Datasets for Dalapicolla et al., 2024. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. Molecular Phylogenetics and Evolution, 107992.

All scripts are available at https://github.com/jdalapicolla/SpeciesDelimitationPermits: SISBIO[#14419-3] and SISGEN [#A58279D]GENOMIC DATA:VCF: proechimys.vcf.gz and proechimys.vcf.gz.tbiLoci data: proechimys_184ind_ipyrad.7zNexus Alignments for SVDQuartets: proechimys_complete_svd_final_speciestrees.nex (complete dataset); proechimys_subset1_svd_indtree.nex (Subset 1); proechimys_subset2_svd_speciestree.nex (Subset 2);Phylip alignments for IQTree: proechimys_MPE1_184.phylip (complete dataset); proechimys_subset1.phylip (Subset 1); proechimys_subset2.phylip (Subset 2).SUPPLEMENTARY MATERIALAppendix A: A brief taxonomic history of the genus Proechimys.Appendix B: Summary of mitochondrial DNA (mtDNA) data available for the genus Proechimys.Appendix C: Details on SNPs calling and filtering steps used in genomic data.Appendix D: Details on repeatability and filtering steps used in morphometric data.Appendix E: Comments on the nomenclatural decisions regarding the species-group taxa of the genus Proechimys.Table S1: Samples used in the genomics analyses.Table S2: Morphometric data consisting of raw values for 22 morphometric variables.Table S3: RAD processing results for 184 genomic samples.Table S4: ICC test for cranial measurements with upper and lower values for the confidence interval.Table S5: Posterior probabilities (PP) found in all demographic scenarios in the iBP&P analyses.Table S6: Patterson’s D (ABBA-BABA), and related statistics.Table S7: Divergence times in millions of years ago (Ma) for the species tree of Proechimys.Table S8: Available cytogenetic, mtDNA, and nuDNA data in the literature for delimited species of Proechimys.Figure S1: Geographical distribution of genomic samples.Figure S2: Geographical distribution of morphometric samples.Figure S3: The 29 cranial measurements with their respective acronyms.Figure S4: Details of clade A in the individual phylogenetic tree.Figure S5: Details of clade B in the individual phylogenetic tree.Figure S6: Details of clade C, D, E, F and G in the individual phylogenetic tree.Figure S7: Partitions used in iBP&P.Figure S8: Species tree and IQTree2 using 17,162 unlinked SNPs subset 2.Figure S9: The branch-specific statisticfb(F-branch).</p

Mammals of a restinga forest in Mataraca, Paraíba, northeastern Brazil, and its affinities to restinga areas in Brazil

<div><p>Abstract The Restinga forests are plant formations associated to the Atlantic Forest which still have not been much studied in terms of their mastofauna. The objective of the present work was to list for the first time the mammal species found in a Restinga on northeastern Brazil and show the similarities on species composition to other areas of the same environment and of Atlantic Forest. Our records were based on several complementary approaches: field survey, interviews, and museum collections. Subsequently, we performed similarity analysis between Restinga areas along Brazil and Atlantic Forest areas. We found a total of 30 species of mammals distributed in 28 genera, 16 families and 7 orders for Restinga of Mataraca. Species richness was similar to other Restinga areas and similarity analyzes pointed out that Restingas are more closely related to adjacent Atlantic Forest areas than to other Restingas in the country. This suggests that Restingas do not exhibit an autochthone fauna, but rather a faunal subsample of neighbor Atlantic Forest. Therefore, conservations policies for the Restinga habitat depends not only on actions focused on this habitat, but on initiatives that encompass nearby Atlantic Forest remnants, allowing the connectivity between these habitats.</p></div

Diversity of ants and mites in the diet of the Brazilian frog Chiasmocleis leucosticta (Anura: Microhylidae)

<div><p>Abstract We describe here the diet of the microhylid frog Chiasmocleis leucosticta based on the stomach contents of 72 individuals (47 males and 25 females) collected in pitfall traps at the Reserva Florestal de Morro Grande, state of São Paulo, southeastern Brazil. We identified 1,981 food items distributed in 13 prey categories of arthropods, mainly ants, mites and collembolans. Formicidae was the most abundant and frequent prey category, including 16 genera from seven subfamilies, and data on ant availability in the habitat suggest that C. leucosticta selects ants actively. The second main prey category was Acari, predominantly represented by mites of the suborder Oribatida. This is the first work identifying mites to the family level in the diet of a Microhylidae. There was no statistical difference between males and females regarding diet composition.</p></div

Human-modified landscape acts as refuge for mammals in Atlantic Forest

<div><p>Abstract: Human-modified landscapes (HMLs) are composed by small, isolated and defaunated forest fragments, which are surrounded by agricultural and urban areas. Information on species that thrives in these HMLs is essential to direct conservation strategies in local and regional scales. Since HMLs are dominant in the Atlantic Forest, we aimed to assess the mammalian diversity in a HML in southeastern Brazil and to propose conservation strategies. We collected data of terrestrial (small-, medium- and large-sized) and volant mammals in three small forest fragments (10, 14 and 26 ha) and adjacent areas, between 2003 and 2016, using complementary methods: active search, camera trapping, live-traps, mist nets and occasional records (i.e., roadkills). In addition, we used secondary data to complement our species list. We recorded 35 native mammal species (6 small-sized, 16 medium- and large-sized, and 13 bats) and seven exotic species in the HML. The recorded mammal assemblage (non-volant and volant), although mainly composed of common and generalist species, includes three medium- and large-sized species nationally threatened (Leopardus guttulus, Puma concolor and Puma yagouaroundi) and two data deficient species (Galictis cuja and Histiotus velatus), highlighting the importance of this HML for the maintenance and conservation of mammal populations. Despite highly impacted by anthropogenic disturbances, the study area harbors a significant richness of medium- and large-sized mammals, being an important biodiversity refuge in the region. However, this biodiversity is threatened by the low quality of the habitats, roadkills and abundant populations of domestic cats and dogs. Therefore, we stress the need of conservation strategies focusing on the medium- and large-sized mammals as an umbrella group, which could benefit all biodiversity in the landscape. We recommend actions that promotes biological restoration, aiming to increase structural composition and connectivity of the forest fragments, reducing roadkills and controlling the domestic cats and dogs' populations, in order to maintain and improve the diversity of mammals in long-term.</p></div