Sandro Luis Bonatto

This study estimates the genetic variability of remaining populations of southern black‐horned capuchin ( Sapajus nigritus cucullatus ) in the Atlantic Forest of Misiones, Argentina and assess connectivity to identify priority conservation units. We evaluated 59 microsatellite loci previously described for other primates, including humans, of which 16 were polymorphic. A total of 81 individuals were genotyped, comprising 33 tissue samples from rescue centers, 3 from capture for radiocollar placement, and 45 non‐invasive fecal samples from two wild populations: Yacutinga Reserve (Fragmented Forest, FF) and the Urugua‐í‐Forester Biological Corridor (Continuous Forest, CF). Structure analysis identified an optimal value K = 3, revealing three major genetic ancestry components with varying degrees of admixture across populations rather than discrete lineages. These components correspond to: (1) a distinctive Continuous Forest (CF) component, (2) a distinctive Yacutinga Fragmented Forest (FF) component, and (3) a widespread background component occurring throughout Misiones Province, which represents the entire distribution range of the species in Argentina. Notably, the CF population exhibited the highest genetic variability, whereas FF showed the lowest. Isolation‐by‐distance analysis via the Mantel test revealed no significant relationship between genetic and geographic distances (R = 0.0336; p = 0.299), suggesting that genetic differentiation may be driven by habitat fragmentation and landscape characteristics rather than geographic distance alone, though historical demographic dynamics may also contribute to these patterns. These results emphasize that forest fragmentation negatively impacts the genetic health of S. n. cucullatus and underscore the urgent need to maintain and restore biological corridors to ensure long‐term genetic viability in the fragmented landscape of Misiones.

Determining the limits of plant species is often challenging, which complicates efforts to preserve biodiversity, especially in transitional zones or areas in constant change due to human activities. The genus Petunia (Solanaceae) is endemic to the open fields of southern South America, an ecosystem strongly impacted by agriculture and livestock. Despite the importance of this ecosystem to Neotropical biodiversity, the genetic diversity of species from these grasslands is still poorly known. Here, we applied genotyping-by-sequencing to multiple individuals to investigate the genetic diversity and population structure in co-occurring Petunia species, aiming to understand the speciation process. We describe the origin of one atypical population and its evolutionary relationships with other Petunia species. Our results suggest that this genetically and ecologically atypical population could constitute a new species, contributing to the recognition and conservation of biodiversity in an understudied Neotropical region. Furthermore, our study highlights the importance of continually assessing the genetic diversity of various populations, particularly those that diverge ecologically, morphologically, or geographically from typical populations, to understand and conserve biodiversity.

Assessing the genetic diversity of a population is critical to evaluate its resilience in the face of anthropogenic impacts. This study aimed to assess the genetic diversity and structure of the spinner dolphins ( Stenella longirostris ) that inhabit the Santos Basin (SB), south and southeast Brazil. Analyses were conducted using seven microsatellite loci and a 686 bp fragment of the mitochondrial DNA (mtDNA) control region. The genetic relationship between SB spinner dolphins with the island‐associated spinner dolphins of Fernando de Noronha and spinner dolphins distributed in the western North Atlantic, including the Wider Caribbean region, was also investigated through a 324 bp fragment of the mtDNA control region. Results indicate that the offshore group of spinner dolphins in the SB has high genetic diversity for both mtDNA and nuclear markers. Based on mtDNA, the SB group has moderate genetic connectivity to the western North Atlantic/Wider Caribbean region spinner dolphins, but high genetic differentiation from their closest neighbors (Fernando de Noronha). These findings indicate that although SB spinner dolphins occur in an area of strong anthropogenic impacts, they present a high level of neutral genetic variation, with subtle matrilineally derived structure in the offshore (not island‐associated) waters of the western Atlantic.

The contemporary genetic diversity of the cheetah (Acinonyx jubatus) has been the focus of several studies, which have revealed very low levels of variation. Different hypotheses have been proposed to explain this pattern of low diversity, and require additional scrutiny. Here, we used published microsatellite data and coalescence-based analytical methods to explore the historical demography of the largest free-ranging cheetah population, aiming to assess whether present-day diversity may have been impacted by a historical demographic decline. Our results support the hypothesis of a historical (and most likely gradual) demographic decline over the past ~10,000 years, leading to a present-day N _e ranging from 700 to 1,600 individuals. This decline was likely induced by climate-driven vegetational shifts affecting habitat suitability and possibly also interspecies interactions with prey and competitors. These results help clarify the demographic history of cheetahs in southern Africa and its impact on the current genetic diversity of this population.

The brown howler, Alouatta guariba, endemic to the Atlantic Forest of Brazil and Argentina, is threatened by habitat loss and fragmentation, hunting, and its susceptibility to yellow fever. Two subspecies have been recognized, but their names, validity, and geographic ranges have been controversial. We obtained samples covering the species' entire distribution in Brazil and Argentina to clarify these issues by investigating their genetic diversity and structure and assessing their evolutionary history. We analyzed, for the first time, a set of ten microsatellite markers (N = 153), plus mitochondrial DNA (mtDNA) segments of the control region (N = 207) and cytochrome b gene (N = 116). The microsatellite data support two to three genetic clusters with biological significance. The southern populations (Argentina, Santa Catarina, and Rio Grande do Sul) presented a homogeneous genetic component, and populations from São Paulo (SP) to the north presented another component, although most presented ∼20% of the southern component. With K = 3, SP emerged as a third component while sharing some ancestry with Rio de Janeiro and Argentina. The mtDNA phylogenies revealed three main clades that diverged almost simultaneously around 250 thousand years ago (kya). Clades A and B are from central SP to the north and east, while clade C is from SP to the south and southwest. Samples from SP presented haplotypes in all three clades, sometimes in the same population. The demographic history of the species estimated with the Bayesian skyline plot of the mtDNA showed a strong expansion ∼40–20 kya and a strong reduction over the last ∼4–2 kya. Although the genetic clusters identified here deserve appropriate management strategies as conservation units, the absence of (i) concordance between the mtDNA and microsatellite data, (ii) reciprocal monophyly in the mtDNA, and (iii) clear-cut non-genetic diagnostic characters advises against considering them as different taxonomic entities. None of the previous taxonomic proposals were corroborated by our data. Our results elucidate the taxonomy of the Atlantic Forest brown howler, indicating it should be considered a monotypic species, A. guariba. We also clarify the evolutionary history of the species regarding its intraspecific genetic diversity, which is crucial information for its conservation and population management.

The 20 ^th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for three great whales in the South Atlantic, the blue, humpback and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20 ^th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all three species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere.

Hybridization is widespread and constitutes an important source of genetic variability and evolution. In animals, its role in generating novel and independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis is a marine apex predator of Pacific and Atlantic waters, with a disjunct set of populations in Peru and Northern Chile [Peruvian fur seal (Pfs)] with controversial taxonomic status. We demonstrate, using complete genome and reduced representation sequencing, that the Pfs is a genetically distinct species with an admixed genome that originated from hybridization between the SAfs and the Galapagos fur seal ( Arctocephalus galapagoensis ) ~400,000 years ago. Our results strongly support the origin of Pfs by homoploid hybrid speciation over alternative introgression scenarios. This study highlights the role of hybridization in promoting species-level biodiversity in large vertebrates.

This study presents the first complete mitogenome of the Brazilian Atlantic bushmaster Lachesis with insights into snake evolution. The total length was 17,177 bp, consisting of 13 PCGs, 22 tRNAs, two rRNAs and a duplicate control region (CRs). Almost all genes were encoded by the heavy-strand, except for the ND6 gene and eight tRNAs (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser[TGA anticodon], Glu, Pro). Only ATG, ATA, and ATC were starting codons for protein-coding sequences. Stop codons mainly were TAA, AGA, AGG, and TAG; whereas ND1, ND3, and CYTB terminated with incomplete stop codons. Phylogeny retrieved Lachesis within the Crotalinae as the sister group of Agkistrodon; and the Lachesis+Agkistrodon clade as the sister group of (Sistrurus+Crotalus)+Bothrops. The tree supports Crotalinae, Viperinae, and Azemiopinae in the Viperidae family, being sister taxa of Colubridae+(Elapidae+Psammophiidae). The mean genetic distance across 15 snake families and 57 nucleotide sequences was 0.37. The overall mean value of genetic distance across the Crotalinae was 0.23, with Lachesis muta exhibiting the shortest distance of 0.2 with Agkistrodon piscivorus, Protobothrops dabieshanensis and P. flavoviridis and the greatest 0.25 with Gloydius blomhoffii, Trimeresurus albolabris, S. miliarius, and Deinagkistrodon acutus. The complete Atlantic L. muta mitogenome presented herein is only the third annotated mitogenome from more than 430 described Brazilian snake species.

Morphological stasis is generally associated with relative constancy in ecological pressures throughout time, producing strong stabilizing selection that retains similar shared morphology. Although climate and vegetation are commonly the main key factors driving diversity and phenotypic diversification in terrestrial vertebrates, fossorial organisms have their morphology mostly defined by their fossorial lifestyle. Among these secretive fossorial organisms, blind snakes of the South American genus Amerotyphlops are considered poorly studied when compared to other taxa. Here, we evaluate the cryptic diversity of Amerotyphlops using phylogenetic and multivariate approaches. We based our phylogenetic analysis on a molecular dataset composed of 12 gene fragments (eight nuclear and four mitochondrial) for 109 species of Typhlopidae. The multivariate analysis was implemented using 36 morphological variables for 377 specimens of Amerotyphlops. Additionally, we contrast our phylogenetic result with the morphological variation found in cranial, external and hemipenial traits. Our phylogenetic results recovered with strong support the following monophyletic groups within Amerotyphlops: (1) a clade formed by A. tasymicris and A. minuisquamus; (2) a clade composed of A. reticulatus; (3) a north-eastern Brazilian clade including A. yonenagae, A. arenensis, A. paucisquamus and A. amoipira; and (4) a clade composed of A. brongersmianus and a complex of cryptic species. Based on these results we describe four new species of Amerotyphlops from north-eastern and south-eastern Brazil, which can be distinguished from the morphologically similar species, A. brongersmianus and A. arenensis.