The Genetic Basis of Primate Behavior: Genetics and Genomics in Field-Based Primatology (original) (raw)

Sequencing primate genomes: What have we learned?

2009

We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation, and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a signiflcant challenge. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into the genetic basis of primate evolution. Nextgeneration sequencing technologies promise to greatly expand the number of available primate genome sequences; however, such draft genome sequences will likely miss critical genetic differences within complex genomic regions unless dedicated efforts are put forward to understand the full spectrum of genetic variation.

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thoug...

Moving primate genomics beyond the chimpanzee genome

Trends in Genetics, 2005

The comparative DNA sequence data that already exist on individual genomic loci depict the phylogenetic relationships of nearly all extant primate genera. Such a phylogenetic representation of the primates, validated by many sequenced primate genomes, and encompassing the full adaptive diversity of the order, is a prerequisite for identifying the genetic basis of humankind, and for testing the proposed human uniqueness of these traits. Some of these traits have been discovered recently, particularly in genes encoding proteins that are important for brain function. has had a makeover, inside and out.

A Primate Genome Project Deserves High Priority

Science, 2000

The initial goals of the Human Genome Project (HGP), to sequence the human genome and identify its constituent genes, are on the verge of being achieved. However, the scientific community recognizes that sequencing must be followed by understanding the manifold functions of human genes throughout the lifespan , in health and in disease. In a Science interview (News Focus, 31 Mar., p. 2396), Francis Collins acknowledged this by saying, "Understanding what the sequence means will require us to make multiple comparisons....The arguments are quite strong for sequencing other mammals besides human and mouse...and for doing another primate."

Primate Comparative Genomics : The Evolution of our Order

2013

We summarize the progress in whole-genome sequencing and analyses of primate genomes. These emerging genome datasets have broadened our understanding of primate genome evolution revealing unexpected and complex patterns of evolutionary change. This includes the characterization of genome structural variation, episodic changes in the repeat landscape, differences in gene expression, new models regarding speciation and the ephemeral nature of the recombination landscape. The functional characterization of genomic differences important in primate speciation and adaptation remains a significant challenge.. Limited access to biological materials, the lack of detailed phenotypic data and the endangered status of many critical primate species have significantly attenuated research into understanding the genetic basis of primate evolution. Next-generation sequencing technologies promise to greatly expand the number of primate genome targets; however, such draft genomes will likely miss critical genetic differences within complex regions of the genome unless dedicated efforts are put forward to understand the full spectrum of genetic variation.

Resource brief: The National Non-Human Primate DNA Bank

Methods, 2009

A National Non-Human Primate (NHP) DNA bank has been established by the National Primate Research Centers and the National Center for Research Resources, NIH, providing a new resource for comparative genomic studies. The collection includes genomic DNA samples from macaques, chimpanzees, baboons, vervets, marmosets, sooty mangabeys and titi monkeys. The repository includes DNAs from 697 unrelated animals, suitable for comparing allele representation within and between species. Another 474 DNAs are derived from family trios (dam, sire, off spring), and are useful for verifying the segregation of genetic variants. The National NHP DNA Bank includes specified holdings within each of the 8 National Primate Research Centers, though detailed information on the entire collection is available through a common website.

A Molecular Phylogeny of Living Primates

PLoS Genetics, 2011

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (,8 Mb) from 186 primates representing 61 (,90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

Prime time for primate functional genomics

Current Opinion in Genetics & Development, 2020

Functional genomics research is continually improving our understanding of genotype-phenotype relationships in humans, and comparative genomics perspectives can provide additional insight into the evolutionary histories of such relationships. To specifically identify conservation or species-specific divergence in humans, we must look to our closest extant evolutionary relatives. Primate functional genomics research has been steadily advancing and expanding, in spite of several limitations and challenges that this field faces. New technologies and cheaper sequencing provide a unique opportunity to enhance and expand primate comparative studies, and we outline possible paths going forward. The potential human-specific insights that can be gained from primate functional genomics research are substantial, and we propose that now is a prime time to expand such endeavors.

Development and annotation of shotgun sequence libraries from New World monkeys

Molecular Ecology Resources, 2012

The draft genome sequences of several primates are available, providing insights into evolutionary and anthropological research. However, genomic resources from New World monkeys are conspicuously lacking. To date, the genomes of only two platyrrhine species, the common marmoset and the Bolivian squirrel monkey, have been fully sequenced. This is especially limiting for comparative genomics research, considering that New World monkeys are the most speciose primate group, and platyrrhine genetic diversity is comparable to that of the catarrhines (i.e. apes and Old World monkeys). Here, we present the generation and annotation of numerous sequence reads from the genomes of Spider monkey (Ateles belzebuth), Owl monkey (Aotus lemurinus) and Uakari (Cacajao calvus), representing the three platyrrhine families, Atelidae, Cebidae and Pitheciidae, respectively. These sequencing reads were developed from gDNA shotgun libraries containing over 3000 individual sequences with an average length of 726 bps. Of these sequences, 1220 contain <20% repeats, and thus are potentially highly useful phylogenetic markers for other platyrrhine species. Among them, a large number of sequencing reads were found to match unique regions within the human (2462 sequences) and the marmoset (2829 sequences) genomes. In particular, the majority of these sequencing reads are from putatively neutrally evolving intergenic regions. Thus, they are likely to be highly informative for inferring neutral evolutionary patterns and genomic evolution for other New World monkeys.