Molecular detection and characterization of Bartonella spp. in small mammals in the Amazonia and Cerrado biomes, midwestern Brazil

Although Bartonella spp. have been worldwide described in rodents and bats, few studies have reported these agents in marsupials. The present work aimed to investigate the occurrence and genetic diversity of Bartonella in small mammals (rodents, marsupials, and bats) and associated ectoparasites in two ecoregions (Amazonia and Cerrado biomes) in midwestern Brazil. For this purpose, DNA samples from 378 specimens of small mammals (128 rodents, 111 marsupials, and 139 bats) and 41 fleas (Siphonaptera) were screened for the Bartonella genus employing a quantitative real-time PCR assay (qPCR) based on the nuoG (nicotinamide adenine dinucleotide dehydrogenase gamma subunit) gene. Then, positive samples in qPCR were submitted to conventional PCR (cPCR) assays targeting the gltA, ftsZ, and rpoB genes. One (0.78 %) rodent, 23 (16.54 %) bats, and 3 (7.31 %) fleas showed positive results in the qPCR for Bartonella sp. After cPCR amplification and sequencing, 13 partial Bartonella DNA sequences of the following genes were obtained only from bats´ blood samples: 9 gltA (citrate synthase), 3 ftsZ (cell division protein), and 1 rpoB (RNA polymerase beta subunit). The maximum likelihood inference based on the gltA gene positioned the obtained sequences in three different clades, closely related to Bartonella genotypes previously detected in other bat species and bat flies sampled in Brazil and other countries from Latin America. Similarly, the ftsZ sequences clustered in two different clades with sequences described in bats from Brazil, other countries from Latin America, and Georgia (eastern Europe). Finally, the Bartonella rpoB from a specimen of Lophostoma silvicolum clustered with a Bartonella sp. sequence obtained from a Noctilio albiventris (KP715475) from French Guiana. The present study provided valuable insights into the diversity of Bartonella genotypes infecting bats from two ecoregions (Amazonia and Cerrado) in midwestern Brazil and emphasized that further studies should be conducted regarding the description and evaluation of different lineages of Bartonella in wild small mammals and their ectoparasites in different Brazilian biomes.

Genetic diversity analysis in the Brazilian Amazon reveals a new evolutionary lineage and new karyotype for the genus Mesomys (Rodentia, Echimyidae, Eumysopinae)

Morphological, molecular and chromosomal studies in the genera Lonchothrix and Mesomys have contributed to a better understanding of taxonomic design, phylogenetic relationships and karyotypic patterns. Recent molecular investigations have shown a yet undescribed diversity, suggesting that these taxa are even more diverse than previously assumed. Furthermore, some authors have questioned the limits of geographic distribution in the Amazon region for the species M. hispidus and M. stimulax. In this sense, the current study sought to understand the karyotypic evolution and geographic limits of the genus Mesomys, based on classical (G- and C-banding) and molecular cytogenetic analysis (FISH using rDNA 18S and telomeric probes) and through the sequencing of mitochondrial genes Cytochrome b (Cytb) and Cytochrome Oxidase-Subunit I (CO using phylogeny, species delimitation and time of divergence, from samples of different locations in the Brazilian Amazon. The species M. stimulax and Mesomys sp. presented 2n = 60/FN = 110, while M. hispidus presented 2n = 60/FN = 112, hitherto unpublished. Molecular dating showed that Mesomys diversification occurred during the Plio-Pleistocene period, with M. occultus diverging at around 5.1 Ma, followed by Mesomys sp. (4.1 Ma) and, more recently, the separation between M. hispidus and M. stimulax (3.5 Ma). The ABGD and ASAP species delimiters support the formation of 7 and 8 potential species of the genus Mesomys, respectively. Furthermore, in both analyzes Mesomys sp. was recovered as a valid species. Our multidisciplinary approach involving karyotypic, molecular and biogeographic analysis is the first performed in Mesomys, with the description of a new karyotype for M. hispidus, a new independent lineage for the genus and new distribution data for M. hispidus and M. stimulax.

New data on the recently described Brazilian Cerrado hotspot endemic Cerradomys akroai Bonvicino, Casado et Weksler, 2014 (Rodentia: Cricetidae)

Cerradomys akroai is a recently described rodent species, known from two localities in the Brazilian Cerrado, in southeastern Tocantins state (type locality), and in southwestern Piauí state. Herein we add a third locality recorded from a specimen collected in central Tocantins state, in a “cerrado sensu stricto” habitat. Morphological and molecular analyses confirm the identification. The three localities now known for the species are restricted to northern Cerrado domain, and two are located in sites severely impacted by anthropogenic activities. Current conservation category of Cerradomys akroai is Data Deficient, and additional information on its distribution and biology is required.

Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)

Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.

The emergence of a new sex-system (XX/XY1Y2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae)

X-autosome translocation (XY₁Y₂) has been reported in distinct groups of vertebrates suggesting that the rise of a multiple sex system within a species may act as a reproductive barrier and lead to speciation. The viability of this system has been linked with repetitive sequences located between sex and autosomal portions of the translocation. Herein, we investigate Oecomys auyantepui, using chromosome banding and Fluorescence In Situ Hybridization with telomeric and Hylaeamys megacephalus whole-chromosome probes, and phylogenetic reconstruction using mtDNA and nuDNA sequences. We describe an amended karyotype for O. auyantepui (2n = 64♀65♂/FNa = 84) and report for the first time a multiple sex system (XX/XY₁Y₂) in Oryzomyini rodents. Molecular data recovered O. auyantepui as a monophyletic taxon with high support and cytogenetic data indicate that O. auyantepui may exist in two lineages recognized by distinct sex systems. The Neo-X exhibits repetitive sequences located between sex and autosomal portions, which would act as a boundary between these two segments. The G-banding comparisons of the Neo-X chromosomes of other Sigmodontinae taxa revealed a similar banding pattern, suggesting that the autosomal segment in the Neo-X can be shared among the Sigmodontinae lineages with a XY₁Y₂ sex system.

Species limits and recent diversification of Cerradomys (Sigmodontinae: Oryzomyini) during the Pleistocene

Cerradomys is a genus of the tribe Oryzomyini with eight species currently recognized, and a controversial taxonomy. These species are mainly distributed in the South America dry diagonal, but some species extend into Atlantic Forest, reaching the coastal sandy plains known as Restingas. This study aimed to address species limits and patterns of diversification of Cerradomys species. For this purpose, we performed cytogenetic and molecular analyses (phylogeny, coalescent species delimitation, barcoding, and divergence times estimation) using multiple mitochondrial and nuclear markers on a comprehensive sampling, representing all nominal taxa reported so far. Chromosomal information was a robust marker recognizing eight Cerradomys species. Reciprocal monophyly was recovered for all the species, except for C. subflavus. These results together with coalescent analyses recovered eight species as the most congruent species delimitation scenario for the genus (mean C _tax : 0.72). Divergence time estimates revealed that Cerradomys' diversification occurred about 1.32 million years ago (Mya) during the Pleistocene. Although our results conservatively support the eight Cerradomys species described so far, different lines of evidence suggest that C. langguthi and C. subflavus could potentially be species-complexes. We discussed this scenario in the light of multiple evolutionary processes within and between species and populations, since Cerradomys comprises a species group with recent diversification affected by Pleistocene climatic changes and by the complex biogeographic history of South America dry diagonal. This work supports that the diversity of Cerradomys is underestimated and reiterates that interdisciplinary approaches are mandatory to identify small rodent species properly, and to unhide cryptic species.

Habitat Heterogeneity and Geographic Location as Major Drivers of Cerrado Small Mammal Diversity Across Multiple Spatial Scales

The Cerrado biome is one of the global hotspots of biodiversity, and non-volant small mammals represent a significant portion of Cerrado species richness (45%) and endemism (86%). Nevertheless, we still lack a comprehensive picture of small mammal diversity patterns and drivers throughout the Cerrado. Here we surveyed small mammals across 45 sites to address species richness, abundance, and composition patterns and their drivers within and across sites, habitats, and localities at the world’s most diverse tropical savanna. As hypothesized, we found: (1) rich assemblages (12–21 species) characterized by few abundant and several intermediate-level and rare species; dominated by oryzomyine and akodontine cricetid rodents, and thylamyine and marmosine within marsupials, each tribe showing distinct habitat requirements; (2) strong habitat selectivity, with assemblages composed of forest dwellers, savanna specialists, and grassland inhabitants; and (3) similar species richness (α-diversity) but high species turnover (β-diversity) across sites, habitats, and localities, suggesting that horizontal stratification (within localities) and geographic location (across the Cerrado) are key drivers of small mammal diversity in tropical savannas. Thus, habitat heterogeneity and geographic location can be inferred as the main factors shaping species richness, abundance, and composition across the analyzed multiple spatial scales. Moreover, we found that geographical distance as well as the distance to neighbor biomes better explained species turnover, indicating landscape history and phylogenetic constraints as the major determinants of Cerrado small mammal diversity, as also evidenced for plants and other animal groups. These data highlight the need to preserve the mosaic of habitats across the different regions of the biome to conserve most of the Cerrado biodiversity.

Cryptic Species Diversity and Phylogenetic Relationship in the Rust Genus Chrysomyxa from China

Chrysomyxa rusts are fungal pathogens widely distributed in the Northern hemisphere, causing spruce needle and cone rust diseases, and they are responsible for significant economic losses in China. Taxonomic delimitation and precise species identification are difficult within this genus because some characters often overlap in several species. Adequate species delimitation, enhanced by the use of DNA-based methodologies, will help to establish well-supported species boundaries and enable the identification of cryptic species. Here, we explore the cryptic species diversity in the rust genus Chrysomyxa from China. Species delimitation analyses are conducted using a distance-based method (ABGD) and three tree-based methods (GMYC, bPTP, and mPTP) based on combined LSU and ITS sequences of over 60 specimens. Although there is some incongruence among species delimitation methods, two new species and three putative cryptic species are identified. The key to 20 Chrysomyxa species distributed in China is presented. These results suggest that a significant level of undiscovered cryptic diversity is likely to be found in Chrysomyxa from China. Future studies should consider multiple analytical methods when dealing with multi-locus datasets.

Prevalence and antifungal drug resistance of dermatophytes in the clinical samples from Pakistan

Dermatophytosis is a major health problem all over the world including Pakistan. This is the first report of detection of dermatophytes and their antifungal drug resistance in the Northern and Western parts of Pakistan. A total of 154 samples were collected from different hospitals of Khyber Pakhtunkhwa, and out of them 136 samples were found positive. Tinea corporis (35%) was the most predominant type of infection followed by Tinea capitis (22%). The fungi identified in Tinea corporis infection types were identified as Trichophyton rubrum, Trichophyton mentagrophytes, Epidermophyton floccosum. The fungi identified in Tinea capitis included Trichophyton violaceum, T. mentagrophytes, Microsporum ferrugineum. The gender wise distribution showed both males (52%) and females (48%) were infected with the fungi. More cases belonged to the rural parts of the country. Age wise distribution showed that the infection was more prevalent in the children and the prevalence decreased with the increase in age. The positive samples were checked against two antifungal agents: fluconazole and nystatin. Among 136 positive samples, none of the isolates showed resistance to nystatin while 7% of the samples showed resistance to fluconazole. The resistant isolates were then identified by amplifying the 18S rRNA gene, using universal primers (ITS1, ITS4). Among the 9 resistant isolates, 5 isolates were identified as Trichophyton spp., 3 as Microsporum spp. and 1 as Epidermophyton spp.

Systematics of the rodent genus Neacomys Thomas (Cricetidae: Sigmodontinae): two new species and a discussion on carotid patterns

The taxonomy of the oryzomyine genus Neacomys currently is in a state of flux: systematic studies in the last 20 years increased its diversity from four to 16 species, with an additional several undescribed phylogenetic lineages. Despite this progress, morphological variation and species limits remain poorly known for several species groups and complexes within the genus, such as N. tenuipes, N. musseri, and N. dubosti. Here we analyze the variation of morphological characters and morphometric patterns of two new candidate species of Neacomys for northern Venezuela and Pará state, Brazil, that are characterized by the presence of derived carotid circulation, a rare character state for the genus. Analyzed material included holotypes, type series, and/or topotypes of almost all described species of Neacomys, including type series of N. musseri, the holotype of N. tenuipes, and sequenced specimens of N. xingu. Qualitative comparison showed that 25 characters are informative for the distinction of the two new forms, and morphometric analyses corroborated the morphological separation of the new species. Results also point that N. tenuipes might represent a species complex. The new forms are sympatric with other species, including N. tenuipes and N. xingu, and can be identified by a suite of morphological characters, including the presence of a derived carotid pattern and, for the Pará form, by a unique morphology of the first upper molar. We review the occurrence of carotid circulation patterns within Sigmodontinae and discuss its use for the systematics of the subfamily. Further studies involving the new Neacomys species will contribute to understanding the biogeographic patterns and evolutionary trends within this distinct and diverse genus.

Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes

Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America.

Integrative analysis supports a new species of the Oecomys catherinae complex (Rodentia, Cricetidae) from Amazonia

The sigmodontine rodent Oecomys catherinae has been recognized as a species complex that includes five different lineages distributed throughout Brazil south of the Amazon river, named in literature according to their geographic position (central, eastern, northern, western, and westernmost). The western lineage also has been referred as Oecomys aff. catherinae in the literature, because it may represent a distinct species. Herein, we used molecular and morphological data to investigate the possible species distinctiveness within the O. catherinae complex. From molecular analyses, we recovered the western lineage as a monophyletic group with high genetic divergence from the other lineages of the complex. This lineage can be differentiated from other lineages of the O. catherinae complex and other congeners through a combination of mensural and morphological characters that includes: smaller size; posterior margin of nasals usually surpassing the maxillary–frontal suture; supraorbital crest moderately developed, similar to the temporal crest; parietal slightly expanded laterally; subsquamosal fenestra present; alisphenoid strut absent; and anterior cingulum of M1 present. The western lineage occurs in the southern Amazonia, in sympatry with the westernmost lineage and other species of Oecomys. Herein we describe this lineage as a new species, increasing to 19 the number of species within Oecomys.

A new species of Akodon Meyen, 1833 (Rodentia: Cricetidae: Sigmodontinae) endemic from the Brazilian Cerrado

Akodon is the second most diverse genus of sigmodontine rodents, comprising 40 extant species. Widely distributed through different environments of South America, the genus ranges from forested to open-vegetation areas, from semiarid to mesic regions, and from Andean altitudes to the lowlands of eastern Brazil. In Brazil, most species are from the Atlantic Forest, inhabiting lowland and montane habitats, with a few taxa also present in areas transitional with the Cerrado and Pantanal. Based on an integrative approach of genetics (cytogenetic and molecular data) and morphology (qualitative and quantitative external and craniodental data), we present in this contribution the hypothesis of a new species of Akodon based on specimens collected in the southwestern limit of the Cerrado domain, in the seasonally dry forests of the Serra da Bodoquena, Mato Grosso do Sul, Brazil. The new species was recovered as a distinct lineage sister to Akodon philipmyersi, a poorly known species from the Northern Campos grasslands of Misiones Province, Argentina, and can be distinguished from its congeners by its karyotype (2n = 40, FN = 40), morphology (morphometric, pelage, and skull characters), as well as by its degree of genetic divergence (above 7.5% in Cytb sequences). This new species is endemic to the Cerrado, one of the world’s biodiversity hotspots, and to Serra da Bodoquena, one of the top priority areas for conservation in Brazil. Moreover, the new species increases the number of lineages of Akodon in Brazil, emphasizing the richness and endemism currently found in the Cerrado domain, and the importance of the open formations to the diversification of Neotropical taxa.

Extensive genomic reshuffling involved in the karyotype evolution of genus Cerradomys (Rodentia: Sigmodontinae: Oryzomyini)

Rodents of the genus Cerradomys belong to the tribe Oryzomyini and present high chromosome variability with diploid numbers ranging from 2n=46 to 60. Classical cytogenetics and fluorescence in situ hybridization (FISH) with telomeric and whole chromosome-specific probes of another Oryzomyini, Oligoryzomys moojeni (OMO), were used to assess the karyotype evolution of the genus. Results were integrated into a molecular phylogeny to infer the hypothetical direction of chromosome changes. The telomeric FISH showed signals in telomeres in species that diverged early in the phylogeny, plus interstitial telomeric signals (ITS) in some species from the most derived clades (C. langguthi,C. vivoi, C. goytaca, and C. subflavus). Chromosome painting revealed homology from 23 segments of C. maracajuensis and C. marinhus to 32 of C. vivoi. Extensive chromosome reorganization was responsible for karyotypic differences in closely related species. Major drivers for genomic reshuffling were in tandem and centric fusion, fission, paracentric and pericentric inversions or centromere repositioning. Chromosome evolution was associated with an increase and decrease in diploid number in different lineages and ITS indicate remnants of ancient telomeres. Cytogenetics results corroborates that C. goytaca is not a junior synonym of C. subflavus since the karyotypic differences found may lead to reproductive isolation.

Updated and annotated checklist of recent mammals from Brazil

An updated and annotated checklist of mammals occurring in Brazil is presented. A total of 751 native species, distributed in 249 genera, 51 families and 11 orders were recorded to the country. The Brazilian mammalian fauna shows an elevated rate of endemism (30%; 223 species). Among the species evaluated by IUCN (668 species; 90%), a total of 80 (10.6% of total mammalian fauna) are Threatened, 28 (3.9%) are considered as Near Threatened, two species (0.3%) are presumable Extinct, 96 (12.8%) are considered with Deficient Data for conservation and 462 (61.6%) are considered as Least Concern. Fifteen new species were described since the last national compilation (published in 2017), which associated to new records to the country and synonimizations resulted in an increment of 30 species. Eight non-native species were introduced to the country, including the recently established Asiatic cervids Rusa unicolor (sambar) and Axis axis (chital). Seven native species (five primates and two hystricomorph rodents) have been translocated from their areas of natural occurrence to other areas inside the country.

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.

Molecular survey of tick-borne pathogens in small mammals from Brazilian Amazonia

Small non-volant mammals (marsupials and small rodents) were captured at three different timepoints from 23 forest fragments across three municipalities (Alta Floresta, Sinop and Cláudia) covering the Amazonian biome of the Mato Grosso State in Midwestern Brazil. The animal tissues (liver and spleen) and blood were screened using molecular tools for the detection of Babesia, Coxiella, Cytauxzoon, Hepatozoon, Theileria, and Anaplasmataceae agents. A total of 230 specimens (78 rodents and 152 marsupials) were trapped. Hepatozoon and Piroplasmorida agents were detected in the common opossums (Didelphis marsupialis). In turn, all samples (blood, liver, or spleen) collected from the small mammals were negative for the genus Coxiella and the family Anaplasmataceae, as detected by polymerase chain reaction (PCR). Phylogenetic analyses inferred from partial sequences of the 18S rRNA gene highlighted the occurrence of new Hepatozoon and Piroplasmorida haplotypes. Future studies determining the role of common opossum (D. marsupialis) in the epidemiological cycles of Hepatozoon and Babesia under natural conditions in the Amazonian biome are necessary.