1
|
Sarakinis KG, Reis-Santos P, Donnellan SC, Ye Q, Earl J, Gillanders BM. Strong philopatry in an estuarine-dependent fish. Ecol Evol 2024; 14:e10989. [PMID: 38500851 PMCID: PMC10945236 DOI: 10.1002/ece3.10989] [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: 07/21/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024] Open
Abstract
Understanding fish movement is critical in determining the spatial scales in which to appropriately manage wild populations. Genetic markers provide a natural tagging approach to assess the degree of gene flow and population connectivity across a species distribution. We investigated the genetic structure of black bream Acanthopagrus butcheri across its entire distribution range in Australia, as well as regional scale gene flow across south-eastern Australia by undertaking a comprehensive analysis of the populations in estuaries across the region. We applied genome-wide sampling of single-nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing. Genetic structure and potential gene flow was assessed using principal component analyses and admixture analyses (STRUCTURE). Using 33,493 SNPs, we detected broad scale genetic structuring, with limited gene flow among regional clusters (i.e. Western Australia, South Australia and western Victoria; and eastern Victoria, Tasmania and New South Wales). This is likely the result of unsuitable habitats, strong ocean currents (e.g. the Leeuwin Current and the East Australian Current), large water bodies (e.g. Bass Strait) and known biogeographical provinces across the continent. Local-scale genetic structuring was also identified across the south-eastern Australian estuaries sampled, reflecting that the coexistence of both migratory and resident individuals within populations (i.e. partial migration), and the movement of fish into coastal waters, still results in strong philopatry across the region. Instances of movement among estuaries at this spatial scale were primarily found between adjacent estuaries and were likely attributed to lone migrants utilising inshore coastal currents for movement beyond nearby habitats. Targeting SNP markers in A. butcheri at this continental scale highlighted how neither spatial proximity of estuaries nor black bream's ability to move into coastal waters reflects increased gene flow. Overall, our findings highlight the importance of location-specific management.
Collapse
Affiliation(s)
- Koster G Sarakinis
- Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | - Patrick Reis-Santos
- Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | | | - Qifeng Ye
- South Australian Research and Development Institute Aquatic and Livestock Sciences Adelaide South Australia Australia
| | - Jason Earl
- South Australian Research and Development Institute Aquatic and Livestock Sciences Adelaide South Australia Australia
| | - Bronwyn M Gillanders
- Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| |
Collapse
|
2
|
Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [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: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
Collapse
Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| |
Collapse
|
3
|
Narváez-Barandica JC, Quintero-Galvis JF, Aguirre-Pabón JC, Castro LR, Betancur R, Acero Pizarro A. A Comparative Phylogeography of Three Marine Species with Different PLD Modes Reveals Two Genetic Breaks across the Southern Caribbean Sea. Animals (Basel) 2023; 13:2528. [PMID: 37570336 PMCID: PMC10417521 DOI: 10.3390/ani13152528] [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: 04/28/2023] [Revised: 07/02/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
The comparative phylogeography of marine species with contrasting dispersal potential across the southern Caribbean Sea was evaluated by the presence of two putative barriers: the Magdalena River plume (MRP) and the combination of the absence of a rocky bottom and the almost permanent upwelling in the La Guajira Peninsula (ARB + PUG). Three species with varying biological and ecological characteristics (i.e., dispersal potentials) that inhabit shallow rocky bottoms were selected: Cittarium pica (PLD < 6 days), Acanthemblemaria rivasi (PLD < 22 days), and Nerita tessellata (PLD > 60 days). We generated a set of SNPs for the three species using the ddRad-seq technique. Samples of each species were collected in five locations from Capurganá to La Guajira. For the first time, evidence of a phylogeographic break caused by the MRP is provided, mainly for A. rivasi (AMOVA: ΦCT = 0.420). The ARB + PUG barrier causes another break for A. rivasi (ΦCT = 0.406) and C. pica (ΦCT = 0.224). Three populations (K = 3) were identified for A. rivasi and C. pica, while N. tessellata presented one population (K = 1). The Mantel correlogram indicated that A. rivasi and C. pica fit the hierarchical population model, and only the A. rivasi and C. pica comparisons showed phylogeographic congruence. Our results demonstrate how the biological traits of these three species and the biogeographic barriers have influenced their phylogeographic structure.
Collapse
Affiliation(s)
- Juan Carlos Narváez-Barandica
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Julián F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile;
| | - Juan Carlos Aguirre-Pabón
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Lyda R. Castro
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Ricardo Betancur
- Biology Department, University of Oklahoma, Norman, OK 73019, USA;
| | - Arturo Acero Pizarro
- Instituto de Estudios en Ciencias del Mar (CECIMAR), Universidad Nacional de Colombia sede Caribe, Santa Marta 470006, Colombia;
| |
Collapse
|
4
|
Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distribution. Sci Rep 2022; 12:22124. [PMID: 36543927 PMCID: PMC9772343 DOI: 10.1038/s41598-022-26651-8] [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: 08/25/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cádiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almería-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.
Collapse
|
5
|
Veliz D, Rojas-Hernández N, Vega-Retter C, Zaviezo C, Garrido I, Pardo LM. Spatial and temporal stability in the genetic structure of a marine crab despite a biogeographic break. Sci Rep 2022; 12:14192. [PMID: 35987816 PMCID: PMC9392802 DOI: 10.1038/s41598-022-18368-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractElucidating the processes responsible for maintaining the population connectivity of marine benthic species mediated by larval dispersal remains a fundamental question in marine ecology and fishery management. Understanding these processes becomes particularly important in areas with a biogeographic break and unidirectional water movement along the sides of the break. Based on variability at 4209 single-nucleotide polymorphisms in 234 individuals, we determine the genetic structure, temporal genetic stability, and gene flow among populations of the commercially important mola rock crab Metacarcinus edwardsii in a system in southern Chile with a biogeographic break at latitude 42°S. Specimens were collected at eight sites within its geographic distribution, with collection at four of these sites was performed twice. Using population genetic approaches, we found no evidence of geographic or temporal population differentiation. Similarly, we found no evidence of an effect on gene flow of the biogeographic break caused by the the West Wind Drift Current. Moreover, migration analyses supported gene flow among all sites but at different rates for different pairs of sites. Overall, our findings indicate that M. edwardsii comprises a single large population with high levels of gene flow among sites separated by over 1700 km and demonstrate temporal stability in its genetic structure.
Collapse
|
6
|
Knutsen H, Catarino D, Rogers L, Sodeland M, Mattingsdal M, Jahnke M, Hutchings JA, Mellerud I, Espeland SH, Johanneson K, Roth O, Hansen MM, Jentoft S, André C, Jorde PE. Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species. Mol Ecol 2022; 31:2562-2577. [PMID: 35229385 PMCID: PMC9311693 DOI: 10.1111/mec.16415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (double‐digest restriction associated DNA) sequencing data to analyse spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds, which are patchily distributed along the study area in southern Norway. Demographic connectivity among populations was inferred from long‐term (~30‐year) population counts that uncovered a rapid decline in spatial correlations in abundance with distance as short as ~2 km. These findings were contrasted with data for two other fish species that have a pelagic larval stage (corkwing wrasse, Symphodus melops; black goby, Gobius niger). For these latter species, we found wider spatial scales of connectivity and weaker genetic isolation‐by‐distance patterns, except where both species experienced a strong barrier to gene flow, seemingly due to lack of suitable habitat. Our findings verify expectations that a fragmented habitat and absence of a pelagic larval stage promote genetic structure, while presence of a pelagic larvae stage increases demographic connectivity and gene flow, except perhaps over extensive habitat gaps.
Collapse
Affiliation(s)
- Halvor Knutsen
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Diana Catarino
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Lauren Rogers
- Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Marte Sodeland
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Morten Mattingsdal
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Marlene Jahnke
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Jeffrey A Hutchings
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Ida Mellerud
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway
| | - Sigurd H Espeland
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Kerstin Johanneson
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Germany
| | - Michael M Hansen
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Sissel Jentoft
- University of Oslo, Department of Biology, 0316, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Per Erik Jorde
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway
| |
Collapse
|
7
|
Klein JD, Asbury TA, da Silva C, Hull KL, Dicken ML, Gennari E, Maduna SN, Bester-van der Merwe AE. Site fidelity and shallow genetic structure in the common smooth-hound shark Mustelus mustelus confirmed by tag-recapture and genetic data. JOURNAL OF FISH BIOLOGY 2022; 100:134-149. [PMID: 34658037 DOI: 10.1111/jfb.14926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/07/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
The common smooth-hound shark, Mustelus mustelus, is a widely distributed demersal shark under heavy exploitation from various fisheries throughout its distribution range. To assist in the development of appropriate management strategies, the authors evaluate stock structure, site fidelity and movement patterns along the species' distribution in southern Africa based on a combination of molecular and long-term tag-recapture data. Eight species-specific microsatellite markers (N = 73) and two mitochondrial genes, nicotinamide adenine dehydrogenase subunit 4 and control region (N = 45), did not reveal any significant genetic structure among neighbouring sites. Nonetheless, tagging data demonstrate a remarkable degree of site fidelity with 76% of sharks recaptured within 50 km of the original tagging location. On a larger geographic scale, dispersal is governed by oceanographic features as demonstrated by the lack of movements across the Benguela-Agulhas transition zone separating the South-East Atlantic Ocean (SEAO) and South-West Indian Ocean (SWIO) populations. Microsatellite data supported very shallow ocean-based structure (SEAO and SWIO) and historical southward gene flow following the Agulhas Current, corroborating the influence of this dynamic oceanographic system on gene flow. Moreover, no movements between Namibia and South Africa were observed, indicating that the Lüderitz upwelling formation off the Namibian coast acts as another barrier to dispersal and gene flow. Overall, these results show that dispersal and stock structure of M. mustelus are governed by a combination of behavioural traits and oceanographic features such as steep temperature gradients, currents and upwelling systems.
Collapse
Affiliation(s)
- Juliana D Klein
- Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Tamaryn A Asbury
- Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Charlene da Silva
- Department of Environment, Forestry and Fisheries, Rogge Bay, South Africa
| | - Kelvin L Hull
- Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Matthew L Dicken
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa
- Department of Development Studies, School of Economics, Development and Tourism, Nelson Mandela University, Port Elizabeth, South Africa
| | - Enrico Gennari
- Oceans Research Institute, Mossel Bay, South Africa
- South African Institute for Aquatic Biodiversity, Grahamstown, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Simo N Maduna
- Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Division of Wildlife Research, Reel Science Coalition, Somerset West, South Africa
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
8
|
Andrews KR, Copus JM, Wilcox C, Williams AJ, Newman SJ, Wakefield CB, Bowen BW. Range-Wide Population Structure of 3 Deepwater Eteline Snappers Across the Indo-Pacific Basin. J Hered 2020; 111:471-485. [PMID: 32803261 DOI: 10.1093/jhered/esaa029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/11/2020] [Indexed: 11/14/2022] Open
Abstract
Deep-sea habitats may drive unique dispersal and demographic patterns for fishes, but population genetic analyses to address these questions have rarely been conducted for fishes in these environments. This study investigates the population structure of 3 tropical deepwater snappers of the genus Etelis that reside at 100-400 m depth, with broad and overlapping distributions in the Indo-Pacific. Previous studies showed little population structure within the Hawaiian Archipelago for 2 of these species: Etelis coruscans and E. carbunculus. Here we extend sampling to the entire geographic range of each species to resolve the population genetic architecture for these 2 species, as well as a recently exposed cryptic species (Etelis sp.). One goal was to determine whether deepwater snappers are more dispersive than shallow-water fishes. A second goal was to determine whether submesophotic fishes have older, more stable populations than shallow reef denizens that are subject to glacial sea-level fluctuations. Both goals are pertinent to the management of these valuable food fishes. A total of 1153 specimens of E. coruscans from 15 geographic regions were analyzed, along with 1064 specimens of E. carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions. The first 2 species were analyzed with mtDNA and 9-11 microsatellite loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a non-significant microsatellite global FST, but significant global mtDNA Ф ST = 0.010 (P = 0.0007), with the isolation of Seychelles in the western Indian Ocean, and intermittent signals of isolation for the Hawaiian Archipelago. Etelis carbunculus had a non-significant microsatellite global FST, and significant global mtDNA Ф ST = 0.021 (P = 0.0001), with low but significant levels of isolation for Hawai'i, and divergence between Tonga and Fiji. Etelis sp. had mtDNA Ф ST = 0.018 (P = 0.0005), with a strong pattern of isolation for both Seychelles and Tonga. Overall, we observed low population structure, shallow mtDNA coalescence (similar to near-shore species), and isolation at the fringes of the Indo-Pacific basin in Hawai'i and the western Indian Ocean. While most shallow-water species have population structure on the scale of biogeographic provinces, deepwater snapper populations are structured on the wider scale of ocean basins, more similar to pelagic fishes than to shallow-water species. This population structure indicates the capacity for widespread dispersal throughout the Indo-Pacific region.
Collapse
Affiliation(s)
- Kimberly R Andrews
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.,Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Christie Wilcox
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Ashley J Williams
- Oceanic Fisheries Programme, The Pacific Community, Noumea, New Caledonia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Corey B Wakefield
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| |
Collapse
|
9
|
Mays HL, Oehler DA, Morrison KW, Morales AE, Lycans A, Perdue J, Battley PF, Cherel Y, Chilvers BL, Crofts S, Demongin L, Fry WR, Hiscock J, Kusch A, Marin M, Poisbleau M, Quillfeldt P, Raya Rey A, Steinfurth A, Thompson DR, Weakley LA. Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi). J Hered 2020; 110:801-817. [PMID: 31737899 DOI: 10.1093/jhered/esz051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/10/2019] [Indexed: 01/05/2023] Open
Abstract
Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.
Collapse
Affiliation(s)
- Herman L Mays
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - David A Oehler
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | | | - Ariadna E Morales
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY
| | - Alyssa Lycans
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Justin Perdue
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Phil F Battley
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| | - B Louise Chilvers
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands
| | | | | | - Jo Hiscock
- Department of Conservation, Invercargill, New Zealand
| | - Alejandro Kusch
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | - Manuel Marin
- Feather Link, Inc., Cincinnati, OH.,Section of Ornithology, Natural History Museum of Los Angeles County, Los Angeles, CA
| | - Maud Poisbleau
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, Antwerp (Wilrijk), Belgium
| | - Petra Quillfeldt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Andrea Raya Rey
- National Scientific and Technical Research Council, Austral Center for Scientific Investigation, Ushuaia, Argentina.,Institute of Polar Science, National University of Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa.,RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Cambridge, UK
| | - David R Thompson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | | |
Collapse
|
10
|
McKeown NJ, Gwilliam MP, Healey AJE, Skujina I, Potts WM, Sauer WHH, Shaw PW. Deep phylogeographic structure may indicate cryptic species within the Sparid genus Spondyliosoma. JOURNAL OF FISH BIOLOGY 2020; 96:1434-1443. [PMID: 32154919 DOI: 10.1111/jfb.14316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/27/2019] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range-wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters. However, the results also indicate that S. cantharus may be a cryptic species complex wherein the various regional lineages represent established/incipient species. A robust multilocus genetic assessment combining morphological data and detailing interactions among lineages is needed to determine the full diversity within Spondyliosoma and the most adequate biological and taxonomic status.
Collapse
Affiliation(s)
- Niall J McKeown
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Michael P Gwilliam
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Amy J E Healey
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ilze Skujina
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Warren M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Warwick H H Sauer
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Paul W Shaw
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| |
Collapse
|
11
|
Neves A, Vieira AR, Sequeira V, Paiva RB, Gordo LS, Paulo OS. Highly regional population structure of Spondyliosoma cantharus depicted by nuclear and mitochondrial DNA data. Sci Rep 2020; 10:4063. [PMID: 32132605 PMCID: PMC7055218 DOI: 10.1038/s41598-020-61050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/20/2020] [Indexed: 12/24/2022] Open
Abstract
Resolution of population structure represents an effective way to define biological stocks and inform efficient fisheries management. In the present study, the phylogeography of the protogynous sparid Spondyliosoma cantharus, in the East Atlantic and Mediterranean Sea, was investigated with nuclear (S7) and mitochondrial (cytochrome b) DNA markers. Significant divergence of four regional genetic groups was observed: North Eastern Atlantic, Mediterranean Sea, Western African Transition (Cape Verde) and Gulf of Guinea (Angola). The two southern populations (Cape Verde and Angola) each comprised reciprocally monophyletic mtDNA lineages, revealed low levels of diversity in Cape Verde and high diversity for Angola despite being represented by only 14 individuals. A complete divergence between North Atlantic and Mediterranean populations was depicted by the mitochondrial marker, but a highly shared nuclear haplotype revealed an incomplete lineage sorting between these regions. Bayesian skyline plots and associated statistics revealed different dynamics among the four regions. Cape Verde showed no expansion and the expansion time estimated for Angola was much older than for the other regions. Mediterranean region seems to have experienced an early population growth but has remained with a stable population size for the last 30000 years while the North Atlantic population has been steadily growing. The lack of genetic structuring within these regions should not be taken as evidence of demographic panmixia in light of potential resolution thresholds and previous evidence of intra-regional phenotypic heterogeneity.
Collapse
Affiliation(s)
- Ana Neves
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal. .,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Ana Rita Vieira
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Vera Sequeira
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Rafaela Barros Paiva
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Leonel Serrano Gordo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Octávio S Paulo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
12
|
Healey AJE, Farthing MW, Nunoo FKE, Potts WM, Sauer WHH, Skujina I, King N, de Becquevort S, Shaw PW, McKeown NJ. Genetic analysis provides insights into species distribution and population structure in East Atlantic horse mackerel (Trachurus trachurus and T. capensis). JOURNAL OF FISH BIOLOGY 2020; 96:795-805. [PMID: 32031244 PMCID: PMC7079130 DOI: 10.1111/jfb.14276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/31/2020] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
Two sister species of horse mackerel (Trachurus trachurus and T. capensis) are described that are intensively harvested in East Atlantic waters. To address long-standing uncertainties as to their respective geographical ranges, overlap and intraspecific population structure this study combined genetic (mitochondrial DNA and microsatellite) analysis and targeted sampling of the hitherto understudied West African coast. mtDNA revealed two reciprocally monophyletic clades corresponding to each species with interspecies nuclear differentiation supported by FST values. The T. trachurus clade was found across the north-east Atlantic down to Ghana but was absent from Angolan and South African samples. The T. capensis clade was found only in South Africa, Angola and a single Ghanaian individual. This pattern suggests that both species may overlap in the waters around Ghana. The potential for cryptic hybridization and/or indiscriminate harvesting of both species in the region is discussed. For T. capensis mtDNA supports high gene flow across the Benguela upwelling system, which fits with the species' ecology. The data add to evidence of a lack of significant genetic structure throughout the range of T. trachurus though the assumption of demographic panmixia is cautioned against. For both species, resolution of stock recruitment heterogeneity relevant to fishery management, as well as potential hybridization, will require more powerful genomic analyses.
Collapse
Affiliation(s)
- Amy J. E. Healey
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Matthew W. Farthing
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | | | - Warren M. Potts
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | - Warwick H. H. Sauer
- Department of Ichthyology & Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
| | - Ilze Skujina
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Nathan King
- School of Ocean SciencesBangor UniversityMenai Bridge, AngleseyUK
| | - Sophie de Becquevort
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Paul W. Shaw
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Niall J. McKeown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| |
Collapse
|
13
|
Kitada S, Nakajima K, Hamasaki K. Population panmixia and demographic expansion of a highly piscivorous marine fish Scomberomorus niphonius. JOURNAL OF FISH BIOLOGY 2017; 91:1435-1448. [PMID: 28990668 DOI: 10.1111/jfb.13466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 08/17/2017] [Indexed: 06/07/2023]
Abstract
Population structure and demographic history of the Japanese Spanish mackerel Scomberomorus niphonius a highly piscivorous and migratory marine fish, were assessed using mitochondrial DNA control region sequences (n = 720) and microsatellite genotypes at five loci (n = 1331) for samples collected on Japanese coasts from 2001 to 2010. The population structure was panmictic and the haplotype and allele frequencies were temporally stable even during the recent recovery process. Demographic expansion was strongly supported throughout the Pleistocene, suggesting that the oscillating glacial and interglacial climate conditions in the Pleistocene had no substantial impact on the demographic history of S. niphonius.
Collapse
Affiliation(s)
- S Kitada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| | - K Nakajima
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| | - K Hamasaki
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| |
Collapse
|
14
|
Farhadi A, Jeffs AG, Farahmand H, Rejiniemon TS, Smith G, Lavery SD. Mechanisms of peripheral phylogeographic divergence in the indo-Pacific: lessons from the spiny lobster Panulirus homarus. BMC Evol Biol 2017; 17:195. [PMID: 28821229 PMCID: PMC5563042 DOI: 10.1186/s12862-017-1050-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/11/2017] [Indexed: 12/03/2022] Open
Abstract
Background There is increasing recognition of the concordance between marine biogeographic and phylogeographic boundaries. However, it is still unclear how population-level divergence translates into species-level divergence, and what are the principal factors that first initiate that divergence, and then maintain reproductive isolation. This study examines the likely forces driving population and lineage divergences in the broadly-distributed Indo-Pacific spiny lobster Panulirus homarus, which has peripheral divergent lineages in the west and east. The study focuses particularly on the West Indian Ocean, which is emerging as a region of unexpected diversity. Mitochondrial control region (mtCR) and COI sequences as well as genotypes of 9 microsatellite loci were examined in 410 individuals from 17 locations grouped into 7 regions from South Africa in the west, and eastward across to Taiwan and the Marquesas Islands. Phylogenetic and population-level analyses were used to test the significance and timing of divergences and describe the genetic relationships among populations. Results Analyses of the mtCR revealed high levels of divergence among the seven regions (ФST = 0.594, P < 0.001). Microsatellite analyses also revealed significant divergence among regions, but at a much lower level (FST = 0.066, P < 0.001). The results reveal different patterns of mtCR v. nDNA divergence between the two distinct peripheral lineages: a subspecies in South Africa and Madagascar, and a phylogeographically diverged population in the Marquesas. The results also expose a number of other more fine-scale population divergences, particularly in the Indian Ocean. Conclusions The divergence of peripheral lineages in the west and east of the species’ range appear to have been initiated and maintained by very different processes. The pattern of mitochondrial and nuclear divergence of the western lineage, implicates processes of parapatric isolation, secondary contact and introgression, and suggests possible maintenance through adaptation and behavioural reproductive isolation. In contrast, the eastern lineage appears to have diverged through a rare colonisation event, maintained through long-term isolation, and matches expectations of the core-periphery hypothesis. The process of active peripheral speciation may be a common force in the Indo-Pacific that helps drive some of the regions’ recognized biogeographic boundaries. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1050-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ahmad Farhadi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand. .,Department of Natural Resources and Environment, School of Agriculture, Shiraz University, Shiraz, Iran.
| | - Andrew G Jeffs
- Institute of Marine Science and School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Hamid Farahmand
- Department of Fisheries and Environment, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | | | - Greg Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Shane D Lavery
- School of Biological Sciences and Institute of Marine Science, University of Auckland, Auckland, New Zealand
| |
Collapse
|
15
|
Feng X, He D, Sui X, Chen Y, Chen Y. Morphological and genetic divergence between lake and river populations of Triplophysa in Ngangtse Co, Tibet. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:778-784. [PMID: 28756717 DOI: 10.1080/24701394.2017.1357711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ngangtse Co (4535 m a.s.l., 840 km2) is a typical endorheic lake in Tibet. In 2015, we investigated the fish resource in this lake and its rivers and collected two Triplophysa species, including T. brevicauda and T. stewarti. To understand the evolutionary dynamics of Triplophysa in Ngangtse Co, the adaptive and genetic divergence between river and lake populations were investigated by analysing their morphological characteristics and mitochondrial COI and Cytb sequences. Among all of 277 samples, the ratios of the number of T. brevicauda to T. stewarti were 27:8, 34:11, 14:24, 37:0, 16:23 and 0:83 in river populations RA, RB, RC, RD, lakeside population LSE and lake population L, respectively. For T. brevicauda, a small but significant genetic divergence (mean FST = 0.0890) was detected between population RD and other three river populations, and significant morphological differences of body length/body height and body length/caudal peduncle length were observed between population RD and RA, RB, suggesting an association between differentiation and geographical distance. For T. stewarti, very high levels of genetic differentiation was observed between population L and other populations with the FST values ranging from 0.4737 (L-RA) to 0.7074 (L-RC). In addition, significant differences of most of morphological characteristics were observed between the lake (L) and river (RC) populations, indicating that lake fish of T. stewarti was a population that showed a long-term adaptation to the saltwater lake. These results provide insights on the evolutionary dynamics of Triplophysa in Ngangtse Co and help us to understand the fish speciation in endorheic lakes on the Qinghai-Tibetan Plateau.
Collapse
Affiliation(s)
- Xiu Feng
- a The Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China
| | - Dekui He
- a The Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China
| | - Xiaoyun Sui
- a The Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China
| | - Yongxia Chen
- b College of Life Sciences , Hebei University , Baoding , China
| | - Yifeng Chen
- a The Key Laboratory of Aquatic Biodiversity and Conservation , Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan , China
| |
Collapse
|