Paul L. Babb

Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection

BackgroundCopy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation.ResultsIn this study, we identified over 2,000 human CNVs that overlap with orthologous chimpanzee or orthologous macaque CNVs. Of these, 170 CNVs overlap with both chimpanzee and macaque CNVs, and these were collapsed into 34 hotspot regions of CNV formation. Many of these hotspot regions of CNV formation are functionally relevant, with a bias toward genes involved in immune function, some of which were previously shown to evolve under balancing selection in humans. The genes in these primate CNV formation hotspots have significant differential expression levels between species and show evidence for positive selection, indicating that they have evolved under species-specific, directional selection.ConclusionsThese hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions.

Correlates of genetic monogamy in socially monogamous mammals: insights from Azara's owl monkeys

Understanding the evolution of mating systems, a central topic in evolutionary biology for more than 50 years, requires examining the genetic consequences of mating and the relationships between social systems and mating systems. Among pair-living mammals, where genetic monogamy is extremely rare, the extent of extra-group paternity rates has been associated with male participation in infant care, strength of the pair bond and length of the breeding season. This study evaluated the relationship between two of those factors and the genetic mating system of socially monogamous mammals, testing predictions that male care and strength of pair bond would be negatively correlated with rates of extra-pair paternity (EPP). Autosomal microsatellite analyses provide evidence for genetic monogamy in a pair-living primate with bi-parental care, the Azaras owl monkey (Aotus azarae). A phylogenetically corrected generalized least square analysis was used to relate male care and strength of the pair bond to their genetic mating system (i.e. proportions of EPP) in 15 socially monogamous mammalian species. The intensity of male care was correlated with EPP rates in mammals, while strength of pair bond failed to reach statistical significance. Our analyses show that, once social monogamy has evolved, paternal care, and potentially also close bonds, may facilitate the evolution of genetic monogamy.

AVPR1A Sequence Variation in Monogamous Owl Monkeys (Aotus azarai) and Its Implications for the Evolution of Platyrrhine Social Behavior

The arginine vasopressin V1a receptor gene (AVPR1A) has been implicated in increased partner preference and pair bonding behavior in mammalian lineages. This observation is of considerable importance for studies of social monogamy, which only appears in a small subset of primate taxa, including the Argentinean owl monkey (Aotus azarai). Thus, to investigate the possible influence of AVPR1A on the evolution of social behavior in owl monkeys, we sequenced this locus in a wild population from the Gran Chaco. We also assessed the interspecific variation of AVPR1A in platyrrhine species that represent a set of phylogenetically and behaviorally disparate taxa. The resulting data revealed A. azarai to have a unique genic structure for AVPR1A that varies in coding sequence and microsatellite repeat content relative to other primate and mammalian species. Specifically, one repetitive region that has been the focus in studies of human AVPR1A diversity, “RS3,” is completely absent in A. azarai and all other platyrrhines examined. This finding suggests that, if AVPR1A modulates behavior in owl monkeys and other neotropical primates, it does so independent of this region. These observations have also provided clues about the process by which the range of social behavior in the Order Primates evolved through lineage-specific neurogenetic variation.

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

Spider silks are the toughest known biological materials, yet are lightweight and virtually invisible to the human immune system, and they thus have revolutionary potential for medicine and industry. Spider silks are largely composed of spidroins, a unique family of structural proteins. To investigate spidroin genes systematically, we constructed the first genome of an orb-weaving spider: the golden orb-weaver (Nephila clavipes), which builds large webs using an extensive repertoire of silks with diverse physical properties. We cataloged 28 Nephila spidroins, representing all known orb-weaver spidroin types, and identified 394 repeated coding motif variants and higher-order repetitive cassette structures unique to specific spidroins. Characterization of spidroin expression in distinct silk gland types indicates that glands can express multiple spidroin types. We find evidence of an alternatively spliced spidroin, a spidroin expressed only in venom glands, evolutionary mechanisms for spidroin diversification, and non-spidroin genes with expression patterns that suggest roles in silk production.

mtDNA diversity in azara's owl monkeys (Aotus azarai azarai) of the Argentinean Chaco

Owl monkeys (Aotus spp.) inhabit much of South America yet represent an enigmatic evolutionary branch among primates. While morphological, cytogenetic, and immunological evidence suggest that owl monkey populations have undergone isolation and diversification since their emergence in the New World, problems with adjacent species ranges, and sample provenance have complicated efforts to characterize genetic variation within the genus. As a result, the phylogeographic history of owl monkey species and subspecies remains unclear, and the extent of genetic diversity at the population level is unknown. To explore these issues, we analyzed mitochondrial DNA (mt DNA) variation in a population of wild Azaras owl monkeys (Aotus azarai azarai) living in the Gran Chaco region of Argentina. We sequenced the complete mitochondrial genome from one individual (16,585 base pairs (bp)) and analyzed 1,099 bp of the hypervariable control region (CR) and 696 bp of the cytochrome oxidase II (COII) gene in 117 others. In addition, we sequenced the mitochondrial genome (16,472 bp) of one Nancy Mas owl monkey (A. nancymaae). Based on the whole mtDNA and COII data, we observed an ancient phylogeographic discontinuity among Aotus species living north, south, and west of the Amazon River that began more than eight million years ago. Our population analyses identified three major CR lineages and detected a high level of haplotypic diversity within A. a. azarai. These data point to a recent expansion of Azaras owl monkeys into the Argentinean Chaco. Overall, we provide a detailed view of owl monkey mtDNA variation at genus, species, and population levels.

An Optimized Microsatellite Genotyping Strategy for Assessing Genetic Identity and Kinship in Azara's Owl Monkeys (Aotus azarai)

In this study, we characterize a panel of 20 microsatellite markers that reproducibly amplify in Azara’s owl monkeys (Aotus azarai) for use in genetic profiling analyses. A total of 128 individuals from our study site in Formosa, Argentina, were genotyped for 20 markers, 13 of which were found to be polymorphic. The levels of allelic variation at these loci provided paternity exclusion probabilities of 0.852 when neither parent was known, and 0.981 when one parent was known. In addition, our analysis revealed that, although genotypes can be rapidly scored using fluorescence-based fragment analysis, the presence of complex or multiple short tandem repeat (STR) motifs at a microsatellite locus could generate similar fragment patterns from alleles that have different nucleotide sequences and perhaps different evolutionary origins. Even so, this collection of microsatellite loci is suitable for parentage analyses and will allow us to test various hypotheses about the relationship between social behavior and kinship in wild owl monkey populations. Furthermore, given the limited number of platyrrhine-specific microsatellite loci available in the literature, this STR panel represents a valuable tool for population studies of other cebines and callitrichines.

Prolactin Receptor Gene Diversity in Azara’s Owl Monkeys (Aotus azarai) and Humans (Homo sapiens) Suggests a Non-Neutral Evolutionary History among Primates

Although paternal care is rare in mammals, males of several primate taxa exhibit high degrees of this behavior. Studies a number of vertebrate species found a positive correlation between prolactin (PRL) levels and paternal care. Studies of maternal care in knockout mice also indicate that the prolactin receptor (PRLR) plays a critical role in the neural regulation of parental care. To better understand the extent of PRLR genetic variation within primates, we characterized intraspecific coding variation in Azara’s owl monkeys (Aotus azarai) from northern Argentina, a species with intensive paternal care. We then examined PRLR variation in 1088 humans (Homo sapiens) from the 1000 Genomes Project. Lastly, we assessed interspecific variation in PRLR in 4 different Aotus spp. and 12 phylogenetically (and behaviorally) disparate primate taxa. Our analyses revealed that the coding region of PRLR exhibits significant variation in all species of primates, with nonsynonymous amino acid substitutions being enriched in the intracellular domain, a region responsible for activation of downstream targets in the PRL pathway. In addition, several species exhibit entire codon deletions in this region. These results suggest a non-neutral evolutionary history of the PRLR locus within different primate lineages, and further imply that the translated PRLR protein has undergone considerable change throughout primate evolution. Such changes may be driven by selection for different behaviors and physiologies resulting from modulations of the pleiotropic prolactin pathway. Yet, the genetic variants in PRLR among primate taxa do not discretely cluster with species-level differences in paternal care behaviors. These observations imply that other mechanisms must be involved in the regulation of paternal care in primates.

Progesterone Response Element Variation in the OXTR Promoter Region and Paternal Care in New World Monkeys

Paternal care is a complex social behavior common in primate species with socially monogamous mating systems and twin births. Evolutionary causes and consequences of such behavior are not well understood, nor are their neuroendocrine and genetic bases. However, the neuropeptide oxytocin (OXT) and its receptor (OXTR) are associated with parental care in mammalian lineages. Here we investigated the interspecific variation in the number of progesterone response elements (PREs) in the OXTR promoter region of 32 primate species, correlating genetic data with behavior, social systems, and ecological/life-history parameters, while controlling for phylogeny. We verified that PREs are only present in New World monkeys and that PRE number is significantly correlated with the presence of paternal care in this branch. We suggest that PRE number could be an essential part of the genetic repertoire that allowed the emergence of taxon-specific complex social behaviors, such as paternal care in marmosets and tamarins.

Multiplexed Targeted Resequencing Identifies Coding and Regulatory Variation Underlying Phenotypic Extremes of High-Density Lipoprotein Cholesterol in Humans

Background: Genome-wide association studies have uncovered common variants at many loci influencing human complex traits, such as high-density lipoprotein cholesterol (HDL-C). However, the contribution of the identified genes is difficult to ascertain from current efforts interrogating common variants with small effects. Thus, there is a pressing need for scalable, cost-effective strategies for uncovering causal variants, many of which may be rare and noncoding. Methods: Here, we used a molecular inversion probe target capture approach to resequence both coding and regulatory regions at 7 HDL-C–associated loci in 797 individuals with extremely high HDL-C versus 735 low-to-normal HDL-C controls. Our targets included protein-coding regions of GALNT2, APOA5, APOC3, SCARB1, CCDC92, ZNF664, CETP, and LIPG (>9 kb) and proximate noncoding regulatory features (>42 kb). Results: Exome-wide genotyping in 1114 of the 1532 participants yielded a >90% genotyping concordance rate with molecular inversion probe-identified variants in ≈90% of participants. This approach rediscovered nearly all established genome-wide association studies associations in GALNT2, CETP, and LIPG loci with significant and concordant associations with HDL-C from our phenotypic extremes design at 0.1% of the sample size of lipid genome-wide association studies. In addition, we identified a novel, rare, CETP noncoding variant enriched in the extreme high HDL-C group (P<0.01, score test). Conclusions: Our targeted resequencing of individuals at the HDL-C phenotypic extremes offers a novel, efficient, and cost-effective approach for identifying rare coding and noncoding variation differences in extreme phenotypes and supports the rationale for applying this methodology to uncover rare variation—particularly noncoding variation—underlying myriad complex traits.

Multiplexed targeted resequencing identifies coding and regulatory variation underlying phenotypic extremes of HDL-cholesterol in humans

Genome-wide association studies have uncovered common variants at many loci influencing human complex traits and diseases, such as high-density lipoprotein cholesterol (HDL-C). However, the contribution of the identified genes is difficult to ascertain from current efforts interrogating common variants with small effects. Thus, there is a pressing need for scalable, cost-effective strategies for uncovering causal variants, many of which may be rare and noncoding. Here, we used a multiplexed inversion probe (MIP) target capture approach to resequence both coding and regulatory regions at seven HDL-C associated loci in 797 individuals with extremely high HDL-C vs. 735 low-to-normal HDL-C controls. Our targets included protein-coding regions of GALNT2, APOA5, APOC3, SCARB1, CCDC92, ZNF664, CETP, and LIPG (>9 kb), and proximate noncoding regulatory features (>42 kb). Exome-wide genotyping in 1,114 of the 1,532 participants yielded a >90% genotyping concordance rate with MIP-identified variants in ~90% of participants. This approach rediscovered nearly all established GWAS associations in GALNT2, CETP, and LIPG loci with significant and concordant associations with HDL-C from our phenotypic-extremes design at 0.1% of the sample size of lipid GWAS studies. In addition, we identified a novel, rare, CETP noncoding variant enriched in the extreme high HDL-C group (P<0.01, Score Test). Our targeted resequencing of individuals at the HDL-C phenotypic extremes offers a novel, efficient, and cost-effective approach for identifying rare coding and noncoding variation differences in extreme phenotypes and supports the rationale for applying this methodology to uncover rare variation—particularly non-coding variation--underlying myriad complex traits.