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Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl‐Wilson A, Benzie JAH, Houston RD, Wiener P. Genetic differentiation following recent domestication events: A study of farmed Nile tilapia ( Oreochromis niloticus) populations. Evol Appl 2023; 16:1220-1235. [PMID: 37360025 PMCID: PMC10286235 DOI: 10.1111/eva.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark Genetics Norway ASBergenNorway
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark GeneticsMidlothianUK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Center of Environment Fisheries and Aquaculture ScienceWeymouthUK
| | | | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| | - John A. H. Benzie
- WorldFishBayan LepasPenangMalaysia
- School of Biological Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Benchmark GeneticsMidlothianUK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
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Arick MA, Grover CE, Hsu CY, Magbanua Z, Pechanova O, Miller ER, Thrash A, Youngblood RC, Ezzell L, Alam MS, Benzie JAH, Hamilton MG, Karsi A, Lawrence ML, Peterson DG. A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination. G3 (Bethesda) 2023; 13:6987299. [PMID: 36639248 PMCID: PMC9997561 DOI: 10.1093/g3journal/jkad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023]
Abstract
Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.
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Affiliation(s)
- Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Zenaida Magbanua
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Olga Pechanova
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Emma R Miller
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Adam Thrash
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Lauren Ezzell
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Md Samsul Alam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - John A H Benzie
- WorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang, Malaysia
| | | | - Attila Karsi
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Mark L Lawrence
- Global Center for Aquatic Health and Food Security, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
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Barría A, Benzie JAH, Houston RD, De Koning DJ, de Verdal H. Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia ( Oreochromis niloticus) Population. Front Genet 2021; 12:737906. [PMID: 34616434 PMCID: PMC8488396 DOI: 10.3389/fgene.2021.737906] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Nile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2) map the genomic regions associated with these traits and identify candidate genes, 3) evaluate the accuracy of breeding value prediction using genomic data, and 4) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; -0.60 and -0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a, ghrh and eif4e3. The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, United Kingdom
| | - John A. H. Benzie
- WorldFish, Bayan Lepas, Malaysia
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, United Kingdom
| | - Dirk-Jan De Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hugues de Verdal
- CIRAD, UMR ISEM, Montpellier, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Barría A, Trịnh TQ, Mahmuddin M, Peñaloza C, Papadopoulou A, Gervais O, Chadag VM, Benzie JAH, Houston RD. Correction to: A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus). Heredity (Edinb) 2021; 127:344. [PMID: 34408297 PMCID: PMC8405769 DOI: 10.1038/s41437-021-00461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, UK
| | | | | | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, UK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, UK
| | - Ophelie Gervais
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, UK
| | | | | | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, UK.
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5
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Yu X, Megens HJ, Mengistu SB, Bastiaansen JWM, Mulder HA, Benzie JAH, Groenen MAM, Komen H. Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus). BMC Genomics 2021; 22:426. [PMID: 34107887 PMCID: PMC8188787 DOI: 10.1186/s12864-021-07486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 16th generation of a Genetically Improved Farmed Tilapia population. Results In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways were involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage. Conclusions There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07486-5.
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Affiliation(s)
- Xiaofei Yu
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
| | - Hendrik-Jan Megens
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Samuel Bekele Mengistu
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.,School of Animal and Range Sciences, College of Agriculture, Hawassa University, Hawassa, Ethiopia
| | - John W M Bastiaansen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Han A Mulder
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - John A H Benzie
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Martien A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Hans Komen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
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Rodde C, de Verdal H, Vandeputte M, Allal F, Nati J, Besson M, Blasco FR, Benzie JAH, McKenzie DJ. An investigation of links between metabolic rate and feed efficiency in European sea bass Dicentrarchus labrax. J Anim Sci 2021; 99:skab152. [PMID: 33966070 PMCID: PMC8219042 DOI: 10.1093/jas/skab152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Feed efficiency (FE) is the amount of body weight gain for a given feed intake. Improving FE through selective breeding is key for sustainable finfish aquaculture but its evaluation at individual level is technically challenging. We therefore investigated whether individual routine metabolic rate (RMR) was a predictor of individual FE in the European sea bass Dicentrarchus labrax, a major species in European mariculture. The European sea bass has three genetically distinct populations across its geographical range, namely Atlantic (AT), West Mediterranean (WM), and East Mediterranean (EM). We compared FE and RMR of fish from these three populations at 18 or 24 °C. We held 200 fish (62 AT, 66 WM, and 72 EM) in individual aquaria and fed them from ad libitum down to fasting. FI was assessed for an ad libitum feeding rate and for a fixed restricted ration (1% of metabolic body weight·day-1, with metabolic body weight = body weight0.8). After being refed 12 wk in a common tank, individual RMR was measured over 36 h by intermittent flow respirometry. There was a significant effect of temperature whereby fish at 18 °C had greater mean FE (P < 0.05) and lower RMR (P < 0.001). There was also a significant effect of population, where AT fish had lower FE (P < 0.05) and greater RMR (P < 0.001) than WM and EM, at both temperatures. Despite these differences in temperature and population means, individual FE and RMR were not significantly correlated (P > 0.05). Therefore, although the results provide evidence of an association between metabolic rate and FE, RMR was not a predictor of individual FE, for reasons that require further investigation.
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Affiliation(s)
- Charles Rodde
- CIRAD, UMR ISEM, 34398 Montpellier, France
- ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
- Worldfish, Jalan Batu Maung, Bayan Lepas, 11960 Penang, Malaysia
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Hugues de Verdal
- CIRAD, UMR ISEM, 34398 Montpellier, France
- ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - Marc Vandeputte
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - François Allal
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Julie Nati
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Mathieu Besson
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
- SYSAAF Section Aquacole, Campus de Beaulieu, 35000 Rennes, France
| | - Felipe R Blasco
- Laboratório de Zoofisiologia e Bioquímica Comparativa, Departamento de Ciências Fisiológicas, Universidade Federal de São Carlos, São Paulo 13565-905, Brasil
| | - John A H Benzie
- Worldfish, Jalan Batu Maung, Bayan Lepas, 11960 Penang, Malaysia
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork T12 K8AF, Ireland
| | - David J McKenzie
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
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7
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Rodde C, Vandeputte M, Trinh TQ, Douchet V, Canonne M, Benzie JAH, de Verdal H. The Effects of Feed Restriction and Isolated or Group Rearing on the Measurement of Individual Feed Intake and Estimation of Feed Conversion Ratio in Juvenile Nile Tilapia ( Oreochromis niloticus) for Selective Breeding Purposes. Front Genet 2021; 11:596521. [PMID: 33519898 PMCID: PMC7844319 DOI: 10.3389/fgene.2020.596521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022] Open
Abstract
Accurately measuring the phenotype at the individual level is critical to the success of selective breeding programs. Feed efficiency is a key sustainability trait and is typically approached through feed conversion ratio (FCR). This requires measurements of body weight gain (BWG) and feed intake (FI), the latter being technically challenging in fish. We assessed two of the principal methods for measuring feed intake in fish over consecutive days: (1) group rearing 10 fish per group and video recording the meals and (2) rearing fish individually on a restricted ration. Juvenile Nile tilapia (Oreochromis niloticus) from the Genetically Improved Farmed Tilapia (GIFT) strain and the Cirad strain were entered into the study (128 GIFT and 109 Cirad). The GIFT strain were reared over three consecutive periods of 7 days each under different feeding, recording, and rearing scenarios (i) in groups fed an optimal ration (g100) or (ii) fed a 50% restricted ration (g50) both with video records of all meals and (iii) reared in isolation and fed a 50% restrictive ration. The Cirad strain were tested similarly but only for scenarios (i) and (iii). All fish were fed twice daily with a calculated ration. Correlations showed the same trends for the GIFT and the Cirad strains. For the GIFT strain, correlations were positive and significant for BWG and FI measured in scenarios (i) and (ii), 0.49 and 0.63, respectively, and FI measured in scenarios (i) and (iii) (0.50) but not for BWG measured in scenarios (i) and (iii) (0.29, NS). The phenotypic correlation estimated for FCR between scenarios (i) and (ii) with fish fed an optimal or a 50% restricted ration was low and not significant (0.22). Feed Conversion Ratio for GIFT fish reared in groups or in isolation and fed with a restricted ration [scenarios (ii) and (iii)] were not significantly correlated either. Social interactions between fish, potentially impacting their efficiency, may explain the results. Therefore, selective breeding programs seeking to improve feed efficiency will need to carefully plan the feeding rate and the rearing system used to estimate FCR in order to optimize selection for the targeted production system.
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Affiliation(s)
- Charles Rodde
- CIRAD, UMR ISEM, Montpellier, France.,ISEM, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France.,WorldFish, Bayan Lepas, Malaysia.,MARBEC, CNRS, Ifremer, IRD, University of Montpellier, Montpellier, France
| | - Marc Vandeputte
- MARBEC, CNRS, Ifremer, IRD, University of Montpellier, Montpellier, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Vincent Douchet
- CIRAD, UMR ISEM, Montpellier, France.,ISEM, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Marc Canonne
- CIRAD, UMR ISEM, Montpellier, France.,ISEM, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - John A H Benzie
- WorldFish, Bayan Lepas, Malaysia.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Hugues de Verdal
- CIRAD, UMR ISEM, Montpellier, France.,ISEM, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
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8
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Hamilton MG, Lind CE, Barman BK, Velasco RR, Danting MJC, Benzie JAH. Distinguishing Between Nile Tilapia Strains Using a Low-Density Single-Nucleotide Polymorphism Panel. Front Genet 2020; 11:594722. [PMID: 33335540 PMCID: PMC7736061 DOI: 10.3389/fgene.2020.594722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most important finfish in aquaculture, particularly in Asia. Numerous genetically improved strains of Nile tilapia have been developed and disseminated through formal and informal channels to hatcheries, many of which operate at a relatively small scale in developing countries. The primary objective of this study was to assess the extent to which molecular genetic tools can identify different and interrelated strains of Nile tilapia in Bangladesh and the Philippines, two globally significant producers. A tool was developed using a low-density panel of single-nucleotide polymorphisms (SNPs), genotyping-by-sequencing and discriminant analysis of principal components (DAPC). When applied to 2,057 samples from 205 hatcheries in Bangladesh and the Philippines, for hatcheries where the hatchery-identified strain was one of the sampled core populations used to develop the tool, hatchery-identified and DAPC-assigned hatchery-level strains were in agreement in 74.1% of cases in Bangladesh and 80.6% of cases in the Philippines. The dominant hatchery-identified and DAPC-assigned strains were GIFT, in Bangladesh, and GET-ExCEL-a composite strain partially derived from GIFT-in the Philippines.
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Affiliation(s)
| | | | | | - Ravelina R. Velasco
- Department of Aquatic Resources, Ecology and Management, College of Fisheries, Central Luzon State University, Muñoz, Philippines
- Freshwater Aquaculture Center, Central Luzon State University, Muñoz, Philippines
| | - Ma. Jodecel C. Danting
- Bureau of Fisheries and Aquatic Resources, National Freshwater Fisheries Technology Center, Central Luzon State University Compound, Science City of Munoz, Philippines
| | - John A. H. Benzie
- WorldFish, Penang, Malaysia
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
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9
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Nayfa MG, Jones DB, Benzie JAH, Jerry DR, Zenger KR. Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia ( Oreochromis niloticus) in Egypt. Front Genet 2020; 11:567969. [PMID: 33193660 PMCID: PMC7593532 DOI: 10.3389/fgene.2020.567969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A H Benzie
- WorldFish, Penang, Malaysia.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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10
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Taslima K, Wehner S, Taggart JB, de Verdal H, Benzie JAH, Bekaert M, McAndrew BJ, Penman DJ. Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23. BMC Genet 2020; 21:49. [PMID: 32349678 PMCID: PMC7189693 DOI: 10.1186/s12863-020-00853-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022] Open
Abstract
Background Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed with O. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins. Results A bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatellite UNH898 and ARO172, and the recently isolated amhy marker for individual fish (n = 284). Conclusions Perhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.
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Affiliation(s)
- Khanam Taslima
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.,Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Stefanie Wehner
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - John B Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - Hugues de Verdal
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,CIRAD, UMR ISEM, F-34398 Montpellier, France; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - John A H Benzie
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - Brendan J McAndrew
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - David J Penman
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.
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11
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Hamilton MG, Mekkawy W, Kilian A, Benzie JAH. Single Nucleotide Polymorphisms (SNPs) Reveal Sibship Among Founders of a Bangladeshi Rohu ( Labeo rohita) Breeding Population. Front Genet 2019; 10:597. [PMID: 31275363 PMCID: PMC6593075 DOI: 10.3389/fgene.2019.00597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/05/2019] [Indexed: 01/04/2023] Open
Abstract
Rohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.
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Affiliation(s)
| | - Wagdy Mekkawy
- WorldFish, Penang, Malaysia
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd., (DArT P/L), University of Canberra, Bruce, ACT, Australia
| | - John A. H. Benzie
- WorldFish, Penang, Malaysia
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
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12
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Hamilton MG, Mekkawy W, Benzie JAH. Sibship assignment to the founders of a Bangladeshi Catla catla breeding population. Genet Sel Evol 2019; 51:17. [PMID: 31035934 PMCID: PMC6489195 DOI: 10.1186/s12711-019-0454-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/06/2019] [Indexed: 01/02/2023] Open
Abstract
Catla catla (Hamilton) fertilised spawn was collected from the Halda, Jamuna and Padma rivers in Bangladesh from which approximately 900 individuals were retained as 'candidate founders' of a breeding population. These fish were fin-clipped and genotyped using the DArTseq platform to obtain, 3048 single nucleotide polymorphisms (SNPs) and 4726 silicoDArT markers. Using SNP data, individuals that shared no putative parents were identified using the program COLONY, i.e. 140, 47 and 23 from the Halda, Jamuna and Padma rivers, respectively. Allele frequencies from these individuals were considered as representative of those of the river populations, and genomic relationship matrices were generated. Then, half-sibling and full-sibling relationships between individuals were assigned manually based on the genomic relationship matrices. Many putative half-sibling and full-sibling relationships were found between individuals from the Halda and Jamuna rivers, which suggests that catla sampled from rivers as spawn are not necessarily representative of river populations. This has implications for the interpretation of past population genetics studies, the sampling strategies to be adopted in future studies and the management of broodstock sourced as river spawn in commercial hatcheries. Using data from individuals that shared no putative parents, overall multi-locus pairwise estimates of Wright's fixation index (FST) were low (≤ 0.013) and the optimum number of clusters using unsupervised K-means clustering was equal to 1, which indicates little genetic divergence among the SNPs included in our study within and among river populations.
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Affiliation(s)
| | - Wagdy Mekkawy
- WorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang Malaysia
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Hadaeq Shubra, Cairo, 11241 Egypt
| | - John A. H. Benzie
- WorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang Malaysia
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
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13
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de Verdal H, Vandeputte M, Mekkawy W, Chatain B, Benzie JAH. Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus. BMC Genet 2018; 19:105. [PMID: 30445908 PMCID: PMC6240178 DOI: 10.1186/s12863-018-0691-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Improving feed efficiency in fish is crucial at the economic, social and environmental levels with respect to developing a more sustainable aquaculture. The important contribution of genetic improvement to achieve this goal has been hampered by the lack of accurate basic information on the genetic parameters of feed efficiency in fish. We used video assessment of feed intake on individual fish reared in groups to estimate the genetic parameters of six growth traits, feed intake, feed conversion ratio (FCR) and residual feed intake in 40 pedigreed families of the GIFT strain of Nile tilapia, Oreochromis niloticus. Feed intake and growth were measured on juvenile fish (22.4 g mean body weight) during 13 consecutive meals, representing 7 days of measurements. We used these data to estimate the FCR response to different selection criteria to assess the potential of genetics as a means of increasing FCR in tilapia. RESULTS Our results demonstrate genetic control for FCR in tilapia, with a heritability estimate of 0.32 ± 0.11. Response to selection estimates showed FCR could be efficiently improved by selective breeding. Due to low genetic correlations, selection for growth traits would not improve FCR. However, weight loss at fasting has a high genetic correlation with FCR (0.80 ± 0.25) and a moderate heritability (0.23), and could be an easy to measure and efficient criterion to improve FCR by selective breeding in tilapia. CONCLUSION At this age, FCR is genetically determined in Nile tilapia. A selective breeding program could be possible and could help enabling the development of a more sustainable aquaculture production.
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Affiliation(s)
- Hugues de Verdal
- CIRAD, UMR116 ISEM, TA B-116/16, 73 rue Jean-François Breton, 34398, Montpellier Cedex 5, France. .,Worldfish, Jalan Batu Maung, 11960, Bayan Lepas, Penang, Malaysia.
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France.,Ifremer, UMR9190 MARBEC, Chemin de Maguelone, F-34250, Palavas-les-Flots, France
| | - Wagdy Mekkawy
- Worldfish, Jalan Batu Maung, 11960, Bayan Lepas, Penang, Malaysia.,Animal Production Department, Faculty of Agriculture, Ain Shams University, Hadaeq Shubra, Cairo, 11241, Egypt
| | - Béatrice Chatain
- Ifremer, UMR9190 MARBEC, Chemin de Maguelone, F-34250, Palavas-les-Flots, France
| | - John A H Benzie
- Worldfish, Jalan Batu Maung, 11960, Bayan Lepas, Penang, Malaysia.,School Of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
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14
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Agha S, Mekkawy W, Ibanez-Escriche N, Lind CE, Kumar J, Mandal A, Benzie JAH, Doeschl-Wilson A. Breeding for robustness: investigating the genotype-by-environment interaction and micro-environmental sensitivity of Genetically Improved Farmed Tilapia (Oreochromis niloticus). Anim Genet 2018; 49:421-427. [PMID: 30058152 PMCID: PMC6175454 DOI: 10.1111/age.12680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2018] [Indexed: 12/03/2022]
Abstract
Robustness has become a highly desirable breeding goal in the globalized agricultural market. Both genotype‐by‐environment interaction (G × E) and micro‐environmental sensitivity are important robustness components of aquaculture production, in which breeding stock is often disseminated to different environments. The objectives of this study were (i) to quantify the degree of G × E by assessing the growth performance of Genetically Improved Farmed Tilapia (GIFT) across three countries (Malaysia, India and China) and (ii) to quantify the genetic heterogeneity of environmental variance for body weight at harvest (BW) in GIFT as a measure of micro‐environmental sensitivity. Selection for BW was carried out for 13 generations in Malaysia. Subsets of 60 full‐sib families from Malaysia were sent to China and India after five and nine generations respectively. First, a multi‐trait animal model was used to analyse the BW in different countries as different traits. The results indicate a strong G × E. Second, a genetically structured environmental variance model, implemented using Bayesian inference, was used to analyse micro‐environmental sensitivity of BW in each country. The analysis revealed the presence of genetic heterogeneity of both BW and its environmental variance in all environments. The presence of genetic variation in residual variance of BW implies that the residual variance can be modified by selection. Incorporating both G × E and micro‐environmental sensitivity information may help in selecting robust genotypes with high performance across environments and resilience to environmental fluctuations.
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Affiliation(s)
- S Agha
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Edinburgh, UK.,Animal Production Department, Faculty of Agriculture, Ain Shams University, Shubra Alkhaima, 11241, Cairo, Egypt
| | - W Mekkawy
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Shubra Alkhaima, 11241, Cairo, Egypt.,WorldFish, Jalan Batu Maung, Batu Maung, Bayan Lepas, 11960, Penang, Malaysia
| | - N Ibanez-Escriche
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Edinburgh, UK.,Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, València, Spain
| | - C E Lind
- WorldFish, Jalan Batu Maung, Batu Maung, Bayan Lepas, 11960, Penang, Malaysia
| | - J Kumar
- Rajiv Gandhi Center for Aquaculture, Vijayawada, Tamil Nadu, India
| | - A Mandal
- Rajiv Gandhi Center for Aquaculture, Vijayawada, Tamil Nadu, India
| | - J A H Benzie
- WorldFish, Jalan Batu Maung, Batu Maung, Bayan Lepas, 11960, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, North Mall Campus, Cork, Ireland
| | - A Doeschl-Wilson
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Edinburgh, UK
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15
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Benzie JAH, Williams ST. GENETIC STRUCTURE OF GIANT CLAM (TRIDACNA MAXIMA) POPULATIONS IN THE WEST PACIFIC IS NOT CONSISTENT WITH DISPERSAL BY PRESENT-DAY OCEAN CURRENTS. Evolution 2017; 51:768-783. [DOI: 10.1111/j.1558-5646.1997.tb03660.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/1995] [Accepted: 01/06/1997] [Indexed: 11/26/2022]
Affiliation(s)
- John A. H. Benzie
- Australian Institute of Marine Science; PMB No 3, Townsville MC Queensland 4810 Australia
| | - Suzanne T. Williams
- Australian Institute of Marine Science; PMB No 3, Townsville MC Queensland 4810 Australia
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16
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Duke NC, Benzie JAH, Goodall JA, Ballment ER. GENETIC STRUCTURE AND EVOLUTION OF SPECIES IN THE MANGROVE GENUSAVICENNIA(AVICENNIACEAE) IN THE INDO-WEST PACIFIC. Evolution 2017; 52:1612-1626. [DOI: 10.1111/j.1558-5646.1998.tb02242.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/1997] [Accepted: 06/25/1998] [Indexed: 11/27/2022]
Affiliation(s)
- Norman C. Duke
- Australian Institute of Marine Science, PMB No. 3; Townsville MC Queensland 4810 Australia
- Botany Department; James Cook University of North Queensland; Townsville Queensland 4811 Australia
| | - John A. H. Benzie
- Australian Institute of Marine Science, PMB No. 3; Townsville MC Queensland 4810 Australia
| | - John A. Goodall
- Australian Institute of Marine Science, PMB No. 3; Townsville MC Queensland 4810 Australia
| | - Elizabeth R. Ballment
- Australian Institute of Marine Science, PMB No. 3; Townsville MC Queensland 4810 Australia
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17
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Benzie JAH. MAJOR GENETIC DIFFERENCES BETWEEN CROWN-OF-THORNS STARFISH (ACANTHASTER PLANCI) POPULATIONS IN THE INDIAN AND PACIFIC OCEANS. Evolution 2017; 53:1782-1795. [PMID: 28565442 DOI: 10.1111/j.1558-5646.1999.tb04562.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/1999] [Accepted: 06/15/1999] [Indexed: 11/26/2022]
Abstract
Spatial variation in allelic frequencies at nine allozyme loci were assayed in 20 populations of the crown-of-thorns starfish, Acanthaster planci, collected throughout the Pacific and Indian Oceans. These data were analyzed together with published data, for the same loci, from an additional 19 populations, giving a total sample size of approximately 1800 individuals. There was a marked discontinuity between the Indian and Pacific Ocean populations, but those off Western Australia and from the Southeast Asian region had a strong Pacific affinity. The genetic groups were congruent with the distributions of two color morph groups: gray-green to red-brown forms in the Pacific and a blue to pale red form in the Indian Ocean. These patterns of genetic structure are similar to those described for the starfish Linckia laevigata, which has similar life-history characteristics. Vicariant events may have influenced some populations within the Pacific, but the allozyme data cannot resolve the effects of these events clearly. Patterns of variation within regions were consistent with isolation by distance, but, at larger scales, were obscured by regional vicariance and some outliers, particularly by apparently high levels of gene flow between Japan and the Great Barrier Reef, Australia. Apparent gene flow between population pairs was not closely related to present-day ocean currents. The results demonstrate a strong influence of allopatric separation on genetic divergence at large geographic scales, but also show evidence of slow rates of change in gene frequencies consistent with the large population sizes of this species. Low levels of divergence between groups demonstrate the genetic structure is recent (Pleistocene) and are likely responses to changes in climate and sea level.
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Affiliation(s)
- John A H Benzie
- Australian Institute of Marine Science, PMB No. 3, Townsville MC, Queensland, 4810, Australia
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18
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Lind CE, Kilian A, Benzie JAH. Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus. Anim Genet 2017; 48:362-364. [PMID: 28094451 DOI: 10.1111/age.12536] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2016] [Indexed: 02/06/2023]
Abstract
The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.
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Affiliation(s)
- C E Lind
- WorldFish, Jalan Batu Maung, 11960, Bayan Lepas, Penang, Malaysia
| | - A Kilian
- Diversity Arrays Technology Pty Ltd (DArT P/L), University of Canberra, Building 3, Bruce, ACT, 2617, Australia
| | - J A H Benzie
- WorldFish, Jalan Batu Maung, 11960, Bayan Lepas, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
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19
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Ma THT, Benzie JAH, He JG, Sun CB, Chan SF. PmPPAF is a pro-phenoloxidase activating factor involved in innate immunity response of the shrimp Penaeus monodon. Dev Comp Immunol 2014; 44:163-172. [PMID: 24345607 DOI: 10.1016/j.dci.2013.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/02/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
One of the major steps in the innate immune response of shrimp includes the activation of serine proteinases of the pro-phenoloxidase pathway by the prophenoloxidase activation enzyme (PPAF). In this study, the cDNA encoding a serine proteinase homologue (SPH) with prophenoloxidase activating activity of Penaeus monodon (PmPPAF) was cloned and characterized. PmPPAF cDNA consists of 1444 nucleotides encoding a protein with 394 amino acid residues. The estimated molecular weight of PmPPAF is 43.5 kDa with an isoelectric point of 5.19. PmPPAF consists of a signal peptide, a CLIP domain and a carboxyl-terminal trypsin-like serine protease domain. It is highly similar to the masquerade-like protein 2A (61% similarity) of the crayfish Pacifastacus leniusculus, other serine proteases (42.9-67% identity) of P. monodon, and the PPAF of the crab (61% similarity). Unlike other SPH of P. monodon, which express mainly in the hemocytes, PmPPAF transcripts were detected in the hemocytes, eyestalk, hypodermis, gill, swimming leg and brain. Similar to the crab PPAF, PmPPAF transcript level is high in shrimp at the premolt stages and PmPPAF expression is up-regulated in shrimp infected with white spot syndrome virus (WSSV). Gene silencing of PmPPAF decreased expression of a prophenoloxidase-like gene and injection of Anti-PmPPAF antibody causes a decrease in PO activity. Taken together, these results provided evidence that PmPPAF is a serine proteinase homologue, and is involved in the pro-PO activation pathway of the shrimp innate immune system.
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Affiliation(s)
- Tracy H T Ma
- Fisheries College, Guangdong Ocen University, Zhanjiang, PR China; School of Biological Sciences, The University of Hong Kong, PR China
| | - John A H Benzie
- University College Cork, Cork, Ireland and WorldFish, Jalan Batu Maung, Batu Maung, 11960 Bayan Lepas, Penang, Malaysia
| | - Jian-Guo He
- School of Life Sciences, Zhongshan University, PR China
| | - Cheng-Bo Sun
- Fisheries College, Guangdong Ocen University, Zhanjiang, PR China.
| | - Siuming F Chan
- Fisheries College, Guangdong Ocen University, Zhanjiang, PR China.
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20
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Benzie JAH. Duplidentitermes furcatidens(Sjöstedt, 1924) (Isoptera, Termitidae) in Northern Guinea savanna habitats, Ghana. Afr J Ecol 2013. [DOI: 10.1111/j.1365-2028.1983.tb01182.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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O'Farrell B, Benzie JAH, McGinnity P, Carlsson J, Eyto ED, Dillane E, Graham C, Coughlan J, Cross T. MHC-mediated spatial distribution in brown trout (Salmo trutta) fry. Heredity (Edinb) 2012; 108:403-9. [PMID: 21934705 PMCID: PMC3313050 DOI: 10.1038/hdy.2011.87] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 07/19/2011] [Accepted: 08/18/2011] [Indexed: 11/08/2022] Open
Abstract
Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5 ± (s.e.)21.03 m; one allele shared, 222.2 ± 14.49 m; two alleles shared, 124.9 ± 23.88 m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r = 0) (no alleles: 457.6 ± 3.58 m; one allele (422.4 ± 3.86 m); two alleles (381.7 ± 10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time.
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Affiliation(s)
- B O'Farrell
- Microbial Phylogeography, Department of Microbiology, Environmental Research Institute, University College Cork, Cork, Ireland
| | - J A H Benzie
- School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork, Ireland
| | - P McGinnity
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Marine Institute, Newport, Co. Mayo, Ireland
| | - J Carlsson
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - E de Eyto
- Marine Institute, Newport, Co. Mayo, Ireland
| | - E Dillane
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - C Graham
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - J Coughlan
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - T Cross
- Aquaculture and Fisheries Development Centre (AFDC), School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
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Nevalainen TJ, Peuravuori HJ, Quinn RJ, Llewellyn LE, Benzie JAH, Fenner PJ, Winkel KD. Phospholipase A2 in Cnidaria. Comp Biochem Physiol B Biochem Mol Biol 2004; 139:731-5. [PMID: 15581805 DOI: 10.1016/j.cbpc.2004.09.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 09/07/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
Phospholipase A2 (PLA2) is an enzyme present in snake and other venoms and body fluids. We measured PLA2 catalytic activity in tissue homogenates of 22 species representing the classes Anthozoa, Hydrozoa, Scyphozoa and Cubozoa of the phylum Cnidaria. High PLA2 levels were found in the hydrozoan fire coral Millepora sp. (median 735 U/g protein) and the stony coral Pocillopora damicornis (693 U/g) that cause skin irritation upon contact. High levels of PLA2 activity were also found in the acontia of the sea anemone Adamsia carciniopados (293 U/g). Acontia are long threads containing nematocysts and are used in defense and aggression by the animal. Tentacles of scyphozoan and cubozoan species had high PLA2 activity levels: those of the multitentacled box jellyfish Chironex fleckeri contained 184 U/g PLA2 activity. The functions of cnidarian PLA2 may include roles in the capture and digestion of prey and defense of the animal. The current observations support the idea that cnidarian PLA2 may participate in the sting site irritation and systemic envenomation syndrome resulting from contact with cnidarians.
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Affiliation(s)
- Timo J Nevalainen
- Department of Pathology, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland.
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Uthicke S, Benzie JAH. Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Mol Ecol 2003; 12:2635-48. [PMID: 12969467 DOI: 10.1046/j.1365-294x.2003.01954.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sea cucumber, Holothuria nobilis, has a long-lived planktotrophic larvae, and previous allozyme surveys have suggested that high dispersal is realized. In contrast, recent ecological studies indicate that dispersal is low. To reconcile these data, and to investigate the evolution of this Indo-Pacific species, we screened geographical variation in 559 bp of a mitochondrial gene (COI) in 360 samples from the Australasian region and La Réunion. Sequences from La Réunion differed by > 7% from others and may constitute another species. Haplotype diversity in other samples was high (0.942, SD = 0.007), but haplotypes were closely related (mean nucleotide diversity: 0.0075, SD = 0.0041). AMOVA, pairwise FST values and exact tests did not detect significant population structure. Nested clade analysis showed that one of two main clades was over-represented in west Australia, whereas the other was more common in the northern Great Barrier Reef. Isolation-by-distance was identified as the main determinant of population structure at several clade levels. Contiguous range expansion was inferred for evolutionary older clade levels and this may correspond to a late Pleistocene (88 000-193 000 years ago) population expansion inferred from haplotype mismatch distributions. Thus, the population genetic structures detected are likely to be formed prior to the last ice age, with some indications for high dispersal on shorter time scales.
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Affiliation(s)
- S Uthicke
- Australian Institute of Marine Science, PMB no. 3, Townsville, Queensland 4810, Australia.
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Benzie JAH, Ballment E, Forbes AT, Demetriades NT, Sugama K, Moria S. Mitochondrial DNA variation in Indo-Pacific populations of the giant tiger prawn, Penaeus monodon. Mol Ecol 2002; 11:2553-69. [PMID: 12453239 DOI: 10.1046/j.1365-294x.2002.01638.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Surveys of mitochondrial DNA (mtDNA) variation in the giant tiger prawn, Penaeus monodon, using restriction fragment length polymorphisms have provided the first clear evidence that the Indo-West Pacific region is a site of accumulation of genetic diversity rather than a site of origin of genetic diversity. No haplotyes were found in common between a group of five southeast African populations and a group of five Australian (including Western Australia) and three southeast Asian populations. The dominant haplotype was different in the Australian and southeast Asian population groups. Genetic diversity (pi) was greatest in Indonesia (pi averaged 0.05), less in the Philippines and Australia (pi averaged 0.01), and markedly less in the southeast African and the West Australian populations (pi averaged 0.003). The high diversity of the southeast Asian populations resulted from the occurrence in those populations of a set of haplotypes found only in southeast Asia but derived from the southeast African haplotypes. These genetic variants therefore evolved in the Indian Ocean and later migrated into the Indo-West Pacific region. Low genetic variation in the geographically marginal populations in southeast Africa and Western Australia is considered to be the result of bottlenecks, but mismatch distributions suggest that large population sizes have been maintained in Indonesian populations for long periods.
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Affiliation(s)
- J A H Benzie
- Australian Institute of Marine Science, PMB 3, Townsville, MC Queensland 4810, Australia.
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Benzie JAH. Major Genetic Differences between Crown-of-Thorns Starfish (Acanthaster planci) Populations in the Indian and Pacific Oceans. Evolution 1999. [DOI: 10.2307/2640440] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Duke NC, Benzie JAH, Goodall JA, Ballment ER. Genetic Structure and Evolution of Species in the Mangrove Genus Avicennia (Avicenniaceae) in the Indo-West Pacific. Evolution 1998. [DOI: 10.2307/2411335] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Benzie JAH, Williams ST. Genetic Structure of Giant Clam (Tridacna maxima) Populations in the West Pacific is Not Consistent with Dispersal by Present-Day Ocean Currents. Evolution 1997. [DOI: 10.2307/2411153] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Benzie JAH, Black KP, Moran PJ, Dixon P. Small-Scale Dispersion of Eggs and Sperm of the Crown-of-Thorns Starfish (Acanthaster planci) in a Shallow Coral Reef Habitat. Biol Bull 1994; 186:153-167. [PMID: 29281365 DOI: 10.2307/1542049] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The dispersal of eggs and sperm of crown-of-thorns starfish, Acanthaster planci (L.), was measured in the field using an array of collectors up to 10 m downstream of a spawning starfish. Hydrodynamic measurements, gamete dispersal numerical models, and the gamete cloud dispersal measurements for the first time quantified the relationship between hydrodynamic conditions and the dispersion of eggs and sperm in the field. In general, gamete concentrations fell rapidly and logarithmically with distance from the spawning starfish; egg concentrations at 3 m were 1% of those near the starfish. Simplified dispersal models showed a good correspondence with these field data, and confirmed the observation that eggs rose higher in the water column and spread more laterally at low current speeds over the short spatial scales being considered. Fertilization rates, predicted from laboratory measurements of fertilization success and the gamete concentrations measured in the field, were estimated to be 90-100% within 1 m and 70-100% at 10 m. These results are explained by high success rates of fertilization (fertilizing capacity) at the measured dilutions, and were similar to fertilization rates previously measured by others for crown-of-thorns starfish in the field. Although the eggs were observed to spread upwards into the water column due to turbulence, laboratory measurements of sinking rates showed eggs to be very slightly negatively buoyant (median fall velocity of 0.072 mm·s-1), whereas sperm were neutrally buoyant. A significant fraction of eggs also entered the seabed near the starfish; the proportion decreased with increasing current strength. This process may provide a mechanism for enhanced fertilization of these gametes and/or a mechanism for self-recruitment to a given reef population.
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Benzie JAH, Dixon P. The Effects of Sperm Concentration, Sperm:Egg Ratio, and Gamete Age on Fertilization Success in Crown-of-Thorns Starfish (Acanthaster planci) in the Laboratory. Biol Bull 1994; 186:139-152. [PMID: 29281364 DOI: 10.2307/1542048] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Laboratory experiments varying gamete concentrations and gamete age demonstrated significant reductions in fertilization success of the starfish Acanthaster planci (L.) with decreasing sperm concentration and increasing age of both eggs and sperm. The effect of aging in sperm was faster than that of eggs, and the speed of sperm aging increased with increasing dilution of sperm. Fertilization success was high over a wide range of sperm: egg ratios but declined rapidly at ratios less than 50, particularly at low sperm concentrations. A. planci gametes aged more slowly, and the loss of fertilizing capacity of sperm with dilution (the respiratory dilution effect) was far less, than in sea urchins. These characteristics provide a mechanism for enhanced fertilization success at given sperm concentrations and at greater distances and times from the point of gamete release, and may explain the higher fertilization rates achieved over longer distances in the wild by A. planci relative to sea urchins. Gametes would remain competent for longer periods at more dilute concentrations and so better achieve long-distance fertilization. Gametes obtained at the end of the breeding season were qualitatively different from those obtained early in the breeding season and showed reduced fertilization success for a given combination of variables, and different fertilization dynamics.
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Benzie JAH. The distribution, abundance, and the effects of fire on mound building termites (Trinervitermes and Cubitermes spp., Isoptera: Termitidae) in northern guinea savanna West Africa. Oecologia 1986; 70:559-567. [PMID: 28311499 DOI: 10.1007/bf00379904] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/1986] [Indexed: 10/26/2022]
Abstract
Termite mound densities in typical guinea savanna, Detarium, and grassland (boval) habitats in northern guinea savanna were determined by random quadratting of 2-3 sites in each habitat (100, 10x10 m quadrats per habitat). Dominant species in guinea savanna were T. geminatus (46 mounds ha-1) and T. oeconomus (21 mounds ha-1), in Detarium T. geminatus (59 mounds ha-1) and C. curtatus (45 mounds ha-1) and in boval C. curtatus (72 mounds ha-1) and T. geminatus (22 mounds ha-1). Only C. curtatus densities and total densities differed significantly between sites within habitats, but all species differed significantly in abundance between habitats. The composition of each community was related to general environment but no particular environmental variable was shown to be a major determinant of termite distribution. Evidence for the limitation of termite populations was obtained from indirect evidence of competition between colonies in Detarium, and by experimental manipulation of fire regimes in the typical guinea savanna habitat. Harvester termites increased four-five fold over two years in fire-protected plots as a result of increased food supplies. Total termite densities in the fire-protected community equilibrated to the new population density (100 mounds ha-1) after only two-three years.
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Affiliation(s)
- John A H Benzie
- Department of Zoology, University of Aberdeen, Tillydrone Avenue, AB9 2TN, Aberdeen, UK
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Benzie JAH. Dismantling of a New Structure Associated With Foraging in the West African Termite Trinervitermes geminatus (Wasmann) (Isoptera: Termitidae: Nasutitermitinae). Biotropica 1984. [DOI: 10.2307/2388060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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