Biology subjects

Arantes, L. S.

Publications and source records attributed to Arantes, L. S..

7 recordsLinked to original sources

bioRxiv2025

Whole-genome resequencing reveals exceptions to panmixia in the exploited top fish predator Antarctic toothfish (Dissostichus mawsoni)

Antarctic toothfish (Dissostichus mawsoni) are a critical top fish predator in the Southern Ocean for whom a changing climate and fishing pressure challenge our understanding of their population dynamics. Their complex, long-lived life history presents challenges to understanding their population dynamics that we endeavor to overcome through the use of both reduced-representation sequencing and whole-genome resequencing data from fish across different cohorts. Our unique sample set allowed us to compare genomic structure, diversity, and demographic changes between cohorts born before and after the year 2000, when changes to fisheries management practices in the Southern Ocean reduced incidences of illegal, unreported, and unregulated fishing. While our population structure analyses corroborate recent studies showing panmixia across circumpolar populations of D. mawsoni, comparisons between cohorts revealed key exceptions. A lack of admixture in fish born before 2000 contrasted with widespread admixture among post-2000 individuals, consistent with increased mixing and/or genotype influx. Concernedly, genome-wide diversity declined over time in the Ross Sea (management area 88), with the significant losses observed in heterozygosity between pre-2000 and post-2000 cohorts. Elevated levels of inbreeding in the Ross Sea, coupled with evidence for recent population contraction from positive Tajimas D values, provided potential explanations for the observed reductions in genomic diversity. Our results reconcile circumpolar panmixia with localized erosion of diversity and elevated inbreeding in the Ross Sea sector, underscoring the value of temporal monitoring and the need to prioritize future research on the interplay between fisheries pressure and environmental change in driving population dynamics and genomic structure in tootfhish.

genomics↗

bioRxiv2025

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

BackgroundReference genomes for the entire sea turtle clade have the potential to reveal the genetic basis of traits driving the ecological and phenotypic diversity in these ancient and iconic marine species. Furthermore, these genomic resources can support conservation efforts and deepen our understanding of their unique evolution. ResultsWe present haplotype-resolved, chromosome-level reference genomes and high-quality gene annotations for five sea turtle species. This completes the catalog of reference genomes of the entire sea turtle clade when combined with our previously published reference genomes. Our analysis reveals remarkable genome synteny and collinearity across all species, despite the clades origin dating back more than 60 million years. Regions of high interspecific genetic distance and intraspecific genetic diversity are consistently clustered in genomic hotspots, which are enriched with genes coding for immune response proteins, olfactory receptors, zinc fingers, and G-protein-coupled receptors. These hotspot regions may offer insights into the genetic mechanisms driving phenotypic divergence among species, and represent areas of significant adaptive potential. Ancient demographic analysis revealed a synchronous population expansion among sea turtle species during the Pleistocene, with varying magnitudes of demographic change, likely shaped by their diverse ecological adaptations, and biogeographic contexts. ConclusionsOur work provides genomic resources for exploring genetic diversity, evolutionary adaptations, and demographic histories of sea turtles. We outline genomic regions with increased diversity, linked to immune response, sensory evolution, and adaptation to varying environments that have historically been subject to strong diversifying selection, and likely will underpin sea turtles responses to future environmental change. These reference genomes can assist conservation by providing insights into the demographic and evolutionary processes that sustain and threaten these iconic species.

genomics↗

bioRxiv2024

Inbreeding depression depends on the body size and environmental conditions in a threatened songbird, the aquatic warbler Acrocephalus paludicola

While inbreeding is known to affect individual fitness and thus population extinction risk, studies have under-represented non-model species of conservation concern, and rarely sought conditionality of inbreeding depression. Here, using SNPs identified with RAD-seq, we determined inbreeding depression in a threatened bird, the aquatic warbler Acrocephalus paludicola, and whether its magnitude depends on phenotypic and environmental factors. We found that the inbreeding coefficient (F) of adults with small tarsi was negatively associated with the seasonal breeding success (in males) and clutch size (in females), with the respective decrease in fitness in the most inbred relative to the least inbred individuals of ~89% and ~12%. In contrast, in adult males, for the average tarsus, wing and mass, support was low for F to be related to the long-term return rate to breeding grounds. For mean phenotypic covariates and male density, we also found low evidence that F is associated with the annual breeding success. Likewise, there was little support that mother F is related to egg hatch success and nestling survival, and - for average phenotypic traits, rainfall, temperature and nest density, and accounting for breeding peak - to clutch and fledged brood sizes. For nestlings, animal models showed that F is more negatively related to tarsus under higher temperatures and its effect varies by study year. However, for average brood size, temperature, rainfall and prey abundance, and when controlling for nestling sex, breeding peak and mother F, evidence for nestling F and tarsus association was weak. We conclude that (1) inbreeding depression on fitness components is stronger in smaller-bodied individuals, (2) considering interaction with phenotypic and environmental variables enables more accurate estimation of inbreeding depression, and (3) the inbreeding depression estimates will inform extinction risk analysis and conservation actions for the aquatic warbler.

evolutionary biology↗

bioRxiv2022

Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids

Hybridization is known to be part of many species evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviors between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behavior. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations besides Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species.

evolutionary biology↗

bioRxiv2022

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 MYA, yet the genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (Dermochelys coriacea) and green (Chelonia mydas) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of non-collinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared to other reptiles, and harbor a higher genetic load compared to green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage. Statement of significanceSea turtle populations have undergone recent global declines. We analyzed de novo assembled genomes for both extant sea turtle families through the Vertebrate Genomes Project to inform their conservation and evolutionary biology. These highly conserved genomes were differentiated by localized gene-rich regions of divergence, particularly within microchromosomes, suggesting that these genomic elements play key functional roles in the evolution of sea turtles and possibly other vertebrates. We further demonstrate that dissimilar evolutionary histories impact standing genomic diversity and genetic load, and are critical to consider when using these metrics to assess adaptive potential and extinction risk. Our results also demonstrate how reference genome quality impacts inferences of comparative and conservation genomics analyses that need to be considered in their application.

genomics↗

bioRxiv2020

New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil

An extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. To understand this atypical phenomenon and its impact on sea turtle conservation, research focused in the evolutionary history of sea turtles is fundamental. We assessed high quality multilocus haplotypes of 143 samples of the five species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill x loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.

genetics↗

bioRxiv2020

Optimization of ddRAD-like data leads to high quality sets of reduced representation single copy orthologs (R2SCOs) in a sea turtle multi-species analysis.

Reduced representation libraries (RRS) allow large scale studies on non-model species to be performed without the need for a reference genome, by building a pseudo-reference locus catalog directly from the data. However, using closely-related high-quality genomes can help maximize nucleotide variation identified from RRS libraries. While chromosome-level genomes remain unavailable for most species, researchers can still invest in building high-quality and project-specific de novo locus catalogs. Among methods that use restriction enzymes (RADSeq), those including fragment size selection to help obtain the desired number of loci - such as double-digest RAD (ddRAD) - are highly flexible but can present important technical issues. Inconsistent size selection reproducibility across libraries and variable coverage across fragment lengths can affect genotyping confidence, number of identified single nucleotide polymorphisms (SNPs), and quality and completeness of the de novo reference catalog. We have developed a strategy to optimize locus catalog building from ddRAD-like data by sequencing overlapping reads that recreate original fragments and add information about coverage per fragment size. Further in silico size selection and digestion steps limit the filtered dataset to well-covered sets of loci and identity thresholds are estimated based on sequence pairwise comparisons. We have developed a full workflow that identifies a set of reduced-representation single-copy orthologs (R2SCOs) for any given species and that includes estimating and evaluating allelic variation in comparison with SNP calling results. We also show how to use our concept in an established RADSeq pipeline - Stacks - and confirm that our approach increases average coverage and number of SNPs called per locus in the final catalog. We have demonstrated our full workflow using newly generated data from five sea turtle species and provided further proof-of-principle using published hybrid sea turtle and primate datasets. Finally, we showed that a project-specific set of R2SCOs perform better than a draft genome as a reference.

evolutionary biology↗