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Verbeeten KC, Tang K, Courtney JM, Bradley BJ, McAssey K, Clarson C, Kirsch S, Curtis JR, Mahmud FH, Richardson C, Cooper T, Lawson ML. Association of Fructosamine Levels with Glycemic Control in Children with Type 1 Diabetes as Determined by Continuous Glucose Monitoring: Results from the CGM TIME Trial. Can J Diabetes 2024:S1499-2671(24)00073-X. [PMID: 38614216 DOI: 10.1016/j.jcjd.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/09/2024] [Accepted: 04/01/2024] [Indexed: 04/15/2024]
Abstract
OBJECTIVES To determine the correlation between fructosamine, used to assess glycemia when HbA1c is not appropriate, with average blood glucose as measured by continuous glucose monitoring (CGM) in children with type 1 diabetes. METHODS 97 blood samples were collected from 70 participants in the CGM TIME Trial. Each eligible participant had 3 weeks of CGM data with at least 60% CGM adherence prior to blood collection. Ordinary least squares linear regression incorporating restricted cubic splines was used to determine association between fructosamine and mean blood glucose. RESULTS An association was found between fructosamine levels and mean blood glucose with F-statistic of 9.543 p-value <0.001). Data were used to create formulae and a conversion chart for calculating mean blood glucose from fructosamine levels for clinical use. CONCLUSIONS There is a complex relationship between average blood glucose and fructosamine.
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Gumber S, Connor-Stroud F, Howard D, Zhang X, Bradley BJ, Sherwood CC, Walker LC. Polyglucosan body disease in an aged chimpanzee (Pan troglodytes). Neuropathology 2023; 43:463-471. [PMID: 37086019 PMCID: PMC10642523 DOI: 10.1111/neup.12906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/23/2023]
Abstract
A 57-year-old female chimpanzee presented with a brief history of increasing lethargy and rapidly progressive lower-limb weakness that culminated in loss of use. Postmortem examination revealed no significant gross lesions in the nervous system or other organ systems. Histological analysis revealed round, basophilic to amphophilic polyglucosan bodies (PGBs) in the white and gray matter of the cervical, thoracic, lumbar, and coccygeal regions of spinal cord. Only rare PGBs were observed in forebrain samples. The lesions in the spinal cord were polymorphic, and they were positively stained with hematoxylin, periodic acid Schiff, Alcian blue, toluidine blue, Bielschowsky silver, and Grocott-Gomori methenamine-silver methods, and they were negative for von Kossa and Congo Red stains. Immunohistochemical evaluation revealed reactivity with antibodies to ubiquitin, but they were negative for glial fibrillary acidic protein, neuron-specific enolase, neurofilaments, tau protein, and Aβ protein. Electron microscopy revealed non-membrane-bound deposits composed of densely packed filaments within axons and in the extracellular space. Intra-axonal PGBs were associated with disruption of the axonal fine structure and disintegration of the surrounding myelin sheath. These findings are the first description of PGBs linked to neurological dysfunction in a chimpanzee. Clinicopathologically, the disorder resembled adult PGB disease in humans.
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Affiliation(s)
- Sanjeev Gumber
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Fawn Connor-Stroud
- Division of Veterinary Medicine, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Dustin Howard
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052, USA
| | - Xiaodong Zhang
- Emory Primate Center Imaging Center, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Brenda J. Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052, USA
| | - Chet C. Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052, USA
| | - Lary C. Walker
- Division of Neuropharmacology and Neurologic Diseases, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
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Sexton CL, Buckley C, Lieberfarb J, Subiaul F, Hecht EE, Bradley BJ. What Is Written on a Dog's Face? Evaluating the Impact of Facial Phenotypes on Communication between Humans and Canines. Animals (Basel) 2023; 13:2385. [PMID: 37508162 PMCID: PMC10376741 DOI: 10.3390/ani13142385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Facial phenotypes are significant in communication with conspecifics among social primates. Less is understood about the impact of such markers in heterospecific encounters. Through behavioral and physical phenotype analyses of domesticated dogs living in human households, this study aims to evaluate the potential impact of superficial facial markings on dogs' production of human-directed facial expressions. That is, this study explores how facial markings, such as eyebrows, patches, and widow's peaks, are related to expressivity toward humans. We used the Dog Facial Action Coding System (DogFACS) as an objective measure of expressivity, and we developed an original schematic for a standardized coding of facial patterns and coloration on a sample of more than 100 male and female dogs (N = 103), aged from 6 months to 12 years, representing eight breed groups. The present study found a statistically significant, though weak, correlation between expression rate and facial complexity, with dogs with plainer faces tending to be more expressive (r = -0.326, p ≤ 0.001). Interestingly, for adult dogs, human companions characterized dogs' rates of facial expressivity with more accuracy for dogs with plainer faces. Especially relevant to interspecies communication and cooperation, within-subject analyses revealed that dogs' muscle movements were distributed more evenly across their facial regions in a highly social test condition compared to conditions in which they received ambiguous cues from their owners. On the whole, this study provides an original evaluation of how facial features may impact communication in human-dog interactions.
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Affiliation(s)
- Courtney L Sexton
- Department of Population Health Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | - Colleen Buckley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | | | - Francys Subiaul
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
- Department of Speech, Language and Hearing Sciences, The George Washington University, Washington, DC 20052, USA
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
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4
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Hopkins WD, Staes N, Guevara EE, Mulholland MM, Sherwood CC, Bradley BJ. Vasopressin, and not oxytocin, receptor gene methylation is associated with individual differences in receptive joint attention in chimpanzees (Pan troglodytes). Autism Res 2023; 16:713-722. [PMID: 36738470 PMCID: PMC10308317 DOI: 10.1002/aur.2895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/15/2023] [Indexed: 02/06/2023]
Abstract
Joint attention (JA) is an important milestone in human infant development and is predictive of the onset of language later in life. Clinically, it has been reported that children at risk for or with a diagnosis of autism spectrum disorder (ASD) perform more poorly on measures of JA compared to neurotypical controls. JA is not unique to humans but has also been reported in great apes and to a lesser extent in more distantly related monkeys. Further, individual differences in JA among chimpanzees are associated with polymorphisms in the vasopressin and oxytocin genes, AVPR1A and OXTR. Here, we tested whether individual variation in DNA methylation of OXTR and AVPR1A were associated with performance on JA tasks in chimpanzees. We found that individual differences in JA performance was associated with AVPR1A methylation, but not OXTR methylation in the chimpanzees. The collective results provide further evidence of the role of AVPR1A in JA abilities in chimpanzees. The results further suggest that methylation values for AVPR1A may be useful biomarkers for identifying individuals at risk for ASD or related neurodevelopmental disorders associated with impairments in JA abilities.
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Affiliation(s)
- William D Hopkins
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Nicky Staes
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
- Behavioral Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Elaine E Guevara
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Michele M Mulholland
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, USA
| | - Chet C Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
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5
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Tapanes E, Kamilar JM, Nukala MA, Irwin MT, Bradley BJ. Melanism in a Wild Sifaka Population: Darker Where Cold and Fragmented. INT J PRIMATOL 2022. [DOI: 10.1007/s10764-022-00323-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Guevara EE, Hopkins WD, Hof PR, Ely JJ, Bradley BJ, Sherwood CC. Epigenetic aging of the prefrontal cortex and cerebellum in humans and chimpanzees. Epigenetics 2022; 17:1774-1785. [PMID: 35603816 DOI: 10.1080/15592294.2022.2080993] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Epigenetic age has emerged as an important biomarker of biological aging. It has revealed that some tissues age faster than others, which is vital to understanding the complex phenomenon of aging and developing effective interventions. Previous studies have demonstrated that humans exhibit heterogeneity in pace of epigenetic aging among brain structures that are consistent with differences in structural and microanatomical deterioration. Here, we add comparative data on epigenetic brain aging for chimpanzees, humans' closest relatives. Such comparisons can further our understanding of which aspects of human aging are evolutionarily conserved or specific to our species, especially given that humans are distinguished by a long lifespan, large brain, and, potentially, more severe neurodegeneration with age. Specifically, we investigated epigenetic aging of the dorsolateral prefrontal cortex and cerebellum, of humans and chimpanzees by generating genome-wide CpG methylation data and applying established epigenetic clock algorithms to produce estimates of biological age for these tissues. We found that both species exhibit relatively slow epigenetic aging in the brain relative to blood. Between brain structures, humans show a faster rate of epigenetic aging in the dorsolateral prefrontal cortex compared to the cerebellum, which is consistent with previous findings. Chimpanzees, in contrast, show comparable rates of epigenetic aging in the two brain structures. Greater epigenetic change in the human dorsolateral prefrontal cortex compared to the cerebellum may reflect both the protracted development of this structure in humans and its greater age-related vulnerability to neurodegenerative pathology.
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Affiliation(s)
- Elaine E Guevara
- Department of Anthropology, University of North Carolina Wilmington, Wilmington, NC 28403, USA.,Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC, 27708, USA
| | - William D Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,New York Consortium in Evolutionary Primatology, New York, NY 10124, USA
| | - John J Ely
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA.,MAEBIOS, Alamogordo, NM 88310, USA
| | - Brenda J Bradley
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
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7
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Staes N, White CM, Guevara EE, Eens M, Hopkins WD, Schapiro SJ, Stevens JM, Sherwood CC, Bradley BJ. Chimpanzee Extraversion scores vary with epigenetic modification of dopamine receptor gene D2 ( DRD2) and early rearing conditions. Epigenetics 2022; 17:1701-1714. [PMID: 35345970 PMCID: PMC9621015 DOI: 10.1080/15592294.2022.2058224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Chimpanzees have consistent individual differences in behaviour, also referred to as personality. Similar to human personality structure, five dimensions are commonly found in chimpanzee studies that show evidence for convergent and predictive validity (Dominance, Openness, Extraversion, Agreeableness, and Reactivity/Undependability). These dimensions are to some extent heritable, indicating a genetic component that explains part of the variation in personality scores, but are also influenced by environmental factors, such as the early social rearing background of the individuals. In this study, we investigated the role of epigenetic modification of the dopamine receptor D2 gene (DRD2) as a potential mechanism underlying personality variation in 51 captive chimpanzees. We used previously collected personality trait rating data and determined levels of DRD2 CpG methylation in peripheral blood samples for these same individuals. Results showed that DRD2 methylation is most strongly associated with Extraversion, and that varying methylation levels at specific DRD2 sites are associated with changes in Extraversion in nursery-reared, but not mother-reared, individuals. These results highlight the role of dopaminergic signalling in chimpanzee personality, and indicate that environmental factors, such as social experiences early in life, can have long-lasting behavioural effects, potentially through modification of the epigenome. These findings add to the growing evidence demonstrating the importance of the experience-dependent methylome for the development of complex social traits like personality.
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Affiliation(s)
- Nicky Staes
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
- Behavioural Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Cassandra M. White
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Elaine E Guevara
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Marcel Eens
- Behavioural Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - William D. Hopkins
- Michale E. Keeling Center for Comparative Medicine and Research, the University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
- Neuroscience Institute and Language Research Center, Georgia State University, Atlanta, GA USA
- Ape Cognition and Conservation Initiative, Des Moines, IA, USA
| | - Steven J. Schapiro
- Michale E. Keeling Center for Comparative Medicine and Research, the University of Texas MD Anderson Cancer Center, Bastrop, TX, USA
| | - Jeroen M.G. Stevens
- Behavioural Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Salto Agro- and Biotechnology, Odisee University College, Sint-Niklaas, Belgium
| | - Chet C. Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
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8
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Städele V, Arandjelovic M, Nixon S, Bergl RA, Bradley BJ, Breuer T, Cameron KN, Guschanski K, Head J, Kyungu JC, Masi S, Morgan DB, Reed P, Robbins MM, Sanz C, Smith V, Stokes EJ, Thalmann O, Todd A, Vigilant L. The complex Y-chromosomal history of gorillas. Am J Primatol 2022; 84:e23363. [PMID: 35041228 DOI: 10.1002/ajp.23363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/27/2021] [Accepted: 01/08/2022] [Indexed: 11/10/2022]
Abstract
Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.
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Affiliation(s)
- Veronika Städele
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Evolutionary and Anthropocene Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Stuart Nixon
- Field Programmes and Conservation Science, Chester Zoo, North of England Zoological Society, Chester, UK
| | | | - Brenda J Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, USA
| | - Thomas Breuer
- WWF Germany, Berlin, Germany.,Mbeli Bai Study, Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | | | - Katerina Guschanski
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Uppsala, Sweden.,Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Shelly Masi
- Eco-Anthropologie, Muséum National d'Histoire Naturelle, CNRS, Musée de l'Homme, Université de Paris, Paris, France
| | - David B Morgan
- Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Crickette Sanz
- Department of Anthropology, Washington University in Saint Louis, Saint Louis, Missouri, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of the Congo
| | | | - Emma J Stokes
- Wildlife Conservation Society, Global Conservation Program, New York City, New York, USA
| | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Bennett AJ, Pierre PJ, Wesley MJ, Latzman R, Schapiro SJ, Mareno MC, Bradley BJ, Sherwood CC, Mullholland MM, Hopkins WD. Predicting their past: Machine language learning can discriminate the brains of chimpanzees with different early-life social rearing experiences. Dev Sci 2021; 24:e13114. [PMID: 34180109 PMCID: PMC8530828 DOI: 10.1111/desc.13114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 11/28/2022]
Abstract
Early life experiences, including separation from caregivers, can result in substantial, persistent effects on neural, behavioral, and physiological systems as is evidenced in a long-standing literature and consistent findings across species, populations, and experimental models. In humans and other animals, differential rearing conditions can affect brain structure and function. We tested for whole brain patterns of morphological difference between 108 chimpanzees reared typically with their mothers (MR; N = 54) and those reared decades ago in a nursery with peers, human caregivers, and environmental enrichment (NR; N = 54). We applied support vector machine (SVM) learning to archival MRI images of chimpanzee brains to test whether we could, with any degree of significant probability, retrospectively classify subjects as MR and NR based on variation in gray matter within the entire brain. We could accurately discriminate MR and NR chimpanzee brains with nearly 70% accuracy. The combined brain regions discriminating the two rearing groups were widespread throughout the cortex. We believe this is the first report using machine language learning as an analytic method for discriminating nonhuman primate brains based on early rearing experiences. In this sense, the approach and findings are novel, and we hope they stimulate application of the technique to studies on neural outcomes associated with early experiences. The findings underscore the potential for infant separation from caregivers to leave a long-term mark on the developing brain.
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Affiliation(s)
| | | | - Michael J. Wesley
- Department of Behavioral Science, University of Kentucky College of Medicine, Lexington, KY 40536
| | - Robert Latzman
- Department of Psychology, Georgia State University, Atlanta, GA 30302
| | - Steven J. Schapiro
- Department of Comparative Medicine, The University of Texas M. D. Anderson Cancer Center, Bastrop, TX 78602
- Department of Experimental Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mary Catherine Mareno
- Department of Comparative Medicine, The University of Texas M. D. Anderson Cancer Center, Bastrop, TX 78602
| | - Brenda J. Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052
| | - Chet C. Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052
| | - Michele M. Mullholland
- Department of Comparative Medicine, The University of Texas M. D. Anderson Cancer Center, Bastrop, TX 78602
- Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA 30302
| | - William D. Hopkins
- Department of Comparative Medicine, The University of Texas M. D. Anderson Cancer Center, Bastrop, TX 78602
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Guevara EE, Greene LK, Blanco MB, Farmer C, Ranaivonasy J, Ratsirarson J, Mahefarisoa KL, Rajaonarivelo T, Rakotondrainibe HH, Junge RE, Williams CV, Rambeloson E, Rasoanaivo HA, Rahalinarivo V, Andrianandrianina LH, Clayton JB, Rothman RS, Lawler RR, Bradley BJ, Yoder AD. Molecular Adaptation to Folivory and the Conservation Implications for Madagascar’s Lemurs. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.736741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The lemurs of Madagascar include numerous species characterized by folivory across several families. Many extant lemuriform folivores exist in sympatry in Madagascar’s remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: (1) bamboo lemurs (family Lemuridae), (2) sportive lemurs (family Lepilemuridae), and (3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a dN/dS value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species’ ecology and, in turn, their resilience to habitat change. Moreover, our results support the body of work demonstrating that not all primate folivores are built the same and reiterate the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.
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11
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Guevara EE, Hopkins WD, Hof PR, Ely JJ, Bradley BJ, Sherwood CC. Comparative analysis reveals distinctive epigenetic features of the human cerebellum. PLoS Genet 2021; 17:e1009506. [PMID: 33956822 PMCID: PMC8101944 DOI: 10.1371/journal.pgen.1009506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying the molecular underpinnings of the neural specializations that underlie human cognitive and behavioral traits has long been of considerable interest. Much research on human-specific changes in gene expression and epigenetic marks has focused on the prefrontal cortex, a brain structure distinguished by its role in executive functions. The cerebellum shows expansion in great apes and is gaining increasing attention for its role in motor skills and cognitive processing, including language. However, relatively few molecular studies of the cerebellum in a comparative evolutionary context have been conducted. Here, we identify human-specific methylation in the lateral cerebellum relative to the dorsolateral prefrontal cortex, in a comparative study with chimpanzees (Pan troglodytes) and rhesus macaques (Macaca mulatta). Specifically, we profiled genome-wide methylation levels in the three species for each of the two brain structures and identified human-specific differentially methylated genomic regions unique to each structure. We further identified which differentially methylated regions (DMRs) overlap likely regulatory elements and determined whether associated genes show corresponding species differences in gene expression. We found greater human-specific methylation in the cerebellum than the dorsolateral prefrontal cortex, with differentially methylated regions overlapping genes involved in several conditions or processes relevant to human neurobiology, including synaptic plasticity, lipid metabolism, neuroinflammation and neurodegeneration, and neurodevelopment, including developmental disorders. Moreover, our results show some overlap with those of previous studies focused on the neocortex, indicating that such results may be common to multiple brain structures. These findings further our understanding of the cerebellum in human brain evolution. Humans are distinguished from other species by several aspects of cognition. While much comparative evolutionary neuroscience has focused on the neocortex, increasing recognition of the cerebellum’s role in cognition and motor processing has inspired considerable new research. Comparative molecular studies, however, generally continue to focus on the neocortex. We sought to characterize potential genetic regulatory traits distinguishing the human cerebellum by undertaking genome-wide epigenetic profiling of the lateral cerebellum, and compared this to the prefrontal cortex of humans, chimpanzees, and rhesus macaque monkeys. We found that humans showed greater differential CpG methylation–an epigenetic modification of DNA that can reflect past or present gene expression–in the cerebellum than the prefrontal cortex, highlighting the importance of this structure in human brain evolution. Humans also specifically show methylation differences at genes involved in neurodevelopment, neuroinflammation, synaptic plasticity, and lipid metabolism. These differences are relevant for understanding processes specific to humans, such as extensive plasticity, as well as pronounced and prevalent neurodegenerative conditions associated with aging.
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Affiliation(s)
- Elaine E. Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
- * E-mail:
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology, New York, New York, United States of America
| | - John J. Ely
- MAEBIOS, Alamogordo, New Mexico, United States of America
| | - Brenda J. Bradley
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
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13
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Verbeeten KC, Chan J, Sourial N, Courtney JM, Bradley BJ, McAssey K, Clarson C, Kirsch S, Curtis JR, Mahmud FH, Cooper T, Richardson C, Lawson ML. Motivational Stage at Continuous Glucose Monitoring (CGM) Initiation in Pediatric Type 1 Diabetes Is Associated With Current Glycemic Control but Does Not Predict Future CGM Adherence or Glycemic Control. Can J Diabetes 2021; 45:466-472.e4. [PMID: 34176610 DOI: 10.1016/j.jcjd.2021.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/28/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES The Timing of Initiation of Continuous Glucose Monitoring in Established Pediatric Diabetes (CGM TIME) Trial is a multicenter, randomized controlled trial in children with type 1 diabetes, comparing simultaneous pump and CGM with CGM initiation 6 months later (Paradigm, Veo, Enlite Sensor, Medtronic Canada). This study addresses the ability of SOCRATES (Stages Of Change Readiness And Treatment Eagerness Scale) to classify children and parents into distinct motivational stages and identify the stages' association with glycated hemoglobin (A1C) at trial entry and outcomes 6 months after CGM initiation. METHODS Ninety-eight of 99 eligible children 10 to 18 years of age and 137 of 141 eligible parents completed SOCRATES at trial entry and 6 months later. Parent-child agreement for motivational stage was determined by weighted kappa. Linear regression was used to examine association between motivational stage and i) A1C at trial entry and ii) change in A1C and CGM adherence 6 months after CGM initiation. RESULTS More than 87% of children and 88% of parents were classified into distinct motivational stages, with weak parent-child agreement. At trial entry, motivational stage was associated with A1C, which was 1.02% higher for children in the Action stage than in the Precontemplation stage (p<0.0001). When compared with children of parents in Precontemplation, A1C for children of parents in the Maintenance and Action stages were 0.83% (p=0.02) and 0.36% (p=0.048) higher, respectively. Precontemplation was associated with shorter diabetes duration. Motivational stage at CGM initiation did not predict change in A1C or CGM adherence 6 months later. CONCLUSIONS SOCRATES can categorize children with type 1 diabetes and their parents into motivational stages. Although motivational stage was associated with glycemic control at trial entry, it did not predict future diabetes-related behaviour or A1C.
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Affiliation(s)
- Kate C Verbeeten
- Division of Endocrinology and Metabolism, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Jason Chan
- CHEO Research Institute, Ottawa, Ontario, Canada
| | | | | | | | - Karen McAssey
- Department of Pediatrics, McMaster Children's Hospital, Toronto, Ontario, Canada
| | - Cheril Clarson
- Children's Hospital, London Health Sciences Centre, Lawson Health Research Institute, London, Ontario, Canada
| | - Susan Kirsch
- Markham-Stouffville Hospital, Markham, Ontario, Canada
| | - Jacqueline R Curtis
- Division of Endocrinology, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Farid H Mahmud
- Division of Endocrinology, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tammy Cooper
- Division of Endocrinology and Metabolism, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Christine Richardson
- Division of Endocrinology and Metabolism, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Margaret L Lawson
- Division of Endocrinology and Metabolism, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; CHEO Research Institute, Ottawa, Ontario, Canada.
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14
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Guevara EE, Webster TH, Lawler RR, Bradley BJ, Greene LK, Ranaivonasy J, Ratsirarson J, Harris RA, Liu Y, Murali S, Raveendran M, Hughes DST, Muzny DM, Yoder AD, Worley KC, Rogers J. Comparative genomic analysis of sifakas ( Propithecus) reveals selection for folivory and high heterozygosity despite endangered status. Sci Adv 2021; 7:7/17/eabd2274. [PMID: 33893095 PMCID: PMC8064638 DOI: 10.1126/sciadv.abd2274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/08/2021] [Indexed: 05/12/2023]
Abstract
Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquereli) and the resequenced genomes of Verreaux's (P. verreauxi), the golden-crowned (P. tattersalli), and the diademed (P. diadema) sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.
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Affiliation(s)
- Elaine E Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, VA 22807, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Lydia K Greene
- Duke Lemur Center, Duke University, Durham, NC 27705, USA
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Jeannin Ranaivonasy
- Département Agroécologie, Biodiversité et Changement Climatique, ESSA, University of Antananarivo, Antananarivo, Madagascar
| | - Joelisoa Ratsirarson
- Département Agroécologie, Biodiversité et Changement Climatique, ESSA, University of Antananarivo, Antananarivo, Madagascar
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shwetha Murali
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Kim C Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
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15
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Verbeeten KC, Perez Trejo ME, Tang K, Chan J, Courtney JM, Bradley BJ, McAssey K, Clarson C, Kirsch S, Curtis JR, Mahmud FH, Richardson C, Cooper T, Lawson ML. Fear of hypoglycemia in children with type 1 diabetes and their parents: Effect of pump therapy and continuous glucose monitoring with option of low glucose suspend in the CGM TIME trial. Pediatr Diabetes 2021; 22:288-293. [PMID: 33179818 PMCID: PMC7983886 DOI: 10.1111/pedi.13150] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/01/2023] Open
Abstract
To determine if pump therapy with continuous glucose monitoring offering low glucose suspend (LGS) decreases fear of hypoglycemia among children with type 1 diabetes and their parents. The CGM TIME trial is a multicenter randomized controlled trial that enrolled 144 children with type 1 diabetes for at least 1 year (mean duration 3.4 ± 3.1 years) starting pump therapy (MiniMed™ Veo™, Medtronic Canada). CGM (MiniMed™ Enlite™ sensor) offering LGS was introduced simultaneously or delayed for 6 months. Hypoglycemia Fear Scale (HFS) was completed by children ≥10 years old and all parents, at study entry and 12 months later. Simultaneous and Delayed Group participants were combined for all analyses. Subscale scores were compared with paired t-tests, and individual items with paired Wilcoxon tests. Linear regression examined association with CGM adherence. 121/140 parents and 91/99 children ≥10 years had complete data. Mean Behavior subscale score decreased from 21.1 (SD 5.9) to 17.2 (SD 6.1) (p < .001) for children, and 20.7 (SD 7.5) to 17.4 (7.4) (p < .001) for parents. Mean Worry subscale score decreased from 17.9 (SD 11.9) to 11.9 (SD 11.4) (p < .001) for children, and 23.1 (SD 13.2) to 17.6 (SD 10.4) (p < .001) for parents. Median scores for 10/25 child items and 12/25 parent items were significantly lower at 12 months (p < .001). Linear regression found no association between HFS scores and CGM adherence. Insulin pump therapy with CGM offering LGS significantly reduced fear of hypoglycemia not related to CGM adherence in children with type 1 diabetes and their parents.
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Affiliation(s)
- Kate C Verbeeten
- Division of Endocrinology and MetabolismChildren's Hospital of Eastern OntarioOttawaCanada
| | | | - Ken Tang
- CHEO Research InstituteOttawaCanada
| | | | | | | | | | - Cheril Clarson
- Department of PediatricsChildren's Hospital, London Health Sciences Centre, Lawson Health Research InstituteLondonCanada
| | - Susan Kirsch
- Department of PediatricsMarkham‐Stouffville HospitalMarkhamCanada
| | - Jacqueline R Curtis
- Division of Endocrinology and MetabolismHospital for Sick ChildrenTorontoCanada
| | - Farid H Mahmud
- Division of Endocrinology and MetabolismHospital for Sick ChildrenTorontoCanada
| | - Christine Richardson
- Division of Endocrinology and MetabolismChildren's Hospital of Eastern OntarioOttawaCanada
| | - Tammy Cooper
- Division of Endocrinology and MetabolismChildren's Hospital of Eastern OntarioOttawaCanada
| | - Margaret L Lawson
- Division of Endocrinology and MetabolismChildren's Hospital of Eastern OntarioOttawaCanada,CHEO Research InstituteOttawaCanada
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16
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Lawson ML, Verbeeten KC, Courtney JM, Bradley BJ, McAssey K, Clarson C, Kirsch S, Curtis JR, Mahmud FH, Richardson C, Cooper T, Chan J, Tang K. Timing of CGM initiation in pediatric diabetes: The CGM TIME Trial. Pediatr Diabetes 2021; 22:279-287. [PMID: 33098212 PMCID: PMC7984035 DOI: 10.1111/pedi.13144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/18/2020] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE To determine whether timing of CGM initiation offering low glucose suspend (LGS) affects CGM adherence in children and youth starting insulin pump therapy. METHODS A 5-site RCT of pump-naïve subjects (aged 5-18 years) with type 1 diabetes (T1D) for at least 1 year compared simultaneous pump and CGM initiation offering LGS vs standard pump therapy with CGM initiation delayed for 6 months. Primary outcome was CGM adherence (hours per 28 days) (MiniMed™ Paradigm™ Veo™ system; CareLink Pro™ software) over 6 months after CGM initiation. Secondary outcome HbA1c was measured centrally. Linear mixed-models and ordinary least squares models were fitted to estimate effect of intervention, and covariates baseline age, T1D duration, HbA1c, gender, ethnicity, hypoglycemia history, clinical site, and association between CGM adherence and HbA1c. RESULTS The trial randomized 144/152 (95%) eligible subjects. Baseline mean age was 11.5 ± 3.3(SD) years, T1D duration 3.4 ± 3.1 years, and HbA1c 7.9 ± 0.9%. Six months after CGM initiation, adjusted mean difference in CGM adherence was 62.4 hours per 28 days greater in the Simultaneous Group compared to Delayed Group (P = .007). There was no difference in mean HbA1c at 6 months. However, for each 100 hours of CGM use per 28-day period, HbA1c was 0.39% (95% CI 0.10%-0.69%) lower. Higher CGM adherence was associated with reduced time with glucose >10 mmol/L (P < .001). CONCLUSION CGM adherence was higher after 6 months when initiated at same time as pump therapy compared to starting CGM 6 months after pump therapy. Greater CGM adherence was associated with improved HbA1c.
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Affiliation(s)
- Margaret L. Lawson
- Division of Endocrinology and Metabolism, Department of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada,Clinical Research UnitCHEO Research InstituteOttawaOntarioCanada
| | - Kate C. Verbeeten
- Division of Endocrinology and Metabolism, Department of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada,Clinical Research UnitCHEO Research InstituteOttawaOntarioCanada
| | | | | | - Karen McAssey
- Department of PediatricsMcMaster Children's HospitalHamiltonOntarioCanada
| | - Cheril Clarson
- Department of Pediatrics, Children's Hospital, London Health Sciences CentreLawson Health Research InstituteLondonOntarioCanada
| | - Susan Kirsch
- Department of PediatricsMarkham‐Stouffville HospitalMarkhamOntarioCanada
| | - Jacqueline R Curtis
- Division of Endocrinology, Department of PediatricsHospital for Sick ChildrenTorontoOntarioCanada
| | - Farid H Mahmud
- Division of Endocrinology, Department of PediatricsHospital for Sick ChildrenTorontoOntarioCanada
| | - Christine Richardson
- Division of Endocrinology and Metabolism, Department of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada
| | - Tammy Cooper
- Division of Endocrinology and Metabolism, Department of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada
| | - Jason Chan
- Clinical Research UnitCHEO Research InstituteOttawaOntarioCanada
| | - Ken Tang
- Clinical Research UnitCHEO Research InstituteOttawaOntarioCanada
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Guevara EE, Lawler RR, Staes N, White CM, Sherwood CC, Ely JJ, Hopkins WD, Bradley BJ. Age-associated epigenetic change in chimpanzees and humans. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190616. [PMID: 32951551 DOI: 10.1098/rstb.2019.0616] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Methylation levels have been shown to change with age at sites across the human genome. Change at some of these sites is so consistent across individuals that it can be used as an 'epigenetic clock' to predict an individual's chronological age to within a few years. Here, we examined how the pattern of epigenetic ageing in chimpanzees compares with humans. We profiled genome-wide blood methylation levels by microarray for 113 samples from 83 chimpanzees aged 1-58 years (26 chimpanzees were sampled at multiple ages during their lifespan). Many sites (greater than 65 000) showed significant change in methylation with age and around one-third (32%) of these overlap with sites showing significant age-related change in humans. At over 80% of sites showing age-related change in both species, chimpanzees displayed a significantly faster rate of age-related change in methylation than humans. We also built a chimpanzee-specific epigenetic clock that predicted age in our test dataset with a median absolute deviation from known age of only 2.4 years. However, our chimpanzee clock showed little overlap with previously constructed human clocks. Methylation at CpGs comprising our chimpanzee clock showed moderate heritability. Although the use of a human microarray for profiling chimpanzees biases our results towards regions with shared genomic sequence between the species, nevertheless, our results indicate that there is considerable conservation in epigenetic ageing between chimpanzees and humans, but also substantial divergence in both rate and genomic distribution of ageing-associated sites. This article is part of the theme issue 'Evolution of the primate ageing process'.
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Affiliation(s)
- Elaine E Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, VA 22807, USA
| | - Nicky Staes
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA.,Behavioural Ecology and Ecophysiology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Cassandra M White
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | - Chet C Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | | | - William D Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
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18
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Tapanes E, Anestis S, Kamilar JM, Bradley BJ. Does facial hair greying in chimpanzees provide a salient progressive cue of aging? PLoS One 2020; 15:e0235610. [PMID: 32663207 PMCID: PMC7360037 DOI: 10.1371/journal.pone.0235610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/18/2020] [Indexed: 11/19/2022] Open
Abstract
The greying of human head hair is arguably the most salient marker of human aging. In wild mammal populations, greying can change with life history or environmental factors (e.g., sexual maturity in silverback gorillas). Yet, whether humans are unique in our pattern of age-related hair depigmentation is unclear. We examined the relationship between pigmentation loss in facial hair (greying) to age, population, and sex in wild and captive chimpanzees (Pan troglodytes). Digital facial photographs representing three chimpanzee populations (N = 145; ages 1–60 years) were scored for hair greying on a scale of one [~100% pigmented] to six [~0% pigmented]. Our data suggest that chimpanzee head and facial hair generally greys with age prior to mid-life (~30 years old), but afterwards, greying ceases to increase incrementally. Our results highlight that chimpanzee pigmentation likely exhibits substantial variation between populations, and that both 'grey' and pigmented phenotypes exist across various age classes. Thus, chimpanzee facial hair greying is unlikely a progressive indicator of age beyond mid-life, and thus facial greying in chimpanzees seems different from the pattern observed in humans. Whether this reflects neutral differences in senescence, or potential differences in selection pressures (e.g. related to conspecific communication), is unclear and worthy of more detailed examination across populations and taxa.
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Affiliation(s)
- Elizabeth Tapanes
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, United States of America
- * E-mail:
| | - Stephanie Anestis
- Department of Anthropology, Yale University, New Haven, CT, United States of America
| | - Jason M. Kamilar
- Department of Anthropology, University of Massachusetts Amherst, Amherst, MA, United States of America
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Brenda J. Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, United States of America
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Staes N, Sherwood CC, Freeman H, Brosnan SF, Schapiro SJ, Hopkins WD, Bradley BJ. Serotonin Receptor 1A Variation Is Associated with Anxiety and Agonistic Behavior in Chimpanzees. Mol Biol Evol 2020; 36:1418-1429. [PMID: 31045220 DOI: 10.1093/molbev/msz061] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Serotonin is a neurotransmitter that plays an important role in regulating behavior and personality in humans and other mammals. Polymorphisms in genes coding for the serotonin receptor subtype 1A (HTR1A), the serotonin transporter (SLC6A4), and the serotonin degrading enzyme monoamine oxidase A (MAOA) are associated with anxiety, impulsivity, and neurotic personality in humans. In primates, previous research has largely focused on SLC6A4 and MAOA, with few studies investigating the role of HTR1A polymorphic variation on behavior. Here, we examined variation in the coding region of HTR1A across apes, and genotyped polymorphic coding variation in a sample of 214 chimpanzees with matched measures of personality and behavior. We found evidence for positive selection at three amino acid substitution sites, one in chimpanzees-bonobos (Thr26Ser), one in humans (Phe33Val), and one in orangutans (Ala274Gly). Investigation of the HTR1A coding region in chimpanzees revealed a polymorphic site, where a C/A single nucleotide polymorphism changes a proline to a glutamine in the amino acid sequence (Pro248Gln). The substitution is located in the third intracellular loop of the receptor, a region important for serotonin signal transduction. The derived variant is the major allele in this population (frequency 0.67), and is associated with a reduction in anxiety, decreased rates of male agonistic behavior, and an increase in socio-positive behavior. These results are the first evidence that the HTR1A gene may be involved in regulating social behavior in chimpanzees and encourage further systematic investigation of polymorphic variation in other primate populations with corresponding data on behavior.
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Affiliation(s)
- Nicky Staes
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC.,Department of Biology, Behavioral Ecology and Ecophysiology Group, University of Antwerp, Antwerp, Belgium.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Chet C Sherwood
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC
| | - Hani Freeman
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer CenterBastrop, TX
| | - Sarah F Brosnan
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer CenterBastrop, TX.,Department of Psychology, Georgia State University, Atlanta, GA.,Neuroscience Institute and Language Research Center, Georgia State University, Atlanta, GA
| | - Steven J Schapiro
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer CenterBastrop, TX
| | - William D Hopkins
- Neuroscience Institute and Language Research Center, Georgia State University, Atlanta, GA.,Ape Cognition and Conservation Initiative, Des Moines, IA
| | - Brenda J Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC
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20
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Baden AL, Mancini AN, Federman S, Holmes SM, Johnson SE, Kamilar J, Louis EE, Bradley BJ. Anthropogenic pressures drive population genetic structuring across a Critically Endangered lemur species range. Sci Rep 2019; 9:16276. [PMID: 31700150 PMCID: PMC6838192 DOI: 10.1038/s41598-019-52689-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
In recent decades Madagascar has experienced significant habitat loss and modification, with minimal understanding of how human land use practices have impacted the evolution of its flora and fauna. In light of ongoing and intensifying anthropogenic pressures, we seek new insight into mechanisms driving genetic variability on this island, using a Critically Endangered lemur species, the black-and-white ruffed lemur (Varecia variegata), as a test case. Here, we examine the relative influence of natural and anthropogenic landscape features that we predict will impose barriers to dispersal and promote genetic structuring across the species range. Using circuit theory, we model functional connectivity among 18 sampling localities using population-based genetic distance (FST). We optimized resistance surfaces using genetic algorithms and assessed their performance using maximum-likelihood population-effects mixed models. The best supported resistance model was a composite surface that included two anthropogenic features, habitat cover and distance to villages, suggesting that rapid land cover modification by humans has driven change in the genetic structure of wild lemurs. Primary conservation priority should be placed on mitigating further forest loss and connecting regions identified as having low dispersal potential to prevent further loss of genetic diversity and promote the survival of other moist forest specialists.
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Affiliation(s)
- Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, 10065, USA.
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA.
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, USA
| | - Sarah Federman
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Sheila M Holmes
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Jason Kamilar
- Department of Anthropology, University of Massachusetts, Amherst, Massachusetts, 01003, USA
| | - Edward E Louis
- Omaha's Henry Doorly Zoo and Aquarium, 3701S 10th St, Omaha, NE68107, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, 20052, USA
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Singh SV, Staes N, Guevara EE, Schapiro SJ, Ely JJ, Hopkins WD, Sherwood CC, Bradley BJ. Evolution of ASPM coding variation in apes and associations with brain structure in chimpanzees. Genes Brain Behav 2019; 18:e12582. [PMID: 31119860 DOI: 10.1111/gbb.12582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/07/2019] [Accepted: 05/21/2019] [Indexed: 12/21/2022]
Abstract
Studying genetic mechanisms underlying primate brain morphology can provide insight into the evolution of human brain structure and cognition. In humans, loss-of-function mutations in the gene coding for ASPM (Abnormal Spindle Microtubule Assembly) have been associated with primary microcephaly, which is defined by a significantly reduced brain volume, intellectual disability and delayed development. However, less is known about the effects of common ASPM variation in humans and other primates. In this study, we characterized the degree of coding variation at ASPM in a large sample of chimpanzees (N = 241), and examined potential associations between genotype and various measures of brain morphology. We identified and genotyped five non-synonymous polymorphisms in exons 3 (V588G), 18 (Q2772K, K2796E, C2811Y) and 27 (I3427V). Using T1-weighted magnetic resonance imaging of brains, we measured total brain volume, cerebral gray and white matter volume, cerebral ventricular volume, and cortical surface area in the same chimpanzees. We found a potential association between ASPM V588G genotype and cerebral ventricular volume but not with the other measures. Additionally, we found that chimpanzee, bonobo, and human lineages each independently show a signature of accelerated ASPM protein evolution. Overall, our results suggest the potential effects of ASPM variation on cerebral cortical development, and emphasize the need for further functional studies. These results are the first evidence suggesting ASPM variation might play a role in shaping natural variation in brain structure in nonhuman primates.
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Affiliation(s)
- Sheel V Singh
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, District of Columbia
| | - Nicky Staes
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, District of Columbia.,Behavioural Ecology & Ecophysiology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Elaine E Guevara
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, District of Columbia
| | - Steven J Schapiro
- Michael E. Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, Texas
| | | | - William D Hopkins
- Michael E. Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, Texas
| | - Chet C Sherwood
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, District of Columbia
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, District of Columbia
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Sherwood CC, Bradley BJ. Brain Evolution: Mapping the Inner Neandertal. Curr Biol 2019; 29:R95-R97. [DOI: 10.1016/j.cub.2018.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Sandor AM, Lindsay RS, Dyjack N, Whitesell JC, Rios C, Bradley BJ, Haskins K, Serreze DV, Geurts AM, Chen YG, Seibold MA, Jacobelli J, Friedman RS. CD11c + Cells Are Gatekeepers for Lymphocyte Trafficking to Infiltrated Islets During Type 1 Diabetes. Front Immunol 2019; 10:99. [PMID: 30766536 PMCID: PMC6365440 DOI: 10.3389/fimmu.2019.00099] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/14/2019] [Indexed: 01/06/2023] Open
Abstract
Type 1 diabetes (T1D) is a T cell mediated autoimmune disease that affects more than 19 million people with incidence increasing rapidly worldwide. For T cells to effectively drive T1D, they must first traffic to the islets and extravasate through the islet vasculature. Understanding the cues that lead to T cell entry into inflamed islets is important because diagnosed T1D patients already have established immune infiltration of their islets. Here we show that CD11c+ cells are a key mediator of T cell trafficking to infiltrated islets in non-obese diabetic (NOD) mice. Using intravital 2-photon islet imaging we show that T cell extravasation into the islets is an extended process, with T cells arresting in the islet vasculature in close proximity to perivascular CD11c+ cells. Antigen is not required for T cell trafficking to infiltrated islets, but T cell chemokine receptor signaling is necessary. Using RNAseq, we show that islet CD11c+ cells express over 20 different chemokines that bind chemokine receptors expressed on islet T cells. One highly expressed chemokine-receptor pair is CXCL16-CXCR6. However, NOD. CXCR6-/- mice progressed normally to T1D and CXCR6 deficient T cells trafficked normally to the islets. Even with CXCR3 and CXCR6 dual deficiency, T cells trafficked to infiltrated islets. These data reinforce that chemokine receptor signaling is highly redundant for T cell trafficking to inflamed islets. Importantly, depletion of CD11c+ cells strongly inhibited T cell trafficking to infiltrated islets of NOD mice. We suggest that targeted depletion of CD11c+ cells associated with the islet vasculature may yield a therapeutic target to inhibit T cell trafficking to inflamed islets to prevent progression of T1D.
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Affiliation(s)
- Adam M Sandor
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Biomedical Research, National Jewish Health, Denver, CO, United States
| | - Robin S Lindsay
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Biomedical Research, National Jewish Health, Denver, CO, United States
| | - Nathan Dyjack
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States
| | - Jennifer C Whitesell
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Biomedical Research, National Jewish Health, Denver, CO, United States
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States
| | - Brenda J Bradley
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kathryn Haskins
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | | | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Yi-Guang Chen
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States.,Department of Pediatrics, National Jewish Health, Denver, CO, United States.,Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jordan Jacobelli
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Biomedical Research, National Jewish Health, Denver, CO, United States
| | - Rachel S Friedman
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Biomedical Research, National Jewish Health, Denver, CO, United States
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25
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Jacobs RL, Frankel DC, Rice RJ, Kiefer VJ, Bradley BJ. Parentage complexity in socially monogamous lemurs (Eulemur rubriventer
): Integrating genetic and observational data. Am J Primatol 2018; 80. [DOI: 10.1002/ajp.22738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/24/2017] [Accepted: 01/07/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Rachel L. Jacobs
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
| | - David C. Frankel
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
| | - Riley J. Rice
- Department of Anthropology; Yale University; New Haven Connecticut
| | - Vera J. Kiefer
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
| | - Brenda J. Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology; The George Washington University; Washington District of Columbia
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Jacobs RL, MacFie TS, Spriggs AN, Baden AL, Morelli TL, Irwin MT, Lawler RR, Pastorini J, Mayor M, Lei R, Culligan R, Hawkins MTR, Kappeler PM, Wright PC, Louis EE, Mundy NI, Bradley BJ. Novel opsin gene variation in large-bodied, diurnal lemurs. Biol Lett 2017; 13:rsbl.2017.0050. [PMID: 28275167 DOI: 10.1098/rsbl.2017.0050] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys.
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Affiliation(s)
- Rachel L Jacobs
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA .,Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar
| | - Tammie S MacFie
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Amanda N Spriggs
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA.,Department of Anthropology, University at Albany-SUNY, Albany, NY 12222, USA
| | - Andrea L Baden
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar.,Department of Anthropology, Hunter College-CUNY, and The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | - Toni Lyn Morelli
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar.,Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, VA 22807, USA
| | - Jennifer Pastorini
- Anthropologisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mireya Mayor
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar
| | - Runhua Lei
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Ryan Culligan
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Melissa T R Hawkins
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Peter M Kappeler
- Behavioural Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, Göttingen 37077, Germany
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar.,Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Edward E Louis
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | | | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC 20052, USA
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Sandor A, Lindsay RS, Gebert MJ, Bradley BJ, Haskins K, Jacobelli J, Friedman RS. CD11c+ cells are required for lymphocyte trafficking into previously infiltrated pancreatic islets during type 1 diabetes. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.143.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Type 1 diabetes (T1D) is a largely T cell mediated autoimmune disease that destroys the beta cells of the pancreatic islets. Inhibition of cell trafficking to an active disease site has been an effective therapy for multiple autoimmune diseases, but the requirements of lymphocyte trafficking to the islets are not fully understood. We show that lymphocyte entry into previously infiltrated islets is dependent on the presence of CD11c+ cells in the islets. T cells and B cells transferred prior to CD11c+ cell depletion were able to enter the islets; whereas, short-term CD11c+ cell depletion rapidly prevented further entry. CD11c+ cells include cells that are highly efficient antigen presenters; however, we show entry of both activated or naïve T cells into previously infiltrated islets was not reliant on antigen. An alternative role for CD11c+ cells in lymphocyte entry into the islets is the production of chemokines and cytokines. These molecules can then either directly recruit lymphocytes through chemoattraction or increased adhesion to the vasculature. Initial experiments show that there are no changes in adhesion to the vasculature after CD11c depletion, suggesting that CD11c+ cells act through recruitment by chemokines following lymphocyte arrest on the vascular endothelium. CD11c+ cells in the islets express high levels of CXCL9, a chemoattractant for T and B lymphocytes. CXCR3, the receptor for CXCL9, is present on both T and B cells in the islets. We hypothesize that CD11c+ cells facilitate the process of extravasation into the islets through chemokine production. Targeting CD11c+ produced chemokine production may be useful therapeutically for the treatment of T1D by preventing T cell entry into remaining or transplanted islets.
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Affiliation(s)
- Adam Sandor
- 1University of Colorado-Anschutz Medical Campus
- 2Natl. Jewish Hlth
| | - Robin S Lindsay
- 1University of Colorado-Anschutz Medical Campus
- 2Natl. Jewish Hlth
| | | | | | | | - Jordan Jacobelli
- 1University of Colorado-Anschutz Medical Campus
- 2Natl. Jewish Hlth
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Guevara EE, Frankel DC, Ranaivonasy J, Richard AF, Ratsirarson J, Lawler RR, Bradley BJ. A simple, economical protocol for DNA extraction and amplification where there is no lab. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0758-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Bradley BJ, Snowdon CT, McGrew WC, Lawler RR, Guevara EE, McIntosh A, O'Connor T. Non-human primates avoid the detrimental effects of prenatal androgen exposure in mixed-sex litters: combined demographic, behavioral, and genetic analyses. Am J Primatol 2016; 78:1304-1315. [PMID: 27434275 DOI: 10.1002/ajp.22583] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 11/10/2022]
Abstract
Producing single versus multiple births has important life history trade-offs, including the potential benefits and risks of sharing a common in utero environment. Sex hormones can diffuse through amniotic fluid and fetal membranes, and females with male littermates risk exposure to high levels of fetal testosterone, which are shown to have masculinizing effects and negative fitness consequences in many mammals. Whereas most primates give birth to single offspring, several New World monkey and strepsirrhine species regularly give birth to small litters. We examined whether neonatal testosterone exposure might be detrimental to females in mixed-sex litters by compiling data from long-term breeding records for seven primate species (Saguinus oedipus; Varecia variegata, Varecia rubra, Microcebus murinis, Mirza coquereli, Cheirogaleus medius, Galago moholi). Litter sex ratios did not differ from the expected 1:2:1 (MM:MF:FF for twins) and 1:2:2:1 (MMM:MMF:MFF:FFF for triplets). Measures of reproductive success, including female survivorship, offspring-survivorship, and inter-birth interval, did not differ between females born in mixed-sex versus all-female litters, indicating that litter-producing non-human primates, unlike humans and rodents, show no signs of detrimental effects from androgen exposure in mixed sex litters. Although we found no evidence for CYP19A1 gene duplications-a hypothesized mechanism for coping with androgen exposure-aromatase protein evolution shows patterns of convergence among litter-producing taxa. That some primates have effectively found a way to circumvent a major cost of multiple births has implications for understanding variation in litter size and life history strategies across mammals.
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Affiliation(s)
- Brenda J Bradley
- Department of Anthropology, The George Washington University, Washington, District of Columbia. .,Department of Anthropology, Yale University, New Haven, Connecticut.
| | - Charles T Snowdon
- Department of Psychology, University of Wisconsin, Madison, Wisconsin
| | - William C McGrew
- Department of Archaeology & Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia
| | - Elaine E Guevara
- Department of Anthropology, Yale University, New Haven, Connecticut
| | - Annick McIntosh
- Department of Anthropology, Yale University, New Haven, Connecticut
| | - Timothy O'Connor
- Institute for Genome Sciences and Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland.,University of Maryland at College Park, College Park, Maryland
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Guevara EE, Veilleux CC, Saltonstall K, Caccone A, Mundy NI, Bradley BJ. Potential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors. Am J Phys Anthropol 2016; 161:181-5. [PMID: 27393125 DOI: 10.1002/ajpa.23046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/10/2016] [Accepted: 06/13/2016] [Indexed: 01/23/2023]
Abstract
OBJECTIVES We explored whether variation in the sweet taste receptor protein T1R3 in primates could contribute to differences in sweet taste repertoire among species, potentially reflecting coevolution with local plants. Specifically, we examined which primates are likely to be sweet "tasters" of brazzein, a protein found in the fruit of the African plant Pentadiplandra brazzeana that tastes intensely sweet to humans, but provides little energy. Sweet proteins like brazzein are thought to mimic the taste of sugars to entice seed dispersers. We examined the evolution of T1R3 and assessed whether primates are likely "deceived" by such biochemical mimicry. METHODS Using published and new sequence data for TAS1R3, we characterized 57 primates and other mammals at the two amino acid sites necessary to taste brazzein to determine which species are tasters. We further used dN/dS-based methods to look for statistical evidence of accelerated evolution in this protein across primate lineages. RESULTS The taster genotype is shared across most catarrhines, suggesting that most African primates can be "tricked" into eating and dispersing P. brazzeana's seeds for little caloric gain. Western gorillas (Gorilla gorilla), however, exhibit derived mutations at the two brazzein-critical positions, and although fruit is a substantial portion of the western gorilla diet, they have not been observed to eat P. brazzeana. Our analyses of protein evolution found no signature of positive selection on TAS1R3 along the gorilla lineage. DISCUSSION We propose that the gorilla-specific mutations at the TAS1R3 locus encoding T1R3 could be a counter-adaptation to the false sweet signal of brazzein.
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Affiliation(s)
- Elaine E Guevara
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052.,Department of Anthropology, Yale University, New Haven, Connecticut, 06511
| | - Carrie C Veilleux
- Department of Anthropology, University of Texas at Austin, Austin, Texas, 78712
| | | | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06511
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Brenda J Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, 20052
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31
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Jacobs RL, Spriggs AN, MacFie TS, Baden AL, Irwin MT, Wright PC, Louis EE, Lawler RR, Mundy NI, Bradley BJ. Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs. Primates 2016; 57:541-7. [DOI: 10.1007/s10329-016-0546-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/13/2016] [Indexed: 01/06/2023]
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32
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Sandor A, Lindsay RS, Gebert M, Bradley BJ, Haskins K, Jacobelli J, Friedman RS. CD11c+ cells are required for lymphocyte trafficking into previously infiltrated pancreatic islets during type 1 diabetes. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.119.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Type 1 diabetes (T1D) is a largely T cell mediated autoimmune disease that destroys the beta cells of the pancreatic islets. Initiation of T1D requires T cell activation in the pancreatic lymph node, and then activated T cells must enter the islets to destroy beta cells. The requirements for lymphocyte entry into islets are not fully understood. We show that lymphocyte entry into previously infiltrated islets is dependent on CD11c+ cells in the islets. T cells and B cells transferred prior to CD11c+ cell depletion were able to enter the islets; whereas, short-term CD11c+ cell depletion rapidly prevented further entry. CD11c+ cells are highly efficient antigen presenters; however, entry into the islets was not reliant on antigen for either activated or naïve T cells. An alternative role for CD11c+ cells in lymphocyte entry into the islets is the production of chemokines and cytokines, which can have direct chemotactic effects on lymphocytes or can activate vascular endothelium. CD11c+ cells in the islets express high levels of CXCL9, a chemoattractant for T and B lymphocytes. CXCR3, the receptor for CXCL9, is present on both T and B lymphocytes in the islets. We hypothesize that CD11c+ cells facilitate lymphocyte recruitment to the islets through a combination of chemokine production and activation of the islet vascular endothelium. Chemokine and cytokine production by CD11c+ cells may be targeted therapeutically for the treatment of T1D to prevent T cell entry into remaining or transplanted islets.
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Affiliation(s)
- Adam Sandor
- 1Univ. of Colorado, Denver
- 2Natl. Jewish Hlth
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Abstract
Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (Eulemur rubriventer, Ranomafana National Park, Madagascar) with a sample size (87 individuals; NX chromosomes = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of Eulemur species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and M-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not M-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates.
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Affiliation(s)
- Rachel L. Jacobs
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, United States of America
- Centre ValBio Research Station, Ranomafana, Fianarantsoa, Madagascar
- * E-mail:
| | - Brenda J. Bradley
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
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Roy J, Arandjelovic M, Bradley BJ, Guschanski K, Stephens CR, Bucknell D, Cirhuza H, Kusamba C, Kyungu JC, Smith V, Robbins MM, Vigilant L. Recent divergences and size decreases of eastern gorilla populations. Biol Lett 2015; 10:20140811. [PMID: 25376805 DOI: 10.1098/rsbl.2014.0811] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Compared with other African apes, eastern gorillas (Gorilla beringei) have been little studied genetically. We used analysis of autosomal DNA genotypes obtained from non-invasively collected faecal samples to estimate the evolutionary histories of the two extant mountain gorilla populations and the closely related eastern lowland gorillas. Our results suggest that eastern lowland gorillas and mountain gorillas split beginning some 10 000 years ago, followed 5000 years ago by the split of the two mountain gorilla populations of Bwindi Impenetrable National Park and the Virungas Massif. All three populations have decreased in effective population size, with particularly substantial 10-fold decreases for the mountain gorillas. These dynamics probably reflect responses to habitat changes resulting from climate fluctuations over the past 20 000 years as well as increasing human influence in this densely populated region in the last several thousand years.
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Affiliation(s)
- Justin Roy
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Brenda J Bradley
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany Department of Anthropology, The George Washington University, Washington, DC 20052, USA
| | - Katerina Guschanski
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Colleen R Stephens
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Dan Bucknell
- The Gorilla Organization, 110 Gloucester Ave, London NW1 8HX, UK
| | - Henry Cirhuza
- The Gorilla Organization, 110 Gloucester Ave, London NW1 8HX, UK
| | | | | | - Vince Smith
- The Gorilla Organization, 110 Gloucester Ave, London NW1 8HX, UK
| | - Martha M Robbins
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
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Lindsay RS, Corbin K, Mahne A, Levitt BE, Gebert MJ, Wigton EJ, Bradley BJ, Haskins K, Jacobelli J, Tang Q, Krummel MF, Friedman RS. Antigen recognition in the islets changes with progression of autoimmune islet infiltration. J Immunol 2014; 194:522-30. [PMID: 25505281 DOI: 10.4049/jimmunol.1400626] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In type 1 diabetes, the pancreatic islets are an important site for therapeutic intervention because immune infiltration of the islets is well established at diagnosis. Therefore, understanding the events that underlie the continued progression of the autoimmune response and islet destruction is critical. Islet infiltration and destruction is an asynchronous process, making it important to analyze the disease process on a single islet basis. To understand how T cell stimulation evolves through the process of islet infiltration, we analyzed the dynamics of T cell movement and interactions within individual islets of spontaneously autoimmune NOD mice. Using both intravital and explanted two-photon islet imaging, we defined a correlation between increased islet infiltration and increased T cell motility. Early T cell arrest was Ag dependent and due, at least in part, to Ag recognition through sustained interactions with CD11c(+) APCs. As islet infiltration progressed, T cell motility became Ag independent, with a loss of T cell arrest and sustained interactions with CD11c(+) APCs. These studies suggest that the autoimmune T cell response in the islets may be temporarily dampened during the course of islet infiltration and disease progression.
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Affiliation(s)
- Robin S Lindsay
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO 80206
| | - Kaitlin Corbin
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143; and
| | - Ashley Mahne
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143
| | - Bonnie E Levitt
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Matthew J Gebert
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Eric J Wigton
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Brenda J Bradley
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO 80206
| | - Kathryn Haskins
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO 80206
| | - Jordan Jacobelli
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO 80206
| | - Qizhi Tang
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143; and
| | - Rachel S Friedman
- Department of Biomedical Research, National Jewish Health, Denver, CO 80206; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO 80206;
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Baden AL, Holmes SM, Johnson SE, Engberg SE, Louis EE, Bradley BJ. Species-level view of population structure and gene flow for a critically endangered primate (Varecia variegata). Ecol Evol 2014; 4:2675-92. [PMID: 25077019 PMCID: PMC4113292 DOI: 10.1002/ece3.1119] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 11/09/2022] Open
Abstract
Lemurs are among the world's most threatened mammals. The critically endangered black-and-white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remaining V. variegata range. We used 10 polymorphic microsatellite loci and ∼550 bp of mtDNA sequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of the Mangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNA haplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high average F ST (0.247) and ΦST (0.544), and followed a pattern of isolation-by-distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re-evaluation of conservation management units moving forward.
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Affiliation(s)
- Andrea L Baden
- Department of Anthropology, Yale University New Haven, Connecticut, 06511 ; Department of Anthropology, Hunter College of City University of New York New York, 10065
| | - Sheila M Holmes
- Department of Anthropology, University of Calgary Calgary, Alberta, Canada
| | - Steig E Johnson
- Department of Anthropology, University of Calgary Calgary, Alberta, Canada
| | - Shannon E Engberg
- Grewcock's Center for Conservation and Research - Omaha's Henry Doorly Zoo and Aquarium Omaha, Nebraska, 68107
| | - Edward E Louis
- Grewcock's Center for Conservation and Research - Omaha's Henry Doorly Zoo and Aquarium Omaha, Nebraska, 68107
| | - Brenda J Bradley
- Department of Anthropology, Yale University New Haven, Connecticut, 06511
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Fünfstück T, Arandjelovic M, Morgan DB, Sanz C, Breuer T, Stokes EJ, Reed P, Olson SH, Cameron K, Ondzie A, Peeters M, Kühl HS, Cipolletta C, Todd A, Masi S, Doran-Sheehy DM, Bradley BJ, Vigilant L. The genetic population structure of wild western lowland gorillas (Gorilla gorilla gorilla) living in continuous rain forest. Am J Primatol 2014; 76:868-78. [PMID: 24700547 DOI: 10.1002/ajp.22274] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/18/2013] [Accepted: 02/10/2014] [Indexed: 11/07/2022]
Abstract
To understand the evolutionary histories and conservation potential of wild animal species it is useful to assess whether taxa are genetically structured into different populations and identify the underlying factors responsible for any clustering. Landscape features such as rivers may influence genetic population structure, and analysis of structure by sex can further reveal effects of sex-specific dispersal. Using microsatellite genotypes obtained from noninvasively collected fecal samples we investigated the population structure of 261 western lowland gorillas (WLGs) (Gorilla gorilla gorilla) from seven locations spanning an approximately 37,000 km(2) region of mainly continuous rain forest within Central African Republic (CAR), Republic of Congo and Cameroon. We found our sample to consist of two or three significantly differentiated clusters. The boundaries of the clusters coincided with courses of major rivers. Moreover, geographic distance detoured around rivers better-explained variation in genetic distance than straight line distance. Together these results suggest that major rivers in our study area play an important role in directing WLG gene flow. The number of clusters did not change when males and females were analyzed separately, indicating a lack of greater philopatry in WLG females than males at this scale.
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Abstract
Reddish pelage and red hair ornaments have evolved many times, independently, during primate evolution. It is generally assumed that these red-coat phenotypes, like red skin phenotypes, play a role in sociosexual signaling and, thus evolved in tandem with conspecific color vision. This study examines the phylogenetic distribution of color vision and pelage coloration across the primate order to ask: (1) did red pelage and trichromacy coevolve; or (2) did trichromacy evolve first, and then subsequently red pelage evolved as an exaptation? We collected quantitative, color-corrected photographic color data for 142 museum research skins from 92 species representing 41 genera spanning all major primate lineages. For each species, we quantified the ratio of Red/Green values (from a RGB color model) at 20 anatomical landmarks. For these same species, we compiled data on color vision type (routine trichromatic, polymorphic, routine dichromatic, monochromatic) and data on variables that potentially covary with visual system (VS) and coloration, including activity pattern and body mass dimorphism (proxy for sexual selection). We also considered whether the long-term storage of research skins might influence coloration. Therefore, we included the time since the specimen was collected as an additional predictor. Analyzing the data with phylogenetic generalized least squares models, we found that the amount of red hair present in primates is associated with differences in VSs, but not in the direction expected. Surprisingly, trichromatic primate species generally exhibited less red hair compared to red-green colorblind species. Thus, our results do not support the general assumption that color vision and red pelage coloration are a coevolutionary product of sociosexual signaling in primates. In addition, we did not find an effect of activity pattern, body mass dimorphism, or time since collection on the redness of primate hair. Our results have important implications for the evolution of primate coloration and visual systems.
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Affiliation(s)
- Jason M Kamilar
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona 85308, USA.
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McIntosh AM, Bennett C, Dickson D, Anestis SF, Watts DP, Webster TH, Fontenot MB, Bradley BJ. The apolipoprotein E (APOE) gene appears functionally monomorphic in chimpanzees (Pan troglodytes). PLoS One 2012; 7:e47760. [PMID: 23112842 PMCID: PMC3480407 DOI: 10.1371/journal.pone.0047760] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/20/2012] [Indexed: 12/21/2022] Open
Abstract
Background The human apolipoprotein E (APOE) gene is polymorphic, with three primary alleles (E2, E3, E4) that differ at two key non-synonymous sites. These alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, Alzheimer’s disease risk, and longevity. The relative frequencies of these alleles vary across human populations, and the evolution and maintenance of this diversity is much debated. Previous studies comparing human and chimpanzee APOE sequences found that the chimpanzee sequence is most similar to the human E4 allele, although the resulting chimpanzee protein might function like the protein coded for by the human E3 allele. However, these studies have used sequence data from a single chimpanzee and do not consider whether chimpanzees, like humans, show intra-specific and subspecific variation at this locus. Methodology and Principal Findings To examine potential intraspecific variation, we sequenced the APOE gene of 32 chimpanzees. This sample included 20 captive individuals representing the western subspecies (P. troglodytes verus) and 12 wild individuals representing the eastern subspecies (P. t. schweinfurthii). Variation in our resulting sequences was limited to one non-coding, intronic SNP, which showed fixed differences between the two subspecies. We also compared APOE sequences for all available ape genera and fossil hominins. The bonobo APOE protein is identical to that of the chimpanzee, and the Denisovan APOE exhibits all four human-specific, non-synonymous changes and appears functionally similar to the human E4 allele. Conclusions We found no coding variation within and between chimpanzee populations, suggesting that the maintenance of functionally diverse APOE polymorphisms is a unique feature of human evolution.
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Affiliation(s)
- Annick M. McIntosh
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Calvin Bennett
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Dara Dickson
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Stephanie F. Anestis
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - David P. Watts
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Timothy H. Webster
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - M. Babette Fontenot
- Division of Behavioral Sciences, New Iberia Research Center, University of Louisiana at Lafayette, Lafayette, Louisiana, United States of America
| | - Brenda J. Bradley
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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Bradley BJ, Gerald MS, Widdig A, Mundy NI. Coat Color Variation and Pigmentation Gene Expression in Rhesus Macaques (Macaca mulatta). J MAMM EVOL 2012. [DOI: 10.1007/s10914-012-9212-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pointer MA, Kamilar JM, Warmuth V, Chester SGB, Delsuc F, Mundy NI, Asher RJ, Bradley BJ. RUNX2 tandem repeats and the evolution of facial length in placental mammals. BMC Evol Biol 2012; 12:103. [PMID: 22741925 PMCID: PMC3438065 DOI: 10.1186/1471-2148-12-103] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 06/28/2012] [Indexed: 01/21/2023] Open
Abstract
Background When simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary ‘tuning knobs’, supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2), which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio) in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length. Results In this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans). We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and a recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans), and we found no correlation between RUNX2 sequence and face length across placental mammals. Conclusions Results of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a ‘tuning knob’ modifying face length in carnivorans, this relationship is not conserved across mammals in general.
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Affiliation(s)
- Marie A Pointer
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature 2012; 483:169-75. [PMID: 22398555 PMCID: PMC3303130 DOI: 10.1038/nature10842] [Citation(s) in RCA: 457] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 01/10/2012] [Indexed: 12/13/2022]
Abstract
Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.
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Affiliation(s)
- Aylwyn Scally
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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Abstract
Life-history theory predicts that reduced extrinsic risk of mortality should increase species longevity over evolutionary time. Increasing group size should reduce an individual's risk of predation, and consequently reduce its extrinsic risk of mortality. Therefore, we should expect a relationship between group size and maximum longevity across species, while controlling for well-known correlates of longevity. We tested this hypothesis using a dataset of 253 mammal species and phylogenetic comparative methods. We found that group size was a poor predictor of maximum longevity across all mammals, as well as within primates and rodents. We found a weak but significant group-size effect on artiodactyl longevity, but in a negative direction. Body mass was consistently the best predictor of maximum longevity, which may be owing to lower predation risk and/or lower basal metabolic rates for large species. Artiodactyls living in large groups may exhibit higher rates of extrinsic mortality because of being more conspicuous to predators in open habitats, resulting in shorter lifespans.
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Affiliation(s)
- Jason M Kamilar
- Department of Anthropology, Yale University, New Haven, CT 06520, USA.
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Bradley BJ, Pedersen A, Mundy NI. Blue eyes in lemurs and humans: same phenotype, different genetic mechanism. Am J Phys Anthropol 2009; 139:269-73. [PMID: 19278018 DOI: 10.1002/ajpa.21010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Almost all mammals have brown or darkly-pigmented eyes (irises), but among primates, there are some prominent blue-eyed exceptions. The blue eyes of some humans and lemurs are a striking example of convergent evolution of a rare phenotype on distant branches of the primate tree. Recent work on humans indicates that blue eye color is associated with, and likely caused by, a single nucleotide polymorphism (rs12913832) in an intron of the gene HERC2, which likely regulates expression of the neighboring pigmentation gene OCA2. This raises the immediate question of whether blue eyes in lemurs might have a similar genetic basis. We addressed this by sequencing the homologous genetic region in the blue-eyed black lemur (Eulemur macaco flavifrons; N = 4) and the closely-related black lemur (Eulemur macaco macaco; N = 4), which has brown eyes. We then compared a 166-bp segment corresponding to and flanking the human eye-color-associated region in these lemurs, as well as other primates (human, chimpanzee, orangutan, macaque, ring-tailed lemur, mouse lemur). Aligned sequences indicated that this region is strongly conserved in both Eulemur macaco subspecies as well as the other primates (except blue-eyed humans). Therefore, it is unlikely that this regulatory segment plays a major role in eye color differences among lemurs as it does in humans. Although convergent phenotypes can sometimes come about via the same or similar genetic changes occurring independently, this does not seem to be the case here, as we have shown that the genetic basis of blue eyes in lemurs differs from that of humans.
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Affiliation(s)
- Brenda J Bradley
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
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Bergl RA, Bradley BJ, Nsubuga A, Vigilant L. Effects of habitat fragmentation, population size and demographic history on genetic diversity: the Cross River gorilla in a comparative context. Am J Primatol 2008; 70:848-59. [PMID: 18521886 DOI: 10.1002/ajp.20559] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In small and fragmented populations, genetic diversity may be reduced owing to increased levels of drift and inbreeding. This reduced diversity is often associated with decreased fitness and a higher threat of extinction. However, it is difficult to determine when a population has low diversity except in a comparative context. We assessed genetic variability in the critically endangered Cross River gorilla (Gorilla gorilla diehli), a small and fragmented population, using 11 autosomal microsatellite loci. We show that levels of diversity in the Cross River population are not evenly distributed across the three genetically identified subpopulations, and that one centrally located subpopulation has higher levels of variability than the others. All measures of genetic variability in the Cross River population were comparable to those of the similarly small mountain gorilla (G. beringei beringei) populations (Bwindi and Virunga). However, for some measures both the Cross River and mountain gorilla populations show lower levels of diversity than a sample from a large, continuous western gorilla population (Mondika, G. gorilla gorilla). Finally, we tested for the genetic signature of a bottleneck in each of the four populations. Only Cross River showed strong evidence of a reduction in population size, suggesting that the reduction in size of this population was more recent or abrupt than in the two mountain gorilla populations. These results emphasize the need for maintaining connectivity in fragmented populations and highlight the importance of allowing small populations to expand.
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Affiliation(s)
- Richard A Bergl
- Anthropology Department, City University of New York Graduate Center, New York, New York, USA.
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Abstract
This review broadly summarizes how molecular biology has contributed to our understanding of human evolution. Molecular anthropology began in the 1960s with immunological comparisons indicating that African apes and humans were closely related and, indeed, shared a common ancestor as recently as 5 million years ago. Although initially dismissed, this finding has proven robust and numerous lines of molecular evidence now firmly place the human-ape divergence at 4-8 Ma. Resolving the trichotomy among humans, chimpanzees and gorillas took a few more decades. Despite the readily apparent physical similarities shared by African apes to the exclusion of modern humans (body hair, knuckle-walking, thin tooth enamel), the molecular support for a human-chimpanzee clade is now overwhelming. More recently, whole genome sequencing and gene mapping have shifted the focus of molecular anthropology from phylogenetic analyses to phenotypic reconstruction and functional genomics. We are starting to identify the genetic basis of the morphological, physiological and behavioural traits that distinguish modern humans from apes and apes from other primates. Most notably, recent comparative genomic analyses strongly indicate that the marked differences between modern humans and chimpanzees are likely due more to changes in gene regulation than to modifications of the genes themselves, an idea first proposed over 30 years ago. Almost weekly, press releases describe newly identified genes and regulatory elements that seem to have undergone strong positive selection along the human lineage. Loci involved in speech (e.g. FOXP2), brain development (e.g. ASPM), and skull musculature (e.g. MYH16) have been of particular interest, but some surprising candidate loci (e.g. those involved in auditory capabilities) have emerged as well. Exciting new research avenues, such as the Neanderthal Genome Project, promise that molecular analyses will continue to provide novel insights about our evolution. Ultimately, however, these molecular findings can only be understood in light of data from field sites, morphology labs, and museum collections. Indeed, molecular anthropology depends on these sources for calibrating molecular clocks and placing genetic data within the context of key morphological and ecological transitions in human evolution.
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Affiliation(s)
- Brenda J Bradley
- Department of Zoology and Christ's College, University of Cambridge, UK.
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Bradley BJ, Stiller M, Doran-Sheehy DM, Harris T, Chapman CA, Vigilant L, Poinar H. Plant DNA sequences from feces: potential means for assessing diets of wild primates. Am J Primatol 2008; 69:699-705. [PMID: 17216626 DOI: 10.1002/ajp.20384] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Analyses of plant DNA in feces provides a promising, yet largely unexplored, means of documenting the diets of elusive primates. Here we demonstrate the promise and pitfalls of this approach using DNA extracted from fecal samples of wild western gorillas (Gorilla gorilla) and black and white colobus monkeys (Colobus guereza). From these DNA extracts we amplified, cloned, and sequenced small segments of chloroplast DNA (part of the rbcL gene) and plant nuclear DNA (ITS-2). The obtained sequences were compared to sequences generated from known plant samples and to those in GenBank to identify plant taxa in the feces. With further optimization, this method could provide a basic evaluation of minimum primate dietary diversity even when knowledge of local flora is limited. This approach may find application in studies characterizing the diets of poorly-known, unhabituated primate species or assaying consumer-resource relationships in an ecosystem.
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Affiliation(s)
- Brenda J Bradley
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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