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Lukhtanov VA, Dantchenko AV. Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran. INSECTS 2024; 15:545. [PMID: 39057277 PMCID: PMC11277131 DOI: 10.3390/insects15070545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Alexander V. Dantchenko
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
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2
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Kulagin DN, Lunina AA, Simakova UV, Vedenin AA, Vereshchaka AL. Revision of the 'Acanthephyra purpurea' species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic. Mol Phylogenet Evol 2024; 195:108070. [PMID: 38574781 DOI: 10.1016/j.ympev.2024.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
We inventoried all nine species of the 'Acanthephyra purpurea' complex, one of the most abundant and cosmopolitan group of mesopelagic shrimps. We used 119 specimens at hand and genetic data for 124 specimens from GenBank and BOLD. Phylogenetic analysis of four genes (COI, 16S, NaK, and enolase) showed that the 'Acanthephyra purpurea' complex is polyphyletic and encompasses two species groups, 'A. purpurea' (mostly Atlantic) and 'A. smithi' (Indo-West Pacific). The 'A. purpurea' species group consists of two major molecular clades A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa. Molecular data suggest that hitherto accepted species A. acanthitelsonis, A. pelagica, and A. sica should be considered as synonyms. The Atlantic is inhabited by at least two cryptic genetic lineages of A. pelagica and A. quadrispinosa. Morphological analyses of qualitative and quantitative (900 measurements) characters resulted in a tabular key to species and in a finding of four evolutionary traits. Atlantic species showed various scenarios of diversification visible on mitochondrial gene level, nuclear gene level, and morphological level. We recorded and discussed similar phylogeographic trends in diversification and in distribution of genetic lineages within two different clades: A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa.
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Affiliation(s)
- Dmitry N Kulagin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Anastasiia A Lunina
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | - Ulyana V Simakova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia
| | | | - Alexander L Vereshchaka
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36 Nakhimovsky Prosp., Moscow 117997, Russia.
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3
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Deng Z, Yao Y, Blair D, Hu W, Yin M. Ceriodaphnia (Cladocera: Daphniidae) in China: Lineage diversity, phylogeography and possible interspecific hybridization. Mol Phylogenet Evol 2022; 175:107586. [PMID: 35810974 DOI: 10.1016/j.ympev.2022.107586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022]
Abstract
The distribution and species/lineage diversity of freshwater invertebrate zooplankton remains understudied in China. Here, we explored the species/lineage diversity and phylogeography of Ceriodaphnia species across China. The taxonomy of this genus is under-explored. Seven morphospecies of Ceriodaphnia (C. cornuta, C. laticaudata, C. megops, C. pulchella, C. quadrangula, C. rotunda and C. spinata) were identified across 45 of 422 water bodies examined. Rather little morphological variation was observed within any single morphospecies regardless of country of origin. Nevertheless, we recognized that some or all of these morphospecies might represent species complexes. To investigate this, phylogenetic relationships within and among these morphospecies were investigated based on mitochondrial (partial cytochrome c oxidase subunit I gene) and nuclear (partial 28S rRNA gene) markers. The mitochondrial marker placed these populations in nine lineages corresponding to the morphospecies: C. laticaudata and C. pulchella were each represented by two lineages, suggesting that both are species complexes. The remaining five morphospecies were each represented by a single mtDNA lineage. Three of the nine mitochondrial lineages (belonging to C. pulchella, C. rotunda and C. megops) are newly reported and exhibited a restricted distribution within China. The nuclear-DNA phylogeny also recognized seven Ceriodaphnia taxa within China. We detected occasional mito-nuclear discordances in Ceriodaphnia taxa across China, suggesting interspecific introgression and hybridization. Our study contributes to an understanding of the species/lineage diversity of Ceriodaphnia, a genus with understudied taxonomy.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Yiyang Yao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China; Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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4
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Deng Z, Yang W, Blair D, Hu W, Yin M. Diversity of Brachionus plicatilis species complex (Rotifera) in inland saline waters from China: presence of a new mitochondrial clade on the Tibetan Plateau. Mol Phylogenet Evol 2022; 171:107457. [DOI: 10.1016/j.ympev.2022.107457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/19/2022] [Accepted: 03/15/2022] [Indexed: 12/12/2022]
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5
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Choo LQ, Bal TMP, Goetze E, Peijnenburg KTCA. Oceanic dispersal barriers in a holoplanktonic gastropod. J Evol Biol 2021; 34:224-240. [PMID: 33150701 PMCID: PMC7894488 DOI: 10.1111/jeb.13735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/02/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large-scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N-36°S) for the pteropod Limacina bulimoides. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI ΦST = 0.230, 28S ΦST = 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15-18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise ΦST comparisons was identified in the equatorial upwelling region (between 15°N and 4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin-scale transect that was sampled 2 years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome-wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.
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Affiliation(s)
- Le Qin Choo
- Plankton Diversity and EvolutionNaturalis Biodiversity CenterLeidenThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Thijs M. P. Bal
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Erica Goetze
- Department of OceanographyUniversity of Hawaiʻi at MānoaHonoluluUSA
| | - Katja T. C. A. Peijnenburg
- Plankton Diversity and EvolutionNaturalis Biodiversity CenterLeidenThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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6
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Laakmann S, Blanco-Bercial L, Cornils A. The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190446. [PMID: 33131432 PMCID: PMC7662206 DOI: 10.1098/rstb.2019.0446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An accurate identification of species and communities is a prerequisite for analysing and recording biodiversity and community shifts. In the context of marine biodiversity conservation and management, this review outlines past, present and forward-looking perspectives on identifying and recording planktonic diversity by illustrating the transition from traditional species identification based on morphological diagnostic characters to full molecular genetic identification of marine assemblages. In this process, the article presents the methodological advancements by discussing progress and critical aspects of the crossover from traditional to novel and future molecular genetic identifications and it outlines the advantages of integrative approaches using the strengths of both morphological and molecular techniques to identify species and assemblages. We demonstrate this process of identifying and recording marine biodiversity on pelagic copepods as model taxon. Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms of biodiversity and ecosystem functioning. Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.
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Affiliation(s)
- Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, 26129 Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | | | - Astrid Cornils
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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7
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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] [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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8
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González-Castellano I, Pons J, González-Ortegón E, Martínez-Lage A. Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans. PLoS One 2020; 15:e0237037. [PMID: 32810189 PMCID: PMC7444591 DOI: 10.1371/journal.pone.0237037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.
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Affiliation(s)
- Inés González-Castellano
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
| | - Joan Pons
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC) and Universitat de les Illes Balears, Esporles, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN), Consejo Superior de Investigaciones Científicas (CSIC), Puerto Real, Spain
| | - Andrés Martínez-Lage
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
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9
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González-Castellano I, González-López J, González-Tizón AM, Martínez-Lage A. Genetic diversity and population structure of the rockpool shrimp Palaemon elegans based on microsatellites: evidence for a cryptic species and differentiation across the Atlantic-Mediterranean transition. Sci Rep 2020; 10:10784. [PMID: 32612210 PMCID: PMC7329806 DOI: 10.1038/s41598-020-67824-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/15/2020] [Indexed: 11/09/2022] Open
Abstract
The rockpool shrimp Palaemon elegans is an ecologically important crustacean species within the European coastline fauna. In the present study, genetic diversity and population structure and connectivity were assessed by examining 21 polymorphic microsatellite loci at 13 sampling sites located along the natural distribution range. All localities showed similar levels of genetic variability. Significant deficits of heterozygosity were recorded, most likely due to the presence of null alleles. Genetic structure analyses revealed two clearly genetically distinct groups within P. elegans but without following any geographical or oceanographic basis. Thus, our results provided nuclear evidence for the existence of a Mediterranean cryptic species within P. elegans, highlighting the need to revise its taxonomic status. Regarding P. elegans sensu stricto, population structuring was reported across the Atlantic-Mediterranean transition area, where the Almería-Orán Front restricts the gene flow between the Atlantic and the Mediterranean population. Moreover, while population connectivity was suggested between all Mediterranean localities, some substructure was found within the Atlantic group. Canary Islands exhibited a weak but significant genetic differentiation from all Atlantic mainland localities, consistent with the isolation-by-distance pattern detected throughout the Atlantic population. Overall, all these findings provided new insights into the population biology of P. elegans complex.
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Affiliation(s)
- Inés González-Castellano
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071, A Coruña, Spain.
| | - Jorge González-López
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071, A Coruña, Spain
| | - Ana M González-Tizón
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071, A Coruña, Spain
| | - Andrés Martínez-Lage
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071, A Coruña, Spain.
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10
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Hirai J, Tachibana A, Tsuda A. Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific. PLoS One 2020; 15:e0233189. [PMID: 32407365 PMCID: PMC7224477 DOI: 10.1371/journal.pone.0233189] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
A clear insight into the large-scale community structure of planktonic copepods is critical to understanding the mechanisms controlling diversity and biogeography of marine taxa in terms of their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed with results from previous morphology-based studies. However, a large-scale metabarcoding approach could detect community changes even under stable environmental conditions, including changes in the north/south subtropical gyres and east/west areas within each subtropical gyre. There were strong effects of the epipelagic environment on mesopelagic communities, and community subdivisions were observed in the environmentally stable mesopelagic layer. In each sampling station, higher operational taxonomic unit (OTU) numbers and lower phylogenetic diversity were observed in the mesopelagic layer than in the epipelagic layer, indicating a recent rapid increase in species numbers in the mesopelagic layer. The phylogenetic analysis utilizing representative sequences of OTUs revealed trends of recent emergence of cold-water OTUs, which are mainly distributed at high latitudes with low water temperatures. Conversely, the high diversity of copepods at low latitudes was suggested to have been formed through long evolution under high water temperature conditions. The metabarcoding results suggest that evolutionary processes have strong impacts on current patterns of copepod diversity, and support the “out of the tropics” theory explaining latitudinal diversity gradients of copepods. Diversity patterns in both epipelagic and mesopelagic copepods was highly correlated to sea surface temperature; thus, predicted global warming may have a significant impact on copepod diversity in both layers.
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Affiliation(s)
- Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- * E-mail:
| | - Aiko Tachibana
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Atsushi Tsuda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
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11
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González CE, Goetze E, Escribano R, Ulloa O, Victoriano P. Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific. Sci Rep 2020; 10:1115. [PMID: 31980660 PMCID: PMC6981114 DOI: 10.1038/s41598-019-56935-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022] Open
Abstract
Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.
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Affiliation(s)
- Carolina E González
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, PO Box 160, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile. .,Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile.
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, Hawaii, USA
| | - Rubén Escribano
- Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
| | - Osvaldo Ulloa
- Instituto Milenio de Oceanografía (IMO) and Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
| | - Pedro Victoriano
- Department of Zoology, Faculty of Natural and Oceanographic Sciences, University of Concepción, PO Box 160 C, Barrio Universitario s/n Concepción, Concepción, 4030000, Chile
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12
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Golestani H, Crocetta F, Padula V, Camacho-García Y, Langeneck J, Poursanidis D, Pola M, yokeş MB, Cervera JL, Jung DW, Gosliner TM, Araya JF, Hooker Y, schrödl M, valdés Á. The little Aplysia coming of age: from one species to a complex of species complexes in Aplysia parvula (Mollusca: Gastropoda: Heterobranchia). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The widespread sea hare species Aplysia parvula includes four genetically distinct lineages, containing a total of ten different species. While the four lineages can be differentiated by their external characteristics, species in each clade are often morphologically indistinguishable. A review of literature and type material revealed that several available names exist for species recognized herein: Aplysia parvula is retained for a species from the north-eastern Atlantic; A. atromarginata, A. elongata, A. nigrocincta and A. japonica are resurrected for species from the western Pacific Ocean, the Hawaiian Islands, the Indian and western Pacific Oceans, and Japan and Korea, respectively. Two new species names are introduced for animals from the eastern Pacific, and the Atlantic and Indian Oceans. Mitochondrial sequences from Mediterranean and eastern Atlantic specimens identified as A. parvula, resulted to be A. punctata. However, two specimens were heterozygotes of histone H3 alleles of A. punctata and of a new Atlantic species described herein, suggesting they could be hybrids. These results contradict the hypothesis that the Mediterranean was colonized by A. parvula. If an invasion occurred, it was a limited introgression of nDNA from an Atlantic species into native A. punctata populations.
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Affiliation(s)
- Haleh Golestani
- Department of Biological Sciences, California State Polytechnic University Pomona, Pomona, California, USA
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Vinicius Padula
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- SNSB-Zoologische Staatssammlung München, München, Germany
| | - Yolanda Camacho-García
- Museo de Zoología, Escuela de Biología, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, Costa Rica
| | | | - Dimitris Poursanidis
- Department of Marine Science, University of the Aegean, University Hill, Lesvos, Mytiline, Greece
| | - Marta Pola
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - M Baki yokeş
- AMBRD Laboratories, Hanimefendi Sok, Istanbul, Turkey
| | - Juan Lucas Cervera
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, Puerto Real (Cádiz), Spain
| | - Dae-Wui Jung
- Department of Biological Sciences, California State Polytechnic University Pomona, Pomona, California, USA
| | - Terrence M Gosliner
- Department of Invertebrate Zoology, California Academy of Sciences, San Francisco, California, USA
| | - Juan Francisco Araya
- Centro de Investigaciones Costeras Universidad de Atacama (CIC-UDA), Universidad de Atacama, Atacama, Chile
| | - Yuri Hooker
- Laboratorio de Biología Marina, Facultad de Ciencias y Filosofía, Universidad Peruana, Cayetano Heredia, Lima, Peru
| | | | - Ángel valdés
- Department of Biological Sciences, California State Polytechnic University Pomona, Pomona, California, USA
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13
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Kerkhove TRH, Boyen J, De Backer A, Mol JH, Volckaert FAM, Leliaert F, De Troch M. Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.
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Affiliation(s)
- Thomas R H Kerkhove
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Jens Boyen
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Annelies De Backer
- Institute for Agricultural and Fisheries Research (ILVO), Animal Sciences, Bio-Environmental Research Group, Ankerstraat, Ostend, Belgium
| | - Jan H Mol
- Anton de Kom University of Suriname, Faculty of Mathematics and Natural Sciences, Department of Biology, Leysweg, Postbus, Paramaribo, Suriname
| | - Filip A M Volckaert
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Ch. Deberiotstraat, Leuven, Belgium
| | - Frederik Leliaert
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
- Meise Botanic Garden, Nieuwelaan, Meise, Belgium
| | - Marleen De Troch
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
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14
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Ni Y, Ma X, Hu W, Blair D, Yin M. New lineages and old species: Lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China. Mol Phylogenet Evol 2019; 134:87-98. [PMID: 30753887 DOI: 10.1016/j.ympev.2019.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 10/27/2022]
Abstract
The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context.
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Affiliation(s)
- Yijun Ni
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Xiaolin Ma
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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15
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Arrigoni R, Berumen ML, Stolarski J, Terraneo TI, Benzoni F. Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean. Cladistics 2018; 35:301-328. [DOI: 10.1111/cla.12346] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
| | - Michael L. Berumen
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
| | - Jaroslaw Stolarski
- Institute of Paleobiology Polish Academy of Sciences Twarda 51/55 Warsaw PL‐00‐818 Poland
| | - Tullia I. Terraneo
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
- College of Marine and Environmental Science James Cook University Townsville QLD 4811 Australia
| | - Francesca Benzoni
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Piazza della Scienza 2 Milano 20126 Italy
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS) Laboratoire d'excellence‐CORAIL Centre IRD de Nouméa 101 Promenade Roger Laroque, BP A5 Noumea Cedex 98848 New Caledonia
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16
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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] [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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17
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18
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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.
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19
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Chen W, Zhong Z, Dai W, Fan Q, He S. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China. BMC Evol Biol 2017; 17:216. [PMID: 28899345 PMCID: PMC5596851 DOI: 10.1186/s12862-017-1058-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively. CONCLUSIONS Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zaixuan Zhong
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei Dai
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qi Fan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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20
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Low VL, Tan TK, Prakash BK, Vinnie-Siow WY, Tay ST, Masmeatathip R, Hadi UK, Lim YAL, Chen CD, Norma-Rashid Y, Sofian-Azirun M. Contrasting evolutionary patterns between two haplogroups of Haematobia exigua (Diptera: Muscidae) from the mainland and islands of Southeast Asia. Sci Rep 2017; 7:5871. [PMID: 28724923 PMCID: PMC5517420 DOI: 10.1038/s41598-017-05921-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/05/2017] [Indexed: 11/17/2022] Open
Abstract
Uncovering the hidden diversity and evolutionary history of arthropods of medico-veterinary importance could have significant implications for vector-borne disease control and epidemiological intervention. The buffalo fly Haematobia exigua is an obligate bloodsucking ectoparasite of livestock. As an initial step towards understanding its population structures and biogeographic patterns, we characterized partial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) sequences of H. exigua from three distinct geographic regions in Southeast Asia. We detected two distinct mitochondrial haplogroups of H. exigua in our surveyed geographic regions. Haplogroup I is widespread in the Southeast Asian mainland whereas haplogroup II is generally restricted to the type population Java Island. Both haplogroups were detected co-occurring on Borneo Island. Additionally, both haplogroups have undergone contrasting evolutionary histories, with haplogroup I exhibited a high level of mitochondrial diversity indicating a population expansion during the Pleistocene era dating back to 98,000 years ago. However, haplogroup II presented a low level of mitochondrial diversity which argues against the hypothesis of recent demographic expansion.
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Affiliation(s)
- Van Lun Low
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia.
| | - Tiong Kai Tan
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Batah Kunalan Prakash
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wei Yin Vinnie-Siow
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sun Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Roungthip Masmeatathip
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Kamphaeng Saen, Thailand
| | - Upik Kesumawati Hadi
- Department of Animal Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University, Bogor, Indonesia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee Dhang Chen
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yusoff Norma-Rashid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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21
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Cheng J, Sha ZL. Cryptic diversity in the Japanese mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae): Allopatric diversification, secondary contact and hybridization. Sci Rep 2017; 7:1972. [PMID: 28512346 PMCID: PMC5434036 DOI: 10.1038/s41598-017-02059-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses. One cryptic species is restricted to cold waters with a distribution range corresponding to temperate affinities, while the other dwelled warm waters influenced by the Kuroshio Current. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the middle Pliocene (c. 3.85 Mya, 95% HPD 2.23–6.07 Mya). Allopatric speciation was maintained by limited genetic exchange due to their habitat preferences. Furthermore, the observation of recombinant nrDNA ITS sequence and intra-individual ITS polymorphism suggested recent hybridization event of the two cryptic species occurred in sympatric areas. Our study also illustrated that the Changjiang River outflow might act as an oceanic barrier to gene flow and promoted allopatric diversification in O. oratoria species complex.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhong-Li Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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22
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Cornils A, Wend-Heckmann B, Held C. Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages? Mol Phylogenet Evol 2016; 107:473-485. [PMID: 28007567 DOI: 10.1016/j.ympev.2016.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 11/19/2022]
Abstract
Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.
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Affiliation(s)
- Astrid Cornils
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Britta Wend-Heckmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Christoph Held
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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23
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Wilk RJ, Horth L. A genetically distinct hybrid zone occurs for two globally invasive mosquito fish species with striking phenotypic resemblance. Ecol Evol 2016; 6:8375-8388. [PMID: 28031790 PMCID: PMC5167044 DOI: 10.1002/ece3.2562] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/11/2016] [Accepted: 09/19/2016] [Indexed: 12/03/2022] Open
Abstract
Hybrid zones allow for the investigation of incipient speciation and related evolutionary processes of selection, gene flow, and migration. Interspecific dynamics, like competition, can impact the size, shape, and directional movement of species in hybrid zones. Hybrid zones contribute to a paradox for the biological species concept because interbreeding between species occurs while parental forms remain distinct. A long‐standing zone of intergradation or introgression exists for eastern and western mosquito fish (Gambusia holbrooki and G. affinis) around Mobile Bay, AL. The region has been studied episodically, over decades, making it perfect for addressing temporal dynamics and for providing a deeper understanding of the genetics of these periodically reclassified fishes (as species or subspecies). We used six microsatellite markers to assess the current population structure and gene flow patterns across 19 populations of mosquito fish and then compared our results with historical data. Genetic evidence demonstrates that the current hybrid zone is located in a similar geographic region as the historical one, even after three decades. Hybrid fish, however, demonstrate relatively low heterozygosity and are genetically distinct from western and eastern mosquito fish populations. Fin ray counts, sometimes used to distinguish the two species from one another, demonstrate more eastern (G. holbrooki) phenotype fish within the molecular genetic hybrid zone today. Mosquito fish are globally invasive, often found on the leading edge of flooded waters that they colonize, so the impact of hurricanes in the wake of climate change was also evaluated. An increase in the frequency and intensity of hurricanes in the hybrid region has occurred, and this point warrants further attention since hurricanes are known to move these aggressive, invasive species into novel territory. This work contributes to our classical understanding of hybrid zone temporal dynamics, refines our understanding of mosquito fish genetics in their native range, evaluates important genotype–phenotype relationships, and identifies a potential new impact of climate change.
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Affiliation(s)
- Rebecca J Wilk
- Department of Biological Sciences Old Dominion University Norfolk VA USA
| | - Lisa Horth
- Department of Biological Sciences Old Dominion University Norfolk VA USA
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Low VL, Takaoka H, Pramual P, Adler PH, Ya'cob Z, Chen CD, Yotopranoto S, Zaid A, Hadi UK, Lardizabal ML, Nasruddin-Roshidi A, Sofian-Azirun M. Three Taxa in One: Cryptic Diversity in the Black Fly Simulium nobile (Diptera: Simuliidae) in Southeast Asia. JOURNAL OF MEDICAL ENTOMOLOGY 2016; 53:972-976. [PMID: 27208009 DOI: 10.1093/jme/tjw058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
We access the molecular diversity of the black fly Simulium nobile De Mejiere, using the universal cytochrome c oxidase subunit I (COI) barcoding gene, across its distributional range in Southeast Asia. Our phylogenetic analyses recovered three well-supported mitochondrial lineages of S. nobile, suggesting the presence of cryptic species. Lineage A is composed of a population from Sabah, East Malaysia (Borneo); lineage B represents the type population from Java, Indonesia; and lineage C includes populations from the mainland of Southeast Asia (Peninsular Malaysia and Thailand). The genetic variation of lineage C on the mainland is greater than that of lineages A and B on the islands of Borneo and Java. Our study highlights the value of a molecular approach in assessing species status of simuliids in geographically distinct regions.
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Affiliation(s)
- Van Lun Low
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia (; ; ; ; ; ),
| | - Hiroyuki Takaoka
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia (; ; ; ; ; )
| | - Pairot Pramual
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Peter H Adler
- Department of Agricultural and Environmental Sciences, Clemson University, Clemson, SC
| | - Zubaidah Ya'cob
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia (; ; ; ; ; )
| | - Chee Dhang Chen
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia (; ; ; ; ; )
| | - Subagyo Yotopranoto
- Laboratory of Entomology, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Adnan Zaid
- University of Technology Yogyakarta, Jalan Ring Road Utara Jombor Sleman, Yogyakarta, Indonesia
| | - Upik Kesumawati Hadi
- Department of Animal Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Bogor Agricultural University, Bogor, Indonesia
| | - Maria Lourdes Lardizabal
- International Tropical Forestry Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Affan Nasruddin-Roshidi
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia (; ; ; ; ; )
| | - Mohd Sofian-Azirun
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia (; ; ; ; ; )
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Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps. BMC Evol Biol 2016; 16:77. [PMID: 27068234 PMCID: PMC4828801 DOI: 10.1186/s12862-016-0643-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/23/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Many species contain evolutionarily distinct groups that are genetically highly differentiated but morphologically difficult to distinguish (i.e., cryptic species). The presence of cryptic species poses significant challenges for the accurate assessment of biodiversity and, if unrecognized, may lead to erroneous inferences in many fields of biological research and conservation. RESULTS We tested for cryptic genetic variation within the broadly distributed alpine mayfly Baetis alpinus across several major European drainages in the central Alps. Bayesian clustering and multivariate analyses of nuclear microsatellite loci, combined with phylogenetic analyses of mitochondrial DNA, were used to assess population genetic structure and diversity. We identified two genetically highly differentiated lineages (A and B) that had no obvious differences in regional distribution patterns, and occurred in local sympatry. Furthermore, the two lineages differed in relative abundance, overall levels of genetic diversity as well as patterns of population structure: lineage A was abundant, widely distributed and had a higher level of genetic variation, whereas lineage B was less abundant, more prevalent in spring-fed tributaries than glacier-fed streams and restricted to high elevations. Subsequent morphological analyses revealed that traits previously acknowledged as intraspecific variation of B. alpinus in fact segregated these two lineages. CONCLUSIONS Taken together, our findings indicate that even common and apparently ecologically well-studied species may consist of reproductively isolated units, with distinct evolutionary histories and likely different ecology and evolutionary potential. These findings emphasize the need to investigate hidden diversity even in well-known species to allow for appropriate assessment of biological diversity and conservation measures.
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Schiffer PH, Herbig HG. Endorsing Darwin: global biogeography of the epipelagic goose barnaclesLepas spp. (Cirripedia, Lepadomorpha) proves cryptic speciation. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philipp H. Schiffer
- Institute for Genetics; University of Cologne; Zülpicher Strasse 47 D-50674 Köln Germany
- EMBL; Meyerhofstraße 1 D-69117 Heidelberg Germany
| | - Hans-Georg Herbig
- Institute of Geology and Mineralogy; University of Cologne; Zülpicher Strasse 49a D-50674 Köln Germany
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Temporal Stability of Genetic Structure in a Mesopelagic Copepod. PLoS One 2015; 10:e0136087. [PMID: 26302332 PMCID: PMC4547763 DOI: 10.1371/journal.pone.0136087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 07/29/2015] [Indexed: 11/19/2022] Open
Abstract
Although stochasticity in oceanographic conditions is known to be an important driver of temporal genetic change in many marine species, little is known about whether genetically distinct plankton populations can persist in open ocean habitats. A prior study demonstrated significant population genetic structure among oceanic gyres in the mesopelagic copepod Haloptilus longicornis in both the Atlantic and Pacific Oceans, and we hypothesized that populations within each gyre represent distinct gene pools that persist over time. We tested this expectation through basin-scale sampling across the Atlantic Ocean in 2010 and 2012. Using both mitochondrial (mtCOII) and microsatellite markers (7 loci), we show that the genetic composition of populations was stable across two years in both the northern and southern subtropical gyres. Genetic variation in this species was partitioned among ocean gyres (FCT = 0.285, P < 0.0001 for mtCOII, FCT = 0.013, P < 0.0001 for microsatellites), suggesting strong spatial population structure, but no significant partitioning was found among sampling years. This temporal persistence of population structure across a large geographic scale was coupled with chaotic genetic patchiness at smaller spatial scales, but the magnitude of genetic differentiation was an order of magnitude lower at these smaller scales. Our results demonstrate that genetically distinct plankton populations persist over time in highly-dispersive open ocean habitats, and this is the first study to rigorously test for temporal stability of large scale population structure in the plankton.
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Lukhtanov VA, Dantchenko AV, Vishnevskaya MS, Saifitdinova AF. Detecting cryptic species in sympatry and allopatry: analysis of hidden diversity inPolyommatus(Agrodiaetus) butterflies (Lepidoptera: Lycaenidae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12596] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics; Zoological Institute of Russian Academy of Sciences; Universitetskaya nab. 1 199034 St. Petersburg Russia
- Department of Entomology; St Petersburg State University; Universitetskaya nab. 7/9 199034 St. Petersburg Russia
| | - Alexander V. Dantchenko
- Department of Entomology; St Petersburg State University; Universitetskaya nab. 7/9 199034 St. Petersburg Russia
| | - Maria S. Vishnevskaya
- Department of Entomology; St Petersburg State University; Universitetskaya nab. 7/9 199034 St. Petersburg Russia
| | - Alsu F. Saifitdinova
- Department of Cytology and Histology; St Petersburg State University; Universitetskaya nab. 7/9 199034 St. Petersburg Russia
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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.
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