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1. Giraffe translocation population viability analysis

Author

Lee, DE, Fienieg, E, Van Oosterhout, C, Muller, Z, Strauss, M, Carter, KD, Scheijen, CPJ, and Deacon, F

Subjects
Zoology, QL1-991, Botany, QK1-989
Abstract

Most populations of giraffes have declined in recent decades, leading to the recent IUCN decision to upgrade the species to Vulnerable status, and some subspecies to Endangered. Translocations have been used as a conservation tool to re-introduce giraffes to previously occupied areas or establish new populations, but guidelines for founding populations are lacking. To provide general guidelines for translocation projects regarding feasibility, we simulated various scenarios of translocated giraffe populations to identify viable age and sex distributions of founding populations using population viability analysis (PVA) implemented in Vortex software. We explored the parameter space for demography and the genetic load, examining how variation in founding numbers and sex ratios affected 100 yr probability of population extinction and genetic diversity. We found that even very small numbers of founders (N ≤ 10 females) can appear to be successful in the first decades due to transient positive population growth, but with moderate population growth rate and moderate genetic load, long-term population viability (probability of extinction 95% genetic diversity of the source population in an isolated population, 50 females and 5 males are recommended to compose the founding population. Sensitivity analyses revealed first-year survival and reproductive rate were the simulation parameters with the greatest proportional influence on probability of extinction and genetic diversity. These simulations highlight important considerations for translocation success and data gaps including true genetic load in wild giraffe populations.

Published
2020
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2. Genomic erosion in a demographically recovered bird species during conservation rescue

Author

Jackson, HA, Percival-Alwyn, L, Ryan, C, Albeshr, MF, Venturi, L, Morales, HE, Mathers, TC, Cocker, J, Speak, SA, Accinelli, GG, Barker, T, Heavens, D, Willman, F, Dawson, D, Ward, L, Tatayah, V, Zuël, N, Young, R, Concannon, L, Whitford, H, Clavijo, B, Bunbury, N, Tyler, KM, Ruhomaun, K, Grace, MK, Bruford, MW, Jones, CG, Tollington, S, Bell, DJ, Groombridge, JJ, Clark, M, and Van Oosterhout, C

Subjects
Birds, Europe, Population Density, Conservation of Natural Resources, Ecology, Endangered Species, H1, Animals, Genetic Variation, Genomics, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive-bred individuals were released into free-living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400-480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993-2008) with restriction site-associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free-living population. However, further genetic rescue with captive-bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.La paloma rosada (Nesoenas mayeri) es una especie endémica de Mauricio que se ha recuperado impresionantemente después de un grave cuello de botella poblacional a principios de la década de 1970 que duró hasta inicios de la década de 1990. Antes de este cuello de botella se había establecido una población ex situ de la cual se liberaban individuos reproducidos en cautiverio a las subpoblaciones en libertad para incrementar la variación genética y el tamaño poblacional. Este rescate de conservación derivó en una recuperación rápida de la población (400-480 individuos) y la especie cambió positivamente de categoría dos veces en la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza (UICN). Analizamos los impactos del cuello de botella y el rescate genético sobre la variación genética neutral durante y después de la recuperación poblacional (de 1993 a 2008) mediante secuenciación RAD, análisis de microsatélites y análisis genéticos cuantitativos de los datos del libro genealógico de 1112 aves ubicadas en zoológicos de Europa y los Estados Unidos. Usamos simulaciones por computadora para estudiar los cambios pronosticados en la variación genética y en la viabilidad poblacional del pasado hacia el futuro. La variación genética declinó rápidamente, a pesar de la recuperación poblacional, y el tamaño efectivo de la población fue aproximadamente un orden de magnitud más pequeño que el tamaño del censo. La especie contó con una carga genética elevada de casi 15 equivalentes letales para la longevidad. Nuestras simulaciones pronostican que la endogamia continua probablemente resultará en un incremento en la expresión de mutaciones deletéreas (es decir, una carga realizada elevada) y en una depresión endogámica severa. Sin acciones continuas para la conservación, es probable que la paloma rosada esté extinta en vida libre dentro de cien años. El rescate de conservación de la paloma rosada ha sido fundamental en la recuperación de la población silvestre; sin embargo, se requiere de un rescate genético adicional con las aves de reproducción en cautiverio de los zoológicos para recuperar la variación perdida, reducir la expresión de la variación deletérea dañina y prevenir la extinción. El uso de la genómica y los datos modelados puede orientar las valoraciones de la UICN sobre la viabilidad y el riesgo de extinción de las especies, además de que ayuda en la evaluación de la dependencia que tienen las poblaciones de la conservación.

Published
2023
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3. Children’s and adolescents’ rising animal-source food intakes in 1990–2018 were impacted by age, region, parental education and urbanicity

Author

Miller, V. Webb, P. Cudhea, F. Zhang, J. Reedy, J. Shi, P. Erndt-Marino, J. Coates, J. Micha, R. Mozaffarian, D. Bas, M. Ali, J.H. Abumweis, S. Krishnan, A. Misra, P. Hwalla, N.C. Janakiram, C. Liputo, N.I. Musaiger, A. Pourfarzi, F. Alam, I. DeRidder, K. Termote, C. Memon, A. Turrini, A. Lupotto, E. Piccinelli, R. Sette, S. Anzid, K. Vossenaar, M. Mazumdar, P. Rached, I. Rovirosa, A. Zapata, M.E. Asayehu, T.T. Oduor, F. Boedecker, J. Aluso, L. Ortiz-Ulloa, J. Meenakshi, J.V. Castro, M. Grosso, G. Waskiewicz, A. Khan, U.S. Thanopoulou, A. Malekzadeh, R. Calleja, N. Ocke, M. Etemad, Z. Nsour, M.A. Waswa, L.M. Nurk, E. Arsenault, J. Lopez-Jaramillo, P. Sibai, A.M. Damasceno, A. Arambepola, C. Lopes, C. Severo, M. Lunet, N. Torres, D. Tapanainen, H. Lindstrom, J. Virtanen, S. Palacios, C. Roos, E. Agdeppa, I.A. Desnacido, J. Capanzana, M. Misra, A. Khouw, I. Ng, S.A. Delgado, E.G. Caballero, M. Otero, J. Lee, H.-J. Koksal, E. Guessous, I. Lachat, C. De Henauw, S. Rahbar, A.R. Tedstone, A. Naska, A. Mathee, A. Ling, A. Tedla, B. Hopping, B. Ginnela, B. Leclercq, C. Duante, C. Haerpfer, C. Hotz, C. Pitsavos, C. Rehm, C. van Oosterhout, C. Cerdena, C. Bradshaw, D. Trichopoulos, D. Gauci, D. Fernando, D. Sygnowska, E. Vartiainen, E. Farzadfar, F. Zajkas, G. Swan, G. Ma, G. Pekcan, G. Ibrahim, H.M. Sinkko, H. Barbieri, H.E. Sioen, I. Myhre, J. Gaspoz, J.-M. Odenkirk, J. Bundhamcharoen, K. Nelis, K. Zarina, K. Biro, L. Johansson, L. Steingrimsdottir, L. Riley, L. Yap, M. Inoue, M. Szabo, M. Ovaskainen, M.-L. Lee, M.-S. Chan, M.F. Cowan, M. Kandiah, M. Kally, O. Jonsdottir, O. Palmer, P. Vollenweider, P. Orfanos, P. Asciak, R. Templeton, R. Don, R. Yaakub, R. Selamat, R. Yusof, S. Al-Zenki, S. Hung, S.-Y. Beer-Borst, S. Wu, S. Lukito, W. Hadden, W. Becker, W. Cao, X. Ma, Y. Lai, Y. Hjdaud, Z. Ali, J. Gravel, R. Tao, T. Veerman, J.L. Chiplonkar, S. Arici, M. Ngoan, L.T. Panagiotakos, D. Li, Y. Trichopoulou, A. Barengo, N. Khadilkar, A. Ekbote, V. Mohammadifard, N. Kovalskys, I and Miller, V. Webb, P. Cudhea, F. Zhang, J. Reedy, J. Shi, P. Erndt-Marino, J. Coates, J. Micha, R. Mozaffarian, D. Bas, M. Ali, J.H. Abumweis, S. Krishnan, A. Misra, P. Hwalla, N.C. Janakiram, C. Liputo, N.I. Musaiger, A. Pourfarzi, F. Alam, I. DeRidder, K. Termote, C. Memon, A. Turrini, A. Lupotto, E. Piccinelli, R. Sette, S. Anzid, K. Vossenaar, M. Mazumdar, P. Rached, I. Rovirosa, A. Zapata, M.E. Asayehu, T.T. Oduor, F. Boedecker, J. Aluso, L. Ortiz-Ulloa, J. Meenakshi, J.V. Castro, M. Grosso, G. Waskiewicz, A. Khan, U.S. Thanopoulou, A. Malekzadeh, R. Calleja, N. Ocke, M. Etemad, Z. Nsour, M.A. Waswa, L.M. Nurk, E. Arsenault, J. Lopez-Jaramillo, P. Sibai, A.M. Damasceno, A. Arambepola, C. Lopes, C. Severo, M. Lunet, N. Torres, D. Tapanainen, H. Lindstrom, J. Virtanen, S. Palacios, C. Roos, E. Agdeppa, I.A. Desnacido, J. Capanzana, M. Misra, A. Khouw, I. Ng, S.A. Delgado, E.G. Caballero, M. Otero, J. Lee, H.-J. Koksal, E. Guessous, I. Lachat, C. De Henauw, S. Rahbar, A.R. Tedstone, A. Naska, A. Mathee, A. Ling, A. Tedla, B. Hopping, B. Ginnela, B. Leclercq, C. Duante, C. Haerpfer, C. Hotz, C. Pitsavos, C. Rehm, C. van Oosterhout, C. Cerdena, C. Bradshaw, D. Trichopoulos, D. Gauci, D. Fernando, D. Sygnowska, E. Vartiainen, E. Farzadfar, F. Zajkas, G. Swan, G. Ma, G. Pekcan, G. Ibrahim, H.M. Sinkko, H. Barbieri, H.E. Sioen, I. Myhre, J. Gaspoz, J.-M. Odenkirk, J. Bundhamcharoen, K. Nelis, K. Zarina, K. Biro, L. Johansson, L. Steingrimsdottir, L. Riley, L. Yap, M. Inoue, M. Szabo, M. Ovaskainen, M.-L. Lee, M.-S. Chan, M.F. Cowan, M. Kandiah, M. Kally, O. Jonsdottir, O. Palmer, P. Vollenweider, P. Orfanos, P. Asciak, R. Templeton, R. Don, R. Yaakub, R. Selamat, R. Yusof, S. Al-Zenki, S. Hung, S.-Y. Beer-Borst, S. Wu, S. Lukito, W. Hadden, W. Becker, W. Cao, X. Ma, Y. Lai, Y. Hjdaud, Z. Ali, J. Gravel, R. Tao, T. Veerman, J.L. Chiplonkar, S. Arici, M. Ngoan, L.T. Panagiotakos, D. Li, Y. Trichopoulou, A. Barengo, N. Khadilkar, A. Ekbote, V. Mohammadifard, N. Kovalskys, I

Abstract

Animal-source foods (ASF) provide nutrition for children and adolescents’ physical and cognitive development. Here, we use data from the Global Dietary Database and Bayesian hierarchical models to quantify global, regional and national ASF intakes between 1990 and 2018 by age group across 185 countries, representing 93% of the world’s child population. Mean ASF intake was 1.9 servings per day, representing 16% of children consuming at least three daily servings. Intake was similar between boys and girls, but higher among urban children with educated parents. Consumption varied by age from 0.6 at <1 year to 2.5 servings per day at 15–19 years. Between 1990 and 2018, mean ASF intake increased by 0.5 servings per week, with increases in all regions except sub-Saharan Africa. In 2018, total ASF consumption was highest in Russia, Brazil, Mexico and Turkey, and lowest in Uganda, India, Kenya and Bangladesh. These findings can inform policy to address malnutrition through targeted ASF consumption programmes. © 2023, The Author(s).

Published
2023

4. Author Correction: Global dietary quality in 185 countries from 1990 to 2018 show wide differences by nation, age, education, and urbanicity (Nature Food, (2022), 3, 9, (694-702), 10.1038/s43016-022-00594-9)

Author

Miller, V. Webb, P. Cudhea, F. Shi, P. Zhang, J. Reedy, J. Erndt-Marino, J. Coates, J. Mozaffarian, D. Bas, M. Ali, J.H. Abumweis, S. Krishnan, A. Misra, P. Hwalla, N.C. Janakiram, C. Liputo, N.I. Musaiger, A. Pourfarzi, F. Alam, I. DeRidder, K. Termote, C. Memon, A. Turrini, A. Lupotto, E. Piccinelli, R. Sette, S. Anzid, K. Vossenaar, M. Mazumdar, P. Rached, I. Rovirosa, A. Zapata, M.E. Asayehu, T.T. Oduor, F. Boedecker, J. Aluso, L. Ortiz-Ulloa, J. Meenakshi, J.V. Castro, M. Grosso, G. Waskiewicz, A. Khan, U.S. Thanopoulou, A. Malekzadeh, R. Calleja, N. Ocke, M. Etemad, Z. Nsour, M.A. Waswa, L.M. Nurk, E. Arsenault, J. Lopez-Jaramillo, P. Sibai, A.M. Damasceno, A. Arambepola, C. Lopes, C. Severo, M. Lunet, N. Torres, D. Tapanainen, H. Lindstrom, J. Virtanen, S. Palacios, C. Roos, E. Agdeppa, I.A. Desnacido, J. Capanzana, M. Misra, A. Khouw, I. Ng, S.A. Delgado, E.G. Caballero, M. Otero, J. Lee, H.-J. Koksal, E. Guessous, I. Lachat, C. De Henauw, S. Rahbar, A.R. Tedstone, A. Naska, A. Mathee, A. Ling, A. Tedla, B. Hopping, B. Ginnela, B. Leclercq, C. Duante, C. Haerpfer, C. Hotz, C. Pitsavos, C. Rehm, C. van Oosterhout, C. Cerdena, C. Bradshaw, D. Trichopoulos, D. Gauci, D. Fernando, D. Sygnowska, E. Vartiainen, E. Farzadfar, F. Zajkas, G. Swan, G. Ma, G. Pekcan, G. Ibrahim, H.M. Sinkko, H. Barbieri, H.E. Sioen, I. Myhre, J. Gaspoz, J.-M. Odenkirk, J. Bundhamcharoen, K. Nelis, K. Zarina, K. Biro, L. Johansson, L. Steingrimsdottir, L. Riley, L. Yap, M. Inoue, M. Szabo, M. Ovaskainen, M.-L. Lee, M.-S. Chan, M.F. Cowan, M. Kandiah, M. Kally, O. Jonsdottir, O. Palmer, P. Vollenweider, P. Orfanos, P. Asciak, R. Templeton, R. Don, R. Yaakub, R. Selamat, R. Yusof, S. Al-Zenki, S. Hung, S.-Y. Beer-Borst, S. Wu, S. Lukito, W. Hadden, W. Becker, W. Cao, X. Ma, Y. Lai, Y. Hjdaud, Z. Garriguet, D. Ali, J. Gravel, R. Tao, T. Veerman, J.L. Chiplonkar, S. Arici, M. Ngoan, L.T. Panagiotakos, D. Li, Y. Trichopoulou, A. Barengo, N. Khadilkar, A. Ekbote, V. Mohammadifard, N. Kovalsky and Miller, V. Webb, P. Cudhea, F. Shi, P. Zhang, J. Reedy, J. Erndt-Marino, J. Coates, J. Mozaffarian, D. Bas, M. Ali, J.H. Abumweis, S. Krishnan, A. Misra, P. Hwalla, N.C. Janakiram, C. Liputo, N.I. Musaiger, A. Pourfarzi, F. Alam, I. DeRidder, K. Termote, C. Memon, A. Turrini, A. Lupotto, E. Piccinelli, R. Sette, S. Anzid, K. Vossenaar, M. Mazumdar, P. Rached, I. Rovirosa, A. Zapata, M.E. Asayehu, T.T. Oduor, F. Boedecker, J. Aluso, L. Ortiz-Ulloa, J. Meenakshi, J.V. Castro, M. Grosso, G. Waskiewicz, A. Khan, U.S. Thanopoulou, A. Malekzadeh, R. Calleja, N. Ocke, M. Etemad, Z. Nsour, M.A. Waswa, L.M. Nurk, E. Arsenault, J. Lopez-Jaramillo, P. Sibai, A.M. Damasceno, A. Arambepola, C. Lopes, C. Severo, M. Lunet, N. Torres, D. Tapanainen, H. Lindstrom, J. Virtanen, S. Palacios, C. Roos, E. Agdeppa, I.A. Desnacido, J. Capanzana, M. Misra, A. Khouw, I. Ng, S.A. Delgado, E.G. Caballero, M. Otero, J. Lee, H.-J. Koksal, E. Guessous, I. Lachat, C. De Henauw, S. Rahbar, A.R. Tedstone, A. Naska, A. Mathee, A. Ling, A. Tedla, B. Hopping, B. Ginnela, B. Leclercq, C. Duante, C. Haerpfer, C. Hotz, C. Pitsavos, C. Rehm, C. van Oosterhout, C. Cerdena, C. Bradshaw, D. Trichopoulos, D. Gauci, D. Fernando, D. Sygnowska, E. Vartiainen, E. Farzadfar, F. Zajkas, G. Swan, G. Ma, G. Pekcan, G. Ibrahim, H.M. Sinkko, H. Barbieri, H.E. Sioen, I. Myhre, J. Gaspoz, J.-M. Odenkirk, J. Bundhamcharoen, K. Nelis, K. Zarina, K. Biro, L. Johansson, L. Steingrimsdottir, L. Riley, L. Yap, M. Inoue, M. Szabo, M. Ovaskainen, M.-L. Lee, M.-S. Chan, M.F. Cowan, M. Kandiah, M. Kally, O. Jonsdottir, O. Palmer, P. Vollenweider, P. Orfanos, P. Asciak, R. Templeton, R. Don, R. Yaakub, R. Selamat, R. Yusof, S. Al-Zenki, S. Hung, S.-Y. Beer-Borst, S. Wu, S. Lukito, W. Hadden, W. Becker, W. Cao, X. Ma, Y. Lai, Y. Hjdaud, Z. Garriguet, D. Ali, J. Gravel, R. Tao, T. Veerman, J.L. Chiplonkar, S. Arici, M. Ngoan, L.T. Panagiotakos, D. Li, Y. Trichopoulou, A. Barengo, N. Khadilkar, A. Ekbote, V. Mohammadifard, N. Kovalsky

Published
2023

6. Global Population Genomics of Two Subspecies of Cryptosporidium hominis during 500 Years of Evolution

Author

Leitner, T, Tichkule, S, Caccio, SM, Robinson, G, Chalmers, RM, Mueller, I, Emery-Corbin, SJ, Eibach, D, Tyler, KM, van Oosterhout, C, Jex, AR, Leitner, T, Tichkule, S, Caccio, SM, Robinson, G, Chalmers, RM, Mueller, I, Emery-Corbin, SJ, Eibach, D, Tyler, KM, van Oosterhout, C, and Jex, AR

Abstract

Cryptosporidiosis is a major global health problem and a primary cause of diarrhea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic Cryptosporidium hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which diverged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis (gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America, and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high diversity and divergence in genomic islands of putative virulence genes, including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This diversity is maintained by balancing selection, suggesting a co-evolutionary arms race with the host. Finally, we find that recent gene flow from C. h. aquapotentis to C. h. hominis, likely associated with increased human migration, maybe driving the evolution of more virulent C. hominis variants.

Published
2022

7. Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum

Author

Corsi, G, Tichkule, S, Sannella, AR, Vatta, P, Asnicar, F, Segata, N, Jex, AR, van Oosterhout, C, Caccio, SM, Corsi, G, Tichkule, S, Sannella, AR, Vatta, P, Asnicar, F, Segata, N, Jex, AR, van Oosterhout, C, and Caccio, SM

Abstract

Cryptosporidium parvum is a globally distributed zoonotic pathogen and a major cause of diarrhoeal disease in humans and ruminants. The parasite's life cycle comprises an obligatory sexual phase, during which genetic exchanges can occur between previously isolated lineages. Here, we compare 32 whole genome sequences from human- and ruminant-derived parasite isolates collected across Europe, Egypt and China. We identify three strongly supported clusters that comprise a mix of isolates from different host species, geographic origins, and subtypes. We show that: (1) recombination occurs between ruminant isolates into human isolates; (2) these recombinant regions can be passed on to other human subtypes through gene flow and population admixture; (3) there have been multiple genetic exchanges, and most are probably recent; (4) putative virulence genes are significantly enriched within these genetic exchanges, and (5) this results in an increase in their nucleotide diversity. We carefully dissect the phylogenetic sequence of two genetic exchanges, illustrating the long-term evolutionary consequences of these events. Our results suggest that increased globalization and close human-animal contacts increase the opportunity for genetic exchanges between previously isolated parasite lineages, resulting in spillover and spillback events. We discuss how this can provide a novel substrate for natural selection at genes involved in host-parasite interactions, thereby potentially altering the dynamic coevolutionary equilibrium in the Red Queens arms race.

Published
2022

8. VIVID A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses

Author

Teeling, E, Tichkule, S, Myung, Y, Naung, MT, Ansell, BRE, Guy, AJ, Srivastava, N, Mehra, S, Caccio, SM, Mueller, I, Barry, AE, van Oosterhout, C, Pope, B, Ascher, DB, Jex, AR, Teeling, E, Tichkule, S, Myung, Y, Naung, MT, Ansell, BRE, Guy, AJ, Srivastava, N, Mehra, S, Caccio, SM, Mueller, I, Barry, AE, van Oosterhout, C, Pope, B, Ascher, DB, and Jex, AR

Abstract

Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of diversity and selection, and 3D visualization of genotypic information encoded in Variant Call Format on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritizing targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.

Published
2022

11. Genome evolution of a non-parasitic secondary heterotroph, the diatom Nitzschia putrida

Author

Oyama K, Joe Win, Shigeki Mayama, Shin-ya Miyagishima, Takako Mochizuki, Ugo Cenci, Sarkozi K, Yasuhiro Tanizawa, Yoji Nakamura, Sophien Kamoun, Toseland A, Toru Nakayama, Ken-Ichiro Ishii, Keitaro Kume, Motoki Kayama, Speak S, Goro Tanifuji, Ryo Onuma, Kato M, Daniel Moog, Hideaki Miyashita, Yuichiro Kashiyama, Thomas Mock, Bernard Henrissat, Tomonori Azuma, Lombard, Ryoma Kamikawa, van Oosterhout C, and Mika Sakamoto

Subjects
Genome evolution, Diatom, Phototroph, biology, Host (biology), Nitzschia, Evolutionary biology, fungi, Heterotroph, biology.organism_classification, Gene, Genome
Abstract

Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a non-photosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms revealed that a combination of genes loss, the horizontal acquisition of genes involved in organic carbon degradation, a unique secretome and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a non-parasitic, free-living secondary heterotroph.

Published
2021
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12. Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa

Author

Tichkule, S, Jex, AR, van Oosterhout, C, Sannella, AR, Krumkamp, R, Aldrich, C, Maiga-Ascofare, O, Dekker, D, Lamshoeft, M, Mbwana, J, Rakotozandrindrainy, N, Borrmann, S, Thye, T, Schuldt, K, Winter, D, Kremsner, PG, Oppong, K, Manouana, P, Mbong, M, Gesase, S, Minja, DTR, Mueller, I, Bahlo, M, Nader, J, May, J, Rakotozandrindrain, R, Adegnika, AA, Lusingu, JPA, Amuasi, J, Eibach, D, Caccio, SM, Tichkule, S, Jex, AR, van Oosterhout, C, Sannella, AR, Krumkamp, R, Aldrich, C, Maiga-Ascofare, O, Dekker, D, Lamshoeft, M, Mbwana, J, Rakotozandrindrainy, N, Borrmann, S, Thye, T, Schuldt, K, Winter, D, Kremsner, PG, Oppong, K, Manouana, P, Mbong, M, Gesase, S, Minja, DTR, Mueller, I, Bahlo, M, Nader, J, May, J, Rakotozandrindrain, R, Adegnika, AA, Lusingu, JPA, Amuasi, J, Eibach, D, and Caccio, SM

Abstract

Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 (gp60) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive exploration of the metapopulation structure and evolution based on whole-genome data has yet to be performed. Here, we sequenced and analysed the genomes of 26 C. hominis isolates, representing different gp60 subtypes, collected at rural sites in Gabon, Ghana, Madagascar and Tanzania. Phylogenetic and cluster analyses based on single-nucleotide polymorphisms showed that isolates predominantly clustered by their country of origin, irrespective of their gp60 subtype. We found a significant isolation-by-distance signature that shows the importance of local transmission, but we also detected evidence of hybridization between isolates of different geographical regions. We identified 37 outlier genes with exceptionally high nucleotide diversity, and this group is significantly enriched for genes encoding extracellular proteins and signal peptides. Furthermore, these genes are found more often than expected in recombinant regions, and they show a distinct signature of positive or balancing selection. We conclude that: (1) the metapopulation structure of C. hominis can only be accurately captured by whole-genome analyses; (2) local anthroponotic transmission underpins the spread of this pathogen in Africa; (3) hybridization occurs between distinct geographical lineages; and (4) genetic introgression provides novel substrate for positive or balancing selection in genes involved in host-parasite coevolution.

Published
2021

20. Exploring NLR diversity in Oryza sativa

Author

Fairhead, S., Kroj, Thomas, Gladieux, Pierre, Jouet, A., Witek, K., Van Oosterhout, C., Morel, Jean-Benoit, Jones, J. D., University of East Anglia, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and International Society for Molecular Plant-Microbe Interactions (IS-MPMI). INT.

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

22. Correction to: Impact of nonoptimal intakes of saturated, polyunsaturated, and trans fat on global burdens of coronary heart disease. [J Am Heart Assoc. (2016) 5, e002891.] Doi:10.1161/JAHA.115.002891

Author

Wang, Q. Afshin, A. Yakoob, M.Y. Singh, G.M. Rehm, C.D. Khatibzadeh, S. Micha, R. Shi, P. Mozaffarian, D. Ezzati, M. Fahimi, S. Wirojratana, P. Powles, J. Elmadfa, I. Rao, M. Alpert, W. Lim, S.S. Engell, R.E. Andrews, K.G. Abbott, P.A. Abdollahi, M. Abeyá Gilardon, E.O. Ahsan, H. Al Nsour, M.A.A. Al-Hooti, S.N. Arambepola, C. Fernando, D.N. Barennes, H. Barquera, S. Baylin, A. Becker, W. Bjerregaard, P. Bourne, L.T. Capanzana, M.V. Castetbon, K. Chang, H.-Y. Chen, Y. Cowan, M.J. Riley, L.M. De Henauw, S. Ding, E.L. Duante, C.A. Duran, P. Barbieri, H.E. Farzadfar, F. Hadziomeragic, A.F. Fisberg, R.M. Forsyth, S. Garriguet, D. Gaspoz, J.-M. Gauci, D. Calleja, N. Ginnela, B.N.V. Guessous, I. Gulliford, M.C. Hadden, W. Haerpfer, C. Hoffman, D.J. Houshiar-Rad, A. Huybrechts, I. Hwalla, N.C. Ibrahim, H.M. Inoue, M. Jackson, M.D. Johansson, L. Keinan-Boker, L. Kim, C.-I. Koksal, E. Lee, H.-J. Li, Y. Lipoeto, N.I. Ma, G. Mangialavori, G.L. Matsumura, Y. McGarvey, S.T. Fen, C.M. Monge-Rojas, R.A. Musaiger, A.O. Nagalla, B. Naska, A. Ocke, M.C. Oltarzewski, M. Szponar, L. Orfanos, P. Ovaskainen, M.-L. Tapanainen, H. Pan, W.-H. Panagiotakos, D.B. Pekcan, G.A. Petrova, S. Piaseu, N. Pitsavos, C. Posada, L.G. Sánchez-Romero, L.M. Selamat, R.B.T. Sharma, S. Sibai, A.M. Sichieri, R. Simmala, C. Steingrimsdottir, L. Swan, G. Sygnowska, E.H. Templeton, R. Thanopoulou, A. Thorgeirsdóttir, H. Thorsdottir, I. Trichopoulou, A. Tsugane, S. Turrini, A. Vaask, S. van Oosterhout, C. Veerman, J.L. Verena, N. Waskiewicz, A. Zaghloul, S. Zajkás, G.

Abstract

In the article by Wang et al, "Impact of Nonoptimal Intakes of Saturated, Polyunsaturated, and Trans Fat on Global Burdens of Coronary Heart Disease," which published online January 20, 2016, and appeared in the January 2016 issue of the journal (J Am Heart Assoc. 2016;5:e002891 doi:10.1161/ JAHA.115.002891), the full list of the Global Burden of Diseases Nutrition and Chronic Diseases Expert Group (NutriCoDE) group were erroneously listed as authors in the HTML version of the article. The publisher regrets the error. The online version of the article has been updated and is available at http://jaha.ahajournals.org/content/5/1/ e002891. © 2016 The Authors.

Published
2016

23. Impact of nonoptimal intakes of saturated, polyunsaturated, and trans fat on global burdens of coronary heart disease

Author

Wang, Q. Afshin, A. Yakoob, M.Y. Singh, G.M. Rehm, C.D. Khatibzadeh, S. Micha, R. Shi, P. Mozaffarian, D. Ezzati, M. Fahimi, S. Wirojratana, P. Powles, J. Elmadfa, I. Rao, M. Alpert, W. Lim, S.S. Engell, R.E. Andrews, K.G. Abbott, P.A. Abdollahi, M. Abeyá Gilardon, E.O. Ahsan, H. Al Nsour, M.A.A. Al-Hooti, S.N. Arambepola, C. Fernando, D.N. Barennes, H. Barquera, S. Baylin, A. Becker, W. Bjerregaard, P. Bourne, L.T. Capanzana, M.V. Castetbon, K. Chang, H.-Y. Chen, Y. Cowan, M.J. Riley, L.M. De Henauw, S. Ding, E.L. Duante, C.A. Duran, P. Barbieri, H.E. Farzadfar, F. Hadziomeragic, A.F. Fisberg, R.M. Forsyth, S. Garriguet, D. Gaspoz, J.-M. Gauci, D. Calleja, N. Ginnela, B.N.V. Guessous, I. Gulliford, M.C. Hadden, W. Haerpfer, C. Hoffman, D.J. Houshiar-Rad, A. Huybrechts, I. Hwalla, N.C. Ibrahim, H.M. Inoue, M. Jackson, M.D. Johansson, L. Keinan-Boker, L. Kim, C.-I. Koksal, E. Lee, H.-J. Li, Y. Lipoeto, N.I. Ma, G. Mangialavori, G.L. Matsumura, Y. McGarvey, S.T. Fen, C.M. Monge-Rojas, R.A. Musaiger, A.O. Nagalla, B. Naska, A. Ocke, M.C. Oltarzewski, M. Szponar, L. Orfanos, P. Ovaskainen, M.-L. Tapanainen, H. Pan, W.-H. Panagiotakos, D.B. Pekcan, G.A. Petrova, S. Piaseu, N. Pitsavos, C. Posada, L.G. Sánchez-Romero, L.M. Selamat, R.B.T. Sharma, S. Sibai, A.M. Sichieri, R. Simmala, C. Steingrimsdottir, L. Swan, G. Sygnowska, E.H. Templeton, R. Thanopoulou, A. Thorgeirsdóttir, H. Thorsdottir, I. Trichopoulou, A. Tsugane, S. Turrini, A. Vaask, S. van Oosterhout, C. Veerman, J.L. Verena, N. Waskiewicz, A. Zaghloul, S. Zajkás, G.

Abstract

Background: Saturated fat (SFA), x-6 (n-6) polyunsaturated fat (PUFA), and trans fat (TFA) influence risk of coronary heart disease (CHD), but attributable CHD mortalities by country, age, sex, and time are unclear. Methods and Results: National intakes of SFA, n-6 PUFA, and TFA were estimated using a Bayesian hierarchical model based on country-specific dietary surveys; food availability data; and, for TFA, industry reports on fats/oils and packaged foods. Etiologic effects of dietary fats on CHD mortality were derived from meta-analyses of prospective cohorts and CHD mortality rates from the 2010 Global Burden of Diseases study. Absolute and proportional attributable CHD mortality were computed using a comparative risk assessment framework. In 2010, nonoptimal intakes of n-6 PUFA, SFA, and TFA were estimated to result in 711 800 (95% uncertainty interval [UI] 680 700-745 000), 250 900 (95% UI 236 900-265 800), and 537 200 (95% UI 517 600-557 000) CHD deaths per year worldwide, accounting for 10.3% (95% UI 9.9%-10.6%), 3.6%, (95% UI 3.5%-3.6%) and 7.7% (95% UI 7.6%-7.9%) of global CHD mortality. Tropical oil-consuming countries were estimated to have the highest proportional n-6 PUFA- and SFAattributable CHD mortality, whereas Egypt, Pakistan, and Canada were estimated to have the highest proportional TFA-attributable CHD mortality. From 1990 to 2010 globally, the estimated proportional CHD mortality decreased by 9% for insufficient n-6 PUFA and by 21% for higher SFA, whereas it increased by 4% for higher TFA, with the latter driven by increases in low- and middle-income countries. Conclusions: Nonoptimal intakes of n-6 PUFA, TFA, and SFA each contribute to significant estimated CHD mortality, with important heterogeneity across countries that informs nation-specific clinical, public health, and policy priorities. © 2016 The Authors.

Published
2016

25. Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

Author

Mock, T., Otillar, R. P., Strauss, Jan, McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., Grigoriev, I. V., Mock, T., Otillar, R. P., Strauss, Jan, McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., and Grigoriev, I. V.

Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Published
2017
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28. Global, regional, and national consumption of sugar-sweetened beverages, fruit juices, and milk: A systematic assessment of beverage intake in 187 countries

Author

Singh, G.M. Micha, R. Khatibzadeh, S. Shi, P. Lim, S. Andrews, K.G. Engell, R.E. Ezzati, M. Mozaffarian, D. Fahimi, S. Powles, J. Elmadfa, I. Rao, M. Wirojratana, P. Abbott, P.A. Abdollahi, M. Gilardon, E.A. Ahsan, H. Al Nsour, M.A.A. Al-Hooti, S.N. Arambepola, C. Arennes, H. Arquera, S. Aylin, A. Becker, W. Bjerregaard, P. Bourne, L.T. Calleja, N. Capanzana, M.V. Castetbon, K. Chang, H.-Y. Chen, Y. Cowan, M.J. De Henauw, S. Ding, E.L. Duante, C.A. Duran, P. Arbieri, H.E. Farzadfar, F. Fernando, D.N. Hadziomeragic, A.F. Fisberg, R.M. Forsyth, S. Garriguet, D. Gaspoz, J.-M. Gauci, D. Ginnela, B.N.V. Guessous, I. Gulliford, M.C. Hadden, W. Haerpfer, C. Hoffman, D.J. Houshiar-Rad, A. Huybrechts, I. Hwalla, N.C. Ibrahim, H.M. Inoue, M. Jackson, M.D. Johansson, L. Keinan-Boker, L. Kim, C.-I. Koksal, E. Lee, H.-J. Li, Y. Lipoeto, N.I. Ma, G. Mangialavori, G.L. Matsumura, Y. McGarvey, S.T. Chan, M.F. Mensink, G.B.M. Monge-Rojas, R.A. Musaiger, A.O. Balakrishna, N. Naska, A. Ocke, M.C. Oltarzewski, M. Orfanos, P. Ovaskainen, M.-L. Pan, W.-H. Panagiotakos, D.B. Pekcan, G.A. Petrova, S. Piaseu, N. Pitsavos, C. Posada, L.G. Riley, L.M. Sánchez-Romero, L.M. Selamat, R.B.T. Sharma, S. Sibai, A.M. Sichieri, R. Simmala, C. Steingrimsdottir, L. Swan, G. Sygnowska, E.H. Szponar, L. Tapanainen, H. Templeton, R. Thanopoulou, A. Thorgeirsdóttir, H. Thorsdottir, I. Trichopoulou, A. Tsugane, S. Turrini, A. Vaask, S. Van Oosterhout, C. Veerman, J.L. Verena, N. Waskiewicz, A. Zaghloul, S. Zajkás, G. and Singh, G.M. Micha, R. Khatibzadeh, S. Shi, P. Lim, S. Andrews, K.G. Engell, R.E. Ezzati, M. Mozaffarian, D. Fahimi, S. Powles, J. Elmadfa, I. Rao, M. Wirojratana, P. Abbott, P.A. Abdollahi, M. Gilardon, E.A. Ahsan, H. Al Nsour, M.A.A. Al-Hooti, S.N. Arambepola, C. Arennes, H. Arquera, S. Aylin, A. Becker, W. Bjerregaard, P. Bourne, L.T. Calleja, N. Capanzana, M.V. Castetbon, K. Chang, H.-Y. Chen, Y. Cowan, M.J. De Henauw, S. Ding, E.L. Duante, C.A. Duran, P. Arbieri, H.E. Farzadfar, F. Fernando, D.N. Hadziomeragic, A.F. Fisberg, R.M. Forsyth, S. Garriguet, D. Gaspoz, J.-M. Gauci, D. Ginnela, B.N.V. Guessous, I. Gulliford, M.C. Hadden, W. Haerpfer, C. Hoffman, D.J. Houshiar-Rad, A. Huybrechts, I. Hwalla, N.C. Ibrahim, H.M. Inoue, M. Jackson, M.D. Johansson, L. Keinan-Boker, L. Kim, C.-I. Koksal, E. Lee, H.-J. Li, Y. Lipoeto, N.I. Ma, G. Mangialavori, G.L. Matsumura, Y. McGarvey, S.T. Chan, M.F. Mensink, G.B.M. Monge-Rojas, R.A. Musaiger, A.O. Balakrishna, N. Naska, A. Ocke, M.C. Oltarzewski, M. Orfanos, P. Ovaskainen, M.-L. Pan, W.-H. Panagiotakos, D.B. Pekcan, G.A. Petrova, S. Piaseu, N. Pitsavos, C. Posada, L.G. Riley, L.M. Sánchez-Romero, L.M. Selamat, R.B.T. Sharma, S. Sibai, A.M. Sichieri, R. Simmala, C. Steingrimsdottir, L. Swan, G. Sygnowska, E.H. Szponar, L. Tapanainen, H. Templeton, R. Thanopoulou, A. Thorgeirsdóttir, H. Thorsdottir, I. Trichopoulou, A. Tsugane, S. Turrini, A. Vaask, S. Van Oosterhout, C. Veerman, J.L. Verena, N. Waskiewicz, A. Zaghloul, S. Zajkás, G.

Abstract

Background Sugar-sweetened beverages (SSBs), fruit juice, and milk are components of diet of major public health interest. To-date, assessment of their global distributions and health impacts has been limited by insufficient comparable and reliable data by country, age, and sex. Objective To quantify global, regional, and national levels of SSB, fruit juice, and milk intake by age and sex in adults over age 20 in 2010. Methods We identified, obtained, and assessed data on intakes of these beverages in adults, by age and sex, from 193 nationally- or subnationally-representative diet surveys worldwide, representing over half the world's population. We also extracted data relevant to milk, fruit juice, and SSB availability for 187 countries from annual food balance information collected by the United Nations Food and Agriculture Organization. We developed a hierarchical Bayesian model to account for measurement incomparability, study representativeness, and sampling and modeling uncertainty, and to combine and harmonize nationally representative dietary survey data and food availability data. Results In 2010, global average intakes were 0.58 (95%UI: 0.37, 0.89) 8 oz servings/day for SSBs, 0.16 (0.10, 0.26) for fruit juice, and 0.57 (0.39, 0.83) for milk. There was significant heterogeneity in consumption of each beverage by region and age. Intakes of SSB were highest in the Caribbean (1.9 servings/day; 1.2, 3.0); fruit juice consumption was highest in Australia and New Zealand (0.66; 0.35, 1.13); and milk intake was highest in Central Latin America and parts of Europe (1.06; 0.68, 1.59). Intakes of all three beverages were lowest in East Asia and Oceania. Globally and within regions, SSB consumption was highest in younger adults; fruit juice consumption showed little relation with age; and milk intakes were highest in older adults. Conclusions Our analysis highlights the enormous spectrum of beverage intakes worldwide, by country, age, and sex. These data are valu

Published
2015

31. Climate model boundary conditions for four Cretaceous time slices

Author

Sewall, J. O., van de Wal, R. S. W., van Der Zwan, K., van Oosterhout, C., Dijkstra, H. A., Scotese, C. R., and EGU, Publication

Subjects
lcsh:GE1-350, lcsh:Environmental pollution, Aardwetenschappen, lcsh:Environmental protection, Natuur- en Sterrenkunde, lcsh:TD172-193.5, [SDU.STU] Sciences of the Universe [physics]/Earth Sciences, lcsh:TD169-171.8, lcsh:Environmental sciences, [SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces, environment
Abstract

General circulation models (GCMs) are useful tools for investigating the characteristics and dynamics of past climates. Understanding of past climates contributes significantly to our overall understanding of Earth's climate system. One of the most time consuming, and often daunting, tasks facing the paleoclimate modeler, particularly those without a geological background, is the production of surface boundary conditions for past time periods. These boundary conditions consist of, at a minimum, continental configurations derived from plate tectonic modeling, topography, bathymetry, and a vegetation distribution. Typically, each researcher develops a unique set of boundary conditions for use in their simulations. Thus, unlike simulations of modern climate, basic assumptions in paleo surface boundary conditions can vary from researcher to researcher. This makes comparisons between results from multiple researchers difficult and, thus, hinders the integration of studies across the broader community. Unless special changes to surface conditions are warranted, researcher dependent boundary conditions are not the most efficient way to proceed in paleoclimate investigations. Here we present surface boundary conditions (land-sea distribution, paleotopography, paleobathymetry, and paleovegetation distribution) for four Cretaceous time slices (120 Ma, 110 Ma, 90 Ma, and 70 Ma). These boundary conditions are modified from base datasets to be appropriate for incorporation into numerical studies of Earth's climate and are available in NetCDF format upon request from the lead author. The land-sea distribution, bathymetry, and topography are based on the 1°×1° (latitude x longitude) paleo Digital Elevation Models (paleoDEMs) of Christopher Scotese. Those paleoDEMs were adjusted using the paleogeographical reconstructions of Ronald Blakey (Northern Arizona University) and published literature and were then modified for use in GCMs. The paleovegetation distribution is based on published data and reconstructions and consultation with members of the paleobotanical community and is represented as generalized biomes that should be easily translatable to many vegetation-modeling schemes.

Published
2007

33. Climate model boundary conditions for four Cretaceous time slices

Author

Geosciences, Sewall, Jacob O., van de Wal, R. S. W., van der Zwan, K., van Oosterhout, C., Dijkstra, H. A., Scotese, C. R., Geosciences, Sewall, Jacob O., van de Wal, R. S. W., van der Zwan, K., van Oosterhout, C., Dijkstra, H. A., and Scotese, C. R.

Abstract

General circulation models (GCMs) are useful tools for investigating the characteristics and dynamics of past climates. Understanding of past climates contributes significantly to our overall understanding of Earth's climate system. One of the most time consuming, and often daunting, tasks facing the paleoclimate modeler, particularly those without a geological background, is the production of surface boundary conditions for past time periods. These boundary conditions consist of, at a minimum, continental configurations derived from plate tectonic modeling, topography, bathymetry, and a vegetation distribution. Typically, each researcher develops a unique set of boundary conditions for use in their simulations. Thus, unlike simulations of modern climate, basic assumptions in paleo surface boundary conditions can vary from researcher to researcher. This makes comparisons between results from multiple researchers difficult and, thus, hinders the integration of studies across the broader community. Unless special changes to surface conditions are warranted, researcher dependent boundary conditions are not the most efficient way to proceed in paleoclimate investigations. Here we present surface boundary conditions (land-sea distribution, paleotopography, paleobathymetry, and paleovegetation distribution) for four Cretaceous time slices (120 Ma, 110 Ma, 90 Ma, and 70 Ma). These boundary conditions are modified from base datasets to be appropriate for incorporation into numerical studies of Earth's climate and are available in NetCDF format upon request from the lead author. The land-sea distribution, bathymetry, and topography are based on the 1 degrees x 1 degrees (latitude x longitude) paleo Digital Elevation Models (paleoDEMs) of Christopher Scotese. Those paleoDEMs were adjusted using the paleogeographical reconstructions of Ronald Blakey (Northern Arizona University) and published literature and were then modified for use in GCMs. The paleovegetation distribution i

Published
2007

34. Population constraints on the Grenada Dove Leptotila wellsi: preliminary findings and proposals from south-west Grenada.

Author

BOLTON, N. M., van OOSTERHOUT, C., COLLAR, N. J., and BELL, D. J.

Abstract

The Critically Endangered Grenada Dove Leptotila wellsi has a very small total population size (< 190 individuals) and faces multiple threats. Over eight weeks in 2012 at the Mount Hartman Estate, we investigated the dove’s habitat selection, established a mongoose index of occupancy and recorded dove use of water sources to help determine key research and conservation needs. Of 12 habitat variables measured, greater levels of canopy cover were the best predictor of dove presence. Tracking tunnels indicated that introduced small Indian mongooses Herpestes auropunctatus, widely known for negatively impacting Caribbean bird populations, have a high level of occupancy in dove habitat, providing baseline mongoose data. Trail cameras revealed that Grenada Doves make good use of water from man-made wells and mongooses scent-mark tunnels. We urge fuller habitat selection studies and water-provision experiments to validate this evidence; strong and immediate control of mongooses and other potential predators, particularly at the nest; and a census backed by a banding programme to establish a monitoring baseline to guide conservation actions. [ABSTRACT FROM PUBLISHER]

Published
2016
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46. Real-time genomics for One Health

Author

Urban, L, Perlas, A, Francino, O, Martí-Carreras, J, Muga, BA, Mwangi, JW, Boykin Okalebo, L, Stanton, J-AL, Black, Amanda, Waipara, N, Fontsere, C, Eccles, D, Urel, H, Reska, T, Morales, HE, Palmada-Flores, M, Marques-Bonet, T, Watsa, M, Libke, Z, Erkenswick, G, and van Oosterhout, C

Published
2023
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47. Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes.

Author

Lobo D, Morales HE, Van Oosterhout C, López-Bao JV, Silva P, Llaneza L, Pacheco C, Castro D, Hernández-Alonso G, Pacheco G, Archer J, Gilbert MTP, Ferrand N, and Godinho R

Abstract

Understanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf ( Canis lupus signatus ), a gray wolf subspecies endemic to the Iberian Peninsula (Portugal and Spain), has uniquely persisted in human-dominated landscapes, unlike many other wolf populations that faced widespread extinction across Europe during the twentieth century. In this study, we conducted a comprehensive genome-wide analysis of 145 historical and contemporary Iberian wolf samples to investigate whether hybridization with domestic dogs resulted in genetic introgression. We identified a dog-derived block on Chromosome 2 in Iberian wolves, displaying signatures consistent with introgression and high nucleotide similarity among introgressed individuals. Additionally, our estimates place the average timing of introgression between 6100 and 3000 years ago, with low sequence divergence to dogs from the Iberian Peninsula suggesting a single local origin for the hybridization event. Using forward genetic simulations, we show that the introgressed haplotype is most likely being maintained in Iberian wolves by selection. The introgressed dog variants are located within the MAST4 gene, which has been linked to neurological disorders, including cognitive and motor developmental delays, hinting at a potential role in cognitive behavior in Iberian wolves. This study uncovers a case of putative adaptive introgression from domestic dogs into wolves, offering new insights into wild canids' adaptation to human-dominated landscapes., (© 2025 Lobo et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2025
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48. Sonification of Genomic Data to Represent Genetic Load in Zoo Populations.

Author

Martin EJ, Speak SA, Urban L, Morales HE, and van Oosterhout C

Subjects
Animals, Genetic Load, Columbidae genetics, Columbidae physiology, Genomics, Endangered Species, Humans, Breeding, Animals, Zoo genetics
Abstract

Maintaining a diverse gene pool is important in the captive management of zoo populations, especially in endangered species such as the pink pigeon (Nesoenas mayeri). However, due to the limited number of breeding individuals and relaxed natural selection, the loss of variation and accumulation of harmful variants is inevitable. Inbreeding results in a loss of fitness (i.e., inbreeding depression), principally because related parents are more likely to transmit a copy of the same recessive deleterious genetic variant to their offspring. Genomics-informed captive breeding can manage harmful variants by artificial selection, reducing the genetic load by avoiding the inheritance of two copies of the same harmful variant. To explain this concept in an interactive way to zoo visitors, we developed a sonification game to represent the fitness impacts of harmful variants by detuning notes in a familiar musical melody (i.e., Beethoven's Für Elise). Conceptually, zoo visitors play a game aiming to create the most optimal pink pigeon offspring in terms of inbreeding depression. They select virtual crosses between pink pigeon individuals and listen for the detuning of the melody, which represents the realised load of the resultant offspring. Here we present the sonification algorithm and the results of an online survey to see whether participants could identify the most and least optimal offspring from three potential pink pigeon offspring. Of our 98 respondents, 85 (86.7%) correctly identified the least optimal offspring, 73 (74.5%) correctly identified the most optimal, and 62 (63.3%) identified both the most and least optimal offspring using only the sonification., (© 2024 The Author(s). Zoo Biology published by Wiley Periodicals LLC.)

Published
2024
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49. Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.

Author

Speak SA, Birley T, Bortoluzzi C, Clark MD, Percival-Alwyn L, Morales HE, and van Oosterhout C

Subjects
Animals, Animals, Zoo, Genetic Load, Genomics, Conservation of Natural Resources, Computer Simulation, Inbreeding Depression, Columbidae genetics, Columbidae physiology, Breeding methods
Abstract

Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations., (© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Published
2024
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50. The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator.

Author

Urban L, Santure AW, Uddstrom L, Digby A, Vercoe D, Eason D, Crane J, Wylie MJ, Davis T, LeLec MF, Guhlin J, Poulton S, Slate J, Alexander A, Fuentes-Cross P, Dearden PK, Gemmell NJ, Azeem F, Weyland M, Schwefel HGL, van Oosterhout C, and Morales HE

Subjects
Animals, New Zealand, Polymorphism, Genetic, Phenotype, Color, Predatory Behavior, Selection, Genetic, Feathers, Pigmentation genetics, Parrots genetics
Abstract

The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living kākāpō to understand the evolution of its feather color polymorphism. The kākāpō is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species' color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the kākāpō a "ghost of selection past.", Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Urban et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Published
2024
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