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Westbrook CE, Daly J, Bowen BW, Hagedorn M. Cryopreservation of the collector urchin embryo, Tripneustes gratilla. Cryobiology 2024; 115:104865. [PMID: 38367796 DOI: 10.1016/j.cryobiol.2024.104865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/19/2024]
Abstract
The collector urchin, Tripneustes gratilla, is an ecologically important member of the grazing community of Hawai'i's coral reefs. Beyond its ability to maintain balance between native seaweeds and corals, T. gratilla has also been used as a food source and a biocontrol agent against alien invasive algae species. Due to overexploitation, habitat degradation, and other stressors, their populations face local extirpation. However, artificial reproductive techniques, such as cryopreservation, could provide more consistent seedstock throughout the year to supplement aquaculture efforts. Although the sperm and larvae of temperate urchins have been successfully cryopreserved, tropical urchins living on coral reefs have not. Here, we investigated the urchin embryos' tolerance to various cryoprotectants and cooling rates to develop a cryopreservation protocol for T. gratilla. We found that using 1 M Me2SO with a cooling rate of 9.7 °C/min on gastrula stage embryos produced the best results with survival rates of up to 85.5% and up to 50.8% maturation to the 4-arm echinopluteus stage, assessed three days after thawing. Continued research could see cryopreservation added to the repertoire of artificial reproductive techniques for T. gratilla, thereby assisting in the preservation of this ecologically important urchin, all while augmenting aquaculture efforts that contribute to coral reef restoration.
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Affiliation(s)
- Charley E Westbrook
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI, 96744, USA.
| | - Jonathan Daly
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI, 96744, USA; Center for Species Survival, Smithsonian National Zoo and Conservation Biology Institute, Smithsonian Institution, Front Royal, VA, 22630, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI, 96744, USA
| | - Mary Hagedorn
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI, 96744, USA; Center for Species Survival, Smithsonian National Zoo and Conservation Biology Institute, Smithsonian Institution, Front Royal, VA, 22630, USA
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2
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Hoban ML, Bunce M, Bowen BW. Plumbing the depths with environmental DNA (eDNA): Metabarcoding reveals biodiversity zonation at 45-60 m on mesophotic coral reefs. Mol Ecol 2023; 32:5590-5608. [PMID: 37728237 DOI: 10.1111/mec.17140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023]
Abstract
Mesophotic coral ecosystems (MCEs) are tropical reefs found at depths of ~30-150 m, below the region most heavily impacted by heat stress and other disturbances. Hence, MCEs may serve as potential refugia for threatened shallow reefs, but they also harbour depth-endemic fauna distinct from shallow reefs. Previous studies have characterized biodiversity patterns along depth gradients, but focussed primarily on conspicuous taxa (fishes, corals, etc.). Environmental DNA (eDNA) metabarcoding offers a more holistic approach to assess biodiversity patterns across the tree of life. Here, we use three metabarcoding assays targeting fishes (16S rRNA), eukaryotes (18S rDNA) and metazoans (COI) to assess biodiversity change from the surface to ~90 m depth across 15-m intervals at three sites within the Hawaiian Archipelago. We observed significant community differences between most depth zones, with distinct zonation centred at 45-60 m for eukaryotes and metazoans, but not for fishes. This finding may be attributable to the higher mobility of reef fishes, although methodological limitations are likely a contributing factor. The possibility for MCEs to serve as refugia is not excluded for fishes, but invertebrate communities >45 m are distinct, indicating limited connectivity for the majority of reef fauna. This study provides a new approach for surveying biodiversity on MCEs, revealing patterns in a much broader context than the limited-taxon studies that comprise the bulk of our present knowledge.
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Affiliation(s)
- Mykle L Hoban
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Michael Bunce
- Department of Conservation, Wellington, New Zealand
- Trace and Environmental DNA Laboratory, Curtin University, Perth, Western Australia, Australia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
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3
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Suchocki CR, Ka'apu-Lyons C, Copus JM, Walsh CAJ, Lee AM, Carter JM, Johnson EA, Etter PD, Forsman ZH, Bowen BW, Toonen RJ. Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae). Sci Rep 2023; 13:15810. [PMID: 37737242 PMCID: PMC10517014 DOI: 10.1038/s41598-023-41719-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture location. Two recent studies applied conservation genomics to assess species boundaries and reached contrasting conclusions: an ezRAD phylogenetic study resolved 5 lineages with poor alignment to species categories and proposed a single species with multiple population partitions. In contrast, a dd-RAD coalescent study concluded that the three nominal species are well-supported evolutionarily lineages. Here we developed a draft genome (~ 1.229 Gbp) to apply genome-wide coverage (10,246 SNPs) with nearly range-wide sampling of specimens (G. robusta N = 266, G. intermedia N = 241, and G. nigra N = 117) to resolve this debate. All three nominal species were polyphyletic, whereas 5 of 8 watersheds were monophyletic. AMOVA partitioned 23.1% of genetic variance among nominal species, 30.9% among watersheds, and the Little Colorado River was highly distinct (FST ranged from 0.79 to 0.88 across analyses). Likewise, DAPC identified watersheds as more distinct than species, with the Little Colorado River having 297 fixed nucleotide differences compared to zero fixed differences among the three nominal species. In every analysis, geography explains more of the observed variance than putative taxonomy, and there are no diagnostic molecular or morphological characters to justify species designation. Our analysis reconciles previous work by showing that species identities based on type location are supported by significant divergence, but natural geographic partitions show consistently greater divergence. Thus, our data confirm Gila robusta as a single polytypic species with roughly a dozen highly isolated geographic populations, providing a strong scientific basis for watershed-based future conservation.
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Affiliation(s)
- Christopher R Suchocki
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cassie Ka'apu-Lyons
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cameron A J Walsh
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Anne M Lee
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Julie Meka Carter
- Arizona Game and Fish Department, 5000 W. Carefree Highway, Phoenix, AZ, 85086, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
- Reefscape Restoration Initiative, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA.
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4
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Kottillil S, Rao C, Bowen BW, Shanker K. Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions. PeerJ 2023; 11:e15396. [PMID: 37283899 PMCID: PMC10239618 DOI: 10.7717/peerj.15396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 04/20/2023] [Indexed: 06/08/2023] Open
Abstract
Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging to 11 genera. Median joining haplotype networks were constructed for each species for the mtDNA cytochrome C oxidase subunit I (COI), and an Analysis of Molecular Variance (AMOVA) was conducted to understand patterns of genetic diversity and structure across the three major ocean basins-the Indian, Atlantic and Pacific Oceans. Haplotype networks showed very shallow coalescence in most species, a finding previously reported for marine teleosts. Star topologies were predominant among sharks while complex mutational topologies predominated among rays, a finding we attribute to extremely limited dispersal in the early life history of rays. Population structuring varied amongst species groups, apparently due to differences in life history traits including reproductive philopatry, site fidelity, pelagic habitat, migratory habits, and dispersal ability. In comparison to reef-associated and demersal species, pelagic and semi pelagic species showed lower levels of structure between and within ocean basins. As expected, there is variation between taxa and groups, but there are also some broad patterns that can guide management and conservation strategies.
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Affiliation(s)
- Sudha Kottillil
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Department of Energy and Environment, TERI School of Advanced Studies, New Delhi, India
| | - Chetan Rao
- Dakshin Foundation, Bengaluru, Karnataka, India
| | - Brian W. Bowen
- Hawai‘i Institute of Marine Biology, University of Hawaii, Kaneohe, Hawai‘i, United States of America
| | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Dakshin Foundation, Bengaluru, Karnataka, India
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5
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Coleman RR, Kraft DW, Hoban ML, Toonen RJ, Bowen BW. Genomic assessment of larval odyssey: self-recruitment and biased settlement in the Hawaiian surgeonfish Acanthurus triostegus sandvicensis. J Fish Biol 2023; 102:581-595. [PMID: 36564830 DOI: 10.1111/jfb.15294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54-77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of O'ahu, Hawai'i. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi-enclosed Kāne'ohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāne'ohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self-recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.
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Affiliation(s)
- Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
| | - Derek W Kraft
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Mykle L Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
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6
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Canfield SJ, Galván-Magaña F, Bowen BW. Little Sharks in a Big World: Mitochondrial DNA Reveals Small-scale Population Structure in the California Horn Shark (Heterodontus francisci). J Hered 2022; 113:298-310. [PMID: 35438775 DOI: 10.1093/jhered/esac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The California horn shark (Heterodontus francisci) is a small demersal species distributed from southern California and the Channel Islands to Baja California and the Gulf of California. These nocturnal reef predators maintain small home-ranges as adults, and lay auger-shaped egg cases that become wedged into the substrate. While population trends are not well documented, this species is subject to fishing pressure through portions of its range and has been identified as vulnerable to overexploitation. Here we present a survey of 318 specimens from across the range, using mtDNA control region sequences to provide the first genetic assessment of H. francisci. Overall population structure (ΦST = 0.266, P < 0.001) is consistent with limited dispersal as indicated by life history, with two distinct features. Population structure along the continuous coastline is low, with no discernable breaks from Santa Barbara, CA to Bahia Tortugas (Baja California Sur, Mexico); however, there is a notable partition at Punta Eugenia (BCS), a well-known biogeographic break between tropical and subtropical marine faunas. In contrast, population structure is much higher (max ΦST = 0.601, P < 0.05) between the coast and adjacent Channel Islands, a minimum distance of 19 km, indicating that horn sharks rarely disperse across deep habitat and open water. Population structure in most elasmobranchs is measured on a scale of hundreds to thousands of kilometers, but the California Horn Shark has population partitions on an unprecedented small scale, indicating a need for localized management strategies which ensure adequate protection of distinct stocks.
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Affiliation(s)
- Sean J Canfield
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, HI, USA
| | - Felipe Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, HI, USA
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7
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Copus JM, Pyle RL, Bowen BW, Kosaki RK, Webster JM. The Habitat Persistence Hypothesis: a new perspective on the distribution of coral-reef organisms. Frontiers of Biogeography 2022. [DOI: 10.21425/f5fbg57427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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8
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Bowen BW, Forsman ZH, Whitney JL, Faucci A, Hoban M, Canfield SJ, Johnston EC, Coleman RR, Copus JM, Vicente J, Toonen RJ. Species Radiations in the Sea: What the Flock? J Hered 2021; 111:70-83. [PMID: 31943081 DOI: 10.1093/jhered/esz075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawai'i is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a "terrestrial" mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.
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Affiliation(s)
- Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Jonathan L Whitney
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI
| | - Anuschka Faucci
- Math & Sciences Division, Leeward Community College, University of Hawai'i, Pearl City, HI
| | - Mykle Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | | | - Erika C Johnston
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Richard R Coleman
- 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
| | - Jan Vicente
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
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9
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Kraft DW, Conklin EE, Barba EW, Hutchinson M, Toonen RJ, Forsman ZH, Bowen BW. Genomics versus mtDNA for resolving stock structure in the silky shark ( Carcharhinus falciformis). PeerJ 2020; 8:e10186. [PMID: 33150082 PMCID: PMC7585369 DOI: 10.7717/peerj.10186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.
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Affiliation(s)
- Derek W. Kraft
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Emily E. Conklin
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Evan W. Barba
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Melanie Hutchinson
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
- Joint Institute of Marine and Atmospheric Research, Pacific Islands Fisheries Science Center, NOAA, University of Hawai’i, Honolulu, HI, USA
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Zac H. Forsman
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Brian W. Bowen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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11
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DiBattista JD, Saenz‐Agudelo P, Piatek MJ, Cagua EF, Bowen BW, Choat JH, Rocha LA, Gaither MR, Hobbs JA, Sinclair‐Taylor TH, McIlwain JH, Priest MA, Braun CD, Hussey NE, Kessel ST, Berumen ML. Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula. Ecol Evol 2020; 10:4314-4330. [PMID: 32489599 PMCID: PMC7246217 DOI: 10.1002/ece3.6199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.
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Affiliation(s)
- Joseph D. DiBattista
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Pablo Saenz‐Agudelo
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Marek J. Piatek
- Computational Bioscience Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Edgar Fernando Cagua
- Centre for Integrative EcologySchool of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - John Howard Choat
- School of Marine and Tropical BiologyJames Cook UniversityTownsvilleQldAustralia
| | - Luiz A. Rocha
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Michelle R. Gaither
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
- Genomics and Bioinformatics ClusterDepartment of BiologyUniversity of Central FloridaOrlandoFLUSA
| | - Jean‐Paul A. Hobbs
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Tane H. Sinclair‐Taylor
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | | | - Mark A. Priest
- Marine Spatial Ecology LabSchool of Biological Sciences and ARC Centre of Excellence for Coral Reef StudiesUniversity of QueenslandSt. LuciaQldAustralia
| | - Camrin D. Braun
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Steven T. Kessel
- Daniel P. Haerther Center for Conservation and ResearchJohn G. Shedd AquariumChicagoILUSA
| | - Michael L. Berumen
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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12
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Kamikawa KT, Humphreys RL, Bowen BW, Friedlander AM. Recruitment dynamics and fishery characteristics of juvenile goatfishes Mulloidichthys spp. in Hawai'i. J Fish Biol 2019; 95:1086-1093. [PMID: 31314922 DOI: 10.1111/jfb.14101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
The most common goatfishes in Hawai'i, Mulloidichthys flavolineatus and M. vanicolensis, comprise a unique resource due to their cultural, ecological and biological significance. These species exhibit pulse-type recruitment to nearshore areas during the summer months. Such pulses of juvenile fishes provide prey for pelagic and nearshore fishes and support a popular directed fishery. However, limited scientific information exists on juvenile stages of these fishes, known locally as oama, despite their contribution to coastal ecology and the extensive nearshore fisheries. Here we resolve growth rates, habitat preferences, hatching dates, size and age structure, as well as fishing catch rates based on new recruits in 2014 and 2015. We sampled 257 M. flavolineatus and 204 M. vanicolensis to compare ecological and fisheries characteristics between species and years. Both show strong habitat segregation, with M. vanicolensis found almost exclusively on hard and M. flavolineatus on soft substrates. Oama recruited in anomalously high numbers in 2014, a trend reflected in a higher catch per unit effort. In contrast, 2015 recruits grew faster, were heavier on average and hatched later than during 2014. Both species have calculated hatch dates in March to July, with M. vanicolensis hatching earlier, recruiting earlier and being consistently larger than M. flavolineatus. This baseline information regarding recruitment and early life-history characteristics can enhance management for other data-limited species that comprise a substantial component of nearshore fisheries in Hawai'i.
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Affiliation(s)
- Keith T Kamikawa
- Fisheries Ecology Research Lab, Department of Biology, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Robert L Humphreys
- Affiliate Faculty, Marine Biology Graduate Program, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Alan M Friedlander
- Fisheries Ecology Research Lab, Department of Biology, University of Hawai'i, Honolulu, Hawai'i, USA
- Pristine Seas, National Geographic Society, Washington, DC, USA
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13
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Wilcox CL, Motomura H, Matsunuma M, Bowen BW. Phylogeography of Lionfishes (Pterois) Indicate Taxonomic Over Splitting and Hybrid Origin of the Invasive Pterois volitans. J Hered 2019. [PMID: 28637254 DOI: 10.1093/jhered/esx056] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The lionfish is an iconic marine fish, and recently renowned for a disastrous introduction into the West Atlantic. Genetic surveys of the putative invaders (Pterois volitans and Pterois miles) in their natural Indo-Pacific range can illuminate both topics. Previous research indicated that P. volitans and P. miles are sister species that hybridize in the invasive range, but hybridization in the native range is unknown. Here, we apply mtDNA COI and 2 nuclear introns (S7 RP1 and Gpd2) from 229 lionfish including the 2 invaders and 2 closely-related taxa (44 P. miles, 91 P. volitans, 31 Pterois lunulata, and 63 Pterois russelii) from 10 locations in their native ranges. Genetic data are supplemented with key morphological characters: dorsal, anal, and pectoral fin ray counts. We observed 2 lineages (d = 4.07%, 0.89%, and 2.75% at COI, S7 RP1, and Gpd2, respectively) among the 4 putative species: an Indian Ocean lineage represented by P. miles, and a Pacific Ocean lineage represented by P. lunulata and P. russelii. All specimens of the invasive P. volitans appear to be hybrids between the Indian Ocean P. miles and a Pacific lineage encompassing P. lunulata/russelii, a conclusion supported by both genetics and morphology. The divergences between Indian and Pacific forms are within the range of species-level partitions in fishes, and we recommend retention of the names P. miles and P. russelii for Indian and Pacific forms. The hybrid origin of the Atlantic invasion invokes the possibility of heterosis as a contributing factor to invasion success.
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Affiliation(s)
- Christie L Wilcox
- Hawai'i Institute of Marine Biology, Kane'ohe, HI.,Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI
| | | | - Mizuki Matsunuma
- Laboratory of Marine Biology, Faculty of Science, Kochi University, Kochi, Japan
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14
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Copus JM, Montgomery WL, Forsman ZH, Bowen BW, Toonen RJ. Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species. PeerJ 2018; 6:e5605. [PMID: 30294509 PMCID: PMC6167970 DOI: 10.7717/peerj.5605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 08/17/2018] [Indexed: 11/20/2022] Open
Abstract
The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions.
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Affiliation(s)
- Joshua M. Copus
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - W. L. Montgomery
- Department of Biology, Northern Arizona University, Flagstaff, AZ, USA
| | - Zac H. Forsman
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Robert J. Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
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15
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Coleman RR, Copus JM, Coffey DM, Whitton RK, Bowen BW. Shifting reef fish assemblages along a depth gradient in Pohnpei, Micronesia. PeerJ 2018; 6:e4650. [PMID: 29707432 PMCID: PMC5922234 DOI: 10.7717/peerj.4650] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
Mesophotic coral ecosystems (MCEs) continue to be understudied, especially in island locations spread across the Indo-Pacific Ocean. Pohnpei is the largest island in the Federated States of Micronesia, with a well-developed barrier reef, and steep slopes that descend to more than 1,000 m. Here we conducted visual surveys along a depth gradient of 0 to 60 m in addition to video surveys that extend to 130 m, with 72 belt transects and 12 roving surveys using closed-circuit rebreathers, to test for changes in reef fish composition from shallow to mesophotic depths. We observed 304 fish species across 47 families with the majority confined to shallow habitat. Taxonomic and trophic positions at 30 m showed similar compositions when compared against all other depths. However, assemblages were comprised of a distinct shallow (<30 m) and deep (>30 m) group, suggesting 30 m as a transition zone between these communities. Shallow specialists had a high probability of being herbivores and deep specialists had a higher probability of being planktivores. Acanthuridae (surgeonfishes), Holocentridae (soldierfishes), and Labridae (wrasses) were associated primarily with shallow habitat, while Pomacentridae (damselfishes) and Serranidae (groupers) were associated with deep habitat. Four species may indicate Central Pacific mesophotic habitat: Chromis circumaurea, Luzonichthys seaver, Odontanthias borbonius, and an undescribed slopefish (Symphysanodon sp.). This study supports the 30 m depth profile as a transition zone between shallow and mesophotic ecosystems (consistent with accepted definitions of MCEs), with evidence of multiple transition zones below 30 m. Disturbances restricted to either region are not likely to immediately impact the other and both ecosystems should be considered separately in management of reefs near human population centers.
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Affiliation(s)
- Richard R Coleman
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, United States of America.,Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, United States of America.,Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Daniel M Coffey
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, United States of America
| | - Robert K Whitton
- Bernice P. Bishop Museum, Honolulu, Hawai'i, United States of America
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, Kāne'ohe, Hawai'i, United States of America
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16
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Whitney JL, Bowen BW, Karl SA. Flickers of speciation: Sympatric colour morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence with gene flow. Mol Ecol 2018; 27:1479-1493. [PMID: 29420860 DOI: 10.1111/mec.14527] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/01/2023]
Abstract
One of the primary challenges of evolutionary research is to identify ecological factors that favour reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive colour polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few metres apart. To test whether ecological barriers have reduced gene flow among dark and light phenotypes, we evaluated genetic variation at 30 microsatellite loci and a nuclear exon (Mc1r) associated with melanistic coloration. We report low, but significant microsatellite differentiation among colour morphs and stronger divergence in the coding region of Mc1r indicating signatures of selection. Critically, we observed greater genetic divergence between colour morphs on the same reefs than that between the same morphs in different geographic locations. We hypothesize that adaptation to the contrasting microhabitats is overriding gene flow and is responsible for the partial reproductive isolation observed between sympatric colour morphs. Combined with complementary studies of hawkfish ecology and behaviour, these genetic results indicate an ecological barrier to gene flow initiated by habitat selection and enhanced by assortative mating. Hence, the arc-eye hawkfish fulfil theoretical expectations for the earliest phase of speciation with gene flow.
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Affiliation(s)
- Jonathan L Whitney
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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17
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Dudoit 'A, Iacchei M, Coleman RR, Gaither MR, Browne WE, Bowen BW, Toonen RJ. The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages. PeerJ 2018. [PMID: 29527409 PMCID: PMC5844259 DOI: 10.7717/peerj.4409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.
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Affiliation(s)
- 'Ale'alani Dudoit
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Matthew Iacchei
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America.,Department of Natural Science, Hawai'i Pacific University, Kāne'ohe, HI, United States of America
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Michelle R Gaither
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Current affiliation: Department of Biology, University of Central Florida, Orlando, FL, United States of America
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
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18
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Krysko KL, Nuñez LP, Newman CE, Bowen BW. Phylogenetics of Kingsnakes, Lampropeltis getula Complex (Serpentes: Colubridae), in Eastern North America. J Hered 2017; 108:226-238. [PMID: 28119446 DOI: 10.1093/jhered/esw086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/08/2016] [Indexed: 01/25/2023] Open
Abstract
Kingsnakes of the Lampropeltis getula complex range throughout much of temperate and subtropical North America. Studies over the last century have used morphology and color pattern to describe numerous subspecies. More recently, DNA analyses have made invaluable contributions to our understanding of their evolution and taxonomy. We use genetic and ecological methods to test previous hypotheses of distinct evolutionary lineages by examining 66 total snakes and 1) analyzing phylogeographic structure using 2 mtDNA loci and 1 nuclear locus, 2) estimating divergence dates and historical demography among lineages in a Bayesian coalescent framework, and 3) applying ecological niche modeling (ENM). Our molecular data and ENMs illustrate that 3 previously recognized subspecies in the eastern United States comprise well-supported monophyletic lineages that diverged during the Pleistocene. The geographic boundaries of these 3 lineages correspond closely to known biogeographic barriers (Florida peninsula, Appalachian Mountains, and Apalachicola River) previously identified for other plants and animals, indicating shared geographic influences on evolutionary history. We conclude that genetic, ecological, and morphological data support recognition of these 3 lineages as distinct species (Lampropeltis floridana, Lampropeltis getula, and Lampropeltis meansi).
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Affiliation(s)
- Kenneth L Krysko
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA
| | - Leroy P Nuñez
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA.,School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA
| | - Catherine E Newman
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
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19
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Bowen BW, Meylan AB, Ross JP, Limpus CJ, Balazs GH, Avise JC. GLOBAL POPULATION STRUCTURE AND NATURAL HISTORY OF THE GREEN TURTLE (
CHELONIA MYDAS
) IN TERMS OF MATRIARCHAL PHYLOGENY. Evolution 2017; 46:865-881. [DOI: 10.1111/j.1558-5646.1992.tb00605.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/1991] [Accepted: 12/17/1991] [Indexed: 11/28/2022]
Affiliation(s)
- Brian W. Bowen
- Department of Genetics University of Georgia Athens GA 30602 USA
| | - Anne B. Meylan
- Department of Natural Resources Florida Marine Research Institute 100 Eighth Ave., S.E. St. Petersburg FL 33701‐5095 USA
| | - J. Perran Ross
- Department of Natural Sciences Florida Museum of Natural History Gainesville FL 32611 USA
| | - Colin J. Limpus
- Queensland National Park and Wildlife Service P.O. Box 155, North Quay Queensland AUSTRALIA 4002
| | - George H. Balazs
- National Marine Fisheries Service Southwest Fisheries Science Center, Honolulu Laboratory 2570 Dole St. Honolulu HI 96822‐2396 USA
| | - John C. Avise
- Department of Genetics University of Georgia Athens GA 30602 USA
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20
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Bowen BW, Kamezaki N, Limpus CJ, Hughes GR, Meylan AB, Avise JC. GLOBAL PHYLOGEOGRAPHY OF THE LOGGERHEAD TURTLE (
CARETTA CARETTA
) AS INDICATED BY MITOCHONDRIAL DNA HAPLOTYPES. Evolution 2017; 48:1820-1828. [DOI: 10.1111/j.1558-5646.1994.tb02217.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/1993] [Accepted: 11/30/1993] [Indexed: 11/28/2022]
Affiliation(s)
- Brian W. Bowen
- BEECS Genetic Analysis Core, P.O. Box 110699 University of Florida Gainesville Florida 32611
- Archie Carr Center for Sea Turtle Research, 223 Bartram Hall University of Florida Gainesville Florida 32611
| | - Naoki Kamezaki
- The Graduate School of Human and Environmental Studies Kyoto University Yoshida Nihonmatsu‐cho, Sakyo Kyoto 606 Japan
| | - Colin J. Limpus
- Queensland Department of Environment and Heritage P.O. Box 155 Brisbane 4002 Queensland Australia
| | - George R. Hughes
- Natal Parks Board P.O. Box 662 Pietermaritzburg 3200 South Africa
| | - Anne B. Meylan
- Florida Marine Research Institute 100 Eighth Avenue, S.E. St. Petersburg Florida 33701‐5095
| | - John C. Avise
- Department of Genetics University of Georgia Athens Georgia 30602
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21
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DiBattista JD, Gaither MR, Hobbs JPA, Rocha LA, Bowen BW. Response to Delrieu-Trottin et al.: Hybrids, Color Variants and the Consistently Devilish Taxonomy of Pygmy Angelfishes. J Hered 2017; 108:337-339. [PMID: 28391308 DOI: 10.1093/jhered/esx009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph D DiBattista
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Michelle R Gaither
- Hawai'i Institute of Marine Biology, Kane'ohe, HI, USA.,Section of Ichthyology, California Academy of Sciences, San Francisco, CA, USA
| | - Jean-Paul A Hobbs
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, San Francisco, CA, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, Kane'ohe, HI, USA
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22
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Pyle RL, Boland R, Bolick H, Bowen BW, Bradley CJ, Kane C, Kosaki RK, Langston R, Longenecker K, Montgomery A, Parrish FA, Popp BN, Rooney J, Smith CM, Wagner D, Spalding HL. A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago. PeerJ 2016; 4:e2475. [PMID: 27761310 PMCID: PMC5068450 DOI: 10.7717/peerj.2475] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 08/23/2016] [Indexed: 11/21/2022] Open
Abstract
Although the existence of coral-reef habitats at depths to 165 m in tropical regions has been known for decades, the richness, diversity, and ecological importance of mesophotic coral ecosystems (MCEs) has only recently become widely acknowledged. During an interdisciplinary effort spanning more than two decades, we characterized the most expansive MCEs ever recorded, with vast macroalgal communities and areas of 100% coral cover between depths of 50–90 m extending for tens of km2 in the Hawaiian Archipelago. We used a variety of sensors and techniques to establish geophysical characteristics. Biodiversity patterns were established from visual and video observations and collected specimens obtained from submersible, remotely operated vehicles and mixed-gas SCUBA and rebreather dives. Population dynamics based on age, growth and fecundity estimates of selected fish species were obtained from laser-videogrammetry, specimens, and otolith preparations. Trophic dynamics were determined using carbon and nitrogen stable isotopic analyses on more than 750 reef fishes. MCEs are associated with clear water and suitable substrate. In comparison to shallow reefs in the Hawaiian Archipelago, inhabitants of MCEs have lower total diversity, harbor new and unique species, and have higher rates of endemism in fishes. Fish species present in shallow and mesophotic depths have similar population and trophic (except benthic invertivores) structures and high genetic connectivity with lower fecundity at mesophotic depths. MCEs in Hawai‘i are widespread but associated with specific geophysical characteristics. High genetic, ecological and trophic connectivity establish the potential for MCEs to serve as refugia for some species, but our results question the premise that MCEs are more resilient than shallow reefs. We found that endemism within MCEs increases with depth, and our results do not support suggestions of a global faunal break at 60 m. Our findings enhance the scientific foundations for conservation and management of MCEs, and provide a template for future interdisciplinary research on MCEs worldwide.
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Affiliation(s)
- Richard L Pyle
- Natural Sciences, Bernice Pauahi Bishop Museum , Honolulu , HI , United States
| | - Raymond Boland
- Pacific Islands Fisheries Science Center, National Oceanographic and Atmospheric Administration, Honolulu, HI, United States; Hawai'i Pacific University, Honolulu, HI, United States
| | - Holly Bolick
- Natural Sciences, Bernice Pauahi Bishop Museum , Honolulu , HI , United States
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa , Honolulu , HI , United States
| | - Christina J Bradley
- Life and Environmental Sciences, University of California at Merced, Merced, CA, United States; Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI, United States
| | - Corinne Kane
- Environmental and Natural Resource Sciences, Washington State University , Pullman , WA , United States
| | - Randall K Kosaki
- Papahānaumokuākea Marine National Monument, National Oceanic and Atmospheric Administration , Honolulu , HI , United States
| | - Ross Langston
- Natural Sciences, Bernice Pauahi Bishop Museum , Honolulu , HI , United States
| | - Ken Longenecker
- Natural Sciences, Bernice Pauahi Bishop Museum , Honolulu , HI , United States
| | - Anthony Montgomery
- Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Honolulu, HI, United States; Pacific Islands Fish and Wildlife Office, U.S. Fish and Wildlife Service, Honolulu, HI, United States
| | - Frank A Parrish
- Pacific Islands Fisheries Science Center, National Oceanographic and Atmospheric Administration , Honolulu , HI , United States
| | - Brian N Popp
- Department of Geology and Geophysics, University of Hawai'i at Manoa , Honolulu , HI , United States
| | - John Rooney
- Joint Institute for Marine and Atmospheric Research, University of Hawai'i at Manoa , Honolulu , HI , United States
| | - Celia M Smith
- Department of Botany, University of Hawai'i at Manoa , Honolulu , HI , United States
| | - Daniel Wagner
- Papahānaumokuākea Marine National Monument, National Oceanic and Atmospheric Administration , Honolulu , HI , United States
| | - Heather L Spalding
- Department of Botany, University of Hawai'i at Manoa , Honolulu , HI , United States
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DiBattista JD, Gaither MR, Hobbs JPA, Rocha LA, Bowen BW. Angelfishes, Paper Tigers, and the Devilish Taxonomy of theCentropyge flavissimaComplex. J Hered 2016; 107:647-653. [DOI: 10.1093/jhered/esw062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/11/2016] [Indexed: 11/13/2022] Open
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DiBattista JD, Whitney J, Craig MT, Hobbs JPA, Rocha LA, Feldheim KA, Berumen ML, Bowen BW. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes. Mol Phylogenet Evol 2016; 101:203-215. [DOI: 10.1016/j.ympev.2016.04.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/12/2016] [Accepted: 04/29/2016] [Indexed: 11/27/2022]
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25
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Salerno JL, Bowen BW, Rappé MS. Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago. FEMS Microbiol Ecol 2016; 92:fiw109. [DOI: 10.1093/femsec/fiw109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 02/07/2023] Open
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26
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Coleman RR, Eble JA, DiBattista JD, Rocha LA, Randall JE, Berumen ML, Bowen BW. Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Mol Phylogenet Evol 2016; 100:243-253. [PMID: 27068838 DOI: 10.1016/j.ympev.2016.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/27/2022]
Abstract
The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.
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Affiliation(s)
- Richard R Coleman
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kāne'ohe, HI 96744, USA; Department of Biology, University of Hawai'i, Mānoa, 2500 Campus Rd, Honolulu, HI 96822, USA.
| | - Jeffrey A Eble
- University of West Florida, 11000 University Pkwy, Pensacola, FL 32514, USA
| | - Joseph D DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; Department of Environment and Agriculture, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr, San Francisco, CA 94118, USA
| | - John E Randall
- Bernice Pauahi Bishop Museum, 1525 Bernice St, Honolulu, HI 96817, USA
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kāne'ohe, HI 96744, USA
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Abstract
The scientific field of conservation biology is dominated by 3 specialties: phylogenetics, ecology, and evolution. Under this triad, phylogenetics is oriented towards the past history of biodiversity, conserving the divergent branches in the tree of life. The ecological component is rooted in the present, maintaining the contemporary life support systems for biodiversity. Evolutionary conservation (as defined here) is concerned with preserving the raw materials for generating future biodiversity. All 3 domains can be documented with genetic case histories in the waters of the Hawaiian Archipelago, an isolated chain of volcanic islands with 2 types of biodiversity: colonists, and new species that arose from colonists. This review demonstrates that 1) phylogenetic studies have identified previously unknown branches in the tree of life that are endemic to Hawaiian waters; 2) population genetic surveys define isolated marine ecosystems as management units, and 3) phylogeographic analyses illustrate the pathways of colonization that can enhance future biodiversity. Conventional molecular markers have advanced all 3 domains in conservation biology over the last 3 decades, and recent advances in genomics are especially valuable for understanding the foundations of future evolutionary diversity.
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Affiliation(s)
- Brian W Bowen
- From the Hawai'i Institute of Marine Biology, PO Box 1346, Kaneohe, HI 96744.
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Gaither MR, Bernal MA, Coleman RR, Bowen BW, Jones SA, Simison WB, Rocha LA. Genomic signatures of geographic isolation and natural selection in coral reef fishes. Mol Ecol 2015; 24:1543-57. [PMID: 25753379 DOI: 10.1111/mec.13129] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 01/17/2023]
Abstract
The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.
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Affiliation(s)
- Michelle R Gaither
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK; Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
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29
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Tenggardjaja KA, Bowen BW, Bernardi G. Vertical and horizontal genetic connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and adjacent Johnston Atoll. PLoS One 2014; 9:e115493. [PMID: 25517964 PMCID: PMC4269425 DOI: 10.1371/journal.pone.0115493] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/13/2014] [Indexed: 11/18/2022] Open
Abstract
Understanding vertical and horizontal connectivity is a major priority in research on mesophotic coral ecosystems (30-150 m). However, horizontal connectivity has been the focus of few studies, and data on vertical connectivity are limited to sessile benthic mesophotic organisms. Here we present patterns of vertical and horizontal connectivity in the Hawaiian Islands-Johnston Atoll endemic threespot damselfish, Chromis verater, based on 319 shallow specimens and 153 deep specimens. The mtDNA markers cytochrome b and control region were sequenced to analyze genetic structure: 1) between shallow (< 30 m) and mesophotic (30-150 m) populations and 2) across the species' geographic range. Additionally, the nuclear markers rhodopsin and internal transcribed spacer 2 of ribosomal DNA were sequenced to assess connectivity between shallow and mesophotic populations. There was no significant genetic differentiation by depth, indicating high levels of vertical connectivity between shallow and deep aggregates of C. verater. Consequently, shallow and deep samples were combined by location for analyses of horizontal connectivity. We detected low but significant population structure across the Hawaiian Archipelago (overall cytochrome b: ΦST = 0.009, P = 0.020; control region: ΦST = 0.012, P = 0.009) and a larger break between the archipelago and Johnston Atoll (cytochrome b: ΦST = 0.068, P < 0.001; control region: ΦST = 0.116, P < 0.001). The population structure within the archipelago was driven by samples from the island of Hawaii at the southeast end of the chain and Lisianski in the middle of the archipelago. The lack of vertical genetic structure supports the refugia hypothesis that deep reefs may constitute a population reservoir for species depleted in shallow reef habitats. These findings represent the first connectivity study on a mobile organism that spans shallow and mesophotic depths and provide a reference point for future connectivity studies on mesophotic fishes.
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Affiliation(s)
- Kimberly A. Tenggardjaja
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, United States of America
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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Coleman RR, Gaither MR, Kimokeo B, Stanton FG, Bowen BW, Toonen RJ. Large-scale introduction of the Indo-Pacific damselfishAbudefduf vaigiensisinto Hawai'i promotes genetic swamping of the endemic congenerA. abdominalis. Mol Ecol 2014; 23:5552-65. [DOI: 10.1111/mec.12952] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Richard R. Coleman
- Hawai'i Institute of Marine Biology; University of Hawai'i; P.O. Box 1346 Kaneohe HI 96744 USA
- Department of Biology; University of Hawai'i; Mānoa, 2450 Campus Road, Dean Hall Room 2 Honolulu HI 96822 USA
| | - Michelle R. Gaither
- Section of Ichthyology; California Academy of Sciences; 55 Music Concourse Drive San Francisco CA 94118 USA
- School of Biological and Biomedical Sciences; Durham University; South Road Durham DH1 3LE UK
| | - Bethany Kimokeo
- Hawai'i Institute of Marine Biology; University of Hawai'i; P.O. Box 1346 Kaneohe HI 96744 USA
| | - Frank G. Stanton
- University of Hawai'i Community Colleges; Leeward Community College; 96-045 Ala Ike Pearl City HI 96782 USA
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology; University of Hawai'i; P.O. Box 1346 Kaneohe HI 96744 USA
| | - Robert J. Toonen
- Hawai'i Institute of Marine Biology; University of Hawai'i; P.O. Box 1346 Kaneohe HI 96744 USA
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Selkoe KA, Gaggiotti OE, Bowen BW, Toonen RJ. Emergent patterns of population genetic structure for a coral reef community. Mol Ecol 2014; 23:3064-79. [DOI: 10.1111/mec.12804] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Kimberly A. Selkoe
- Hawai ̀i Institute of Marine Biology; University of Hawai ̀i; Kāne ̀ohe HI 97644 USA
- National Center for Ecological Analysis and Synthesis; 735 State St. Santa Barbara CA 93101 USA
| | - Oscar E. Gaggiotti
- Scottish Oceans Institute; School of Biology; University of St Andrews; St Andrews Fife KY16 8LB UK
| | - Brian W. Bowen
- Hawai ̀i Institute of Marine Biology; University of Hawai ̀i; Kāne ̀ohe HI 97644 USA
| | - Robert J. Toonen
- Hawai ̀i Institute of Marine Biology; University of Hawai ̀i; Kāne ̀ohe HI 97644 USA
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Andrews KR, Moriwake VN, Wilcox C, Grau EG, Kelley C, Pyle RL, Bowen BW. Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago. PLoS One 2014; 9:e91665. [PMID: 24722193 PMCID: PMC3982960 DOI: 10.1371/journal.pone.0091665] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 02/13/2014] [Indexed: 11/18/2022] Open
Abstract
The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m) in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m) in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787) and E. "marshi" (formerly E. carbunculus; N = 770) with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals) had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus) and a submesophotic grouper (Hyporthodus quernus). Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management plans.
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Affiliation(s)
- Kimberly R. Andrews
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- School of Biological & Biomedical Sciences, Durham University, South Road, United Kingdom
| | - Virginia N. Moriwake
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- Department of Oceanography, University of Hawai'i, Honolulu, Hawaii, United States of America
| | - Christie Wilcox
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- Cell and Molecular Biology Graduate Program, University of Hawai'i, Honolulu, Hawaii, United States of America
| | - E. Gordon Grau
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
| | - Christopher Kelley
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
- Hawai'i Undersea Research Lab, University of Hawai'i, Honolulu, Hawaii, United States of America
| | - Richard L. Pyle
- Bernice P. Bishop Museum, Honolulu, Hawaii, United States of America
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kane'ohe, Hawaii, United States of America
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Toonen RJ, Wilhelm T'A, Maxwell SM, Wagner D, Bowen BW, Sheppard CRC, Taei SM, Teroroko T, Moffitt R, Gaymer CF, Morgan L, Lewis N, Sheppard ALS, Parks J, Friedlander AM. One size does not fit all: the emerging frontier in large-scale marine conservation. Mar Pollut Bull 2013; 77:7-10. [PMID: 24246654 DOI: 10.1016/j.marpolbul.2013.10.039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
On the 20th anniversary of the Convention on Biological Diversity, a network of very large marine protected areas (the Big Ocean network) has emerged as a key strategy in the move to arrest marine decline and conserve some of the last remaining relatively undisturbed marine areas on the globe. Here we outline the ecological, economic and policy benefits of very large-scale MPAs and show their disproportionate value to global marine conservation targets. In particular we point out that very large-scale MPAs are a critical component of reaching the Aichi targets of protecting 10% of global marine habitats by 2020, because in addition to encompassing entire ecosystems, they will bring forward the expected date of achievement by nearly three decades (2025 as opposed to 2054). While the need for small MPAs remains critical, large MPAs will complement and enhance these conservation efforts. Big Ocean sites currently contain more than 80% of managed area in the sea, and provide our best hope for arresting the global decline in marine biodiversity.
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Affiliation(s)
- Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, P.O. Box 1346, Kāne'ohe, HI 96744, USA.
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Bowen BW, Rocha LA, Toonen RJ, Karl SA. The origins of tropical marine biodiversity. Trends Ecol Evol 2013; 28:359-66. [DOI: 10.1016/j.tree.2013.01.018] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/30/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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Abstract
Forecasting invasion success remains a fundamental challenge in invasion biology. The effort to identify universal characteristics that predict which species become invasive has faltered in part because of the diversity of taxa and systems considered. Here, we use an alternative approach focused on the spread stage of invasions. FST, a measure of alternative fixation of alleles, is a common proxy for realized dispersal among natural populations, summarizing the combined influences of life history, behaviour, habitat requirements, population size, history and ecology. We test the hypothesis that population structure in the native range (FST) is negatively correlated with the geographical extent of spread of marine species in an introduced range. An analysis of the available data (29 species, nine phyla) revealed a significant negative correlation (R(2) = 0.245-0.464) between FST and the extent of spread of non-native species. Mode FST among pairwise comparisons between populations in the native range demonstrated the highest predictive power (R(2) = 0.464, p < 0.001). There was significant improvement when marker type was considered, with mtDNA datasets providing the strongest relationship (n = 21, R(2) = 0.333-0.516). This study shows that FST can be used to make qualitative predictions concerning the geographical extent to which a non-native marine species will spread once established in a new area.
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Affiliation(s)
- Michelle R Gaither
- Section of Ichthyology, California Academy of Sciences, , 55 Music Concourse Drive, San Francisco, CA 94118, USA.
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36
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Andrews KR, Perrin WF, Oremus M, Karczmarski L, Bowen BW, Puritz JB, Toonen RJ. The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers. Mol Ecol 2013; 22:2408-23. [DOI: 10.1111/mec.12193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/30/2012] [Accepted: 12/04/2012] [Indexed: 11/26/2022]
Affiliation(s)
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service; NOAA; 8901 La Jolla Shores Drive La Jolla CA 92037 USA
| | - Marc Oremus
- Opération Cétacés; 16 rue Henri Niautou 98800 Nouméa New Caledonia
| | - Leszek Karczmarski
- The Swire Institute of Marine Science; School of Biological Sciences; The University of Hong Kong; Cape d'Aguilar Shek O Hong Kong
| | - Brian W. Bowen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
| | | | - Robert J. Toonen
- Hawai'i Institute of Marine Biology; PO Box 1346 Kāne'ohe HI 96744 USA
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37
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Gaither MR, Aeby G, Vignon M, Meguro YI, Rigby M, Runyon C, Toonen RJ, Wood CL, Bowen BW. An invasive fish and the time-lagged spread of its parasite across the Hawaiian archipelago. PLoS One 2013; 8:e56940. [PMID: 23468894 PMCID: PMC3584140 DOI: 10.1371/journal.pone.0056940] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/18/2013] [Indexed: 11/23/2022] Open
Abstract
Efforts to limit the impact of invasive species are frustrated by the cryptogenic status of a large proportion of those species. Half a century ago, the state of Hawai'i introduced the Bluestripe Snapper, Lutjanus kasmira, to O'ahu for fisheries enhancement. Today, this species shares an intestinal nematode parasite, Spirocamallanus istiblenni, with native Hawaiian fishes, raising the possibility that the introduced fish carried a parasite that has since spread to naïve local hosts. Here, we employ a multidisciplinary approach, combining molecular, historical, and ecological data to confirm the alien status of S. istiblenni in Hawai'i. Using molecular sequence data we show that S. istiblenni from Hawai'i are genetically affiliated with source populations in French Polynesia, and not parasites at a geographically intermediate location in the Line Islands. S. istiblenni from Hawai'i are a genetic subset of the more diverse source populations, indicating a bottleneck at introduction. Ecological surveys indicate that the parasite has found suitable intermediate hosts in Hawai'i, which are required for the completion of its life cycle, and that the parasite is twice as prevalent in Hawaiian Bluestripe Snappers as in source populations. While the introduced snapper has spread across the entire 2600 km archipelago to Kure Atoll, the introduced parasite has spread only half that distance. However, the parasite faces no apparent impediments to invading the entire archipelago, with unknown implications for naïve indigenous Hawaiian fishes and the protected Papahānaumokuākea Marine National Monument.
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Affiliation(s)
- Michelle R Gaither
- Ichthyology, California Academy of Sciences, San Francisco, California, USA.
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Fernandez-Silva I, Whitney J, Wainwright B, Andrews KR, Ylitalo-Ward H, Bowen BW, Toonen RJ, Goetze E, Karl SA. Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. PLoS One 2013; 8:e55990. [PMID: 23424642 PMCID: PMC3570555 DOI: 10.1371/journal.pone.0055990] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 01/04/2013] [Indexed: 11/18/2022] Open
Abstract
Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.
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Affiliation(s)
- Iria Fernandez-Silva
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, United States of America.
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DiBattista JD, Rocha LA, Craig MT, Feldheim KA, Bowen BW. Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites. ACTA ACUST UNITED AC 2012; 103:617-29. [PMID: 22888133 DOI: 10.1093/jhered/ess056] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography.
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Gaither MR, Toonen RJ, Bowen BW. Coming out of the starting blocks: extended lag time rearranges genetic diversity in introduced marine fishes of Hawai'i. Proc Biol Sci 2012; 279:3948-57. [PMID: 22874747 DOI: 10.1098/rspb.2012.1481] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biological invasions with known histories are rare, especially in the sea, and empirical studies of the genetic consequences are even rarer. Fifty-five years ago, the state of Hawai'i began a remarkable, if unintentional, 'experiment' with the introduction of three reef fishes, Lutjanus fulvus, Cephalopholis argus and Lutjanus kasmira. All have since expanded from the initial introduction of 2204 to 3163 individuals; however, historical records show that initially L. fulvus remained scarce, C. argus had modest population expansion and L. kasmira experienced rapid population growth. The consequences of differential population growth rates are apparent in F-statistics: Hawaiian L. fulvus demonstrate strong and significant haplotype frequency shifts from the founder location (F(ST) = 0.449), C. argus shows low but significant differentiation (F(ST) = 0.066) and L. kasmira is nearly identical to the founder location (F(ST) = 0.008). All three species had higher mtDNA diversity in the introduced range, which can be explained by multiple sources for L. fulvus and L. kasmira, but not for C. argus. We conclude that lag time before population expansion, in conjunction with genetic drift, has defined the genetic architecture of these three species in the introduced range.
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Affiliation(s)
- Michelle R Gaither
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, PO Box 1346, Kane'ohe, HI 96744, USA.
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Ludt WB, Bernal MA, Bowen BW, Rocha LA. Living in the past: phylogeography and population histories of Indo-Pacific wrasses (genus Halichoeres) in shallow lagoons versus outer reef slopes. PLoS One 2012; 7:e38042. [PMID: 22701597 PMCID: PMC3368945 DOI: 10.1371/journal.pone.0038042] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 05/01/2012] [Indexed: 11/19/2022] Open
Abstract
Sea level fluctuations during glacial cycles affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes on oceanic islands. In these circumstances we expect that species inhabiting lagoons should show shallow genetic architecture relative to species inhabiting more stable outer reefs. Here we test this expectation on an ocean-basin scale with four wrasses (genus Halichoeres): H. claudia (N = 194, with ocean-wide distribution) and H. ornatissimus (N = 346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N = 239) and H. margaritaceus (N = 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations. Mismatch distributions and significant negative Fu's F values indicate Pleistocene population expansion for all species, and (contrary to expectations) shallower histories in the outer slope species. We conclude that lagoonal wrasses may persist through glacial habitat disruptions, but are restricted to refugia during lower sea level stands. In contrast, outer reef slope species have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles.
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Affiliation(s)
- William B Ludt
- Department of Marine Science, University of Texas, Austin, Texas, United States of America.
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Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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Daly-Engel TS, Randall JE, Bowen BW. Is the Great Barracuda ( Sphyraena barracuda) a reef fish or a pelagic fish? The phylogeographic perspective. Mar Biol 2012; 159:975-985. [PMID: 25594680 PMCID: PMC3784357 DOI: 10.1007/s00227-012-1878-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Current taxonomy indicates a single global species of the Great Barracuda (Sphyraena barracuda) despite differences in color and behavior between Atlantic and Pacific forms. To investigate these differences and qualify the dispersal characteristics of this unique coastal- pelagic teleost (bony fish), we conducted a global phylogeographic survey of 246 specimens from thirteen sampling locations using a 629-base pair fragment of mtDNA cytochrome b. Data indicate high overall gene flow in the Indo-Pacific over large distances (>16,500 km) bridging several biogeographic barriers. The West Atlantic population contains an mtDNA lineage that is divergent from the Indo-Pacific (d = 1.9%), while the East Atlantic (N = 23) has two mutations (d = 0.6%) apart from the Indo-Pacific. While we cannot rule out distinct evolutionary partitions among ocean basins based on behavior, coloration, and near-monophyly between Atlantic and Indo-Pacific subpopulations, more investigation is required before taxonomic status is revised. Overall, the pattern of high global dispersal and connectivity in S. barracuda more closely resembles those reported for large oceanic predators than reef-associated teleosts.
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Affiliation(s)
- Toby S Daly-Engel
- Department of Zoology, University of Hawaii at Mānoa, Honolulu, HI 96822, USA
| | - John E Randall
- Bishop Museum, 1525 Bernice Street, Honolulu, HI 96817-2704, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
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Bowen BW. Interview with John C. Briggs, recipient of the 2005 Alfred Russel Wallace award. Frontiers of Biogeography 2012. [DOI: 10.21425/f5fbg12349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Daly-Engel TS, Seraphin KD, Holland KN, Coffey JP, Nance HA, Toonen RJ, Bowen BW. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini). PLoS One 2012; 7:e29986. [PMID: 22253848 PMCID: PMC3254628 DOI: 10.1371/journal.pone.0029986] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022] Open
Abstract
Background The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA) markers demonstrated strong genetic partitioning overall (global ΦST = 0.749) and significant population separations across oceans and between discontinuous continental coastlines. Methodology/Principal Findings We surveyed the same global range with increased sample coverage (N = 403) and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (FST = 0.035) over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (ΦST = 0.749). Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. Conclusions/Significance These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.
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Affiliation(s)
- Toby S Daly-Engel
- Department of Zoology, University of Hawaii at Mānoa, Honolulu, Hawaii, United States of America.
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Gaither MR, Jones SA, Kelley C, Newman SJ, Sorenson L, Bowen BW. High connectivity in the deepwater snapper Pristipomoides filamentosus (Lutjanidae) across the Indo-Pacific with isolation of the Hawaiian archipelago. PLoS One 2011; 6:e28913. [PMID: 22216141 PMCID: PMC3245230 DOI: 10.1371/journal.pone.0028913] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/17/2011] [Indexed: 11/18/2022] Open
Abstract
In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100-400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N=1,222) collected across 17,000 km from Hawai'i to the western Indian Ocean. Results indicate that P. filamentosus is a highly dispersive species with low but significant population structure (mtDNA Φ(ST)=0.029, microsatellite F(ST)=0.029) due entirely to the isolation of Hawai'i. No population structure was detected across 14,000 km of the Indo-Pacific from Tonga in the Central Pacific to the Seychelles in the western Indian Ocean, a pattern rarely observed in reef species. Despite a long pelagic phase (60-180 days), interisland dispersal as adults, and extensive gene flow across the Indo-Pacific, P. filamentosus is unable to maintain population connectivity with Hawai'i. Coalescent analyses indicate that P. filamentosus may have colonized Hawai'i 26 K-52 K y ago against prevailing currents, with dispersal away from Hawai'i dominating migration estimates. P. filamentosus harbors low genetic diversity in Hawai'i, a common pattern in marine fishes, and our data indicate a single archipelago-wide stock. However, like the Hawaiian Grouper, Hyporthodus quernus, this snapper had several significant pairwise comparisons (F(ST)) clustered around the middle of the archipelago (St. Rogatien, Brooks Banks, Gardner) indicating that this region may be isolated or (more likely) receives input from Johnston Atoll to the south.
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Affiliation(s)
- Michelle R Gaither
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, Hawai'i, USA.
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Gaither MR, Bowen BW, Bordenave TR, Rocha LA, Newman SJ, Gomez JA, van Herwerden L, Craig MT. Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the Indo-Pacific Barrier with contemporary overlap in The Coral Triangle. BMC Evol Biol 2011; 11:189. [PMID: 21722383 PMCID: PMC3145601 DOI: 10.1186/1471-2148-11-189] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 07/01/2011] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The Coral Triangle (CT), bounded by the Philippines, the Malay Peninsula, and New Guinea, is the epicenter of marine biodiversity. Hypotheses that explain the source of this rich biodiversity include 1) the center of origin, 2) the center of accumulation, and 3) the region of overlap. Here we contribute to the debate with a phylogeographic survey of a widely distributed reef fish, the Peacock Grouper (Cephalopholis argus; Epinephelidae) at 21 locations (N = 550) using DNA sequence data from mtDNA cytochrome b and two nuclear introns (gonadotropin-releasing hormone and S7 ribosomal protein). RESULTS Population structure was significant (ΦST = 0.297, P < 0.001; FST = 0.078, P < 0.001; FST = 0.099, P < 0.001 for the three loci, respectively) among five regions: French Polynesia, the central-west Pacific (Line Islands to northeastern Australia), Indo-Pacific boundary (Bali and Rowley Shoals), eastern Indian Ocean (Cocos/Keeling and Christmas Island), and western Indian Ocean (Diego Garcia, Oman, and Seychelles). A strong signal of isolation by distance was detected in both mtDNA (r = 0.749, P = 0.001) and the combined nuclear loci (r = 0.715, P < 0.001). We detected evidence of population expansion with migration toward the CT. Two clusters of haplotypes were detected in the mtDNA data (d = 0.008), corresponding to the Pacific and Indian Oceans, with a low level of introgression observed outside a mixing zone at the Pacific-Indian boundary. CONCLUSIONS We conclude that the Indo-Pacific Barrier, operating during low sea level associated with glaciation, defines the primary phylogeographic pattern in this species. These data support a scenario of isolation on the scale of 105 year glacial cycles, followed by population expansion toward the CT, and overlap of divergent lineages at the Pacific-Indian boundary. This pattern of isolation, divergence, and subsequent overlap likely contributes to species richness at the adjacent CT and is consistent with the region of overlap hypothesis.
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Affiliation(s)
- Michelle R Gaither
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Tiana-Rae Bordenave
- Hawaii Institute of Marine Biology University of Hawaii PO Box 1346, Kaneohe, HI 96744, USA
| | - Luiz A Rocha
- Department of Ichthyology California Academy of Sciences 55 Music Concourse Drive San Francisco, CA 94118, USA
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Government of Western Australia P.O. Box 20, North Beach, WA 6920, Australia
| | - Juan A Gomez
- School of Marine & Tropical Biology James Cook University Townsville, QLD 4811, Australia
| | - Lynne van Herwerden
- School of Marine & Tropical Biology James Cook University Townsville, QLD 4811, Australia
| | - Matthew T Craig
- Department of Marine Sciences University of Puerto Rico Mayagüez P.O. Box 9000, Mayagüez PR 00681, USA
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Bjorndal KA, Bowen BW, Chaloupka M, Crowder LB, Heppell SS, Jones CM, Lutcavage ME, Policansky D, Solow AR, Witherington BE. Better Science Needed for Restoration in the Gulf of Mexico. Science 2011; 331:537-8. [PMID: 21292956 DOI: 10.1126/science.1199935] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Karen A. Bjorndal
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Brian W. Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
| | - Milani Chaloupka
- Ecological Modelling Services Pty. Ltd., University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Larry B. Crowder
- Center for Marine Conservation, Duke University Marine Lab, Beaufort, NC 28516, USA
| | - Selina S. Heppell
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA
| | - Cynthia M. Jones
- Center for Quantitative Fisheries Ecology, Old Dominion University, Norfolk, VA 23529, USA
| | - Molly E. Lutcavage
- Large Pelagics Research Center, Department of Environmental Conservation, University of Massachusetts, Amherst, Gloucester, MA 01930, USA
| | | | - Andrew R. Solow
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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Schultz JK, Baker JD, Toonen RJ, Harting AL, Bowen BW. Range-wide genetic connectivity of the Hawaiian monk seal and implications for translocation. Conserv Biol 2011; 25:124-132. [PMID: 21166713 DOI: 10.1111/j.1523-1739.2010.01615.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Hawaiian monk seal (Monachus schauinslandi) is one of the most critically endangered marine mammals. Less than 1200 individuals remain, and the species is declining at a rate of approximately 4% per year as a result of juvenile starvation, shark predation, and entanglement in marine debris. Some of these problems may be alleviated by translocation; however, if island breeding aggregates are effectively isolated subpopulations, moving individuals may disrupt local adaptations. In these circumstances, managers must balance the pragmatic need of increasing survival with theoretical concerns about genetic viability. To assess range-wide population structure of the Hawaiian monk seal, we examined an unprecedented, near-complete genetic inventory of the species (n =1897 seals, sampled over 14 years) at 18 microsatellite loci. Genetic variation was not spatially partitioned ((w) =-0.03, p = 1.0), and a Bayesian clustering method provided evidence of one panmictic population (K =1). Pairwise F(ST) comparisons (among 7 island aggregates over 14 annual cohorts) did not reveal temporally stable, spatial reproductive isolation. Our results coupled with long-term tag-resight data confirm seal movement and gene flow throughout the Hawaiian Archipelago. Thus, human-mediated translocation of seals among locations is not likely to result in genetic incompatibilities.
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Affiliation(s)
- Jennifer K Schultz
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii, Kaneohe, HI 96744, U.S.A.
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