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Borecki P, Rosenberger J, Mucha A, Partyka A. Breeding behavior analysis in a large captive colony of African penguins (Spheniscus demersus) and its implications for population management and conservation. Sci Rep 2024; 14:3589. [PMID: 38351247 PMCID: PMC10864276 DOI: 10.1038/s41598-024-54105-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
The African penguin Spheniscus demersus, frequently housed in zoos, holds potential for future reintroduction efforts due to its declining wild population. This paper aims to explore various aspects of reproductive performance in African penguins within a large ex situ colony at Zoo Wrocław in Poland, covering 9 years of breeding behaviors. The analysis reveals parallels in colony growth and partner change patterns with those observed in the wild. Positive correlations were found between breeding success and pair-bond duration, with the increasing colony size influencing reproductive performance. Contrary to their wild counterparts, captive African penguins initiate breeding attempt and produce a fertilized egg at a younger age. However, successful breeding still requires gaining experience or forming pairs with more experienced partners. Our research indicates that providing captive African penguins with unlimited food resources and sufficient nesting space results in rapid colony growth. The increased colony size facilitates breeding behaviors that positively influence population dynamics, particularly through the maintenance of long-term pair bond relationships and the potential for partner changes when necessary or desirable to enhance breeding success. We present compelling case studies in pair fidelity, offering valuable insights and implications for the management of captive populations and conservation efforts.
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Affiliation(s)
- Paweł Borecki
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 49, 50-366, Wrocław, Poland
- Zoo Wrocław, Ul. Wróblewskiego 1-5, 51-618, Wrocław, Poland
| | - Joanna Rosenberger
- Division of Poultry Breeding, Institute of Animal Breeding, Wroclaw University of Environmental and Life Sciences, Ul. Chełmońskiego 38C, 51-630, Wrocław, Poland
| | - Anna Mucha
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Ul. Kożuchowska 7, 51-631, Wrocław, Poland
| | - Agnieszka Partyka
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 49, 50-366, Wrocław, Poland.
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2
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Omondi SF, Githae EW, Khasa DP. Long-distance gene flow in Acacia senegal: Hope for disturbed and fragmented populations. Ecol Evol 2023; 13:e10292. [PMID: 37449018 PMCID: PMC10337015 DOI: 10.1002/ece3.10292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Even though pollen and seed dispersals are some of the important factors that determine tree species survival across landscapes, gene dispersal data of important tropical dryland tree species such as Acacia senegal that are undergoing various population disturbances remain scarce. Understanding patterns of gene dispersal in these ecosystems is important for conservation, landscape restoration and tree improvement. We investigated pollen and seed mediated gene flow in two A. senegal populations of contrasting state (less disturbed and heavily undisturbed) using nine microsatellites and 128 genotyping-by-sequencing single nucleotide polymorphism (SNPs) multilocus genotypes of two growth stages (juvenile and adult trees) and their spatial locations. We performed parentage assignments using likelihood approach and undertook spatial genetic structure (SGS) analyses for the two growth stages through correlation among kinship coefficients and geographical distances between pair of individuals. The SNPs showed higher resolving power and assignment rates than microsatellites; however, a combination of the two marker-types improved the assignment rate and provided robust parentage assessments. We found evidence of long-distance (up to 210 m) pollination events for both populations; however, the majority of seed dispersal was found closer to the putative maternal parent. On average, parentage analysis showed high amounts of pollen (40%) and seed (20%) immigration in both populations. Significant positive SGS was found only for the adult cohorts in the less disturbed population for distance classes 20 and 40 m, indicating historical short-distance seed dispersals. Our results suggest long-distance gene flow within the species and we recommend conservation of remnant and isolated populations or individual trees to promote genetic connectivity.
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Affiliation(s)
- Stephen F. Omondi
- Department of Forest Genetics and Tree ImprovementKenya Forestry Research InstituteNairobiKenya
| | | | - Damase P. Khasa
- Centre for Forest Research and Institute for Systems and Integrative BiologyUniversité LavalSainte‐FoyQuébecCanada
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Khan A, Singh K, Jaiswal S, Raza M, Jasrotia RS, Kumar A, Gurjar AKS, Kumari J, Nayan V, Iquebal MA, Angadi UB, Rai A, Datta TK, Kumar D. Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis). Front Genet 2022; 13:809741. [PMID: 35480326 PMCID: PMC9035531 DOI: 10.3389/fgene.2022.809741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.
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Affiliation(s)
- Aamir Khan
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kalpana Singh
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mustafa Raza
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Animesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anoop Kishor Singh Gurjar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Juli Kumari
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- *Correspondence: Mir Asif Iquebal,
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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4
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Hauser SS, Athrey G, Leberg PL. Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics. Ecol Evol 2021; 11:15800-15814. [PMID: 34824791 PMCID: PMC8601879 DOI: 10.1002/ece3.8250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/07/2022] Open
Abstract
Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.
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Affiliation(s)
- Samantha S. Hauser
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
| | - Giridhar Athrey
- Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Paul L. Leberg
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
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5
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Iglesias Pastrana C, Navas González FJ, Ruiz Aguilera MJ, Dávila García JA, Delgado Bermejo JV, Abelló MT. White-naped mangabeys' viable insurance population within European Zoo Network. Sci Rep 2021; 11:674. [PMID: 33436901 PMCID: PMC7804940 DOI: 10.1038/s41598-020-80281-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
The success and viability of an ex-situ conservation program lie in the establishment and potential maintenance of a demographically and genetically viable insurance population. Such population reserve may support reintroduction and reinforcement activities of wild populations. White-naped mangabeys are endangered restricted-range African primates which have experienced a dramatic population decrease in their natural habitats over the last few decades. Since 2001, some European zoos singularly monitor an ex-situ population aiming to seek the recovery of the current wild population. The aim of the present paper is to evaluate the genetic status and population demographics of European zoo-captive white-naped mangabeys based on pedigree data. The captive population is gradually growing and preserves specific reproductive and demographic parameters linked to the species. The intensive management program that is implemented has brought about the minimization of inbreeding and average relatedness levels, thus maintaining high levels of genetic diversity despite the existence of fragmented populations. This finding suggests white-naped mangabey ex-situ preservation actions may be a good example of multifaceted conservation throughout studbook management which could be used as a model for other ex-situ live-animal populations.
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Affiliation(s)
| | | | | | | | | | - María Teresa Abelló
- White-naped mangabey EEP Coordination (EAZA: European Association of Zoos & Aquariums), Parc Zoològic de Barcelona, Barcelona, Spain
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6
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Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole. Sci Rep 2020; 10:21905. [PMID: 33318526 PMCID: PMC7736592 DOI: 10.1038/s41598-020-78397-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/20/2020] [Indexed: 11/08/2022] Open
Abstract
The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
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7
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Genome-wide screening of microsatellites in golden snub-nosed monkey (Rhinopithecus roxellana), for the development of a standardized genetic marker system. Sci Rep 2020; 10:10614. [PMID: 32606319 PMCID: PMC7326997 DOI: 10.1038/s41598-020-67451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/27/2020] [Indexed: 11/08/2022] Open
Abstract
Golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered primate endemic to China. The lack of standardized genetic markers limits its conservation works. In the present study, a total of 1,400,552 perfect STRs was identified in the reference genome of R. roxellana. By comparing it with the 12 resequencing genomes of four geographical populations, a total of 1,927 loci were identified as perfect tetranucleotides and shared among populations. We randomly selected 74 loci to design primer pairs. By using a total of 64 samples from the Chengdu Zoo captive population and the Pingwu wild population, a set of 14 novel STR loci were identified with good polymorphism, strong stability, high repeatability, low genotyping error rate that were suitable for non-invasive samples. These were used to establish a standardized marker system for golden snub-nosed monkeys. The genetic diversity analysis showed the average HO, HE, and PIC was 0.477, 0.549, and 0.485, respectively, in the Chengdu Zoo population; and 0.516, 0.473, and 0.406, respectively, in Pingwu wild population. Moreover, an individual identification method was established, which could effectively distinguish individuals with seven markers. The paternity tests were conducted on seven offspring with known mothers from two populations, and their fathers were determined with high confidence. A genotyping database for the captive population in the Chengdu Zoo (n = 25) and wild population in Pingwu country (n = 8) was acquired by using this marker system.
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8
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Zhang Y, Zhou Y, Liu X, Yu H, Li D, Zhang Y. Genetic diversity of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Shennongjia National Park, China using RAD-seq analyses. Genetica 2019; 147:327-335. [DOI: 10.1007/s10709-019-00073-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/12/2019] [Indexed: 12/30/2022]
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9
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Tahoor A, Khan JA, Mahfooz S. A comparative survey of microsatellites among wild and domestic cat provides valuable resources for marker development. Mol Biol Rep 2019; 46:3025-3033. [PMID: 30864111 DOI: 10.1007/s11033-019-04739-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
Information on the level and distribution of genetic variation is important for conservation plan of captive population of an endangered species such as tiger and cheetah. We assayed the frequency of microsatellites in the genomic and genic sequences of wild cats (Panthera tigris, Acinonyx jubatus) and compared it with the domestic cat (Felis catus). Frequency, relative abundance and density of microsatellites were highest in the domestic cat when compared with wild cats. The frequency of microsatellites was positively correlated with the G+C content of genomic and genic sequences. The maximum frequency of microsatellites among all three sequence sets was of di-nucleotide repeats (genomic-88.1%; genic-70.4%), whereas the hexa-nucleotide repeat represents < 0.5%. Motif conservation study among the genomic and genic sequences revealed conservation of 81.3% and 51.0% motif within the members of family Felidae. A total 40,233 primers from genic sequences were designed in order to enrich the members of family Felidae with genomic resources. The designed primers could be useful in determining the molecular genetics of population structure and individualization of a particular cat.
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Affiliation(s)
- Azram Tahoor
- Department of Wildlife Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Jamal Ahmad Khan
- Department of Wildlife Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Sahil Mahfooz
- Department of Biotechnology, V.B.S. Purvanchal University, Jaunpur, Uttar Pradesh, 222003, India. .,Division of Plant Microbe Interaction, CSIR-National Botanical Research Institute, Ranapratap Marg, Lucknow, Uttar Pradesh, 226001, India.
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10
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Flanagan SP, Jones AG. The future of parentage analysis: From microsatellites to SNPs and beyond. Mol Ecol 2019; 28:544-567. [PMID: 30575167 DOI: 10.1111/mec.14988] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022]
Abstract
Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
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Lee L, Tirrell N, Burrell C, Chambers S, Vogel S, Domyan ET. Genetic tests reveal extra-pair paternity among Gentoo penguins (Pyogoscelis papua ellsworthii) at Loveland Living Planet Aquarium: Implications for ex situ colony management. Zoo Biol 2018; 37:236-244. [PMID: 29998463 DOI: 10.1002/zoo.21432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/25/2018] [Indexed: 11/10/2022]
Abstract
Maintenance of ex situ populations for species conservation is a collaborative effort involving multiple agencies, institutions, and individuals around the world. Gentoo penguins (Pyogoscelis papua) are one species involved in such a conservation effort, and a Species Survival Plan (SSP) has been put in place by the Association of Zoos and Aquariums (AZA) to foster their long-term sustainability. As a part of their SSP, a Breeding and Transfer Plan has been created to support interagency exchanges of specimens. These transfers are vital to the demographic health and stability of ex situ populations, as well as the maintenance of genetic diversity. In populations such as the Gentoo, where social monogamy exists, paternal inferences of offspring are usually made through observation of birds' social behavior. However, social monogamy does not guarantee reproductive monogamy. In this study, we utilize Illumina high-throughput DNA sequencing to genetically test the postulated paternity of Gentoo penguins born at Loveland Living Planet Aquarium (LLPA) in Draper, UT. While our data support the majority of the postulated relationships, we did identify two offspring that were the result of extra-pair paternity (EPP). The results of this research highlight the importance of genetic tests to validate pedigrees used in SSPs, to provide more-accurate data for the support of species conservation.
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Affiliation(s)
- Lauren Lee
- Department of Biology, Utah Valley University, Orem, Utah
| | - Nathan Tirrell
- Department of Biology, Utah Valley University, Orem, Utah
| | | | | | - Steve Vogel
- Loveland Living Planet Aquarium, Draper, Utah
| | - Eric T Domyan
- Department of Biology, Utah Valley University, Orem, Utah
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12
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Oleński K, Kamiński S, Tokarska M, Hering DM. Subset of SNPs for parental identification in European bison Lowland-Białowieża line (Bison bonasus bonasus). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0768-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Attard CRM, Beheregaray LB, Möller LM. Genotyping‐by‐sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias. Mol Ecol Resour 2018; 18:381-390. [DOI: 10.1111/1755-0998.12739] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Catherine R. M. Attard
- Molecular Ecology Lab College of Science and Engineering Flinders University Adelaide SA Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Lab College of Science and Engineering Flinders University Adelaide SA Australia
| | - Luciana M. Möller
- Molecular Ecology Lab College of Science and Engineering Flinders University Adelaide SA Australia
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14
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Coetzer WG, Downs CT, Perrin MR, Willows-Munro S. Testing of microsatellite multiplexes for individual identification of Cape Parrots ( Poicephalus robustus): paternity testing and monitoring trade. PeerJ 2017; 5:e2900. [PMID: 28344897 PMCID: PMC5363265 DOI: 10.7717/peerj.2900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/12/2016] [Indexed: 12/04/2022] Open
Abstract
Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic.
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Affiliation(s)
- Willem G Coetzer
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Colleen T Downs
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Mike R Perrin
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Sandi Willows-Munro
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
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15
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Puckett EE. Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0643-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Kaiser SA, Taylor SA, Chen N, Sillett TS, Bondra ER, Webster MS. A comparative assessment of
SNP
and microsatellite markers for assigning parentage in a socially monogamous bird. Mol Ecol Resour 2016; 17:183-193. [DOI: 10.1111/1755-0998.12589] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Sara A. Kaiser
- Macaulay Library Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Migratory Bird Center Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington DC 20013 USA
| | - Scott A. Taylor
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder 1900 Pleasant Street 334 UCB Boulder CO 80309 USA
| | - Nancy Chen
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall 215 Tower Road Ithaca NY 14853 USA
| | - T. Scott Sillett
- Migratory Bird Center Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington DC 20013 USA
| | - Eliana R. Bondra
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall 215 Tower Road Ithaca NY 14853 USA
| | - Michael S. Webster
- Macaulay Library Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
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Labuschagne C, Nupen L, Kotzé A, Grobler PJ, Dalton DL. Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations. Ecol Evol 2015; 5:4389-99. [PMID: 26819703 PMCID: PMC4667824 DOI: 10.1002/ece3.1600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/10/2015] [Accepted: 06/14/2015] [Indexed: 11/11/2022] Open
Abstract
Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested.
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Affiliation(s)
- Christiaan Labuschagne
- Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa; Inqaba Biotechnical Industries (Pty) Ltd P.O. Box 14356 Hatfield 0028 South Africa
| | - Lisa Nupen
- National Zoological Gardens of South Africa P.O. Box 754 Pretoria 0001 South Africa; Department of Biological Sciences Percy FitzPatrick Institute University of Cape Town Rondebosch Cape Town 7701 South Africa
| | - Antoinette Kotzé
- Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa; National Zoological Gardens of South Africa P.O. Box 754 Pretoria 0001 South Africa
| | - Paul J Grobler
- Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
| | - Desiré L Dalton
- Department of Genetics University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa; National Zoological Gardens of South Africa P.O. Box 754 Pretoria 0001 South Africa
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