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Introduction
Sandro L. Bonatto currently works at the School of Sciences, Pontifícia Universidade Católica do Rio Grande do Sul. Sandro does research in Biological Evolution, Conservation Genomics and Systematics.
Publications
Publications (619)
Rivers are prominent landscape features, acting as key promoters of diversification among freshwater organisms. Albeit generally considered potential barriers to species movement, they may also facilitate gene flow and structure populations of semiaquatic species (Riverine Thruway Hypothesis, RTH). We evaluated the role of rivers on the processes r...
The South American bushmaster Lachesis muta is currently considered a valid taxon with no recognized subspecies. However, its wide distribution with discontinuous populations, the restricted sampling of molecular data in previous studies, and the inherent difficulty in obtaining diagnostic data, preclude a detailed evaluation of the taxonomic statu...
Background
In prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutati...
Delimiting species is challenging in recently diverged species, and adaptive radiation is fundamental to understanding the evolutionary processes because it requires multiple ecological opportunities associated with adaptation to biotic and abiotic environments. The young Petunia genus (Solanaceae) is an excellent opportunity to study speciation be...
Delimiting species is challenging in recently diverged species, and adaptive radiation is fundamental to understanding the evolutionary processes because it requires multiple ecological opportunities associated with adaptation to biotic and abiotic environments. The young Petunia genus (Solanaceae) is an excellent opportunity to study speciation be...
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...
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 gre...
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 o...
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 organism...
Although the recent advances on the relationship of its major groups, the systematics of the rich fauna of Neotropical snakes is far from being a consensus. In this sense, derived groups presenting continental distributions have represented a main challenge. The taxonomy of the snake tribe Echinantherini is one of the most contentious among the div...
Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and 'Critically Endangered' Kemp's ridley (L. kempii). To i...
Pinnipeds found across islands provide an ideal opportunity to examine the evolutionary process of population subdivision affected by several mechanisms. Here, we report the genetic consequences of the geographic distribution of rookeries in Galapagos fur seals (GFS: Arctocephalus galapagoensis) in creating population structure. We show that rooker...
Black and gold howler monkeys (Alouatta caraya) inhabit several eco-regions in South America with the highest population densities in riverine forests. Dam construction for electricity production represents a severe human alteration of ecosystems with consequences for primate conservation. To evaluate the possible loss of genetic diversity in A. ca...
Population genetic structure results from the interaction between historical events, current ecological conditions and life traits. The genetic structure and gene flow between populations are important to species dynamics, mainly for rare and endangered species that are more vulnerable to landscape changes and fragmentation. Here we evaluated the g...
Gene flow via seed or pollen dispersal is fundamental for establishing population diversity and structure of plants, especially in naturally fragmented environments. Petunia exserta (Solanaceae) is endemic to small shelters in rocky towers in the Brazilian Pampa grassland, an ancient and isolated region. The landscape is a long-term fragmented habi...
The recent publication of the genomes of a 24,000-years-old Mal'ta individual (MA-1) from Siberia, and the 13-12,000-years-old Hoyo Negro specimen from Yucatan Peninsule (among other recent paleogenetic evidences) reopens the discussion about the pre-Columbian peopling of Americas. Specifically, the availability of extensive genetic data along with...
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely...
South American racers of the tribe Philodryadini are a widespread and diverse group of Neotropical snakes with a complex taxonomic and systematic history. Recent studies failed to present a robust phylogenetic hypothesis for the tribe, mainly due to incomplete taxon sampling. Here we provide the most extensive molecular phylogenetic analysis of Phi...
It corrects the article: http://doi.org/10.11606/1807-0205/2020.60.53
The Brazilian Atlantic Forest (BAF) is one of the most impacted biomes in the world, and in this region, there are several examples of the effects of Pleistocene climate changes among the species found there. Athenaea fasciculata (Solanaceae) is a forest component distributed mainly throughout the BAF extension. Here, we investigated the genetic di...
A bstract
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance pointing at strong gene-tree species tree discordance. Divergence times in the group also vary largely...
The taxonomy of muriquis, the largest extant primates in the New World, is controversial. While some specialists argue for a monotypic genus (Brachyteles arachnoides), others favor a two-species classification, splitting northern muriquis (Brachyteles hypoxanthus) from southern muriquis (B. arachnoides). This uncertainty affects how we study the di...
Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and...
Plant hybridization is frequently observed in nature and considered an important driver of angiosperm diversity. Species are thought to arise through the accumulation of morphological and genetic differences that promote their evolutionary independence, even in the presence of hybridization. Natural hybrid zones yield an excellent system to study t...
The black-and-gold howler monkey ( Alouatta caraya ) is widely distributed in Brazil, Bolivia, Paraguay, and northeastern Argentina. Despite this wide distribution, it is locally threatened in some parts of its southern range by forest loss and fragmentation, and yellow fever outbreaks. We present 14 new localities of A. caraya occurrence in the Pa...
We assessed the level of genetic variability and population structure of the common bottlenose dolphin (Tursiops truncatus) in the tropical and subtropical portions of the southwestern Atlantic Ocean and compared the results with previous morphological findings. We analyzed 109 samples of common bottlenose dolphins that were sequenced for control r...
Hybridization is relatively well documented among Old World primates, but poorly investigated among New World monkeys. We investigated hybridization between the sexually dichromatic howlers Alouatta caraya and Alouatta guariba clamitans, whose lineages diverged ca. 5 million years ago. These taxa show allopatric distributions with a few recently di...
Typhlopidae is the most diverse family of Scolecophidia, with 269 species. Amerotyphlops was recently erected within subfamily Typhlopinae and comprises fifteen species distributed from Mexico to Argentina and the southern Lesser Antilles. Despite recent advances, affinities among typhlopines remain poorly explored, and the phylogenetic relationshi...
The systematics and phylogeny of Otariidae have been extensively studied for over two centuries. Yet, several relationships, in particular, the monophyly within Arctocephalus, remain unclear. Recent molecular phylogenies only used few concatenated mitochondrial or nuclear genes. Here we reconstructed the Otariidae phylogeny based on whole-genome se...
Gal apagos snakes are among the least studied terrestrial vertebrates of the Archipelago. Here, we provide a phylogenetic analysis and a time calibrated tree for the group, based on a sampling of the major populations known to occur in the Archipelago. Our study revealed the presence of two previously unknown species from Santiago and R abida Islan...
Chiroxiphia and Antilophia manakins are recognized as closely related genera. Nonetheless, Chiroxiphia has been recovered as paraphyletic in some studies with limited taxonomic coverage. This genus currently comprises five species, although this arrangement is still unsettled. Chiroxiphia pareola is the most widespread species, with four recognized...
Southern Hemisphere humpback whales breed in tropical waters and migrate to Antarctica to forage. While the breeding grounds are well defined, the population structure on Antarctic feeding grounds is poorly described. The Western Antarctic Peninsula (WAP) is of particular interest, where rapidly changing environmental conditions could alter prey di...
In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populati...
Genotypes of 10 microsatellite loci of 420 humpback whales from the Southwestern Atlantic Ocean population were used to estimate for the first time its contemporary effective (Ne) and census (Nc) population sizes and to test the genetic effect of commercial whaling. The results are in agreement with our previous studies that found high genetic dive...
- Posterior density for the splitting parameter s for all scenarios.
- Posterior density for the effective size of the founder population for Native Americans, from Siberians, with or without migration.
- Posterior density of effective population sizes for Chinese vs. Native Americans.
- Posterior density of effective population sizes for Siberian vs. Native Americans.
- Posterior density for the effective size of the founder population for Siberians, from Chinese, with or without migration.
- Pairwise ΦST for each locus.
- Posterior density for migration parameters for all scenarios.
- Posterior density for the effective size of the founder population for Native Americans, from Asia, with or without migration.
- Genetic diversity statistics for each locus.
- Estimated substitution rates (μ) for each locus.
- Posterior density of effective population sizes for Asian vs. Native Americans.
- Posterior density of effective population sizes for Chinese vs. Siberians.
- Posterior density for divergence times (in years) for all scenarios.
- Posterior density for the effective size of the founder population for Native Americans, from Chinese, with or without migration.
The process of colonization and range expansion to novel environments involves both demographic and selective processes that can be traceable in the genetic diversity of the organisms. Nevertheless, it can be difficult to disentangle the signatures of the demographic and selective in the current genetic diversity of the populations. In this work, w...
The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial...
List of individuals that bear each mitochondrial DNA control region haplotype, and the respective GenBank number.
Absolute frequency in the sample and geographic distribution of haplotypes for South American sea lion.
(DOCX)
List of individuals that bear each mitochondrial DNA cytochrome b haplotype.
Absolute frequency in the sample and geographic distribution of haplotypes for South American sea lion.
(DOCX)
Extended Bayesian skyline plot showing the effective population size fluctuation of South American sea lions populations throughout time based on the mtDNA control region.
Internal dashed lines are median estimates and thin lines and coloured areas are the 95% Central Posterior Density (CPD) intervals. Nef, effective female population size (log sca...
Extended Bayesian skyline plot showing the effective population size fluctuation of South American sea lions populations throughout time based on the mtDNA control region.
Internal black dashed lines are median estimates and thin lines are the 95% CPD intervals. Thin green lines are the individual population trajectories. Nef, effective female popu...
Species and access number of sequences downloaded from GenBank used to estimate the Bayesian phylogeny (Fig 3).
(DOCX)
Genetic diversity of South American sea lions for each locus per clustered localities and for the species as whole.
(A) Number of alleles, (E) = exclusive alleles, (Ho) observed heterozygosity, (He) expected heterozygosity.* Loci that deviated from HW equilibrium after Bonferroni correction.
(DOCX)
Plots from STRUCTURE HARVESTER performed with Evanno’s method.
(A) Highest value of (ΔK) = 79.20 on K = 2. (B) Mean of estimated Ln probability of data (± sd) averaging ten runs from K = 1 to K = 10.
(TIF)
STRUCTURE bar plot from the test for migrants or hybrids between oceans using the sampling locations (in this case the ocean basin) and the USEPOPINFO model.
Each bar is one individual and each colour represents the assignment probability of the individual to belong to that genetic cluster.
(TIF)
Humpback whales wintering in tropical waters along the Atlantic and Pacific coasts of the South American continent are thought to represent distinct populations or “stocks.” Here we present the first analysis of genetic differentiation and estimates of gene flow between these breeding stocks, based on both mitochondrial DNA (mtDNA) control region s...
- Phylogenetic trees based on ITS sequences for Decaloba, ITS1.
- Phylogenetic trees based on ITS sequences for Passiflora, ITS1.
- Phylogenetic trees based on ITS sequences for Astrophea, ITS1.
- Phylogenetic trees based on ITS sequences for Astrophea, ITS2.
- Phylogenetic trees based on ITS sequences for Deidamioides, ITS1.
- ITS1 and ITS2 sequences parameters analyzed
- Phylogenetic trees based on ITS sequences for Deidamioides, ITS2.
- Phylogenetic trees based on ITS sequences for Passiflora, ITS2.
- Phylogenetic trees based on ITS sequences for Decaloba, ITS2.
- Random sequences parameters analyzed.
Recently, it has been suggested that internal transcribed spacer (ITS) sequences are under selective constraints to preserve their secondary structure. Here, we investigate the patterns of the ITS nucleotide and secondary structure conservation across the Passiflora L. genus to evaluate the potential use of secondary structure data as a helpful too...
The São Pedro and São Paulo Archipelago (SPSPA) (00°56’N, 29°22’W) lies approximately 1010km northeast off the coast of Rio Grande do Norte State in Brazilian waters. Recently, through photo-identification and group size analysis, around 20-30 individual bottlenose dolphins, Tursiops truncatus, from SPSPA were recognized as a resident, and potentia...
The Omura's whale (Balaenoptera omurai), previously referred to as a small form of Bryde's whale, was described in 2003 as a distinct baleen whale species of the family Balaenopteridae. Omura's whales are currently confirmed to occur in three of the world's oceans; the western Pacific, Indian, and northeastern Atlantic. Here we report the genetic i...