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Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S, Eichler EE, Levine JE, Rogers J. Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets ( Callithrix jacchus). Genes (Basel) 2023; 14:2185. [PMID: 38137007 PMCID: PMC10742769 DOI: 10.3390/genes14122185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
The common marmoset (Callithrix jacchus) is one of the most widely used nonhuman primate models of human disease. Owing to limitations in sequencing technology, early genome assemblies of this species using short-read sequencing suffered from gaps. In addition, the genetic diversity of the species has not yet been adequately explored. Using long-read genome sequencing and expert annotation, we generated a high-quality genome resource creating a 2.898 Gb marmoset genome in which most of the euchromatin portion is assembled contiguously (contig N50 = 25.23 Mbp, scaffold N50 = 98.2 Mbp). We then performed whole genome sequencing on 84 marmosets sampling the genetic diversity from several marmoset research centers. We identified a total of 19.1 million single nucleotide variants (SNVs), of which 11.9 million can be reliably mapped to orthologous locations in the human genome. We also observed 2.8 million small insertion/deletion variants. This dataset includes an average of 5.4 million SNVs per marmoset individual and a total of 74,088 missense variants in protein-coding genes. Of the 4956 variants orthologous to human ClinVar SNVs (present in the same annotated gene and with the same functional consequence in marmoset and human), 27 have a clinical significance of pathogenic and/or likely pathogenic. This important marmoset genomic resource will help guide genetic analyses of natural variation, the discovery of spontaneous functional variation relevant to human disease models, and the development of genetically engineered marmoset disease models.
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Affiliation(s)
- R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
| | - Wes Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;
| | - Hillier W. LaDeana
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98104, USA; (H.W.L.); (E.E.E.)
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA; (C.T.); (T.G.-L.)
| | - Tina Graves-Lindsay
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA; (C.T.); (T.G.-L.)
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA;
| | - Jenna K. Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Julia C. Colwell
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Allison T. Makulec
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Shelley A. Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Ian H. Cheeseman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Corinna N. Ross
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98104, USA; (H.W.L.); (E.E.E.)
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jon E. Levine
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
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Ziegler TE, Tardif SD, Ross CN, Snowdon CT, Kapoor A, Rutherford JN. Timing of the luteal-placental shift is delayed with additional fetuses in litter-bearing callitrichid monkeys, Saguinus oedipus and Callithrix jacchus. Gen Comp Endocrinol 2023; 333:114195. [PMID: 36563863 PMCID: PMC10089085 DOI: 10.1016/j.ygcen.2022.114195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The luteal-placental shift is an important milestone of mammalian pregnancy signifying when endocrine control of pregnancy shifts from the corpus luteum of the ovary to the placenta. The corpus luteum is maintained by chorionic gonadotropin (CG). Upon sufficient placental maturation, CG production wanes, the corpus luteum involutes, and control is shifted to the placenta, one consequence of which is a midgestational rise in glucocorticoid production, especially cortisol and cortisone, by both mother and fetus. Glucocorticoids are involved in initiating parturition, prenatal programming of offspring phenotype, and maturing fetal organs. Limited evidence from human pregnancy suggests that the timing of this shift is delayed in twin pregnancies, but little is known about the timing of the luteal-placental shift in litter-bearing monkeys from the primate family Callitrichidae. Here we provide evidence from cotton-top tamarins (Saguinus oedipus) and common marmosets (Callithrix jacchus) of longer duration of elevated CG associated with multiple infant births compared to single births. Urinary profiles from cotton-top tamarins demonstrate that the decline of the extended elevation of CG precedes the onset of the midpregnancy sustained rise in glucocorticoids; this shift occurs later with an increase from one to two fetuses carried to term. In the common marmoset, the onset of the sustained rise of glucocorticoids in maternal urine is also delayed with an increase in infant number. Total urinary glucocorticoid levels during the last half of gestation increase monthly but do not differ by infant number. The significant delay in the luteal-placental shift suggests a longer period of placental maturation is needed to support a greater number of fetuses.
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Affiliation(s)
- Toni E Ziegler
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 53715, United States
| | - Suzette D Tardif
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78245, United States
| | - Corinna N Ross
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78245, United States
| | - Charles T Snowdon
- Department of Psychology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Amita Kapoor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 53715, United States
| | - Julienne N Rutherford
- Division of Biobehavioral Health Sciences, College of Nursing, University of Arizona, Tucson, AZ 85721, United States.
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Masilkova M, Boukal D, Ash H, Buchanan-Smith HM, Konečná M. Linking personality traits and reproductive success in common marmoset (Callithrix jacchus). Sci Rep 2022; 12:13341. [PMID: 35922528 PMCID: PMC9349211 DOI: 10.1038/s41598-022-16339-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/08/2022] [Indexed: 01/22/2023] Open
Abstract
Animal personality can affect individual fitness and population growth. Personality traits of either parent or parents' combination may facilitate reproduction and offspring survival across species. However, previous studies focused mainly on the role of only one sex, and the link between personality and fitness has not been confirmed in primates. We examined this link in both sexes of captive common marmosets (Callithrix jacchus), a cooperatively breeding primate with extensive paternal care. We studied the effects of five personality traits of the parents (Agreeableness, Assertiveness, Conscientiousness, Inquisitiveness, and Patience), including their absolute and directional differences within pairs, on key components of reproductive performance. We expected pairs with more similar personality scores to have higher reproductive success as found in other species with long-term pairs and biparental care, but found no evidence for this hypothesis. Instead, we detected strong effects of female traits on inter-birth intervals, which were shorter in more agreeable females, and fecundity rates, which were higher in more inquisitive females. Male traits appeared to have only a limited effect on reproductive success of the pair. Our study demonstrates that various aspects of animal personality underpin reproductive performance in captive common marmosets and provides novel insights into the possible ultimate causes of personality in cooperatively breeding species.
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Affiliation(s)
- Michaela Masilkova
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic.
| | - David Boukal
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, České Budějovice, Czech Republic
| | - Hayley Ash
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, USA
| | - Hannah M Buchanan-Smith
- Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
- Scottish Primate Research Group, Stirling, Scotland, UK
| | - Martina Konečná
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Veile A, Christopher L, Azcorra H, Dickinson F, Kramer K, Varela‐Silva I. Differences in nutritional status between rural and urban Yucatec Maya children: The importance of early life conditions. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [PMCID: PMC9314705 DOI: 10.1002/ajpa.24510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Early‐life conditions shape childhood growth and are affected by urbanization and the nutritional transition. To investigate how early‐life conditions (across the “first” and “second” 1000 days) are associated with rural and urban children's nutritional status, we analyzed anthropometric data from Maya children in Yucatan, Mexico. We collected weight, height and triceps skinfold measures, then computed body mass and fat mass indices (BMI/FMI), in a cross‐sectional sample of 6‐year‐olds (urban n = 72, rural n = 66). Demographic, socioeconomic and early‐life variables (birthweight/mode, rural/urban residence, household crowding) were collected by maternal interview. We statistically analyzed rural‐urban differences in demographic, socioeconomic, early‐life, and anthropometric variables, then created linear mixed models to evaluate associations between early‐life variables and child anthropometric outcomes. Two‐way interactions were tested between early‐life variables and child sex, and between early‐life variables and rural‐urban residence. Results showed that rural children were shorter‐statured, with lower overweight/obesity and cesarean delivery rates, compared to urban children. Household crowding was a negative predictor of anthropometric outcomes; the strongest effect was in boys and in urban children. Birthweight positively predicted anthropometric outcomes, especially weight/BMI. Birth mode was positively (not statistically) associated with any anthropometric outcome. Cesarean delivery was more common in boys than in girls, and predicted increased height in urban boys. In conclusion, urbanization and household crowding were the most powerful predictors of Maya 6‐year‐old anthropometry. The negative effects of crowding may disproportionately affect Maya boys versus girls and urban versus rural children. Early‐life conditions shape Maya children's nutritional status both in the “first” and “second” 1000 days.
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Affiliation(s)
- Amanda Veile
- Department of Anthropology Purdue University West Lafayette Indiana USA
| | | | - Hugo Azcorra
- Centro de Investigaciones Silvio Zavala Universidad Modelo Mérida Mexico
| | - Federico Dickinson
- Departamento de Ecología Humana Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Mérida Mexico
| | - Karen Kramer
- Department of Anthropology University of Utah Salt Lake City Utah USA
| | - Inês Varela‐Silva
- Departamento de Ecología Humana Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Mérida Mexico
- School of Sport, Exercise and Health Sciences Loughborough University Loughborough UK
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