Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer.

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 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression. RESULTS: Using genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into "High" and "Low" expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa. CONCLUSIONS: These data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses.

Shades of white: The Petunia long corolla tube clade evolutionary history.

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 because of its association with pollinators and unique microenvironments. This study evaluated the phylogenetic relationships among a Petunia clade species with different floral syndromes that inhabit several environments. We based our work on multiple individuals per lineage and employed nuclear and plastid phylogenetic markers and nuclear microsatellites. The phylogenetic tree revealed two main groups regarding the elevation of the distribution range, whereas microsatellites showed high polymorphism-sharing splitting lineages into three clusters. Isolation by distance, migration followed by new environment colonization, and shifts in floral syndrome were the motors for lineage differentiation, including infraspecific structuring, which suggests the need for taxonomic revision in the genus.

The Brazilian Atlantic Bushmaster Lachesis (Linnaeus, 1766) Mitogenome With Insights On Snake Evolution And Divergence (Serpentes: Viperidae: Crotalinae).

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.

Diversity of mitochondrial DNA in 3 species of great whales before and after modern whaling.

The 20th 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 3 great whales in the South Atlantic, such as 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 20th 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 3 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.

Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator.

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.

Global phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation.

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 investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp's (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (< 1 Mya) with low within- clade diversity, supporting a recurrent extinction-recolonization model for these ocean regions. All data showed that ATL and IWP groups were more closely related than those in the EP, with mtDNA data supporting recent recolonization of the ATL from the IWP. Individual olive ridley dispersal between the ATL, EP, and IN/IWP could be interpreted as more male- than female-biased, and genetic diversity was lowest in the Atlantic Ocean. All populations showed signs of recent expansion, and estimated time frames were concordant with their recent colonization history. Investigating species abundance and distribution changes over time is central to evolutionary biology, and this study provides a historical biogeographic context for marine vertebrate conservation and management. Supplementary Information: The online version contains supplementary material available at 10.1007/s10592-022-01465-3.

Population Genetics and Phylogeography of Galapagos Fur Seals.

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 rookeries across four islands (nine rookeries) are genetically structured into the following major groups: 1) a western cluster of individuals from Fernandina; 2) a central group from north and east Isabela, Santiago, and Pinta; and possibly, 3) a third cluster in the northeast from Pinta. Furthermore, asymmetric levels of gene flow obtained from eight microsatellites found migration from west Isabela to Fernandina islands (number of migrants Nm = 1), with imperceptible Nm in any other direction. Our findings suggest that the marked structuring of populations recovered in GFS is likely related to an interplay between long-term site fidelity and long-distance migration in both male and female individuals, probably influenced by varying degrees of marine productivity.

Revealing the cryptic diversity of the widespread and poorly known South American blind snake genus Amerotyphlops (Typhlopidae: Scolecophidia) through integrative taxonomy

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.

Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere.

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 between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].

Phylogeographic evidence for two species of muriqui (genus Brachyteles).

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 differences between these highly endangered and charismatic primates, as well as the design of more effective conservation programs. To address this issue, between 2003 and 2017 we collected over 230 muriqui fecal samples across the genus' distribution in the Brazilian Atlantic Forest, extracted DNA from these samples, and sequenced 423 base pairs of the mitochondrial DNA (mtDNA) control region. Phylogenetic and species delimitation analyses of our sequence dataset robustly support two reciprocally monophyletic groups corresponding to northern and southern muriquis separated by an average 12.7% genetic distance. The phylogeographic break between these lineages seems to be associated with the Paraíba do Sul River and coincides with the transition between the north and south Atlantic Forest biogeographic zones. Published divergence estimates from whole mitochondrial genomes and nuclear loci date the split between northern and southern muriquis to the Early Pleistocene (ca. 2.0 mya), and our new mtDNA dataset places the coalescence time for each of these two clades near the last interglacial (ca. 120-80 kya). Our results, together with both phenotypic and ecological differences, support recognizing northern and southern muriquis as sister species that should be managed as distinct evolutionarily significant units. Given that only a few thousand muriquis remain in nature, it is imperative that conservation strategies are tailored to protect both species from extinction.

How diverse can rare species be on the margins of genera distribution?

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 structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

Molecular phylogeny and hemipenial diversity of South American species of Amerotyphlops (Typhlopidae, Scolecophidia)

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 relationships and morphology of the South American (SA) species were never accessed before. Here, we performed a phylogenetic analysis including 106 species of Typhlopidae and ten genes. Our dataset represents the most comprehensive for SA species, containing seven of eight recognized species. Corroborating previous studies, we recovered the main groups of Typhlopoidea, and for typhlopines, we recovered with strong support two clades: (a) the Greater Antilles radiation, and the (b) Lesser Antilles and SA radiation. Within the SA radiation, we recovered four main lineages: (a) a clade formed by A. tasymicris and A. minuisquamus; (b) a clade composed by A. reticulatus as the sister group of all other SA species; (c) a clade composed by A. brongersmianus as the sister group of a clade comprising all Northeast Brazilian Species (NBS); and (d) a clade of the NBS, including A. yonenagae, A. arenensis, A. paucisquamus, and A. amoipira. We supplemented our phylogenetic result with the description of hemipenial morphology for seven SA species and comment their relevance to the systematics of Typhlopinae. Hemipenes of SA Amerotyphlops follow the general pattern in scolecophidians (single organ with undivided sulcus). Only A. reticulatus and A. minuisquamus have organs with calcified spines. According to our results, hemipenial ornamentation have shown highly informative and could represent a potential source of systematic and taxonomic characters in that group. We also present an extensive review of the geographical distribution for all SA species. Our study represents the first integrative analysis of a poorly known evolutionary radiation of one of the most widespread SA fossorial snakes.

Molecular phylogeny and hemipenial diversity of South American species of Amerotyphlops (Typhlopidae, Scolecophidia)

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 relationships and morphology of the South American (SA) species were never accessed before. Here, we performed a phylogenetic analysis including 106 species of Typhlopidae and ten genes. Our dataset represents the most comprehensive for SA species, containing seven of eight recognized species. Corroborating previous studies, we recovered the main groups of Typhlopoidea, and for typhlopines, we recovered with strong support two clades: (a) the Greater Antilles radiation, and the (b) Lesser Antilles and SA radiation. Within the SA radiation, we recovered four main lineages: (a) a clade formed by A. tasymicris and A. minuisquamus; (b) a clade composed by A. reticulatus as the sister group of all other SA species; (c) a clade composed by A. brongersmianus as the sister group of a clade comprising all Northeast Brazilian Species (NBS); and (d) a clade of the NBS, including A. yonenagae, A. arenensis, A. paucisquamus, and A. amoipira. We supplemented our phylogenetic result with the description of hemipenial morphology for seven SA species and comment their relevance to the systematics of Typhlopinae. Hemipenes of SA Amerotyphlops follow the general pattern in scolecophidians (single organ with undivided sulcus). Only A. reticulatus and A. minuisquamus have organs with calcified spines. According to our results, hemipenial ornamentation have shown highly informative and could represent a potential source of systematic and taxonomic characters in that group. We also present an extensive review of the geographical distribution for all SA species. Our study represents the first integrative analysis of a poorly known evolutionary radiation of one of the most widespread SA fossorial snakes.

Phylogeny and systematics of Chiroxiphia and Antilophia manakins (Aves, Pipridae).

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 subspecies, but their taxonomic status are also uncertain. Finally, the phylogenetic relationships amongst the majority of Chiroxiphia and Antilophia taxa are unknown. Here, we use multilocus DNA sequences from multiple individuals of all currently accepted species and subspecies of both genera to infer their phylogenetic relationships and its implications on their classification. Our results suggest Chiroxiphia, as currently defined, is a paraphyletic group, since C. boliviana is more closely related to Antilophia than to the remaining Chiroxiphia taxa. Within C. pareola, our results support that C. p. regina and C. p. napensis should be treated as independent species. We found three divergent clades in C. p. pareola likely corresponding to distinct subspecies: one in which the isolated and endemic Tobago Island C. p. atlantica individuals are grouped with C. p. pareola from the north bank of the lower Amazon River; and two sister clades comprising individuals distributed south of the Amazon river, and those from the Atlantic Forest.

Effective population size and the genetic consequences of commercial whaling on the humpback whales (Megaptera novaeangliae) from Southwestern Atlantic Ocean.

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 diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation Nc (Ne multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term Nc in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.

How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data.

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 populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.

Origin and hidden diversity within the poorly known Galápagos snake radiation (Serpentes: Dipsadidae)

Galápagos 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 Rábida Islands, and one from Tortuga, Isabela, and Fernandina. We also recognize six additional species of Pseudalsophis in the Galápagos Archipelago (Pseudalsophis biserialis from San Cristobal, Floreana and adjacent islets; Pseudalsophis hoodensis from Española and adjacent islets; Pseudalsophis dorsalis from Santa Cruz, Baltra, Santa Fé, and adjacent islets; Pseudalsophis occidentalis from Fernandina, Isabela, and Tortuga; Pseudalsophis slevini from Pinzon, and Pseudalsophis steindachneri from Baltra, Santa Cruz and adjacent islets). Our time calibrated tree suggests that the genus Pseudalsophis colonized the Galápagos Archipelago through a single event of oceanic dispersion from the coast of South America that occurred at approximately between 6.9?Ma and 4.4?Ma, near the Miocene/Pliocene boundary.

Origin and hidden diversity within the poorly known Galápagos snake radiation (Serpentes: Dipsadidae)

Galápagos 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 Rábida Islands, and one from Tortuga, Isabela, and Fernandina. We also recognize six additional species of Pseudalsophis in the Galápagos Archipelago (Pseudalsophis biserialis from San Cristobal, Floreana and adjacent islets; Pseudalsophis hoodensis from Española and adjacent islets; Pseudalsophis dorsalis from Santa Cruz, Baltra, Santa Fé, and adjacent islets; Pseudalsophis occidentalis from Fernandina, Isabela, and Tortuga; Pseudalsophis slevini from Pinzon, and Pseudalsophis steindachneri from Baltra, Santa Cruz and adjacent islets). Our time calibrated tree suggests that the genus Pseudalsophis colonized the Galápagos Archipelago through a single event of oceanic dispersion from the coast of South America that occurred at approximately between 6.9?Ma and 4.4?Ma, near the Miocene/Pliocene boundary.

How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data

Abstract 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 populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.

Effective population size and the genetic consequences of commercial whaling on the humpback whales (Megaptera novaeangliae) from Southwestern Atlantic Ocean

Abstract 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 diversity for this breeding population. Using an approximate Bayesian computation approach, the scenario of constant Ne was significantly supported over scenarios with moderate to strong size changes during the commercial whaling period. The previous generation Nc (Ne multiplied by 3.6), which should corresponds to the years between around 1980 and 1990, was estimated between ~2,600 and 6,800 whales (point estimate ~4,000), and is broadly compatible with the recent abundance surveys extrapolated to the past using a growth rate of 7.4% per annum. The long-term Nc in the constant scenario (point estimate ~15,000) was broadly compatible (considering the confidence interval) with pre-whaling catch records estimates (point estimate ~25,000). Overall, our results shown that the Southwestern Atlantic Ocean humpback whale population is genetically very diverse and resisted well to the strong population reduction during commercial whaling.