Papers by Jane Phillips-Conroy
International Journal of Primatology, Dec 1, 2008
Science, Apr 2, 1999
The article by Jon Cohen (News of the Week, 5 Feb. p. 772) reporting that human immunodeficiency ... more The article by Jon Cohen (News of the Week, 5 Feb. p. 772) reporting that human immunodeficiency virus-type 1 (HIV-1) probably originated in central African chimpanzees has prompted calls for collaboration between biomedical scientists and field-workers to investigate the natural ...
Mobile Dna, Apr 5, 2018
Background: Since the completion of the human genome project, the diversity of genome sequencing ... more Background: Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. Papio baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of Papio, the systematics of these species has been widely debated, and the evolutionary history of Papio diversity is not fully understood. Alu elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of Alu insertion polymorphisms unique to the Papio lineage. To complete these analyses, we created a computational algorithm to identify novel Alu insertions in next-generation sequencing data. Results: We identified 187,379 Alu insertions present in the Papio lineage, yet absent from M. mulatta [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve Papio baboons: two from each of the six extant Papio species. These data were used to construct a whole genome Alu-based phylogeny of Papio baboons. The resulting cladogram fully-resolved relationships within Papio. Conclusions: These data represent the most comprehensive Alu-based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved Alu-based phylogeny of Papio baboons.
The Journal of Clinical Endocrinology and Metabolism, Sep 1, 2001
Leptin has emerged as the major lipostat, regulating adiposity by affecting feeding behavior and ... more Leptin has emerged as the major lipostat, regulating adiposity by affecting feeding behavior and thermogenesis. Leptin levels in normal-weight Western humans and in captive rodents are 5-15 ng/ml. But evidence suggests that these levels are abnormally high and that leptin may have evolved as a more general metabolic signal, with its most robust effects at lower levels. If this is true, then wild, healthy animal populations should have lower levels of leptin than captive populations and Western Man. We examined leptin levels in wild, East African populations of baboons (Papio anubis, P. hamadryas, and anubis/hamadryas hybrids). Serum leptin levels averaged less than 1 ng/ml, and no differences occurred in leptin levels among the species. In wild baboons, serum leptin levels were highest in the youngest baboons, with a trend toward an inverse relation between dental age and serum leptin levels. In comparison, captive baboons had levels about three times higher than wild baboons, with a clear inverse relation between age and leptin levels. These results support the view that leptin evolved to be effective at low levels.
AIDS Research and Human Retroviruses, Jun 1, 1989
We have documented rare infection of baboons in their native habitat with simian immunodeficiency... more We have documented rare infection of baboons in their native habitat with simian immunodeficiency virus (SIV). Of 124 sera collected from yellow baboons in central Tanzania, two gave high readings by SIVagm ELISA (greater than 1.0) and moderate by SIVmac ELISA (0.5-1.0). These two sera gave strong reactions to the major SIVagm proteins, including gp130, by western blot analysis; their reactivity to SIVmac protein was considerably weaker. Similar testing of 155 sera from olive baboons of Ethiopia revealed no clearly positive sera. Thus, 2 of 279 baboon sera or 0.7% were positive for antibodies to SIV. The strong reactivity of the two positive yellow baboon sera with SIVagm proteins raises questions about whether these animals may have been infected by green monkeys in their native habitat; baboons occasionally prey upon and eat green monkeys. In addition to these two clearly positive samples, one olive baboon serum and one yellow baboon serum reacted only with major gag protein (p24-p26). Continued study of prevalence and diversity of SIV in primates will be important for understanding the history and evolution of primate lentiviruses and, it is hoped, the origins of viruses that cause AIDS in humans.
mSphere, Apr 26, 2017
Zika virus (ZIKV) has recently spread through the Americas and has been associated with a range o... more Zika virus (ZIKV) has recently spread through the Americas and has been associated with a range of health effects, including birth defects in children born to women infected during pregnancy. Although the natural reservoir of ZIKV remains poorly defined, the virus was first identified in a captive "sentinel" macaque monkey in Africa in 1947. However, the virus has not been reported in humans or nonhuman primates (NHPs) in Africa outside Gabon in over a decade. Here, we examine ZIKV infection in 239 wild baboons and African green monkeys from South Africa, the Gambia, Tanzania, and Zambia using combinations of unbiased deep sequencing, quantitative reverse transcription-PCR (qRT-PCR), and an antibody capture assay that we optimized using serum collected from captive macaque monkeys exposed to ZIKV, dengue virus, and yellow fever virus. While we did not find evidence of active ZIKV infection in wild NHPs in Africa, we found variable ZIKV seropositivity of up to 16% in some of the NHP populations sampled. We anticipate that these results and the methodology described within will help in continued efforts to determine the prevalence, natural reservoir, and transmission dynamics of ZIKV in Africa and elsewhere. IMPORTANCE Zika virus (ZIKV) is a mosquito-borne virus originally discovered in a captive monkey living in the Zika Forest of Uganda, Africa, in 1947. Recently, an outbreak in South America has shown that ZIKV infection can cause myriad health effects, including birth defects in the children of women infected during pregnancy. Here, we sought to investigate ZIKV infection in wild African primates to better understand its emergence and spread, looking for evidence of active or prior infection. Our results suggest that up to 16% of some populations of nonhuman primate were, at some point, exposed to ZIKV. We anticipate that this study will be useful for future studies that examine the spread of infections from wild animals to humans in general and those studying ZIKV in primates in particular. KEYWORDS false-positive reactions, Flavivirus, sensitivity and specificity, seroepidemiologic studies, Zika virus, Zika virus infection Z ika virus (ZIKV) is a positive-sense single-stranded RNA virus (family Flaviviridae, genus Flavivirus) that recently emerged to cause widespread human infection in Micronesia, French Polynesia, Singapore, and the Americas. The cause of ZIKV's recent global spread is poorly understood, and its natural reservoir remains poorly defined.
Molecular Phylogenetics and Evolution, Jul 1, 2004
International Journal of Primatology, Aug 1, 1992
Since 1983, we have observed 11 individually identified adult hamadryas immigrants in four anubis... more Since 1983, we have observed 11 individually identified adult hamadryas immigrants in four anubis groups above the Awash Falls and have trapped and tagged 9 of them. One subadult male was also captured and marked. Repeated visits to the study site allow us to document long-term residence of these "'cross-migrant" males in their host groups. The longest-resident male has been in the same group for 5 years or more; a conservative estimate of the average length of residence is 3 years. We estimate that 25 hamadryas males have moved into this zone over the last 15 years. Although larger than the hamadryas males captured in 1973, all but one of our cross-migrants appear phenotypical(y hamadryas. By comparing the ages of our cross-migrants with Abegglen's account of the typical hamadryas male life-history, we have found that the adult hamadryas males seem to immigrate at ages consistent with having left their
bioRxiv (Cold Spring Harbor Laboratory), May 2, 2023
bioRxiv (Cold Spring Harbor Laboratory), May 2, 2023
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys ... more Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
bioRxiv (Cold Spring Harbor Laboratory), Sep 1, 2021
Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. ... more Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.
The 82nd Annual Meeting of the American Association of Physical Anthropologists, Knoxville, Tennessee, 2013
The 82nd Annual Meeting of the American Association of Physical Anthropologists, Knoxville, Tennessee, 2013
Personalized genome sequencing has revealed millions of genetic differences between individuals, ... more Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicit...
Kinda and gray-footed chacma baboons occupy opposite extremes of the body size distribution in ex... more Kinda and gray-footed chacma baboons occupy opposite extremes of the body size distribution in extant baboons (genusPapio). In order to detect signatures of natural selection in these two species, we genotyped 24,790 genome-wide autosomal SNPs from populations of Zambian baboons using double digest RADseq. We scanned the genome for evidence of selection by identifying regions with extreme differentiation between populations. We find evidence of selection on body size influencing multiple genes in one or both species, includingFGF1, ATXN2, andPRKCE. We also find an enriched signal of selection associated with biological processes involved in multicellular organism growth and development, cell proliferation and cell growth, nutrient metabolism, and chondrocyte differentiation. Finally, we find that selection has impacted components of the CCKR signaling pathway, which regulates food intake and metabolism, and the JAK/STAT signaling pathway, which mediates the effect of cytokine signal...
Hybridization in nature offers unique insights into the process of natural selection in incipient... more Hybridization in nature offers unique insights into the process of natural selection in incipient species and their hybrids. In order to evaluate the patterns and targets of selection, we examine a recently discovered baboon hybrid zone in the Kafue River valley of Zambia, where Kinda baboons (Papio kindae) and gray-footed chacma baboons (P. ursinus griseipes) coexist with hybridization. We genotyped baboons at 14,962 variable genome-wide autosomal markers using double-digest RADseq. We compare ancestry patterns from this genome-wide dataset to previously reported ancestry from mitochondrial-DNA and Y-chromosome sources. We also fit a Bayesian genomic cline model to scan for genes with extreme patterns of introgression. We show that the Kinda baboon Y chromosome has penetrated the species boundary to a greater extent than either mitochondrial DNA or the autosomal chromosomes. We also find evidence for overall restricted introgression in the JAK/STAT signaling pathway. Echoing result...
Genome Biology and Evolution, 2017
Membership in the Baboon Genome Analysis Consortium is listed in the supplementary file S1, Suppl... more Membership in the Baboon Genome Analysis Consortium is listed in the supplementary file S1, Supplementary Material online.
The rich diversity of morphology and behavior displayed across primate species provides an inform... more 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...
An excel file containing a figure and table representing possible basal divergence model reconstr... more An excel file containing a figure and table representing possible basal divergence model reconstructions generated using all six extant Papio species. A maximum of 31 rooted monophyletic models can be generated from such a genus comprised of six species. These models can be further organized into three distinct groups based on the number of species contained in the subsequent clades. Group I depicts the six different scenarios when one of the six species diverges prior to the other five. Group I-A) illustrates P. kindae diverging first, followed by B) P. ursinus first, then C-F) P. cynocephalus, P. papio, P. hamadryas, and P. anubis diverging first, respectively. Group II depicts the 15 different models when two of the six species diverge prior to the other four. All possible combinations of this scenario are illustrated in Group II A-O. Group III depicts the ten different models generated from a basal divergence that forms two clades each comprised of three species. All ten combina...
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Papers by Jane Phillips-Conroy