232 results on '"van Hooft, Pim"'
Search Results
2. A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: Possible implications for disease management.
- Author
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Greyling, Barend, Bastos, Armanda, van Hooft, Pim, and Getz, Wayne
- Subjects
Alleles ,Animals ,Buffaloes ,Cattle ,Disease Susceptibility ,Female ,Gene Frequency ,Genetic Association Studies ,Haplotypes ,Male ,Microsatellite Repeats ,South Africa ,Tuberculosis ,Bovine ,Y Chromosome - Abstract
Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002-2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.
- Published
- 2019
3. A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: Possible implications for disease management
- Author
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van Hooft, Pim, Getz, Wayne M, Greyling, Barend J, and Bastos, Armanda DS
- Subjects
Zoology ,Genetics ,Biological Sciences ,Rare Diseases ,2.1 Biological and endogenous factors ,Aetiology ,Good Health and Well Being ,Alleles ,Animals ,Buffaloes ,Cattle ,Disease Susceptibility ,Female ,Gene Frequency ,Genetic Association Studies ,Haplotypes ,Male ,Microsatellite Repeats ,South Africa ,Tuberculosis ,Bovine ,Y Chromosome ,General Science & Technology - Abstract
Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002-2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.
- Published
- 2019
4. Breeding den selection by Arctic foxes (Vulpes lagopus) in southern Yamal Peninsula, Russia
- Author
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Hofhuis, Stijn P., Ehrich, Dorothee, Sokolova, Natalia A., van Hooft, Pim, and Sokolov, Aleksandr A.
- Published
- 2021
- Full Text
- View/download PDF
5. Genetic responsiveness of African buffalo to environmental stressors: A role for epigenetics in balancing autosomal and sex chromosome interactions?
- Author
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van Hooft, Pim, Dougherty, Eric R, Getz, Wayne M, Greyling, Barend J, Zwaan, Bas J, and Bastos, Armanda DS
- Subjects
Sex Chromosomes ,Animals ,Buffaloes ,Logistic Models ,Cohort Studies ,Epigenesis ,Genetic ,Female ,Male ,Stress ,Physiological ,General Science & Technology - Abstract
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distorter-suppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequency-dependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.
- Published
- 2018
6. Sympatric speciation in structureless environments
- Author
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Getz, Wayne M, Salter, Richard, Seidel, Dana Paige, and van Hooft, Pim
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Biological Sciences ,Ecology ,Genetics ,Animals ,Behavior ,Animal ,Environment ,Feeding Behavior ,Genetic Speciation ,Models ,Theoretical ,Phenotype ,Reproduction ,Selection ,Genetic ,Sexual Behavior ,Animal ,Sympatry ,Magic traits ,Foraging guilds ,Disruptive selection ,Genetic algorithms ,Agent-based models ,Evolutionary Biology ,Evolutionary biology - Abstract
BackgroundDarwin and the architects of the Modern Synthesis found sympatric speciation difficult to explain and suggested it is unlikely to occur. Increasingly, evidence over the past few decades suggest that sympatric speciation can occur under ecological conditions that require at most intraspecific competition for a structured resource. Here we used an individual-based population model with variable foraging strategies to study the evolution of mating behavior among foraging strategy types. Initially, individuals were placed at random on a structureless resource landscape, with subsequent spatial variation induced through foraging activity itself. The fitness of individuals was determined by their biomass at the end of each generational cycle. The model incorporates three diallelic, codominant foraging strategy genes, and one mate-choice or m-trait (i.e. incipient magic trait) gene, where the latter is inactive when random mating is assumed.ResultsUnder non-random mating, the m-trait gene promotes increasing levels of either disassortative or assortative mating when the frequency of m respectively increases or decreases from 0.5. Our evolutionary simulations demonstrate that, under initial random mating conditions, an activated m-trait gene evolves to promote assortative mating because the system, in trying to fit a multipeak adaptive landscape, causes heterozygous individuals to be less fit than homozygous individuals.ConclusionOur results extend our theoretical understanding that sympatric speciation can evolve under nicheless or gradientless resource conditions: i.e. the underlying resource is monomorphic and initially spatially homogeneous. Further the simplicity and generality of our model suggests that sympatric speciation may be more likely than previously thought to occur in mobile, sexually-reproducing organisms.
- Published
- 2016
7. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.
- Author
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van Hooft, Pim, Greyling, Ben J, Getz, Wayne M, van Helden, Paul D, Zwaan, Bas J, and Bastos, Armanda DS
- Subjects
Chromosomes ,Y Chromosome ,Animals ,Buffaloes ,Sex Ratio ,Microsatellite Repeats ,Gene Frequency ,Genotype ,Heterozygote ,Quantitative Trait ,Heritable ,Alleles ,Genes ,Suppressor ,Female ,Male ,Selection ,Genetic ,General Science & Technology - Abstract
Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important implications for our understanding not only of the evolutionary and ecological dynamics of sex-ratio distorters and suppressors, but also of the functioning of deleterious and sexually-antagonistic alleles, and their impact on population viability.
- Published
- 2014
8. An inbreeding perspective on the effectiveness of wildlife population defragmentation measures - a case study on wild boar (Sus scrofa) of Veluwe, The Netherlands.
- Author
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de Jong, Joost F., de Jong, Menno J., Megens, Hendrik-Jan, van Hooft, Pim, Crooijmans, Richard P. M. A., de Groot, G. Arjen, Prins, Herbert H. T., Vilaca, Sibelle Torres, and Laliotis, George P.
- Subjects
WILD boar ,INBREEDING ,ANIMAL populations ,CORRIDORS (Ecology) ,MAMMAL populations ,GENE flow - Abstract
Pervasive inbreeding is a major genetic threat of population fragmentation and can undermine the efficacy of population connectivity measures. Nevertheless, few studies have evaluated whether wildlife crossings can alleviate the frequency and length of genomic autozygous segments. Here, we provided a genomic inbreeding perspective on the potential effectiveness of mammal population defragmentation measures. We applied a SNP-genotyping case study on the ~2500 wild boar Sus scrofa population of Veluwe, The Netherlands, a 1000-km
2 Natura 2000 protected area with many fences and roads but also, increasingly, fence openings and wildlife crossings. We combined a 20K genotyping assessment of genetic status and migration rate with a simulation that examined the potential for alleviation of isolation and inbreeding. We found that Veluwe wild boar subpopulations are significantly differentiated (FST -values of 0.02-0.13) and have low levels of gene flow. One noteworthy exception was the Central and Southeastern subpopulation, which were nearly panmictic and appeared to be effectively connected through a highway wildlife overpass. Estimated effective population sizes were at least 85 for the meta-population and ranged from 31 to 52 for the subpopulations. All subpopulations, including the two connected subpopulations, experienced substantial inbreeding, as evidenced through the occurrence of many long homozygous segments. Simulation output indicated that whereas one or few migrants per generation could undo genetic differentiation and boost effective population sizes rapidly, genomic inbreeding was only marginally reduced. The implication is that ostensibly successful connectivity restoration projects may fail to alleviate genomic inbreeding of fragmented mammal populations. We put forward that defragmentation projects should allow for (i) monitoring of levels of differentiation, migration and genomic inbreeding, (ii) anticipation of the inbreeding status of the meta-population, and, if inbreeding levels are high and/or haplotypes have become fixed, (iii) consideration of enhancing migration and gene flow among meta-populations, possibly through translocation. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
9. A new species of living peccary (Mammalia: Tayassuidae) from the Brazilian Amazon
- Author
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Van Roosmalen, Marc G M, Frenz, Lothar, Van Hooft, Pim, De Iongh, Hans H, Leirs, Herwig, and BioStor
- Published
- 2007
10. Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods
- Author
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de Winter, Iris I., Qurkhuli, Tamar, de Groot, Nanine, de Vos-Rouweler, Annemiek J. M., van Hooft, Pim, Heitkönig, Ignas M. A., Prins, Herbert H. T., Bontrop, Ronald E., and Doxiadis, Gaby G. M.
- Published
- 2019
- Full Text
- View/download PDF
11. Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio
- Author
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van Hooft, Pim, Prins, Herbert HT, Getz, Wayne M, Jolles, Anna E, van Wieren, Sipke E, Greyling, Barend J, van Helden, Paul D, and Bastos, Armanda DS
- Abstract
Abstract Background The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio. These sex-ratio (SR) genes modify (suppress) gamete transmission in their own favour at a fitness cost, allowing for stable polymorphism. Results Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. Frequencies varied by a factor of five; too high to be alternatively explained by Y-chromosomal effects on pregnancy loss. Sex ratios were male-biased during wet and female-biased during dry periods (male proportion: 0.47-0.53), seasonally and annually. Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. Conclusions The distinctive properties suggested for explaining Y-chromosomal polymorphism in African buffalo may not be restricted to this species alone. SR genes may play a broader and largely overlooked role in mammalian sex-ratio variation.
- Published
- 2010
12. Selection at the Y chromosome of the African buffalo driven by rainfall.
- Author
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van Hooft, Pim, Greyling, Barend J, Prins, Herbert HT, Getz, Wayne M, Jolles, Anna E, and Bastos, Armanda DS
- Subjects
Y Chromosome ,Animals ,Buffaloes ,Behavior ,Animal ,Ecology ,Rain ,Tandem Repeat Sequences ,Gene Frequency ,Haplotypes ,Polymorphism ,Genetic ,Models ,Genetic ,Male ,Genetic Variation ,Selection ,Genetic ,Behavior ,Animal ,Models ,Genetic ,Polymorphism ,Selection ,General Science & Technology - Abstract
Selection coefficients at the mammalian Y chromosome typically do not deviate strongly from neutrality. Here we show that strong balancing selection, maintaining intermediate frequencies of DNA sequence variants, acts on the Y chromosome in two populations of African buffalo (Syncerus caffer). Significant correlations exist between sequence variant frequencies and annual rainfall in the years before conception, with five- to eightfold frequency changes over short time periods. Annual rainfall variation drives the balancing of sequence variant frequencies, probably by affecting parental condition. We conclude that sequence variants confer improved male reproductive success after either dry or wet years, making the population composition and dynamics very sensitive to climate change. The mammalian Y chromosome, interacting with ecological processes, may affect male reproductive success much more strongly than previously thought.
- Published
- 2007
13. Birds in a bush : Toward an avian phylogenetic network
- Author
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Ottenburghs, Jente, van Hooft, Pim, van Wieren, Sipke E., Ydenberg, Ronald C., and Prins, Herbert H. T.
- Published
- 2016
14. Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
- Author
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Smitz, Nathalie, Van Hooft, Pim, Heller, Rasmus, Cornélis, Daniel, Chardonnet, Philippe, Kraus, Robert, Greyling, Ben, Crooijmans, Richard, Groenen, Martien, and Michaux, Johan
- Published
- 2016
- Full Text
- View/download PDF
15. Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa
- Author
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van Hooft, Pim, Keet, Dewald F., Brebner, Diana K., and Bastos, Armanda D. S.
- Published
- 2018
- Full Text
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16. Increased Mycoplasma hyopneumoniae Disease Prevalence in Domestic Hybrids Among Free-Living Wild Boar
- Author
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Goedbloed, Daniel J., van Hooft, Pim, Lutz, Walburga, Megens, Hendrik-Jan, van Wieren, Sip E., Ydenberg, Ron C., and Prins, Herbert H.T.
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- 2015
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17. A renewed call for conservation leadership 10 years further in the feral cat Trap-Neuter-Return debate and new opportunities for constructive dialogue
- Author
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Debrot, A.O., Ruijter, Martin, Endarwin, Wempy, van Hooft, Pim, Wulf, K., Delnevo, Adrian J., Debrot, A.O., Ruijter, Martin, Endarwin, Wempy, van Hooft, Pim, Wulf, K., and Delnevo, Adrian J.
- Abstract
It has been 10 years since a seminal paper in the journal Conservation Biology called for stronger leadership from the conservation community in countering the growing inappropriate use of Trap-Neuter-Return (TNR) as a method to control feral cat, Felis catus, populations. The practice is rapidly spreading to areas of wildlife and conservation significance, and the need to counter this development is extremely urgent. So far, the promulgation of TNR has been based on a narrow, single-species approach to animal welfare. However, a new, yet little-noticed, species-inclusive perspective on animal welfare includes the consideration of collateral animal suffering for a more equitable assessment of TNR. Each setting, depending on the level of conservation required, may call for different methods for the management of free-roaming cats. TNR is just one such method and its appropriateness depends on the specific wildlife conservation needs for each area specified.
- Published
- 2022
18. A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium
- Author
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van Hooft, Pim, primary, Getz, Wayne M., additional, Greyling, Barend J., additional, Zwaan, Bas, additional, and Bastos, Armanda D. S., additional
- Published
- 2021
- Full Text
- View/download PDF
19. Context dependence of risk effects: wolves and tree logs create patches of fear in an old-growth forest
- Author
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Kuijper, Dries P.J., Bubnicki, Jakub W., Churski, Marcin, Mols, Bjorn, and van Hooft, Pim
- Published
- 2015
- Full Text
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20. A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium
- Author
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van Hooft, Pim, Getz, Wayne M., Greyling, Barend J., Zwaan, Bas, Bastos, Armanda D.S., van Hooft, Pim, Getz, Wayne M., Greyling, Barend J., Zwaan, Bas, and Bastos, Armanda D.S.
- Abstract
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
- Published
- 2021
21. Wildlife roadkill patterns in a fragmented landscape of the Western Amazon
- Author
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Filius, Jonathan, van der Hoek, Yntze, Jarrin-V, Pablo, van Hooft, Pim, Filius, Jonathan, van der Hoek, Yntze, Jarrin-V, Pablo, and van Hooft, Pim
- Abstract
One of the most evident and direct effects of roads on wildlife is the death of animals by vehicle collision. Understanding the spatial patterns behind roadkill helps to plan mitigation measures to reduce the impacts of roads on animal populations. However, although roadkill patterns have been extensively studied in temperate zones, the potential impacts of roads on wildlife in the Neotropics have received less attention and are particularly poorly understood in the Western Amazon. Here, we present the results of a study on roadkill in the Amazon region of Ecuador; a region that is affected by a rapidly increasing development of road infrastructure. Over the course of 50 days, in the wet season between September and November 2017, we searched for road-killed vertebrates on 15.9 km of roads near the city of Tena, Napo province, for a total of 1590 surveyed kilometers. We recorded 593 dead specimens, predominantly reptiles (237 specimens, 40%) and amphibians (190, 32%), with birds (102, 17%) and mammals (64, 11%) being less common. Recorded species were assigned to three functional groups; based on their movement behavior and habitat use (‘slow’, ‘intermediate’ and ‘fast’). Using Ripley’s K statistical analyses and 2D HotSpot Identification Analysis, we found multiple distinct spatial clusters or hotspots, where roadkill was particularly frequent. Factors that potentially determined these clusters, and the prevalence of roadkill along road segments in general, differed between functional groups, but often included land cover variables such as native forest and waterbodies, and road characteristics such as speed limit (i.e. positive effect on roadkill frequency). Our study, which provides a first summary of species that are commonly found as roadkill in this part of the Amazon region, contributes to a better understanding of the negative impacts of roads on wildlife and is an important first step towards conservation efforts to mitigate these impacts.
- Published
- 2021
22. Temporal dynamics of cloacal microbiota in adult laying chickens with and without access to an outdoor range
- Author
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Schreuder, Janneke, Velkers, Francisca C., Bossers, A., Bouwstra, R.J., de Boer, Willem F., van Hooft, Pim, Stegeman, Jan Arend, Jurburg, S.D., Schreuder, Janneke, Velkers, Francisca C., Bossers, A., Bouwstra, R.J., de Boer, Willem F., van Hooft, Pim, Stegeman, Jan Arend, and Jurburg, S.D.
- Abstract
Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.
- Published
- 2021
23. An observational field study of the cloacal microbiota in adult laying hens with and without access to an outdoor range
- Author
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FAH veterinaire epidemiologie, dFAH I&I, FAH GZ pluimvee, dFAH AVR, Schreuder, J., Velkers, F.C., Bouwstra, Ruth, Beerens, Nancy, Stegeman, J.A., de Boer, Fred, van Hooft, Pim, Elbers, Armin, Bossers, Alex, Jurburg, Stephanie D, FAH veterinaire epidemiologie, dFAH I&I, FAH GZ pluimvee, dFAH AVR, Schreuder, J., Velkers, F.C., Bouwstra, Ruth, Beerens, Nancy, Stegeman, J.A., de Boer, Fred, van Hooft, Pim, Elbers, Armin, Bossers, Alex, and Jurburg, Stephanie D
- Published
- 2020
24. Microsatellite data from various African buffalo (Syncerus caffer) populations throughout Africa
- Author
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van Hooft, Pim, Getz, Wayne, Greyling, Ben, Heller, Rasmus, Røed, Knut, Bastos, Armanda, van Hooft, Pim, Getz, Wayne, Greyling, Ben, Heller, Rasmus, Røed, Knut, and Bastos, Armanda
- Abstract
1280 African buffalo (Syncerus caffer) samples genotyped with up to 19 microsatellites. 1275 samples are from East (12 populations) and southern Africa (4 populations). 5 samples are from central Africa (2 populations). Dataset consists of previously published genotypes from four different laboratories, using microsatellites originally developed for cattle (Bos taurus) and randomly chosen with respect to genomic location (microsatellite sets A, B, C and E). For various populations, microsatellite sets from two different laboratories were available, which permitted allele alignment by matching (allele size shift) each microsatellite's allele frequencies while preserving size order. Aligning microsatellite alleles from different laboratories based on frequency information is a valid standardization method when data sets are reasonably large and coming from the same population. Both the original microsatellite allele sizes and the aligned (standardized) microsatellite allele sizes are provided. Missing values are denoted with 0.
- Published
- 2020
25. A cross-sectional observational study of the fecal microbiota in adult laying hens with and without an outdoor range
- Author
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Schreuder, Janneke, Velkers, Francisca C., Bouwstra, R.J., Beerens, Nancy, Stegeman, J.A., de Boer, Fred, van Hooft, Pim, Elbers, Armin, Bossers, Alex, Jurburg, S.D., Schreuder, Janneke, Velkers, Francisca C., Bouwstra, R.J., Beerens, Nancy, Stegeman, J.A., de Boer, Fred, van Hooft, Pim, Elbers, Armin, Bossers, Alex, and Jurburg, S.D.
- Abstract
Background: Laying hens with access to outdoor ranges are exposed to additional environmental micro-organisms, including potential pathogens from wild birds. Alterations in the fecal microbiota or the relative abundance of individual genera of outdoor-housed layers may serve as an indicator for risks of exposure to potential pathogens. We therefore performed a cross-sectional field study to evaluate differences in the fecal microbiota of outdoor- vs indoor-layers across farms. Eight layer flocks (four indoor and four outdoor), from five poultry farms were sampled. Indoor and outdoor flocks were selected that had the same rearing flock of origin, and breed. In each flock, cloacal swabs were taken from ten layers, and microbiota compositions were analysed with 16S rRNA gene amplicon sequencing (region V3-V4). Conclusions: Our study shows that the cloacal microbial composition of adult laying hens in field conditions is to a limited extent, affected by the access to an outdoor range (i.e. housing type), but that the poultry house, farm, and rearing flock play a greater role in determining microbial composition. Overall, our study indicates that measuring differences in the cloacal fecal microbiota of layers as an indicator for the level of exposure to potential pathogens and the level of biosecurity seems of limited practical use.
- Published
- 2020
26. Temporal dynamics of cloacal microbiota in adult laying chickens with and without access to an outdoor range
- Author
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Schreuder, Janneke, Velkers, Francisca C., Bossers, Alex, Bouwstra, R.J., de Boer, Fred, van Hooft, Pim, Schreuder, Janneke, Velkers, Francisca C., Bossers, Alex, Bouwstra, R.J., de Boer, Fred, and van Hooft, Pim
- Abstract
Associations between animal health and performance, and the host its microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host its immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 % and 4.4 % of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens immediate environment affects the microbiota composition.
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- 2020
27. An observational field study of the cloacal microbiota in adult laying hens with and without access to an outdoor range
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Schreuder, Janneke, Velkers, Francisca C., Bouwstra, R.J., Beerens, N., Stegeman, J.A., de Boer, Willem F., van Hooft, Pim, Elbers, A.R.W., Bossers, A., Jurburg, S.D., Schreuder, Janneke, Velkers, Francisca C., Bouwstra, R.J., Beerens, N., Stegeman, J.A., de Boer, Willem F., van Hooft, Pim, Elbers, A.R.W., Bossers, A., and Jurburg, S.D.
- Abstract
Background: Laying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Differences in composition of the cloacal microbial community between indoor- and outdoor-housed layers may serve as an indicator for exposure to the outdoor environment, including its pathogens, and may yield insights into factors affecting the chickens’ microbiota community dynamics. However, little is known about the influence of outdoor housing on microbiota community composition in commercial layer flocks. We performed a cross-sectional field study to evaluate differences in the cloacal microbiota of indoor- vs outdoor-layers across farms. Eight layer flocks (four indoor, four outdoor) from five commercial poultry farms were sampled. Indoor and outdoor flocks with the same rearing flock of origin, age, and breed were selected. In each flock, cloacal swabs were taken from ten layers, and microbiota were analysed with 16S rRNA gene amplicon sequencing.Results: Housing type (indoor vs outdoor), rearing farm, farm and poultry house within the farm all significantly contributed to bacterial community composition. Poultry house explained most of the variation (20.9%), while housing type only explained 0.2% of the variation in community composition. Bacterial diversity was higher in indoor-layers than in outdoor-layers, and indoor-layers also had more variation in their bacterial community composition. No phyla or genera were found to be differentially abundant between indoor and outdoor poultry houses. One amplicon sequence variant was exclusively present in outdoor-layers across all outdoor poultry houses, and was identified as Dietzia maris.Conclusions: This study shows that exposure to an outdoor environment is responsible for a relatively small proportion of the community variation in the microbiota of layers. The poultry house, farm, and rearing flock play a much greater role in determining the cloacal microbiot
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- 2020
28. Fragmentation and Translocation Distort the Genetic Landscape of Ungulates : Red Deer in the Netherlands
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de Jong, Joost F., van Hooft, Pim, Megens, Hendrik Jan, Crooijmans, Richard P.M.A., de Groot, Gerard Arjen, Pemberton, Josephine M., Huisman, Jisca, Bartoš, Luděk, Iacolina, Laura, van Wieren, Sip E., Ydenberg, Ronald C., Prins, Herbert H.T., de Jong, Joost F., van Hooft, Pim, Megens, Hendrik Jan, Crooijmans, Richard P.M.A., de Groot, Gerard Arjen, Pemberton, Josephine M., Huisman, Jisca, Bartoš, Luděk, Iacolina, Laura, van Wieren, Sip E., Ydenberg, Ronald C., and Prins, Herbert H.T.
- Abstract
Many ungulate populations have a complex history of isolation and translocation. Consequently, ungulate populations may have experienced substantial reductions in the level of overall gene flow, yet simultaneously have augmented levels of long-distance gene flow. To investigate the effect of this dual anthropogenic effect on the genetic landscape of ungulates, we genotyped 35K SNPs in 47 red deer (Cervus elaphus) of Netherlands, including putative autochthonous relic populations as well as allochthonous populations established in private estates and rewilding areas. We applied FST and ordination analyses to determine the meta-population genetic structure and thereby the occurrence of hybridization. At population level, we investigated levels of inbreeding through individual-based diversity measures, including Runs of Homozygosity. We documented that both spatial genetic structure and within-population genetic variation differed markedly from patterns assumed from present-day abundance and distribution. Notwithstanding the small spatial scale, red deer populations formed distinct genetic clusters, and some had higher genetic similarity to distant than to nearby populations. Moreover, the putative autochthonous relic deer populations had much reduced levels of polymorphism and multi-locus heterozygosity, despite relatively large current population sizes. Accordingly, genomes of these deer contained a high proportion of long (>5 Mb) Runs of Homozygosity. Whereas the observed high levels of inbreeding warrant defragmentation measures, the presence of adjacent autochthonous and allochthonous genetic stocks imply that facilitation of gene flow would cause genetic homogenization. Such distortions of the genetic landscape of ungulates creates management dilemmas that cannot be properly anticipated without baseline genetic monitoring.
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- 2020
29. Wildlife roadkill patterns in a fragmented landscape of the Western Amazon
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Filius, Jonathan, van der Hoek, Yntze, Jarrín-V, Pablo, van Hooft, Pim, Filius, Jonathan, van der Hoek, Yntze, Jarrín-V, Pablo, and van Hooft, Pim
- Abstract
One of the most evident and direct effects of roads on wildlife is the death of animals by vehicle collision. Understanding the spatial patterns behind roadkill helps to plan mitigation measures to reduce the impacts of roads on animal populations. However, although roadkill patterns have been extensively studied in temperate zones, the potential impacts of roads on wildlife in the Neotropics have received less attention and are particularly poorly understood in the Western Amazon. Here, we present the results of a study on roadkill in the Amazon region of Ecuador; a region that is affected by a rapidly increasing development of road infrastructure. Over the course of 50 days, in the wet season between September and November 2017, we searched for road-killed vertebrates on 15.9 km of roads near the city of Tena, Napo province, for a total of 1,590 surveyed kilometers. We recorded 593 dead specimens, predominantly reptiles (237 specimens, 40%) and amphibians (190, 32%), with birds (102, 17%) and mammals (64, 11%) being less common. Recorded species were assigned to three functional groups, based on their movement behavior and habitat use (“slow,” “intermediate,” and “fast”). Using Ripley's K statistical analyses and 2D HotSpot Identification Analysis, we found multiple distinct spatial clusters or hotspots, where roadkill was particularly frequent. Factors that potentially determined these clusters, and the prevalence of roadkill along road segments in general, differed between functional groups, but often included land cover variables such as native forest and waterbodies, and road characteristics such as speed limit (i.e., positive effect on roadkill frequency). Our study, which provides a first summary of species that are commonly found as roadkill in this part of the Amazon region, contributes to a better understanding of the negative impacts of roads on wildlife and is an important first step toward conservation efforts to mitigate these impacts.
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- 2020
30. Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range
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Schreuder, Janneke, primary, Velkers, Francisca C., additional, Bossers, Alex, additional, Bouwstra, Ruth J., additional, de Boer, Willem F., additional, van Hooft, Pim, additional, Stegeman, J. Arjan, additional, and Jurburg, Stephanie D., additional
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- 2021
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31. A renewed call for conservation leadership 10 years further in the feral cat Trap‐Neuter‐Return debate and new opportunities for constructive dialogue.
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Debrot, Adolphe O., Ruijter, Martin N. M., Endarwin, Wempy, van Hooft, Pim, Wulf, Kai, and Delnevo, Adrian J.
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FERAL cats ,WILDLIFE conservation ,CATS ,ANIMAL welfare ,CONSERVATION biology ,ANIMAL rights ,BIODIVERSITY conservation - Abstract
It has been 10 years since a seminal paper in the journal Conservation Biology called for stronger leadership from the conservation community in countering the growing inappropriate use of Trap‐Neuter‐Return (TNR) as a method to control feral cat, Felis catus, populations. The practice is rapidly spreading to areas of wildlife and conservation significance, and the need to counter this development is extremely urgent. So far, the promulgation of TNR has been based on a narrow, single‐species approach to animal welfare. However, a new, yet little‐noticed, species‐inclusive perspective on animal welfare includes the consideration of collateral animal suffering for a more equitable assessment of TNR. Each setting, depending on the level of conservation required, may call for different methods for the management of free‐roaming cats. TNR is just one such method and its appropriateness depends on the specific wildlife conservation needs for each area specified. [ABSTRACT FROM AUTHOR]
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- 2022
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32. Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands
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de Jong, Joost F., primary, van Hooft, Pim, additional, Megens, Hendrik-Jan, additional, Crooijmans, Richard P. M. A., additional, de Groot, Gerard Arjen, additional, Pemberton, Josephine M., additional, Huisman, Jisca, additional, Bartoš, Luděk, additional, Iacolina, Laura, additional, van Wieren, Sip E., additional, Ydenberg, Ronald C., additional, and Prins, Herbert H. T., additional
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- 2020
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33. Limited changes in the fecal microbiome composition of laying hens after oral inoculation with wild duck feces
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Schreuder, Janneke, primary, Velkers, Francisca C., additional, Bouwstra, Ruth J., additional, Beerens, Nancy, additional, Stegeman, J. Arjan, additional, de Boer, Willem F., additional, Elbers, Armin R.W., additional, van Hooft, Pim, additional, Feberwee, Anneke, additional, Bossers, Alex, additional, and Jurburg, Stephanie D., additional
- Published
- 2019
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34. Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods
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Theoretical Biology and Bioinformatics, Sub Onderwijsinstituut Biologie, Sub Theoretical Biology, Afd Biologie Algemeen, de Winter, Iris I., Qurkhuli, Tamar, de Groot, Nanine, de Vos-Rouweler, Annemiek J.M., van Hooft, Pim, Heitkönig, Ignas M.A., Prins, Herbert H.T., Bontrop, Ronald E., Doxiadis, Gaby G.M., Theoretical Biology and Bioinformatics, Sub Onderwijsinstituut Biologie, Sub Theoretical Biology, Afd Biologie Algemeen, de Winter, Iris I., Qurkhuli, Tamar, de Groot, Nanine, de Vos-Rouweler, Annemiek J.M., van Hooft, Pim, Heitkönig, Ignas M.A., Prins, Herbert H.T., Bontrop, Ronald E., and Doxiadis, Gaby G.M.
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- 2019
35. Limited changes in the fecal microbiome composition of laying hens after oral inoculation with wild duck feces
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LS GZ Landbouwhuisdieren, dFAH I&I, Sub GZ Varken/Pluimvee, Sub GZ Herkauwer, Schreuder, Janneke, Velkers, Francisca C, Bouwstra, Ruth J, Beerens, Nancy, Stegeman, J Arjan, de Boer, Willem F, Elbers, Armin R W, van Hooft, Pim, Feberwee, Anneke, Bossers, Alex, Jurburg, Stephanie D, LS GZ Landbouwhuisdieren, dFAH I&I, Sub GZ Varken/Pluimvee, Sub GZ Herkauwer, Schreuder, Janneke, Velkers, Francisca C, Bouwstra, Ruth J, Beerens, Nancy, Stegeman, J Arjan, de Boer, Willem F, Elbers, Armin R W, van Hooft, Pim, Feberwee, Anneke, Bossers, Alex, and Jurburg, Stephanie D
- Published
- 2019
36. Panthera leo D-loop, partial sequence; mitochondrial
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van Hooft, Pim, Keet, Dewald F., Brebner, Diana K., Bastos, Armanda D.S., van Hooft, Pim, Keet, Dewald F., Brebner, Diana K., and Bastos, Armanda D.S.
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- 2019
37. Limited changes in the fecal microbiome composition of laying hens after oral inoculation with wild duck feces
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Schreuder, Janneke, Velkers, Francisca C., Bouwstra, Ruth J., Beerens, N., Stegeman, J.A., de Boer, Willem F., Elbers, A.R.W., van Hooft, Pim, Feberwee, Anneke, Bossers, A., Jurburg, Stephanie, Schreuder, Janneke, Velkers, Francisca C., Bouwstra, Ruth J., Beerens, N., Stegeman, J.A., de Boer, Willem F., Elbers, A.R.W., van Hooft, Pim, Feberwee, Anneke, Bossers, A., and Jurburg, Stephanie
- Abstract
Interspecies transmission of fecal microbiota can serve as an indicator for (indirect) contact between domestic and wild animals to assess risks of pathogen transmission, e.g., avian influenza. Here, we investigated whether oral inoculation of laying hens with feces of wild ducks (mallards, Anas platyrhynchos) resulted in a hen fecal microbiome that was detectably altered on community parameters or relative abundances of individual genera. To distinguish between effects of the duck inoculum and effects of the inoculation procedure, we compared the fecal microbiomes of adult laying hens resulting from 3 treatments: inoculation with wild duck feces (duck), inoculation with chicken feces (auto), and a negative control group with no treatment. We collected cloacal swabs from 7 hens per treatment before (day 0), and 2 and 7 D after inoculation, and performed 16S rRNA amplicon sequencing. No distinguishable effect of inoculation with duck feces on microbiome community (alpha and beta diversity) was found compared to auto or control treatments. At the individual taxonomic level, the relative abundance of the genus Alistipes (phylum Bacteroidetes) was significantly higher in the inoculated treatments (auto and duck) compared to the control 2 D after inoculation. Seven days after inoculation, the relative abundance of Alistipes had increased in the control and no effect was found anymore across treatments. These effects might be explained by the perturbation of the hen's microbiome caused by the inoculation procedure itself, or by intrinsic temporal variation in the hen's microbiome. This experiment shows that a single inoculation of fecal microbiota from duck feces to laying hens did not cause a measurable alteration of the gut microbiome community. Furthermore, the temporary change in relative abundance for Alistipes could not be attributed to the duck feces inoculation. These outcomes suggest that the fecal microbiome of adult laying hens may not be a useful indicator for
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- 2019
38. Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
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Kraus, Robert HS, Kerstens, Hindrik HD, Van Hooft, Pim, Crooijmans, Richard PMA, Van Der Poel, Jan J, Elmberg, Johan, Vignal, Alain, Huang, Yinhua, Li, Ning, Prins, Herbert HT, and Groenen, Martien AM
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- 2011
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39. Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks
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Kraus Robert HS, Kerstens Hindrik HD, van Hooft Pim, Megens Hendrik-Jan, Elmberg Johan, Tsvey Arseny, Sartakov Dmitry, Soloviev Sergej A, Crooijmans Richard PMA, Groenen Martien AM, Ydenberg Ronald C, and Prins Herbert HT
- Subjects
Evolution ,QH359-425 - Abstract
Abstract Background The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct. Results We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years. Conclusions By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal gene transfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group of animals. There is large evolutionary potential in the ability to exchange genes among species and the resulting dramatic increase of effective population size to counter selective constraints.
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- 2012
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40. Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA
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Kraus Robert HS, Zeddeman Anne, van Hooft Pim, Sartakov Dmitry, Soloviev Sergei A, Ydenberg Ronald C, and Prins Herbert HT
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Genetics ,QH426-470 - Abstract
Abstract Background Main waterfowl migration systems are well understood through ringing activities. However, in mallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere. Results Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (FST = 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero). Conclusions Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration.
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- 2011
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41. Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
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Huang Yinhua, Vignal Alain, Elmberg Johan, Van Der Poel Jan J, Crooijmans Richard PMA, Van Hooft Pim, Kerstens Hindrik HD, Kraus Robert HS, Li Ning, Prins Herbert HT, and Groenen Martien AM
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.
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- 2011
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42. Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in south Africa
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van Hooft Pim, Lamb Jennifer M, von Maltitz Emil, Mostert Elmarie, Kirsten Frikkie, Brettschneider Helene, Taylor Peter J, Nair Deenadayalan, Bastos Armanda D, Belmain Steven R, Contrafatto Giancarlo, Downs Sarah, and Chimimba Christian T
- Subjects
Genetics ,QH426-470 - Abstract
Abstract Background South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present. Results To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species. Conclusions This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.
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- 2011
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43. Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio
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Greyling Barend J, van Wieren Sipke E, Jolles Anna E, Getz Wayne M, Prins Herbert HT, van Hooft Pim, van Helden Paul D, and Bastos Armanda DS
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Evolution ,QH359-425 - Abstract
Abstract Background The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio. These sex-ratio (SR) genes modify (suppress) gamete transmission in their own favour at a fitness cost, allowing for stable polymorphism. Results Here we show temporal correlations between Y-chromosomal haplotype frequencies and foetal sex ratios in the KNP buffalo population, suggesting SR genes. Frequencies varied by a factor of five; too high to be alternatively explained by Y-chromosomal effects on pregnancy loss. Sex ratios were male-biased during wet and female-biased during dry periods (male proportion: 0.47-0.53), seasonally and annually. Both wet and dry periods were associated with a specific haplotype indicating a SR distorter and SR suppressor, respectively. Conclusions The distinctive properties suggested for explaining Y-chromosomal polymorphism in African buffalo may not be restricted to this species alone. SR genes may play a broader and largely overlooked role in mammalian sex-ratio variation.
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- 2010
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44. Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods
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de Winter, Iris I., primary, Qurkhuli, Tamar, additional, de Groot, Nanine, additional, de Vos-Rouweler, Annemiek J. M., additional, van Hooft, Pim, additional, Heitkönig, Ignas M. A., additional, Prins, Herbert H. T., additional, Bontrop, Ronald E., additional, and Doxiadis, Gaby G. M., additional
- Published
- 2018
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45. Anthropogenic disturbance effects remain visible in forest structure, but not in lemur abundances
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de Winter, Iris, primary, van der Hoek, Sebastiaan, additional, Schütt, Jeroen, additional, Heitkönig, Ignas M.A., additional, van Hooft, Pim, additional, Gort, Gerrit, additional, Prins, Herbert H.T., additional, and Sterck, Frank, additional
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- 2018
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46. Occupancy strongly influences faecal microbial composition of wild lemurs
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Umanets, Alexander, primary, de Winter, Iris, additional, IJdema, Freek, additional, Ramiro-Garcia, Javier, additional, van Hooft, Pim, additional, Heitkönig, Ignas M A, additional, Prins, Herbert H T, additional, and Smidt, Hauke, additional
- Published
- 2018
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47. Avian introgression in the genomic era
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Ottenburghs, Jente, primary, Kraus, Robert H. S., additional, van Hooft, Pim, additional, van Wieren, Sipke E., additional, Ydenberg, Ronald C., additional, and Prins, Herbert H. T., additional
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- 2017
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48. Avian introgression in the genomic era
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Ottenburghs, Jente, Kraus, Robert H.S., van Hooft, Pim, van Wieren, Sipke E., Ydenberg, Ronald C., Prins, Herbert H.T., Ottenburghs, Jente, Kraus, Robert H.S., van Hooft, Pim, van Wieren, Sipke E., Ydenberg, Ronald C., and Prins, Herbert H.T.
- Abstract
Introgression, the incorporation of genetic material from one (sub)species into the gene pool of another by means of hybridization and backcrossing, is a common phenomenon in birds and can provide important insights into the speciation process. In the last decade, the toolkit for studying introgression has expanded together with the development of molecular markers. In this review, we explore how genomic data, the most recent step in this methodological progress, impacts different aspects in the study of avian introgression. First, the detection of hybrids and backcrosses has improved dramatically. The most widely used software package is STRUCTURE. Phylogenetic discordance (i.e. different loci resulting in discordant gene trees) is another means for the detection of introgression, although it should be regarded as a starting point for further analyses, not as a definitive proof of introgression. Specifically, disentangling introgression from other biological processes, such as incomplete lineage sorting, remains a challenging endeavour, although new techniques, such as the D-statistic, are being developed. In addition, phylogenetics might require a shift from trees to networks. Second, the study of hybrid zones by means of geographical or genomic cline analysis has led to important insights into the complex interplay between hybridization and speciation. However, because each hybrid zone study is just a single snapshot of a complex and continuously changing interaction, hybrid zones should be studied across different temporal and/or spatial scales. A third powerful tool is the genome scan. The debate on which evolutionary processes underlie the genomic landscape is still ongoing, as is the question whether loci involved in reproductive isolation cluster together in 'islands of speciation' or whether they are scattered throughout the genome. Exploring genomic landscapes across the avian tree of life will be an exciting field for further research. Finally, the findin
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- 2017
49. A history of hybrids? Genomic patterns of introgression in the True Geese
- Author
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Ottenburghs, Jente, Megens, Hendrik Jan, Kraus, Robert H.S., van Hooft, Pim, van Wieren, Sipke E., Crooijmans, Richard P.M.A., Ydenberg, Ronald C., Groenen, Martien A.M., Prins, Herbert H.T., Ottenburghs, Jente, Megens, Hendrik Jan, Kraus, Robert H.S., van Hooft, Pim, van Wieren, Sipke E., Crooijmans, Richard P.M.A., Ydenberg, Ronald C., Groenen, Martien A.M., and Prins, Herbert H.T.
- Abstract
Background: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results: We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hy
- Published
- 2017
50. A history of hybrids? Genomic patterns of introgression in the True Geese
- Author
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Ottenburghs, Jente, primary, Megens, Hendrik-Jan, additional, Kraus, Robert H. S., additional, van Hooft, Pim, additional, van Wieren, Sipke E., additional, Crooijmans, Richard P. M. A., additional, Ydenberg, Ronald C., additional, Groenen, Martien A. M., additional, and Prins, Herbert H. T., additional
- Published
- 2017
- Full Text
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