identified as plague reservoirs, in addition to one lagomorph and two marsupials. To review the nomenclature of plague reservoirs, we examined specimens collected in plague foci, carried out new surveys in Brazilian plague regions, and re-evaluated the nomenclature of South American reservoirs on the basis of the current literature. Five of the 15 species involved with plague in Argentina, three of 10 species involved with plague in Bolivia, three of the seven species involved with plague in Peru, five of the nine species involved with plague in Ecuador, and six of the nine species involved with plague in Brazil have undergone taxonomic changes. In the last 20 years, plague cases were recorded in Bolivia, Brazil, Ecuador, and Peru. These four countries have a high rodent species richness in plague foci, a fact that may be decisive for the maintenance of plague in the wild.

A new species of Cerradomys (Mammalia: Rodentia: Cricetidae) from Central Brazil, with remarks on the taxonomy of the genus

Cerradomys is a Neotropical genus of cricetid rodents with seven recognized species, Cerradomys subflavus, C. maracajuensis, C. marinhus, C. scotti, C. langguthi, C. vivoi, and C. goytaca. Species of the genus are distributed throughout the open vegetation belt across South America, from northeastern and southeastern Atlantic coast of Brazil to eastern Paraguay and Western Bolivia. Here we describe a new species of Cerradomys from the state of Tocantins in Central Brazil, based on morphological, karyological and mitochondrial DNA analyses. This species is characterized by a medium body size and long tail, dense dorsal pelage, overall dorsal color gray olive lined with yellow, color of head and dorsum continuous, ventral body color slightly yellowish, skull with deep rostral depression, mesopterygoid fossa with long and wide sphenopalatine vacuities, presence of alisphenoid strut and of complex posterolateral palatal pits, and a unique chromosomal formula (2n = 60 and FNa = 74). Phylogenetic analyses based on cytochrome b sequences, including for the first time all known Cerradomys species, indicate that the new species is more closely related to C. scotti. The new species is found in sympatry with C. marinhus, while C. marinhus, C. scotti, and C. subflavus are found in sympatry (but not in syntopy) in one locality in the state of Minas Gerais. Finally, analysis of cytochrome b sequences indicates that C. subflavus and C. goytaca are very closely related genetically and might be conspecific. Alternatively, these results can also be explained by incomplete lineage sorting due to a recent speciation event.

A new species of Cerradomys (Mammalia: Rodentia: Cricetidae) from Central Brazil, with remarks on the taxonomy of the genus

Cerradomys is a Neotropical genus of cricetid rodents with seven recognized species, Cerradomys subflavus, C. maracajuensis, C. marinhus, C. scotti, C. langguthi, C. vivoi, and C. goytaca. Species of the genus are distributed throughout the open vegetation belt across South America, from northeastern and southeastern Atlantic coast of Brazil to eastern Paraguay and Western Bolivia. Here we describe a new species of Cerradomys from the state of Tocantins in Central Brazil, based on morphological, karyological and mitochondrial DNA analyses. This species is characterized by a medium body size and long tail, dense dorsal pelage, overall dorsal color gray olive lined with yellow, color of head and dorsum continuous, ventral body color slightly yellowish, skull with deep rostral depression, mesopterygoid fossa with long and wide sphenopalatine vacuities, presence of alisphenoid strut and of complex posterolateral palatal pits, and a unique chromosomal formula (2n = 60 and FNa = 74). Phylogenetic analyses based on cytochrome b sequences, including for the first time all known Cerradomys species, indicate that the new species is more closely related to C. scotti. The new species is found in sympatry with C. marinhus, while C. marinhus, C. scotti, and C. subflavus are found in sympatry (but not in syntopy) in one locality in the state of Minas Gerais. Finally, analysis of cytochrome b sequences indicates that C. subflavus and C. goytaca are very closely related genetically and might be conspecific. Alternatively, these results can also be explained by incomplete lineage sorting due to a recent speciation event.(AU)

Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict.

Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The evolution of NP has been intensively investigated in the last decade by studies focusing on their phylogeny and timescale. However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene trees within the proposed phylogenies. We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids. The molecular phylogeny of NP has been difficult to solve because of population-level phenomena at the early evolution of the lineage. The association of evolutionary variation with the distribution of gene trees within proposed phylogenies is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time. This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms.

Hepatitis B virus lineages in mammalian hosts: potential for bidirectional cross-species transmission.

The hepatitis B virus (HBV) is a cosmopolitan infectious agent currently affecting over 350 million people worldwide, presently accounting for more than two billion infections. In addition to man, other hepatitis virus strains infect species of several mammalian families of the Primates, Rodentia and Chiroptera orders, in addition to birds. The mounting evidence of HBV infection in African, Asian and neotropical primates draws attention to the potential cross-species, zoonotic transmission of these viruses to man. Moreover, recent evidence also suggests the humans may also function as a source of viral infection to other mammals, particularly to domestic animals like poultry and swine. In this review, we list all evidence of HBV and HBV-like infection of nonhuman mammals and discuss their potential roles as donors or recipients of these viruses to humans and to other closely-related species.