1
|
Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
Collapse
Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
| |
Collapse
|
2
|
Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 2022; 10:e13790. [PMID: 35959477 PMCID: PMC9359134 DOI: 10.7717/peerj.13790] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
Collapse
Affiliation(s)
- Mykle L. Hoban
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, Hawai‘i, United States of America
| | - Jonathan Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Allen G. Collins
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine R. Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Abigail J. Reft
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine E. Bemis
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| |
Collapse
|
3
|
Lim HC, Habib A, Chen WJ. Comparative Phylogeography and Phylogeny of Pennah Croakers (Teleostei: Sciaenidae) in Southeast Asian Waters. Genes (Basel) 2021; 12:genes12121926. [PMID: 34946874 PMCID: PMC8701226 DOI: 10.3390/genes12121926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/28/2021] [Accepted: 11/28/2021] [Indexed: 11/16/2022] Open
Abstract
A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals from the three species, and an additional eight and six individuals of P. argentata and P. pawak were employed in this study. Two genetically divergent lineages each of P. argentata and P. anea (lineages L1 and L2) were respectively detected from the analyses based on mitochondrial cytochrome b gene data. Historical biogeography analysis with a multi-gene dataset revealed that Pennahia species most likely originated in the South China Sea and expanded into the eastern Indian Ocean, East China Sea, and northwestern Pacific Ocean through three separate range expansions. The main diversifications of Pennahia species occurred during Miocene and Pliocene periods, and the occurrences of lineage divergences within P. anea and P. argentata were during the Pleistocene, likely as a consequence of cyclical glaciations. The population expansions that occurred after the sea level rise might be the reason for the population homogeneity observed in P. macrocephalus and most P. anea L2 South China Sea populations. The structure observed between the two populations of P. ovata, and the restricted distributions of P. anea lineage L1 and P. ovata in the eastern Indian Ocean, might have been hampered by the northward flowing ocean current at the Malacca Strait and by the distribution of coral reefs or rocky bottoms. While our results support S. Ekman’s center-of-origin hypothesis taking place in the South China Sea, the Malacca Strait serving as the center of overlap is a supplementary postulation for explaining the present-day high diversity of pennah croakers centered in these waters.
Collapse
Affiliation(s)
- Hong-Chiun Lim
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan;
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Sungai Petan 08100, Kedah, Malaysia
| | - Ahasan Habib
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia;
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Sonapur 3814, Bangladesh
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan;
- Correspondence:
| |
Collapse
|
4
|
Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters. Sci Rep 2021; 11:14874. [PMID: 34290296 PMCID: PMC8295251 DOI: 10.1038/s41598-021-94257-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
The demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.
Collapse
|
5
|
Delrieu-Trottin E, Hubert N, Giles EC, Chifflet-Belle P, Suwalski A, Neglia V, Rapu-Edmunds C, Mona S, Saenz-Agudelo P. Coping with Pleistocene climatic fluctuations: Demographic responses in remote endemic reef fishes. Mol Ecol 2020; 29:2218-2233. [PMID: 32428327 DOI: 10.1111/mec.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that species endemic to Rapa Nui share a common demographic history, as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level lowstands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
Collapse
Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France
| | - Emily C Giles
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Arnaud Suwalski
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Valentina Neglia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| |
Collapse
|
6
|
Liedke AM, Pinheiro HT, Floeter SR, Bernardi G. Phylogeography of the banded butterflyfish, Chaetodon striatus, indicates high connectivity between biogeographic provinces and ecosystems in the western Atlantic. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2019-0054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
ABSTRACT Among the four butterflyfishes of the genus Chaetodon present in the western Atlantic, the banded butterflyfish Chaetodon striatus has the largest distribution range, spanning 44 degrees of latitude (from Massachusetts, USA to Santa Catarina, Brazil). Although the ecology of the banded butterflyfish has been well studied over its entire range, nothing is known about its phylogeography and how biogeographic barriers structure its populations. To assess the level of genetic connectivity among populations from distinct biogeographic provinces and environmental conditions, we collected samples from seven localities: Puerto Rico, in the Caribbean, and Tamandaré, Salvador, Abrolhos, Trindade Island, Arraial do Cabo and Florianópolis, in Brazil. One nuclear (rag 2) and two mitochondrial (control region and cyt b) molecular markers were sequenced. Our findings are consistent with a recent population expansion, around 30-120 thousand years ago, which was found for all populations. Haplotype network analyses point to the Caribbean as a refugium before the population expansion. Results show no geographic pattern of genetic diversity. Indeed, a lack of population structure was found and no isolation was observed across oceanographic barriers, as well as between coral and rocky reef ecosystems. Furthermore, no directionality in the migration pattern was found among populations. Since ecological and environmental characteristics are very diverse across such a vast geographic range, the lack of genetic differentiation suggests that C. striatus evolved ecological plasticity rather than local adaptation in the western Atlantic.
Collapse
Affiliation(s)
- Ana M.R. Liedke
- Universidade Federal do Paraná, Brazil; Universidade Federal de Santa Catarina, Brazil
| | - Hudson T. Pinheiro
- University of California Santa Cruz, USA; California Academy of Sciences, USA
| | | | | |
Collapse
|
7
|
Otwoma LM, Reuter H. Do differences in mating behaviour lead to differences in connectivity patterns of reef fishes? Insights from two sympatric surgeonfish species in the Indian Ocean. MARINE ENVIRONMENTAL RESEARCH 2019; 151:104760. [PMID: 31358313 DOI: 10.1016/j.marenvres.2019.104760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Disentangling the contribution of biotic and abiotic factors in the structuring of the genetic diversity of reef species is critical to illuminate the diversification of evolutionary lineages in marine environment. Howevr, previous studies have mainly focused on determining the influence of pelagic larval duration on the connectivity and demographic history of reef fishes, whereas few studies have examined the effects of other biotic factors, such as mating behaviour and habitat preference. Here, we use mitochondrial DNA (ATPase 6/8) and ten microsatellite loci to compare the population genetic structure and demographic history of the spawning aggregating Acanthurus triostegus with the monogamous spawning Acanthurus leucosternon. Pairwise comparisons and discriminant analysis of principal components showed that the genetic structuring patterns of the two species are not consistent with the influence of mating behaviour, suggesting the possible role of other biotic and abiotic factors. However, demographic history estimates revealed that these species may have responded differently to sea level fluctuations during the glacial maxima.
Collapse
Affiliation(s)
- Levy Michael Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany; Faculty Biology and Chemistry, University of Bremen, Germany; Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya.
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany; Faculty Biology and Chemistry, University of Bremen, Germany
| |
Collapse
|
8
|
Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
Collapse
Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| |
Collapse
|
9
|
Putra ING, Syamsuni YF, Subhan B, Pharmawati M, Madduppa H. Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA. PeerJ 2018; 6:e4315. [PMID: 29576933 PMCID: PMC5855881 DOI: 10.7717/peerj.4315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/11/2018] [Indexed: 11/20/2022] Open
Abstract
The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.
Collapse
Affiliation(s)
- I Nyoman Giri Putra
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia.,Department of Marine Science, Faculty of Marine Science and Fisheries, Udayana University, Bukit Jimbaran, Bali, Indonesia
| | | | - Beginer Subhan
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia
| | - Made Pharmawati
- Biology Department, Faculty of Mathematics and Natural Sciences, Udayana University, Bukit Jimbaran, Bali, Indonesia
| | - Hawis Madduppa
- Department of Marine Science and Technology, Faculty Fisheries and Marine Sciences, Bogor Agricultural University (IPB), Bogor, Indonesia.,Center for Coastal and Marine Resources Studies, Bogor Agricultural University (IPB), Bogor, Indonesia
| |
Collapse
|
10
|
Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian Ocean. PLoS One 2018. [PMID: 29522547 PMCID: PMC5844546 DOI: 10.1371/journal.pone.0193825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci. Analysis included estimation of genetic diversity and population differentiation. A haplotype network was inferred using mtDNA. Nuclear markers were used in Bayesian clustering and a principal component analysis. Both markers confirmed strong genetic differentiation between WIO and Eastern Indian Ocean (EIO) populations, and a shallower population structure among Malagasy and East African mainland populations. Limited gene flow across the Mozambique Channel may be explained by its complex oceanography, which could cause local retention of larvae, limiting dispersal between Madagascar and the East African coast. Two other potential current-mediated barriers to larval dispersal suggested in the WIO, the split of the SEC at approximately 10° S and the convergence of the Somali Current with the East African Coast Current at approximately 3° S, were not found to form a barrier to gene flow in this species.
Collapse
|
11
|
Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii). Sci Rep 2018; 8:1498. [PMID: 29367590 PMCID: PMC5784092 DOI: 10.1038/s41598-018-19430-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022] Open
Abstract
The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservation.
Collapse
|
12
|
Abstract
Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
Collapse
|
13
|
Ni G, Kern E, Dong YW, Li Q, Park JK. More than meets the eye: The barrier effect of the Yangtze River outflow. Mol Ecol 2017; 26:4591-4602. [DOI: 10.1111/mec.14235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Gang Ni
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| | - Elizabeth Kern
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen Fujian Province China
- Marine Biodiversity and Global Change Laboratory; College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian Province China
| | - Qi Li
- The Key Laboratory of Mariculture; Ministry of Education; Ocean University of China; Qingdao China
| | - Joong-Ki Park
- Division of EcoScience; Ewha Womans University; Seodaemun-gu Seoul Korea
| |
Collapse
|
14
|
Bertrand JAM, Borsa P, Chen WJ. Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Mol Ecol 2017; 26:2527-2542. [PMID: 28160340 DOI: 10.1111/mec.14044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 01/02/2023]
Abstract
On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species.
Collapse
Affiliation(s)
- Joris A M Bertrand
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement, UMR 250 'Ecologie marine tropicale des océans Pacifique et Indien', 101 promenade Roger-Laroque Anse Vata, BP A5, 98848 Nouméa cedex, New Caledonia
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| |
Collapse
|
15
|
Montecinos AE, Couceiro L, Peters AF, Desrut A, Valero M, Guillemin ML. Species delimitation and phylogeographic analyses in the Ectocarpus subgroup siliculosi (Ectocarpales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2017; 53:17-31. [PMID: 27454456 DOI: 10.1111/jpy.12452] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
The genus Ectocarpus (Ectocarpales, Phaeophyceae) contains filamentous algae widely distributed in marine and estuarine habitats of temperate regions in both hemispheres. While E. siliculosus has become a model organism for genomics and genetics of the brown macroalgae, accurate species delineation, distribution patterns and diversity for the genus Ectocarpus remain problematic. In this study, we used three independent species delimitation approaches to generate a robust species hypothesis for 729 Ectocarpus specimens collected mainly along the European and Chilean coasts. These approaches comprised phylogenetic reconstructions and two bioinformatics tools developed to objectively define species boundaries (General Mixed Yule Coalescence Method and Automatic Barcode Gap Discovery). Our analyses were based on DNA sequences of two loci: the mitochondrial cytochrome oxidase subunit 1 and the nuclear internal transcribed spacer 1 of the ribosomal DNA. Our analyses showed the presence of at least 15 cryptic species and suggest the existence of incomplete lineage sorting or introgression between five of them. These results suggested the possible existence of different levels of reproductive barriers within this species complex. We also detected differences among species in their phylogeographic patterns, range and depth distributions, which may suggest different biogeographic histories (e.g., endemic species or recent introductions).
Collapse
Affiliation(s)
- Alejandro E Montecinos
- CNRS, Sorbonne Universités, UPMC University Paris VI, PUC, UACH, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Teissier, 29680, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Lucia Couceiro
- CNRS, Sorbonne Universités, UPMC University Paris VI, PUC, UACH, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Teissier, 29680, Roscoff, France
| | - Akira F Peters
- Bezhin Rosko, 40 rue des pêcheurs, 29250, Santec, France
| | - Antoine Desrut
- CNRS, Sorbonne Universités, UPMC University Paris VI, PUC, UACH, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Teissier, 29680, Roscoff, France
| | - Myriam Valero
- CNRS, Sorbonne Universités, UPMC University Paris VI, PUC, UACH, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Teissier, 29680, Roscoff, France
| | - Marie-Laure Guillemin
- CNRS, Sorbonne Universités, UPMC University Paris VI, PUC, UACH, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Teissier, 29680, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| |
Collapse
|
16
|
Negi RK, Joshi BD, Johnson JA, De R, Goyal SP. Phylogeography of freshwater fish Puntius sophore in India. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:256-265. [PMID: 28117612 DOI: 10.1080/24701394.2016.1275598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts of its distribution range. Total 20 haplotypes with the intra-species sequence divergence ranging from 0.004 to 0.025 were observed and they were split into two major clades (North and Northeastern to Central India). Two distant geographic (North and Northeastern to Central India) regions shared haplotype suggesting ancient river connectivity or introduction of species from Northeast and Central India. Overall nucleotide and haplotype diversities were 0.00971 and 0.915. The Tajima's D and Fu's Fs values were found negative but non-significant thus rejecting the population expansion model followed by the multimodal mode of mismatch distribution. Bayesian skyline plots from both the clade showed steady population history over time; and start of decline in recent years in the clade B (∼1000-1500 years). The present finding is in support to the 'Satpura hypothesis' proposed to explain species movement patterns from Southeast Asian countries to Indian subcontinent, seconded by P. sophore showing high genetic diversity within Northern India clade (high genetic splits) because of presence of high river network in comparison to other parts of the country.
Collapse
Affiliation(s)
- R K Negi
- a Department of Zoology , University of Delhi , Delhi , India
| | - Bheem Dutt Joshi
- b Department of Zoology and Environmental Sciences , Gurukula Kangri University , Haridwar , India.,c Wildlife Institute of India , Dehradun , India
| | - J A Johnson
- c Wildlife Institute of India , Dehradun , India
| | - Rahul De
- c Wildlife Institute of India , Dehradun , India
| | | |
Collapse
|
17
|
Delrieu-Trottin E, Mona S, Maynard J, Neglia V, Veuille M, Planes S. Population expansions dominate demographic histories of endemic and widespread Pacific reef fishes. Sci Rep 2017; 7:40519. [PMID: 28091580 PMCID: PMC5238389 DOI: 10.1038/srep40519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Despite the unique nature of endemic species, their origin and population history remain poorly studied. We investigated the population history of 28 coral reef fish species, close related, from the Gambier and Marquesas Islands, from five families, with range size varying from widespread to small-range endemic. We analyzed both mitochondrial and nuclear sequence data using neutrality test and Bayesian analysis (EBSP and ABC). We found evidence for demographic expansions for most species (24 of 28), irrespective of range size, reproduction strategy or archipelago. The timing of the expansions varied greatly among species, from 8,000 to 2,000,000 years ago. The typical hypothesis for reef fish that links population expansions to the Last Glacial Maximum fit for 14 of the 24 demographic expansions. We propose two evolutionary processes that could lead to expansions older than the LGM: (a) we are retrieving the signature of an old colonization process for widespread, large-range endemic and paleoendemic species or (b) speciation; the expansion reflects the birth of the species for neoendemic species. We show for the first time that the demographic histories of endemic and widespread reef fish are not distinctly different and suggest that a number of processes drive endemism.
Collapse
Affiliation(s)
- Erwan Delrieu-Trottin
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Stefano Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Jeffrey Maynard
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- SymbioSeas and Marine Applied Research Center, Wilmington NC 28411, United States of America
| | - Valentina Neglia
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Michel Veuille
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, Paris Sorbonne Universités, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Serge Planes
- Laboratoire d’Excellence «CORAIL», EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, F-66360 Perpignan, France
| |
Collapse
|
18
|
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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/12/2016] [Accepted: 04/29/2016] [Indexed: 11/27/2022]
|
19
|
Tornabene L, Valdez S, Erdmann MV, Pezold FL. Multi-locus sequence data reveal a new species of coral reef goby (Teleostei: Gobiidae: Eviota), and evidence of Pliocene vicariance across the Coral Triangle. JOURNAL OF FISH BIOLOGY 2016; 88:1811-1834. [PMID: 27021219 DOI: 10.1111/jfb.12947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
Here, multi-locus sequence data are coupled with observations of live colouration to recognize a new species, Eviota punyit from the Coral Triangle, Indian Ocean and Red Sea. Relaxed molecular clock divergence time estimation indicates a Pliocene origin for the new species, and the current distribution of the new species and its sister species Eviota sebreei supports a scenario of vicariance across the Indo-Pacific Barrier, followed by subsequent range expansion and overlap in the Coral Triangle. These results are consistent with the 'centre of overlap' hypothesis, which states that the increased diversity in the Coral Triangle is due in part to the overlapping ranges of Indian Ocean and Pacific Ocean faunas. These findings are discussed in the context of other geminate pairs of coral reef fishes separated by the Indo-Pacific Barrier.
Collapse
Affiliation(s)
- L Tornabene
- College of Science and Engineering, Texas A&M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, U.S.A
| | - S Valdez
- College of Science and Engineering, Texas A&M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, U.S.A
| | - M V Erdmann
- Conservation International Indonesia Marine Program, Jl. Dr. Muwardi No. 17, Renon, Denpasar, 80235 Bali, Indonesia
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr, Golden Gate Park, San Francisco, CA 94118-4599, U.S.A
| | - F L Pezold
- College of Science and Engineering, Texas A&M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, U.S.A
| |
Collapse
|
20
|
Comparative phylogeography of the western Indian Ocean reef fauna. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2016. [DOI: 10.1016/j.actao.2015.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
21
|
Bowen BW. The Three Domains of Conservation Genetics: Case Histories from Hawaiian Waters. J Hered 2016; 107:309-17. [PMID: 27001936 DOI: 10.1093/jhered/esw018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/17/2016] [Indexed: 11/14/2022] Open
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.
Collapse
Affiliation(s)
- Brian W Bowen
- From the Hawai'i Institute of Marine Biology, PO Box 1346, Kaneohe, HI 96744.
| |
Collapse
|
22
|
Andrews KR, Norton EL, Fernandez-Silva I, Portner E, Goetze E. Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod. Mol Ecol 2015; 23:5462-79. [PMID: 25283587 DOI: 10.1111/mec.12950] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022]
Abstract
Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.
Collapse
Affiliation(s)
- Kimberly R Andrews
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA; School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | | | | | | | | |
Collapse
|
23
|
Spaet JLY, Jabado RW, Henderson AC, Moore ABM, Berumen ML. Population genetics of four heavily exploited shark species around the Arabian Peninsula. Ecol Evol 2015; 5:2317-32. [PMID: 26120422 PMCID: PMC4475365 DOI: 10.1002/ece3.1515] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 01/31/2023] Open
Abstract
The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.
Collapse
Affiliation(s)
- Julia L Y Spaet
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology23955-6900, Thuwal, Saudi Arabia
| | - Rima W Jabado
- Gulf Elasmo ProjectP.O. Box 29588, Dubai, United Arab Emirates
| | - Aaron C Henderson
- Department of Marine Science & Fisheries, College of Agricultural & Marine Sciences, Sultan Qaboos UniversityMuscat, Oman
| | - Alec B M Moore
- RSK Environment Ltd, Spring LodgeHelsby, Cheshire, WA6 0AR, UK
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology23955-6900, Thuwal, Saudi Arabia
| |
Collapse
|
24
|
Dohna TA, Timm J, Hamid L, Kochzius M. Limited connectivity and a phylogeographic break characterize populations of the pink anemonefish, Amphiprion perideraion, in the Indo-Malay Archipelago: inferences from a mitochondrial and microsatellite loci. Ecol Evol 2015; 5:1717-33. [PMID: 25937914 PMCID: PMC4409419 DOI: 10.1002/ece3.1455] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 11/25/2022] Open
Abstract
To enhance the understanding of larval dispersal in marine organisms, species with a sedentary adult stage and a pelagic larval phase of known duration constitute ideal candidates, because inferences can be made about the role of larval dispersal in population connectivity. Members of the immensely diverse marine fauna of the Indo-Malay Archipelago are of particular importance in this respect, as biodiversity conservation is becoming a large concern in this region. In this study, the genetic population structure of the pink anemonefish, Amphiprion perideraion, is analyzed by applying 10 microsatellite loci as well as sequences of the mitochondrial control region to also allow for a direct comparison of marker-derived results. Both marker systems detected a strong overall genetic structure (ΦST = 0.096, P < 0.0001; mean D est = 0.17; F ST = 0.015, P < 0.0001) and best supported regional groupings (ΦCT = 0.199 P < 0.0001; F CT = 0.018, P < 0.001) that suggested a differentiation of the Java Sea population from the rest of the archipelago. Differentiation of a New Guinea group was confirmed by both markers, but disagreed over the affinity of populations from west New Guinea. Mitochondrial data suggest higher connectivity among populations with fewer signals of regional substructure than microsatellite data. Considering the homogenizing effect of only a few migrants per generation on genetic differentiation between populations, marker-specific results have important implications for conservation efforts concerning this and similar species.
Collapse
Affiliation(s)
- Tina A Dohna
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Janne Timm
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Lemia Hamid
- Biotechnology and Molecular Genetics, UFT, University of BremenBremen, 28359, Germany
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit BrusselBrussel, Belgium
| |
Collapse
|
25
|
Delrieu-Trottin E, Maynard J, Planes S. Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity. Proc Biol Sci 2014; 281:20141068. [PMID: 25355471 PMCID: PMC4240976 DOI: 10.1098/rspb.2014.1068] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/25/2014] [Indexed: 11/12/2022] Open
Abstract
Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.
Collapse
Affiliation(s)
- Erwan Delrieu-Trottin
- CRIOBE-USR 3278, CNRS-EPHE-UPVD, 58 Avenue Paul Alduy, 66860 Perpignan cedex, France Laboratoire d'Excellence 'CORAIL', 58 Avenue Paul Alduy, 66860 Perpignan cedex, France
| | - Jeffrey Maynard
- CRIOBE-USR 3278, CNRS-EPHE-UPVD, 58 Avenue Paul Alduy, 66860 Perpignan cedex, France Laboratoire d'Excellence 'CORAIL', 58 Avenue Paul Alduy, 66860 Perpignan cedex, France Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Serge Planes
- CRIOBE-USR 3278, CNRS-EPHE-UPVD, 58 Avenue Paul Alduy, 66860 Perpignan cedex, France Laboratoire d'Excellence 'CORAIL', 58 Avenue Paul Alduy, 66860 Perpignan cedex, France
| |
Collapse
|
26
|
McLean CA, Stuart-Fox D, Moussalli A. Phylogeographic structure, demographic history and morph composition in a colour polymorphic lizard. J Evol Biol 2014; 27:2123-37. [DOI: 10.1111/jeb.12464] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 07/14/2014] [Accepted: 07/21/2014] [Indexed: 12/22/2022]
Affiliation(s)
- C. A. McLean
- Department of Zoology; The University of Melbourne; Parkville Vic. Australia
- Sciences Department; Museum Victoria; Carlton Gardens Vic. Australia
| | - D. Stuart-Fox
- Department of Zoology; The University of Melbourne; Parkville Vic. Australia
| | - A. Moussalli
- Sciences Department; Museum Victoria; Carlton Gardens Vic. Australia
| |
Collapse
|
27
|
Thinking outside the barrier: neutral and adaptive divergence in Indo-Pacific coral reef faunas. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9724-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Ravinet M, Harrod C, Eizaguirre C, Prodöhl PA. Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization? Ecol Evol 2014; 4:2488-504. [PMID: 25360281 PMCID: PMC4203293 DOI: 10.1002/ece3.853] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/06/2013] [Indexed: 11/24/2022] Open
Abstract
Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.
Collapse
Affiliation(s)
- Mark Ravinet
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K ; Lovén Centre-Tjärnö, Department of Biology and Environmental Sciences, University of Gothenburg Gothenburg, Sweden
| | - Chris Harrod
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K ; Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta Chile
| | - Christophe Eizaguirre
- GEOMAR
- Helmholtz Centre for Ocean Research Duesternbrooker weg 20, 24105, Kiel, Germany ; Max Planck Institute for Evolutionary Biology August Thienemannstr. 2, 24306, Ploen, Germany
| | - Paulo A Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K
| |
Collapse
|
29
|
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] [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.
Collapse
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
| |
Collapse
|
30
|
Poortvliet M, Longo GC, Selkoe K, Barber PH, White C, Caselle JE, Perez-Matus A, Gaines SD, Bernardi G. Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality. Ecol Evol 2013; 3:4558-71. [PMID: 24340195 PMCID: PMC3856754 DOI: 10.1002/ece3.840] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 11/06/2022] Open
Abstract
In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well as the population genetic characteristics within S. pulcher. While S. pulcher and S. darwini are found in the temperate eastern Pacific regions of the northern and southern hemispheres, respectively, their genetic divergence was very small (estimated to have occurred between 200 and 600 kya). Within S. pulcher, genetic structuring was generally weak, especially along mainland California, but showed weak differentiation between Sea of Cortez and California, and between mainland California and Channel Islands. We highlight the congruence of weak genetic differentiation both within and between species and discuss possible causes for maintenance of high gene flow. In particular, we argue that deep and cooler water refugia are used as stepping stones to connect distant populations, resulting in low levels of genetic differentiation.
Collapse
Affiliation(s)
- Marloes Poortvliet
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta Cruz, California, 95076
- Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of GroningenNijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Gary C Longo
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta Cruz, California, 95076
| | - Kimberly Selkoe
- Marine Science Institute, University of California Santa BarbaraSanta Barbara, California, 93106
- Hawai'i Institute of Marine Biology, University of Hawai'iKane'ohe, Hawaii, 96744
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology and the Institute of the Environment and Sustainability, University of California Los Angeles621 Charles E. Young Dr. South, Los Angeles, California, 90095
| | - Crow White
- Marine Science Institute, University of California Santa BarbaraSanta Barbara, California, 93106
- Biological Sciences Department, California Polytechnic State UniversitySan Luis Obispo, California, 93407
| | - Jennifer E Caselle
- Marine Science Institute, University of California Santa BarbaraSanta Barbara, California, 93106
| | - Alejandro Perez-Matus
- Subtidal Ecology Laboratory & Center for Marine Conservation, Pontificia Universidad Católica de Chile, Estación Costera de Investigaciones MarinasCasilla 114-D, Santiago, Las Cruces, Chile
| | - Steven D Gaines
- Bren School of Environmental Science and Management, University of CaliforniaSanta Barbara, California, 93106
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta Cruz, California, 95076
| |
Collapse
|
31
|
High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis. PLoS One 2013; 8:e77011. [PMID: 24167556 PMCID: PMC3805563 DOI: 10.1371/journal.pone.0077011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/28/2013] [Indexed: 11/25/2022] Open
Abstract
Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide.
Collapse
|
32
|
Gaither MR, Bowen BW, Toonen RJ. Population structure in the native range predicts the spread of introduced marine species. Proc Biol Sci 2013; 280:20130409. [PMID: 23595272 PMCID: PMC3652461 DOI: 10.1098/rspb.2013.0409] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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.
Collapse
Affiliation(s)
- Michelle R Gaither
- Section of Ichthyology, California Academy of Sciences, , 55 Music Concourse Drive, San Francisco, CA 94118, USA.
| | | | | |
Collapse
|
33
|
Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0456-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
34
|
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] [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.
Collapse
Affiliation(s)
- Michelle R Gaither
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, Hawai'i, USA.
| | | | | | | | | | | |
Collapse
|