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Bringloe TT, Bourret A, Cote D, Marie-Julie R, Herbig J, Robert D, Geoffroy M, Parent GJ. Genomic architecture and population structure of Boreogadus saida from Canadian waters. Sci Rep 2024; 14:19331. [PMID: 39164428 PMCID: PMC11336163 DOI: 10.1038/s41598-024-69782-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024] Open
Abstract
The polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4-16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.
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Affiliation(s)
- Trevor T Bringloe
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada.
| | - Audrey Bourret
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada
| | - David Cote
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, A0G 2M0, Canada
| | - Roux Marie-Julie
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada
| | - Jennifer Herbig
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, A1C 5R3, Canada
| | - Dominique Robert
- Institut Des Sciences de La Mer, Université du Québec à Rimouski, Rimouski, QC, G5L 3A1, Canada
| | - Maxime Geoffroy
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, A1C 5R3, Canada
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9036, Tromsø, Norway
| | - Geneviève J Parent
- Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, QC, G5H 3Z4, Canada.
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Wang X, Reid K, Chen Y, Dudgeon D, Merilä J. Ecological genetics of isolated loach populations indicate compromised adaptive potential. Heredity (Edinb) 2024; 133:88-98. [PMID: 38961235 PMCID: PMC11286901 DOI: 10.1038/s41437-024-00695-0] [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: 01/10/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.
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Affiliation(s)
- Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Chen
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - David Dudgeon
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, FI-00014 University of Helsinki, Helsinki, Finland.
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Wróbel A, Klichowska E, Nowak A, Nobis M. Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot. Syst Biol 2024; 73:263-278. [PMID: 38141222 PMCID: PMC11282368 DOI: 10.1093/sysbio/syad073] [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: 03/06/2023] [Revised: 11/23/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023] Open
Abstract
Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.
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Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza 11, 30-348 Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
| | - Arkadiusz Nowak
- Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973 Warszawa, Poland
- Botanical Garden of the Wrocław University, Sienkiewicza 23, 50-335 Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland
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Vega-Retter C, Rojas-Hernández N, Cortés-Miranda J, Véliz D, Rico C. Genome scans reveal signals of selection associated with pollution in fish populations of Basilichthys microlepidotus, an endemic species of Chile. Sci Rep 2024; 14:15727. [PMID: 38977738 PMCID: PMC11231317 DOI: 10.1038/s41598-024-66121-x] [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: 01/19/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
The Maipo River catchment is one of Chile's most polluted basins. In recent decades, discharges of untreated sewage and organic matter have caused eutrophication and water quality degradation. We employed the indigenous silverfish species Basilichthys microlepidotus as a model organism to investigate the process of adaptation and selection on genes influenced by pollution. Using variation at single nucleotide polymorphisms (SNPs), we determined the temporal stability of the population structure patterns previously identified in this species by varying SNPs. We also examined local adaptation to pollution-selected genes. Using the genotypes of 7684 loci in 180 individuals, we identified 429 and 700 loci that may be undergoing selection. We detected these loci using the FSTHET and ARLEQUIN outlier detection software, respectively. Both software packages simultaneously identified a total of 250 loci. B. microlepidotus' population structure did not change over time at contaminated or unpolluted sites. In addition, our analysis found: (i) selection of genes associated with pollution, consistent with observations in other organisms; (ii) identification of candidate genes that are functionally linked to the same biological processes, molecular functions and/or cellular components that previously showed differential expression in the same populations; and (iii) a candidate gene with differential expression and a non-synonymous substitution.
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Affiliation(s)
- Caren Vega-Retter
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago, Chile
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago, Chile
| | - Jorge Cortés-Miranda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago, Chile
- Centro de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Coquimbo, Chile
| | - Ciro Rico
- Instituto de Ciencias Marinas de Andalucía (ICMAN), CSIC. Campus Universitario Río San Pedro, C. Republica Saharaui, 4, 11519, Puerto Real, Cádiz, Spain.
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5
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Kokarev V, Dufour SC, Raeymaekers JAM, Mailli AA, Reiss H. Thyasirid species composition (Bivalvia: Thyasiridae) and genetic connectivity of Parathyasira equalis (A. E. Verrill & K. J. Bush, 1898) in deep basins of sub-Arctic fjords. BMC Ecol Evol 2024; 24:91. [PMID: 38965473 PMCID: PMC11223403 DOI: 10.1186/s12862-024-02278-3] [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: 04/12/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Thyasirid bivalves are often recorded as a dominant component of macrobenthic infaunal communities in depositional environments such as fjord basins. Fjord basins comprise patchy soft-bottom habitats bounded by steep walls and sills; however, little is known how this semi-isolated nature of fjords affects benthic populations. Accordingly, data on the composition and population connectivity of thyasirids can provide valuable information on the ecology of these ecosystems. RESULTS The species composition of thyasirid bivalves has been studied in the basins of three sub-Arctic fjords (Nordland, Northern Norway). Overall, six thyasirid species were recorded: Parathyasira equalis, Parathyasira dunbari, Mendicula ferruginosa, Genaxinus eumyarius, Thyasira sarsii, and Thyasira obsoleta. The species composition remained stable within the basins during the sampling period (2013-2020) and suggested the importance of local reproduction over advection of individuals for population dynamics. Only one species, Parathyasira equalis, was common in all fjords. We have further investigated the population genetics of this species by combining two types of genetic markers: a 579 bp fragment of the cytochrome c oxidase subunit I (COI) gene and 4043 single-nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing. The latter provided a more in-depth resolution on the population genetics of this species and revealed a weak but significant differentiation of populations within fjords, further indicating limited connectivity between basins. CONCLUSION Based on our findings, we conclude that limited dispersal between the basin communities results in weakly connected populations and might be an important structuring factor for macrobenthic communities.
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Affiliation(s)
- Valentin Kokarev
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway.
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | | | - Amalia A Mailli
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
| | - Henning Reiss
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
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6
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Stringer EJ, Gruber B, Sarre SD, Wardle GM, Edwards SV, Dickman CR, Greenville AC, Duncan RP. Boom-bust population dynamics drive rapid genetic change. Proc Natl Acad Sci U S A 2024; 121:e2320590121. [PMID: 38621118 PMCID: PMC11067018 DOI: 10.1073/pnas.2320590121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype-by-sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse (Pseudomys hermannsburgensis) experiences marked boom-bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation (FST) increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy-footed dunnart (Sminthopsis youngsoni), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts.
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Affiliation(s)
- Emily J. Stringer
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, CanberraACT2617, Australia
| | - Bernd Gruber
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, CanberraACT2617, Australia
| | - Stephen D. Sarre
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, CanberraACT2617, Australia
| | - Glenda M. Wardle
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, SydneyNSW2006, Australia
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
| | - Christopher R. Dickman
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, SydneyNSW2006, Australia
| | - Aaron C. Greenville
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, SydneyNSW2006, Australia
| | - Richard P. Duncan
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, CanberraACT2617, Australia
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7
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Hagan T, Ding G, Buchmann G, Oldroyd BP, Gloag R. Serial founder effects slow range expansion in an invasive social insect. Nat Commun 2024; 15:3608. [PMID: 38684711 PMCID: PMC11058855 DOI: 10.1038/s41467-024-47894-1] [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: 07/16/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Invasive populations often experience founder effects: a loss of genetic diversity relative to the source population, due to a small number of founders. Even where these founder effects do not impact colonization success, theory predicts they might affect the rate at which invasive populations expand. This is because secondary founder effects are generated at advancing population edges, further reducing local genetic diversity and elevating genetic load. We show that in an expanding invasive population of the Asian honey bee (Apis cerana), genetic diversity is indeed lowest at range edges, including at the complementary sex determiner, csd, a locus that is homozygous-lethal. Consistent with lower local csd diversity, range edge colonies had lower brood viability than colonies in the range centre. Further, simulations of a newly-founded and expanding honey bee population corroborate the spatial patterns in mean colony fitness observed in our empirical data and show that such genetic load at range edges will slow the rate of population expansion.
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Affiliation(s)
- Thomas Hagan
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Guiling Ding
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Gabriele Buchmann
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Benjamin P Oldroyd
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Rosalyn Gloag
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
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8
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Wróbel A, Klichowska E, Nobis M. Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia. FRONTIERS IN PLANT SCIENCE 2024; 15:1369732. [PMID: 38693932 PMCID: PMC11061500 DOI: 10.3389/fpls.2024.1369732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Hybridization is one of the key processes shaping lineage diversification, particularly in regions that experienced strong climate oscillations. The alpine biome with its rich history of glacial-interglacial cycles and complex patterns of species distribution shifts offers an excellent system to investigate the impact of gene flow on population dynamics and speciation, important issues for evolutionary biology and biodiversity conservation. In this study, we combined genomic data (DArTseq), chloroplast markers, and morphology to examine phylogenetic relationships and the permeability of species boundaries and their evolutionary outcomes among the alpine extremophilic species of Puccinellia (Poaceae) in the Pamir Mountains, a part of the Mountains of Central Asia biodiversity hotspot. We determined the occurrence of interspecific hybrids between P. himalaica and P. pamirica, which demonstrated almost symmetric ancestry from their parental species and did not show signals of introgression. According to our integrative revision, the natural hybrids between P. himalaica and P. pamirica should be classified as Puccinellia ×vachanica (pro species). Using approximate Bayesian computation for population history inference, we uncovered that P. himalaica hybridized with P. pamirica independently in multiple localities over the Holocene. Hybrids inherited the fine-scale genetic structure from their parental species, which developed these patterns earlier, during the Late Pleistocene. Hybridization had different consequences for the involved parental lineages, likely playing an important role in a continuing decline of P. himalaica in the Pamir Mountains over the Holocene. Our results show that P. himalaica should be considered a critically endangered species in the Pamir Mountains and could also be retreating across its entire range of distribution in High Mountain Asia. Using a comparative phylogeographic framework, we revealed the risk of extinction of a cold-adapted alpine species in a global biodiversity hotspot. This study highlights that genomics could unravel diversity trends under climate change and provides valuable evidence for conservation management.
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Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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Segura-García I, Olson JB, Gochfeld DJ, Brandt ME, Chaves-Fonnegra A. Severe hurricanes increase recruitment and gene flow in the clonal sponge Aplysina cauliformis. Mol Ecol 2024; 33:e17307. [PMID: 38444224 DOI: 10.1111/mec.17307] [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: 09/11/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 03/07/2024]
Abstract
Upright branching sponges, such as Aplysina cauliformis, provide critical three-dimensional habitat for other organisms and assist in stabilizing coral reef substrata, but are highly susceptible to breakage during storms. Breakage can increase sponge fragmentation, contributing to population clonality and inbreeding. Conversely, storms could provide opportunities for new genotypes to enter populations via larval recruitment, resulting in greater genetic diversity in locations with frequent storms. The unprecedented occurrence of two Category 5 hurricanes in close succession during 2017 in the U.S. Virgin Islands (USVI) provided a unique opportunity to evaluate whether recolonization of newly available substrata on coral reefs was due to local (e.g. re-growth of remnants, fragmentation, larval recruitment) or remote (e.g. larval transport and immigration) sponge genotypes. We sampled A. cauliformis adults and juveniles from four reefs around St. Thomas and two in St. Croix (USVI). Using a 2bRAD protocol, all samples were genotyped for single-nucleotide polymorphisms (SNPs). Results showed that these major storm events favoured sponge larval recruitment but did not increase the genetic diversity of A. cauliformis populations. Recolonization of substratum post-storms via clonality was lower (15%) than expected and instead was mainly due to sexual reproduction (85%) via local larval recruitment. Storms did enhance gene flow among and within reef sites located south of St. Thomas and north of St. Croix. Therefore, populations of clonal marine species with low pelagic dispersion, such as A. cauliformis, may benefit from increased frequency and magnitude of hurricanes for the maintenance of genetic diversity and to combat inbreeding, enhancing the resilience of Caribbean sponge communities to extreme storm events.
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Affiliation(s)
- Iris Segura-García
- Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, Florida, USA
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Deborah J Gochfeld
- National Center for Natural Products Research, University of Mississippi, Oxford, Mississippi, USA
| | - Marilyn E Brandt
- Center for Marine and Environmental Studies, University of the Virgin Islands, St. Thomas, Virgin Islands, USA
| | - Andia Chaves-Fonnegra
- Harbor Branch Oceanographic Institution, Florida Atlantic University, Fort Pierce, Florida, USA
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida, USA
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10
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Pavlova A, Schneller NM, Lintermans M, Beitzel M, Robledo‐Ruiz DA, Sunnucks P. Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression. Evol Appl 2024; 17:e13679. [PMID: 38617824 PMCID: PMC11009430 DOI: 10.1111/eva.13679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 04/16/2024] Open
Abstract
Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch Macquaria australasica, which over 3 years (2017-2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome-wide genotypes were used to assess individual ancestry, heterozygosity, short-term effective population size and identify parent-offspring and full-sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half-sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low-flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.
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Affiliation(s)
- Alexandra Pavlova
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Nadja M. Schneller
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Mark Lintermans
- Centre for Applied Water ScienceInstitute for Applied Ecology, University of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Matt Beitzel
- Environment, Planning & Sustainable Development Directorate (ACT Government)CanberraAustralian Capital TerritoryAustralia
| | | | - Paul Sunnucks
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
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11
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Gose MA, Humble E, Brownlow A, Wall D, Rogan E, Sigurðsson GM, Kiszka JJ, Thøstesen CB, IJsseldijk LL, Ten Doeschate M, Davison NJ, Øien N, Deaville R, Siebert U, Ogden R. Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts. Heredity (Edinb) 2024; 132:192-201. [PMID: 38302666 PMCID: PMC10997624 DOI: 10.1038/s41437-024-00672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.
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Affiliation(s)
- Marc-Alexander Gose
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Dave Wall
- Irish Whale and Dolphin Group (IWDG), Kilrush, Ireland
| | - Emer Rogan
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | | | - Jeremy J Kiszka
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL, USA
| | | | - Lonneke L IJsseldijk
- Division of Pathology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Mariel Ten Doeschate
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, UK
| | - Nils Øien
- Institute of Marine Research (IMR), Bergen, Norway
| | - Rob Deaville
- Institute of Zoology, Zoological Society of London, London, UK
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
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12
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Kyu KL, Taylor CM, Douglas CA, Malik AI, Colmer TD, Siddique KHM, Erskine W. Genetic diversity and candidate genes for transient waterlogging tolerance in mungbean at the germination and seedling stages. FRONTIERS IN PLANT SCIENCE 2024; 15:1297096. [PMID: 38584945 PMCID: PMC10996369 DOI: 10.3389/fpls.2024.1297096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/26/2024] [Indexed: 04/09/2024]
Abstract
Mungbean [Vigna radiata var. radiata (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini-core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome-wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully-expanded). In a temperature-controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high-quality DArTseq-derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain-containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad-sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker-trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker-assisted selection of tolerance traits to accelerate breeding of climate-resilient mungbean varieties.
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Affiliation(s)
- Khin Lay Kyu
- Centre for Plant Genetics and Breeding (PGB), UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | | | - Colin Andrew Douglas
- Department of Agriculture and Fisheries, Gatton Research Facility, Gatton, QLD, Australia
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding (PGB), UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- International Center for Tropical Agriculture (CIAT-Asia), Lao PDR Office, Vientiane, Lao People’s Democratic Republic
| | - Timothy David Colmer
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding (PGB), UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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13
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Ramirez-Ramirez AR, Mirzaei K, Menéndez-Grenot M, Clapé-Borges P, Espinosa-Lopéz G, Bidot-Martínez I, Bertin P. Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes. FRONTIERS IN PLANT SCIENCE 2024; 15:1367632. [PMID: 38504901 PMCID: PMC10948478 DOI: 10.3389/fpls.2024.1367632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.
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Affiliation(s)
- Angel Rafael Ramirez-Ramirez
- Faculty of Agroforestry, University of Guantánamo, Guantánamo, Cuba
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-neuve, Belgium
| | - Khaled Mirzaei
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-neuve, Belgium
| | - Miguel Menéndez-Grenot
- Unidad de Ciencia y Técnica de Base-Baracoa / Instituto de Investigaciones Agroforestales (UCTBBaracoa / INAF), Baracoa, Cuba
| | - Pablo Clapé-Borges
- Unidad de Ciencia y Técnica de Base-Baracoa / Instituto de Investigaciones Agroforestales (UCTBBaracoa / INAF), Baracoa, Cuba
| | | | | | - Pierre Bertin
- Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-neuve, Belgium
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14
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Vašut RJ, Pospíšková M, Lukavský J, Weger J. Detection of Hybrids in Willows ( Salix, Salicaceae) Using Genome-Wide DArTseq Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:639. [PMID: 38475486 DOI: 10.3390/plants13050639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024]
Abstract
The genus Salix, comprising some 400-500 species, is important in various alluvial or wet habitats of the northern hemisphere. It is a promising crop for applications such as biomass production, biofuels, or environmental projects. Clear species delimitation is crucial in ecology, biotechnology, and horticulture. DArTseq markers, a genome-wide technique, were tested for species and hybrid identification. A total of 179 willow samples were analysed, including six species of Salix subgen. Salix and four species of Salix subgen. Vetrix, including those used in biomass crop production, representing important European taxa. Identification of species-specific markers, clustering analyses (principal coordinate analysis, neighbor-joining) and Bayesian methods (Structure) unambiguously identified putative hybrids. In addition to demonstrating the high efficiency of DArT-seq markers in identifying willow hybrids, we also opened-up new questions about hybridisation processes and systematics. We detected unidirectional hybridisation between S. alba and S. fragilis, forming backcross hybrids, and we rejected the hypothesis that S. fragilis does not occur naturally in Europe. Further, the isolated position of Salix triandra within the genus was confirmed.
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Affiliation(s)
- Radim J Vašut
- Department of Biology, Faculty of Education, Palacky University Olomouc, 779 00 Olomouc, Czech Republic
- Department of Botany, Faculty of Science, Palacky University Olomouc, 783 71 Olomouc, Czech Republic
| | - Markéta Pospíšková
- Department of Phytoenergy, Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Public Research Institute, 252 43 Průhonice, Czech Republic
| | - Jan Lukavský
- Department of Botany, Faculty of Science, Palacky University Olomouc, 783 71 Olomouc, Czech Republic
- The Nature Conservation Agency of the Czech Republic, Moravian-Silesian Regional Branch, 756 61 Rožnov pod Radhoštěm, Czech Republic
| | - Jan Weger
- Department of Phytoenergy, Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Public Research Institute, 252 43 Průhonice, Czech Republic
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15
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Johnson NA, Henderson AR, Jones JW, Beaver CE, Ahlstedt SA, Dinkins GR, Eckert NL, Endries MJ, Garner JT, Harris JL, Hartfield PD, Hubbs DW, Lane TW, McGregor MA, Moles KR, Morrison CL, Wagner MD, Williams JD, Smith CH. Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex. J Hered 2024; 115:72-85. [PMID: 38015800 DOI: 10.1093/jhered/esad075] [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: 06/20/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023] Open
Abstract
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America's Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia-a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Andrew R Henderson
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jess W Jones
- U.S. Fish and Wildlife Service, Virginia Tech University, Blacksburg, VA, United States
| | - Caitlin E Beaver
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Steven A Ahlstedt
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Gerald R Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Nathan L Eckert
- U.S. Fish and Wildlife Service, Neosho National Fish Hatchery, Neosho, MO, United States
| | - Mark J Endries
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jeffrey T Garner
- Alabama Division of Wildlife and Freshwater Fisheries, Florence, AL, United States
| | - John L Harris
- Arkansas State University Museum of Zoology, Jonesboro, AR, United States
| | - Paul D Hartfield
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - Don W Hubbs
- DJH Environmental Services, Camden, TN, United States
| | - Timothy W Lane
- Virginia Department of Wildlife Resources, Marion, VA, United States
| | - Monte A McGregor
- Kentucky Department of Fish and Wildlife Resources, Frankfort, KY, United States
| | - Kendall R Moles
- Arkansas Game and Fish Commission, Benton, AR, United States
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV, United States
| | - Matthew D Wagner
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - James D Williams
- Florida Museum, University of Florida, Gainesville, FL, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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16
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Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [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: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
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Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
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17
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Carvajal-Yepes M, Ospina JA, Aranzales E, Velez-Tobon M, Correa Abondano M, Manrique-Carpintero NC, Wenzl P. Identifying genetically redundant accessions in the world's largest cassava collection. FRONTIERS IN PLANT SCIENCE 2024; 14:1338377. [PMID: 38304449 PMCID: PMC10830726 DOI: 10.3389/fpls.2023.1338377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
Crop diversity conserved in genebanks facilitates the development of superior varieties, improving yields, nutrition, adaptation to climate change and resilience against pests and diseases. Cassava (Manihot esculenta) plays a vital role in providing carbohydrates to approximately 500 million people in Africa and other continents. The International Center for Tropical Agriculture (CIAT) conserves the largest global cassava collection, housing 5,963 accessions of cultivated cassava and wild relatives within its genebank. Efficient genebank management requires identifying and eliminating genetic redundancy within collections. In this study, we optimized the identification of genetic redundancy in CIAT's cassava genebank, applying empirical distance thresholds, and using two types of molecular markers (single-nucleotide polymorphism (SNP) and SilicoDArT) on 5,302 Manihot esculenta accessions. A series of quality filters were applied to select the most informative and high-quality markers and to exclude low-quality DNA samples. The analysis identified a total of 2,518 and 2,526 (47 percent) distinct genotypes represented by 1 to 87 accessions each, using SNP or SilicoDArT markers, respectively. A total of 2,776 (SNP) and 2,785 (SilicoDArT) accessions were part of accession clusters with up to 87 accessions. Comparing passport and historical characterization data, such as pulp color and leaf characteristic, we reviewed clusters of genetically redundant accessions. This study provides valuable guidance to genebank curators in defining minimum genetic-distance thresholds to assess redundancy within collections. It aids in identifying a subset of genetically distinct accessions, prioritizing collection management activities such as cryopreservation and provides insights for follow-up studies in the field, potentially leading to removal of duplicate accessions.
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Affiliation(s)
- Monica Carvajal-Yepes
- Genetic Resources Program, Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | | | | | | | | | - Peter Wenzl
- Genetic Resources Program, Alliance Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
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18
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Rojas-Araos F, Rojas-Hernández N, Cornejo-Guzmán S, Ernst B, Dewitte B, Parada C, Veliz D. Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster Jasus frontalis inhabiting oceanic islands. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106253. [PMID: 37979403 DOI: 10.1016/j.marenvres.2023.106253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/20/2023]
Abstract
Knowledge about connectivity between populations is essential for the fisheries management of commercial species. The lobster Jasus frontalis inhabits two oceanic island groups, the Juan Fernández Archipelago and the Desventuradas Islands, separated by 800 km. Since this species is primarily exploited in the Juan Fernández Archipelago, knowledge of the connectivity patterns among islands is foundational for species management. Here, we used variability at single-nucleotide polymorphisms (SNPs) and individual-based modeling (IBM) to estimate the genetic structure and connectivity between J. frontalis populations in these island groups. The variability at 9090 SNPs suggests two genetic populations, one in the Juan Fernández Archipelago and one in the Desventuradas Islands. Furthermore, IBM suggests an asymmetric connectivity pattern, with particles moving from the Juan Fernández Archipelago to the Desventuradas Islands but not vice versa. Since the IBM analysis suggests asymmetric larval movement between the islands, and the genetic analysis indicates isolation between the Juan Fernández Archipelago and the Desventuradas Islands, larval retention mechanisms such as small-scale oceanographic processes or behavior could hinder larval movement between islands. This study highlights the importance of using more than one methodology to estimate population connectivity.
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Affiliation(s)
- Felipe Rojas-Araos
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Billy Ernst
- Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile; Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Boris Dewitte
- Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile; Université de Toulouse III, CERFACS/CNRS, Toulouse, France
| | - Carolina Parada
- Departamento de Geofísica, Universidad de Concepción, Concepción, Chile; Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
| | - David Veliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile; Centro Milenio de Ecología y Manejo Sustentable (ESMOI), Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
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19
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Croft L, Matheson P, Flemming C, Butterworth NJ, McGaughran A. Population structure and interspecific hybridisation of two invasive blowflies (Diptera: Calliphoridae) following replicated incursions into New Zealand. Ecol Evol 2024; 14:e10832. [PMID: 38192906 PMCID: PMC10772223 DOI: 10.1002/ece3.10832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Rates of biological invasion are increasing globally, with associated negative effects on native biodiversity and ecosystem services. Among other genetic processes, hybridisation can facilitate invasion by producing new combinations of genetic variation that increase adaptive potential and associated population fitness. Yet the role of hybridisation (and resulting gene flow) in biological invasion in invertebrate species is under-studied. Calliphora hilli and Calliphora stygia are blowflies proposed to have invaded New Zealand separately from Australia between 1779 and 1841, and are now widespread throughout the country. Here, we analysed genome-wide single nucleotide polymorphisms (SNPs), generating genotyping-by-sequencing data for 154 individuals collected from 24 populations across New Zealand and Australia to assess the extent of gene flow and hybridisation occurring within and between these blowflies and to better understand their overall population structure. We found that New Zealand populations of both species had weak genetic structure, suggesting high gene flow and an absence of dispersal limitations across the country. We also found evidence that interspecific hybridisation is occurring in the wild between C. hilli and C. stygia in both the native and invasive ranges, and that intraspecific admixture is occurring among populations at appreciable rates. Collectively, these findings provide new insights into the population structure of these two invasive invertebrates and highlight the potential importance of hybridisation and gene flow in biological invasion.
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Affiliation(s)
- Lilly Croft
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Paige Matheson
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Chloe Flemming
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | | | - Angela McGaughran
- Te Aka Mātuatua – School of ScienceUniversity of WaikatoHamiltonNew Zealand
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Nimbs MJ, Champion C, Lobos SE, Malcolm HA, Miller AD, Seinor K, Smith SD, Knott N, Wheeler D, Coleman MA. Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change. PeerJ 2023; 11:e16498. [PMID: 38025735 PMCID: PMC10676721 DOI: 10.7717/peerj.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.
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Affiliation(s)
- Matt J. Nimbs
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Curtis Champion
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Simon E. Lobos
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Hamish A. Malcolm
- NSW Department of Primary Industries, Fisheries Research, Coffs Harbour, NSW, Australia
| | - Adam D. Miller
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Kate Seinor
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Stephen D.A. Smith
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Aquamarine Australia, Mullaway, NSW, Australia
| | - Nathan Knott
- NSW Department of Primary Industries, Fisheries Research, Huskisson, NSW, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange, NSW, Australia
| | - Melinda A. Coleman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
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21
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Suetsugu K, Nozaki T, Hirota SK, Funaki S, Ito K, Isagi Y, Suyama Y, Kaneko S. Phylogeographical evidence for historical long-distance dispersal in the flightless stick insect Ramulus mikado. Proc Biol Sci 2023; 290:20231708. [PMID: 37817589 PMCID: PMC10565398 DOI: 10.1098/rspb.2023.1708] [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: 07/30/2023] [Accepted: 09/13/2023] [Indexed: 10/12/2023] Open
Abstract
Exploring how organisms overcome geographical barriers to dispersal is a fundamental question in biology. Passive long-distance dispersal events, although infrequent and unpredictable, have a considerable impact on species range expansions. Despite limited active dispersal capabilities, many stick insect species have vast geographical ranges, indicating that passive long-distance dispersal is vital for their distribution. A potential mode of passive dispersal in stick insects is via the egg stage within avian digestive tracts, as suggested by experimental evidence. However, detecting such events under natural conditions is challenging due to their rarity. Therefore, to indirectly assess the potential of historical avian-mediated dispersal, we examined the population genetic structure of the flightless stick insect Ramulus mikado across Japan, based on a multifaceted molecular approach [cytochrome oxidase subunit I (COI) haplotypes, nuclear simple sequence repeat markers and genome-wide single nucleotide polymorphisms]. Subsequently, we identified unique phylogeographic patterns, including the discovery of identical COI genotypes spanning considerable distances, which substantiates the notion of passive long-distance genotypic dispersal. Overall, all the molecular data revealed the low and mostly non-significant genetic differentiation among populations, with identical or very similar genotypes across distant populations. We propose that long-distance dispersal facilitated by birds is the plausible explanation for the unique phylogeographic pattern observed in this flightless stick insect.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
- Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
| | - Tomonari Nozaki
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shun K. Hirota
- Botanical Gardens, Osaka Metropolitan University, 2000 Kisaichi, Katano City, Osaka 576-0004, Japan
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Shoichi Funaki
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobeotsu, Nankoku, Kochi 783-8502, Japan
| | - Katsura Ito
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobeotsu, Nankoku, Kochi 783-8502, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Shingo Kaneko
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, Fukushima, Fukushima 960-1296, Japan
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22
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Bertola LV, Hoskin CJ, Jones DB, Zenger KR, McKnight DT, Higgie M. The first linkage map for Australo-Papuan Treefrogs (family: Pelodryadidae) reveals the sex-determination system of the Green-eyed Treefrog (Litoria serrata). Heredity (Edinb) 2023; 131:263-272. [PMID: 37542195 PMCID: PMC10539516 DOI: 10.1038/s41437-023-00642-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023] Open
Abstract
Amphibians represent a useful taxon to study the evolution of sex determination because of their highly variable sex-determination systems. However, the sex-determination system for many amphibian families remains unknown, in part because of a lack of genomic resources. Here, using an F1 family of Green-eyed Treefrogs (Litoria serrata), we produce the first genetic linkage map for any Australo-Papuan Treefrogs (family: Pelodryadidae). The resulting linkage map contains 8662 SNPs across 13 linkage groups. Using an independent set of sexed adults, we identify a small region in linkage group 6 matching an XY sex-determination system. These results suggest Litoria serrata possesses a male heterogametic system, with a candidate sex-determination locus on linkage group 6. Furthermore, this linkage map represents the first genomic resource for Australo-Papuan Treefrogs, an ecologically diverse family of over 220 species.
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Affiliation(s)
- Lorenzo V Bertola
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia.
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - David B Jones
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - Kyall R Zenger
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - Donald T McKnight
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Department of Environment and Genetics, School of Agriculture, Biomedicine and Environment, West Wodonga, La Trobe University, Melbourne, VIC, 3690, Australia
| | - Megan Higgie
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
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23
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dos Santos CC, de Andrade LRB, do Carmo CD, de Oliveira EJ. Development of cassava core collections based on morphological and agronomic traits and SNPS markers. FRONTIERS IN PLANT SCIENCE 2023; 14:1250205. [PMID: 37745996 PMCID: PMC10511765 DOI: 10.3389/fpls.2023.1250205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]
Abstract
Cassava (Manihot esculenta Crantz) holds significant importance as one of the world's key starchy crop species. This study aimed to develop core collections by utilizing both phenotypic data (15 quantitative and 33 qualitative descriptors) and genotypic data (20,023 single-nucleotide polymorphisms) obtained from 1,486 cassava accessions. Six core collections were derived through two optimization strategies based on genetic distances: Average accession-to-nearest-entry and Average entry-to-nearest-entry, along with combinations of phenotypic and genotypic data. The quality of the core collections was evaluated by assessing genetic parameters such as genetic diversity Shannon-Weaver Index, inbreeding (Fis), observed (Ho), and expected (Hs) heterozygosity. While the selection of accessions varied among the six core collections, a seventh collection (consolidated collection) was developed, comprising accessions selected by at least two core collections. Most collections exhibited genetic parameters similar to the complete collection, except for those developed by the Average accession-to-nearest-entry algorithm. However, the variations in the maximum and minimum values of Ho, Hs, and Fis parameters closely resembled the complete collection. The consolidated collection and the collection constructed using genotypic data and the Average entry-to-nearest-entry algorithm (GenEN) retained the highest number of alleles (>97%). Although the differences were not statistically significant (above 5%), the consolidated collection demonstrated a distribution profile and mean trait values most similar to the complete collection, with a few exceptions. The Shannon-Weaver Index of qualitative traits exhibited variations exceeding ±10% when compared to the complete collection. Principal component analysis revealed that the consolidated collection selected cassava accessions with a more uniform dispersion in all four quadrants compared to the other core collections. These findings highlight the development of optimized and valuable core collections for efficient breeding programs and genomic association studies.
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Affiliation(s)
- Caroline Cardoso dos Santos
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
| | | | - Cátia Dias do Carmo
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
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24
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Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, Martienssen RA. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554647. [PMID: 37662366 PMCID: PMC10473749 DOI: 10.1101/2023.08.24.554647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.
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Affiliation(s)
| | | | - Cristiane de Santis Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Laís Araujo Coelho
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Gil Eshel
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Samantha Frangos
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Katherine Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaojin Wang
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Yin Peng Lee
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Stella Loke
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Australian Botanic Garden, Mount Annan, NSW 2567, Australia
| | - Sebastiano Nigris
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Silvia Moschin
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Damon P. Little
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Manpreet S. Katari
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Kranthi Varala
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Barbara Ambrose
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Larry J. Croft
- School of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Gloria M. Coruzzi
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Michael Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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25
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Slobodova N, Sharko F, Gladysheva-Azgari M, Petrova K, Tsiupka S, Tsiupka V, Boulygina E, Rastorguev S, Tsygankova S. Genetic Diversity of Common Olive ( Olea europaea L.) Cultivars from Nikita Botanical Gardens Collection Revealed Using RAD-Seq Method. Genes (Basel) 2023; 14:1323. [PMID: 37510228 PMCID: PMC10379327 DOI: 10.3390/genes14071323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
In different countries, interest in the commercial cultivation of the olive has recently greatly increased, which has led to the expansion of its range. The Crimean Peninsula is the northern limit of the common olive (Olea europaea L.) range. A unique collection of common olive's cultivars and hybrids has been collected in the Nikitsky Botanical Gardens (NBG). The aim of this study was to assess the genetic diversity of 151 samples (total of several biological replicates of 46 olive cultivars including 29 introduced and 11 indigenous genotypes) using the ddRAD sequencing method. Structural analysis showed that the studied samples are divided into ten groups, each of which mainly includes cultivars of the same origin. Cultivars introduced to the Crimean Peninsula from different regions formed separate groups, while local cultivars joined different groups depending on their origin. Cultivars of Crimean origin contain admixtures of mainly Italian and Caucasian cultivars' genotypes. Our study showed that the significant number of Crimean cultivars contains an admixture of the Italian cultivar "Coreggiolo". Genetic analysis confirmed the synonymy for the cv. "Otur" and "Nikitskaya 2", but not for the other four putative synonyms. Our results revealed the genetic diversity of the olive collection of NBG and provided references for future research studies, especially in selection studies for breeding programs.
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Affiliation(s)
- Natalia Slobodova
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
- Faculty of Biology and Biotechnology, HSE University, Moscow 101000, Russia
| | - Fedor Sharko
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | | | | | - Sergey Tsiupka
- Nikita Botanical Gardens-National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Russia
| | - Valentina Tsiupka
- Nikita Botanical Gardens-National Scientific Centre of the Russian Academy of Sciences, Yalta 298648, Russia
| | - Eugenia Boulygina
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Sergey Rastorguev
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
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26
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van Mantgem PJ, Milano ER, Dudney J, Nesmith JCB, Vandergast AG, Zald HSJ. Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California. Ecol Evol 2023; 13:e10072. [PMID: 37206686 PMCID: PMC10191741 DOI: 10.1002/ece3.10072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/21/2023] Open
Abstract
Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease-free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate-associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens.
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Affiliation(s)
| | - Elizabeth R. Milano
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
- Present address:
USDA Forest ServiceRocky Mountain Research StationMoscowIdahoUSA
| | - Joan Dudney
- Environmental Studies ProgramUC Santa BarbaraSanta BarbaraCaliforniaUSA
- Department of Environmental Science, Policy, & ManagementUC BerkeleyBerkeleyCaliforniaUSA
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Amy G. Vandergast
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Harold S. J. Zald
- USDA Forest ServicePacific Northwest Research StationCorvallisOregonUSA
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27
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Fu YB. Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data. PLANTS (BASEL, SWITZERLAND) 2023; 12:1476. [PMID: 37050102 PMCID: PMC10096604 DOI: 10.3390/plants12071476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Assessing genetic distinctness and redundancy is an important part of plant germplasm characterization. Over the last decade, such assessment has become more feasible and informative, thanks to the advances in genomic analysis. An attempt was made here to search for genebank germplasm with published genomic data and to assess their genetic distinctness and redundancy based on average pairwise dissimilarity (APD). The effort acquired 12 published genomic data sets from CIMMYT, IPK, USDA-ARS, IRRI, and ICRISAT genebanks. The characterized collections consisted of 661 to 55,879 accessions with up to 2.4 million genome-wide SNPs. The assessment generated an APD estimate for each sample. As a higher or lower APD is indicative of more genetic distinctness or redundance for an accession, respectively, these APD estimates helped to identify the most genetically distinct and redundant groups of 100 accessions each and a genetic outlier group with APD estimates larger than five standard deviations in each data set. An APD-based grouping of the conserved germplasm in each data set revealed among-group variances ranging from 1.5 to 53.4% across all data sets. Additional analyses showed that these APD estimations were more sensitive to SNP number, minor allele frequency, and missing data. Generally, 5000 to 10,000 genome-wide SNPs were required for an effective APD analysis. These findings together are encouraging and useful for germplasm management, utilization, and conservation, particularly in the genetic categorization of conserved germplasm.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
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28
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Manrique-Carpintero NC, Berdugo-Cely JA, Cerón-Souza I, Lasso-Paredes Z, Reyes-Herrera PH, Yockteng R. Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1046400. [PMID: 37180391 PMCID: PMC10173156 DOI: 10.3389/fpls.2023.1046400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023]
Abstract
The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions - an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC's genetic diversity. The analysis of molecular variance confirmed the CCC's diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count.
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Affiliation(s)
| | - Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Montería, Colombia
| | - Ivania Cerón-Souza
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Zahara Lasso-Paredes
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Paula H. Reyes-Herrera
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
- *Correspondence: Roxana Yockteng,
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Mijangos JL, Bino G, Hawke T, Kolomyjec SH, Kingsford RT, Sidhu H, Grant T, Day J, Dias KN, Gongora J, Sherwin WB. Fragmentation by major dams and implications for the future viability of platypus populations. Commun Biol 2022; 5:1127. [PMID: 36329312 PMCID: PMC9633709 DOI: 10.1038/s42003-022-04038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
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Affiliation(s)
- Jose L. Mijangos
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia ,grid.1039.b0000 0004 0385 7472Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Gilad Bino
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Tahneal Hawke
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Stephen H. Kolomyjec
- grid.258898.60000 0004 0462 9201College of Science and the Environment, Lake Superior State University, Sault Sainte Marie, USA
| | - Richard T. Kingsford
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Harvinder Sidhu
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia
| | - Tom Grant
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Jenna Day
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Kimberly N. Dias
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Jaime Gongora
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - William B. Sherwin
- grid.1005.40000 0004 4902 0432Evolution & Ecology Research Centre, UNSW, Sydney, Australia
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