A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

Mitochondrial DNA for Phylogeny Building: Assessing Individual and Grouped mtGenes as Proxies for the mtGenome in Platyrrhines

Phylogenetic trees are analytic tools used in primate studies to elucidate evolutionary relationships. Because of its relative ease to sequence and rapid evolution compared to nuclear genomes, mitochondrial DNA is frequently used for phylogeny building. This project evaluated the effectiveness of using individual or grouped mitochondrial genes (mtGenes) as a proxy for the mitochondrial genome (mtGenome) in phylogeny building within two nested primate datasets, Cebidae and Platyrrhini, with differing divergence dates. mtGene utility rankings were determined based on congruence values to the mtGenome tree. mtGenes trees were also assessed on tree resolution and ability to sort nested clades. We found that most individual mtGenes, including ribosomal genes (12S and 16S), COX genes, most ND genes, and d-Loop are not appropriate for use as proxies for the mtGenome when tree building in either the Cebidae or Platyrrhini set. On average, grouped mtGenes outperformed individual mtGenes in both sets, and mtGene and grouped mtGene rankings varied between sets. Pairing CYB and COX3 together or pairing ND2 and CYB worked well in both the Cebidae set and the Platyrrhini set. We also found that nucleotide diversity is not a predictor of mtGene performance. Instead, it may be that unique mtGene or mtGene system evolutionary history impacts mtGene performance.

Genetic Determination of a Cryptic Species in the Littoraria Genus With Whole-Genome Molecular Resolution

Recognizing cryptic species is crucial for understanding global biodiversity. The intertidal snail Littoraria flammea is potentially a cryptic species of L. melanostoma widely distributed in the Northwest Pacific. However, the evidence from traditional morphology and single genetic markers is inconsistent. Our study combined quantitative morphological and whole-genome molecular data to clarify the phylogenetic relationship of three species (L. flammea, L. aff. melanostoma, and L. melanostoma). Three-dimensional models of shells revealed significant differences in morphology between L. flammea and L. melanostoma. Neutral SNPs indicated that individuals of L. flammea and L. melanostoma were in different clusters. The ratio of interspecific F ST to intraspecific F ST between L. flammea and L. melanostoma (16) was much larger than the lowest ratio (2.31) in six published genera with cryptic species in gastropods. Non-neutral SNPs disclosed divergence in functional genes related to reproduction and protein binding. The morphological and phylogenetic analyses corroborated the transitional status of L. aff. melanostoma. These results confirmed that the L. flammea snails north of the Yangtze River Estuary is a cryptic species of L. melanostoma, and allopatric speciation occurs in the L. melanostoma complex.

Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.

A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation

Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the number of discrete species supported. Our results support the recognition of three species from the Atlantic Forest south of the São Francisco River, with these species being the first splits in the robust capuchin radiation. Our results were congruent in recovering the Pantanal and Amazonian Sapajus as structured into three monophyletic clades, though new morphological assessments are necessary, as the Amazonian clades do not agree with previous morphology-based taxonomic distributions. Phylogenetic reconstructions for Sapajus occurring in the Cerrado, Caatinga, and northeastern Atlantic Forest were less congruent with morphology-based phylogenetic reconstructions, as the bearded capuchin was recovered as a paraphyletic clade, with samples from the Caatinga biome being either a monophyletic clade or nested with the blond capuchin monkey.

2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics

Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.

Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation

Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N's in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.

Signatures of adaptive evolution in platyrrhine primate genomes

The platyrrhine family Cebidae (capuchin and squirrel monkeys) exhibit among the largest primate encephalization quotients. Each cebid lineage is also characterized by notable lineage-specific traits, with capuchins showing striking similarities to Hominidae such as high sensorimotor intelligence with tool use, advanced cognitive abilities, and behavioral flexibility. Here, we take a comparative genomics approach, performing genome-wide tests for positive selection across five cebid branches, to gain insight into major periods of cebid adaptive evolution. We uncover candidate targets of selection across cebid evolutionary history that may underlie the emergence of lineage-specific traits. Our analyses highlight shifting and sustained selective pressures on genes related to brain development, longevity, reproduction, and morphology, including evidence for cumulative and diversifying neurobiological adaptations across cebid evolution. In addition to generating a high-quality reference genome assembly for robust capuchins, our results lend to a better understanding of the adaptive diversification of this distinctive primate clade.

Molecular phylogeny and systematics of bald uakaris, genus Cacajao Lesson, 1840 (Primates: Pitheciidae), with the description of a new species

Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species.

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish

The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.

Species distribution and conservation assessment of the black-headed night monkey (Aotus nigriceps): a species of Least Concern that faces widespread anthropogenic threats

Deforestation rates in the Brazilian Amazon have been steadily increasing since 2007. Recent government policy, the projected growth of agriculture, and the expansion of the cattle industry are expected to further pressure primates within the Amazon basin. In this study, we examined the anthropogenic impact on the widely distributed black-headed night monkey, Aotus nigriceps, whose distribution and population status have yet to be assessed. We (1) modeled potential species distribution in A. nigriceps, (2) estimated the impact of habitat loss on population trends, and (3) highlight landscape-based conservation actions that maximize the potential for their long-term sustainability. We found the black-headed night monkey to be restricted by several biotic and environmental factors including forest cover, isothermality, precipitation, temperature, and elevation. Over the last two decades, over 132,908 km² of tree cover (18%) has been lost within their currently recognized range based on satellite imagery. Based on a balance training omission, predicted area, and threshold values (BPTP), suitable habitat was only 67% (1,069,948 km²) of their hypothesized range, a loss of 16.5% from 2000, with just nearly a third of suitable habitat currently within protected areas. Over the last two decades, an estimated minimum 1.6 million individuals have been lost due to loss of suitable habitat. Projected deforestation rates equate to an additional loss of 94,458 km² of suitable habitat over the next decade. Although classified as a species of Least Concern, we suggest that A. nigriceps may likely be more at risk than previously described. The future impact of the continued expansion of monoculture crops, cattle ranching, and wildfires is still unknown. However, we outline several steps to ensure the long-term viability of this nocturnal primate and other sympatric species throughout the Amazon Basin.

Hepatitis C outreach project and cross-sectional epidemiology in high-risk populations in Trondheim, Norway

BACKGROUND

Hepatitis C is highly prevalent among people who use drugs (PWUD), and the hepatitis C virus (HCV) epidemic is less characterised in Norway. The aims of the study were to assess the prevalence and treatment willingness in high-risk populations by reaching out to frequently visited sites for high-risk populations.

METHODS

Individuals from high-risk populations were included from September 2015 to March 2017. Two dedicated study nurses frequently visited the local opioid substitution clinic, outpatient clinics, PWUD day centres, local prison, and refugee centre in Trondheim, Norway. Demographic data, risk behaviour, and clinical symptoms were obtained by study questionnaire. Subjects with anti-HCV+ rapid test were subsequently tested for HCV RNA and genotyped. Viraemic patients were offered referral for HCV treatment evaluation.

RESULTS

A total of 381 participants were included in the study: 52 immigrants, 62 prisoners, and 267 PWUD. The anti-HCV prevalence rates were 0% (n = 0) in immigrants, 40% (n = 25) in prisoners, and 61% (n = 164) in PWUD, with 24% (n = 15) of prisoners and 42% (n = 108) of PWUD being viraemic. Of those qualifying for treatment (n = 31), 30 wished to be evaluated.

CONCLUSION

This study showed high HCV prevalence in prisoners and PWUD and that infected high-risk patients were interested in treatment evaluation.

Historical antecedents and recent innovations in pitheciid (titi, saki, and uakari) feeding ecology

The modern pitheciids (titis, sakis, and uakaris) of northern South America represent one of the earliest radiations of platyrrhines and demonstrate morphological adaptations and ecological strategies for seed eating. While seeds can provide reliable resources for relatively long periods of time, they are often well protected by thick husks and hard seed coverings. Seeds also tend to be rich in lipids, but they may also be high in indigestible fiber. Even though seed eaters are found in each major primate radiation, only the pitheciids demonstrate primary adaptations for eating seeds. In this partly historical, partly contemporary review, I examine the ecological and anatomical correlates of seed eating. It is dedicated to two well-known field primatologists: ecologist and conservationist J. Márcio Ayres; and anatomist and ecologist Warren G. Kinzey. Using observations in Kinzey (1992, Am J Phys Anthropol, 88, pp. 499-514) as a framework, I provide context and analysis for the intervening three decades of pitheciid research to identify what we know about this understudied group of primates and propose directions for future work.