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BioRxiv : the Preprint Server For... May 2023Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying...
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying these patterns within hybrid populations have been lacking. Here, we develop methods based on the Wavelet Transform to understand the spatial genomic scale of local ancestry variation and its association with recombination rates. We present theory and use simulations to show how wavelet-based decompositions of ancestry variance along the genome and the correlation between ancestry and recombination reflect the joint effects of recombination, genetic drift, and genome-wide selection against introgressed alleles. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of local ancestry variation at varying spatial genomic scales through time. Using wavelet approaches to identify the genomic scale of variance in ancestry and its correlates, we show that these methods can detect temporally localized effects of drift and selection. We apply these methods to previously published datasets from hybrid populations of swordtail fish () and baboons (), and to inferred Neanderthal introgression in modern humans. Across systems, we find that upwards of 20% of the variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. We also see signals of selection at fine genomic scales and much longer time scales. However, we show that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available, and can help shed light on generalities of the genomic consequences of interspecific hybridization.
PubMed: 37337589
DOI: 10.1101/2023.05.25.542345 -
Learning & Behavior Dec 2023When human and non-human animals learn sequences, they manage to implicitly extract statistical regularities through associative learning mechanisms. In two experiments...
When human and non-human animals learn sequences, they manage to implicitly extract statistical regularities through associative learning mechanisms. In two experiments conducted with a non-human primate species (Guinea baboons, Papio papio), we addressed simple questions on the learning of simple AB associations appearing in longer noisy sequences. Using a serial reaction time task, we manipulated the position of AB within the sequence, such that it could be either fixed (by appearing always at the beginning, middle, or end of a four-element sequence; Experiment 1) or variable (Experiment 2). We also tested the effect of sequence length in Experiment 2 by comparing the performance on AB when it was presented at a variable position within a sequence of four or five elements. The slope of RTs from A to B was taken for each condition as a measurement of learning rate. While all conditions differed significantly from a no-regularity baseline, we found strong evidence that the learning rate did not differ between the conditions. These results indicate that regularity extraction is not impacted by the position of the regularity within a sequence and by the length of the sequence. These data provide novel general empirical constraints for modeling associative mechanisms in sequence learning.
Topics: Animals; Learning; Reaction Time; Papio papio
PubMed: 37284936
DOI: 10.3758/s13420-023-00579-z -
Science (New York, N.Y.) Jun 2023Baboons (genus ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically...
Baboons (genus ) 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 interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal 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.
Topics: Animals; Male; Biological Evolution; Gene Flow; Papio; Phenotype; Phylogeny; Species Specificity; Sex Characteristics
PubMed: 37262153
DOI: 10.1126/science.abn8153 -
Biology Letters May 2023While anthropogenic pollutants are known to be a threat to primates, our understanding of exposure to pollutants and their sub-lethal effects is still limited. We used...
While anthropogenic pollutants are known to be a threat to primates, our understanding of exposure to pollutants and their sub-lethal effects is still limited. We used non-invasive biomonitoring to examine associations between faecal concentrations of 97 chemical pollutants and faecal hormone metabolites of cortisol and oestradiol in four primate species inhabiting Kibale National Park, Uganda (chimpanzees-, olive baboons-, red colobus- and red-tailed monkeys-). Across all species ( = 71 samples), results demonstrated positive associations of organochlorine pesticides (OCPs) ( = 0.143, = 0.020) and organophosphate esters ( = 0.112, = 0.003) with cortisol in adult females. Additionally, we observed positive associations of OCPs ( = 0.192, = 0.013) and brominated flame retardants ( = 0.176, = 0.004) with cortisol in juveniles. Results suggest that cumulative pesticides and flame retardants are disruptive to endocrine function in these populations, which could have implications for development, metabolism and reproduction. Our study further demonstrates that faeces can be an important, non-invasive matrix for examining pollutant-hormone associations in wild primates and other critical wildlife populations.
Topics: Female; Animals; Hydrocortisone; Uganda; Flame Retardants; Parks, Recreational; Environmental Pollutants; Feces; Pan troglodytes; Pesticides; Primates
PubMed: 37221860
DOI: 10.1098/rsbl.2023.0005 -
BioRxiv : the Preprint Server For... May 2023Baboons (genus ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically...
UNLABELLED
Baboons (genus ) 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.
ONE-SENTENCE SUMMARY
Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
PubMed: 37205419
DOI: 10.1101/2023.05.02.539112 -
Ecology and Evolution May 2023Species with slow life history strategies that invest in few offspring with extended parental care need to adapt their behavior to cope with anthropogenic changes that...
Species with slow life history strategies that invest in few offspring with extended parental care need to adapt their behavior to cope with anthropogenic changes that occur within their lifetime. Here we show that a female chacma baboon () that commonly ranges within urban space in the City of Cape Town, South Africa, stops using urban space after giving birth. This change of space use occurs without any significant change in daily distance traveled or social interactions that would be expected with general risk-sensitive behavior after birth. Instead, we suggest this change occurs because of the specific and greater risks the baboons experience within the urban space compared to natural space, and because leaving the troop (to enter urban space) may increase infanticide risk. This case study can inform methods used to manage the baboons' urban space use in Cape Town and provides insight into how life history events alter individuals' use of anthropogenic environments.
PubMed: 37200910
DOI: 10.1002/ece3.9963 -
Science Advances May 2023Adverse conditions in early life can have negative consequences for adult health and survival in humans and other animals. What variables mediate the relationship...
Adverse conditions in early life can have negative consequences for adult health and survival in humans and other animals. What variables mediate the relationship between early adversity and adult survival? Adult social environments represent one candidate: Early life adversity is linked to social adversity in adulthood, and social adversity in adulthood predicts survival outcomes. However, no study has prospectively linked early life adversity, adult social behavior, and adult survival to measure the extent to which adult social behavior mediates this relationship. We do so in a wild baboon population in Amboseli, Kenya. We find weak mediation and largely independent effects of early adversity and adult sociality on survival. Furthermore, strong social bonds and high social status in adulthood can buffer some negative effects of early adversity. These results support the idea that affiliative social behavior is subject to natural selection through its positive relationship with survival, and they highlight possible targets for intervention to improve human health and well-being.
Topics: Animals; Humans; Adult; Adverse Childhood Experiences; Interpersonal Relations; Social Behavior; Social Environment; Papio
PubMed: 37196090
DOI: 10.1126/sciadv.ade7172 -
Reproductive Sciences (Thousand Oaks,... Oct 2023MicroRNAs (miRs) play an important role in the pathophysiology of endometriosis; however, the role of miR-210 in endometriosis remains unclear. This study explores the...
MicroRNAs (miRs) play an important role in the pathophysiology of endometriosis; however, the role of miR-210 in endometriosis remains unclear. This study explores the role of miR-210 and its targets, IGFBP3 and COL8A1, in ectopic lesion growth and development. Matched eutopic (EuE) and ectopic (EcE) endometrial samples were obtained for analysis from baboons and women with endometriosis. Immortalized human ectopic endometriotic epithelial cells (12Z cells) were utilized for functional assays. Endometriosis was experimentally induced in female baboons (n = 5). Human matched endometrial and endometriotic tissues were obtained from women (n = 9, 18-45 years old) with regular menstrual cycles. Quantitative reverse transcript polymerase chain reaction (RT-qPCR) analysis was performed for in vivo characterization of miR-210, IGFBP3, and COL8A1. In situ hybridization and immunohistochemical analysis were performed for cell-specific localization. Immortalized endometriotic epithelial cell lines (12Z) were utilized for in vitro functional assays. MiR-210 expression was decreased in EcE, while IGFBP3 and COL8A1 expression was increased in EcE. MiR-210 was expressed in the glandular epithelium of EuE but attenuated in those of EcE. IGFBP3 and COL8A1 were expressed in the glandular epithelium of EuE and were increased compared to EcE. MiR-210 overexpression in 12Z cells suppressed IGFBP3 expression and attenuated cell proliferation and migration. MiR-210 repression and subsequent unopposed IGFBP3 expression may contribute to endometriotic lesion development by increasing cell proliferation and migration.
Topics: Animals; Humans; Female; Adolescent; Young Adult; Adult; Middle Aged; Endometriosis; Papio; MicroRNAs; Endometrium; Cell Line; Insulin-Like Growth Factor Binding Protein 3
PubMed: 37188982
DOI: 10.1007/s43032-023-01253-5 -
BMC Zoology Apr 2022The study on medium and large-sized mammalian species' diversity and distribution is important for conservation efforts in the different protected areas of Ethiopia. The...
The study on medium and large-sized mammalian species' diversity and distribution is important for conservation efforts in the different protected areas of Ethiopia. The present study was intended to investigate the species diversity of medium and large-sized mammalian fauna between October 2019 and July 2020 in Michole Community Protected Forest, southern Ethiopia. The study was conducted by stratification of the study area into three habitat types: riverine forest (3.37 km), woodland (4.14 km), and grassland with scattered trees (2.33 km) based on the vegetation cover. A diurnal transect survey method was implemented to record the mammalian species diversity. A total of 18 representative sample transect lines (six in riverine forest, four in grassland with scattered trees, and eight in woodland habitats) that varied in length and width were used. A total of 17 species of medium and large-sized mammalian species were identified and recorded in the study area. As a result, the orders Carnivora and Primates have the greatest abundance, while the order Lagomorpha has the least. Anubis baboon (Papio anubis) was the most abundant species (15.14%), followed by Spotted hyena (Crocuta crocuta) (12.98%), Crested porcupine (Hystrix cristata) (12.51%), Vervet monkey (Chlorocebus aethiops) (10.35%), Common duiker (Sylvicapra grimmia) (8.80%), and Giant root-rat (Tachyoryctes macrocephalus) (8.65%). The distributions of mammals among the three habitat types were comparable. The riverine forest harbored the highest mammalian diversity index (H' = 2.35) followed by the woodland (H' = 2.32), and the grassland with scattered trees (H' = 2.30), respectively. The greatest species similarity was recorded in woodland (0.902). The study area harbors considerable mammalian species that are threatened by interacting anthropogenic factors. So, urgent conservation measures by concerned sectors are needed to safeguard these animals and their habitat.
PubMed: 37170351
DOI: 10.1186/s40850-022-00121-0 -
Primates; Journal of Primatology Jul 2023In this "tale" I summarize the major landmarks of my 50-year career watching wild olive baboons (Papio anubis). I review some major discoveries, like baboon hunting and... (Review)
Review
In this "tale" I summarize the major landmarks of my 50-year career watching wild olive baboons (Papio anubis). I review some major discoveries, like baboon hunting and baboon social strategies of competition and defense, that only a creature with a "mind" could manage. My efforts expanded beyond science to include community-based conservation because quite early on these baboons experienced many of the threats of the Anthropocene. My research expanded to include studying crop-raiding by naïve groups of baboons, the first scientific translocation of a primate species, and a detour to study the invasion of a non-indigenous cactus, Opuntia stricta. Throughout I worked with local communities to find solutions to problems that the baboons created, and also to develop new options for their livelihoods. As the baboon research became a long-term project, it depended on a team of Kenyan research assistants who made possible the simultaneous monitoring of up to six baboon troops as well as extensive ecological monitoring. Knowing the ecology, including the impact of the sedentarization of pastoralists in the area, meant we could interpret the process of invasion by a non-indigenous cactus for the first time. Ecological periods allowed comparisons of the same troop over time and different baboon groups during the same ecological phase. Although I began my work before hypothesis testing was the preferred approach, once the paradigm changed, I continued to study and learn what matters to baboons from their perspective. As a result of observing them for 50 years, the baboons showed me that evolution often does not work the way that I had been taught, and it took all my detours and studies to convince me that anecdotes, when they are systematic and comparative, are not stories to be discounted, but evidence, much like Darwin's natural history. Natural history can reassemble the pieces that quantitative hypothesis testing has teased apart to provide its larger meaning. Today, the lone scientist, like me, is an anachronism because no one person has expertise in the many fields needed to understand and save the primates we care about.
Topics: Animals; Papio; Kenya; Papio anubis
PubMed: 37165179
DOI: 10.1007/s10329-023-01060-1