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Gao P, Khong HY, Wibowo A, Zhen Y, Peng C, Miao W. Chemical compositions and nutritional profiles of two edible tunicate species ( Halocynthia roretzi and Halocynthia aurantium). Heliyon 2024; 10:e32321. [PMID: 38948036 PMCID: PMC11209008 DOI: 10.1016/j.heliyon.2024.e32321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/22/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
As an abundant marine bioresource, tunicates could be exploited in the food industry. However, limited knowledge of their chemical composition and nutritional profiles prohibited further application. In this study, two common edible tunicate species, Halocynthia roretzi (HR) and Halocynthia aurantium (HA), were subjected to comprehensive composition analysis in terms of moisture, protein, lipids, cellulose, ash, amino acids, fatty acids, non-cellulose carbohydrates and minerals. Reddish HR was much bigger than purple HA with respect to body length and weight, and their moisture fell within 82.98 %-90.92 %. The non-edible outer shell part (OS) and edible internal organs part (IO) had a dry weight ratio of around 3:2 for both two species. Generally, for both HR and HA, IO was more abundant in protein and lipids. In contrast, OS had much higher cellulose contents, confirming the better suitability of IO as a nutritional seafood. IO was richer in essential amino acids and unsaturated fatty acids, while OS had more abundant saturated fatty acids. The detected non-cellulose monosugars ranged from 0.47 % to 1.18 % and indicated the presence of some sulfated glycans. IO of HR had higher contents of essential minerals, such as Cu, Zn, and Fe, while IO of HA showed a higher K content. To sum up, this study identified the chemical composition and nutritional profile variations among different tunicate species and various dissected parts, guiding the development of specific strategies to exploit tunicates for proper food applications.
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Affiliation(s)
- Pingping Gao
- Faculty of Applied Sciences, Universiti Teknologi MARA Sarawak Branch, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Heng Yen Khong
- Faculty of Applied Sciences, Universiti Teknologi MARA Sarawak Branch, 94300, Kota Samarahan, Sarawak, Malaysia
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Selangor Branch, Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Agustono Wibowo
- Faculty of Applied Sciences, Universiti Teknologi MARA Pahang Branch, 26400, Bandar Tun Razak, Pahang, Malaysia
- Organic Synthesis Laboratory, Institute of Science (IOS), Universiti Teknologi MARA (UiTM), 42300 Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Yixiang Zhen
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Chengcheng Peng
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wenhua Miao
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China
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2
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Haye PA, Segovia NI. Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel. Heredity (Edinb) 2023; 130:402-413. [PMID: 37024547 PMCID: PMC10238476 DOI: 10.1038/s41437-023-00615-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.
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Affiliation(s)
- Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile
| | - Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile.
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3
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Haye PA, Segovia NI, Vera R, Acuña E. Phylogeography reveals a panmictic population of the Chilean nylon shrimp along its exploitation range in the southeast Pacific Ocean. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00589-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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4
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Segovia NI, González-Wevar CA, Naretto J, Rosenfeld S, Brickle P, Hüne M, Bernal V, Haye PA, Poulin E. The right tool for the right question: contrasting biogeographic patterns in the notothenioid fish Harpagifer spp. along the Magellan Province. Proc Biol Sci 2022; 289:20212738. [PMID: 35382596 PMCID: PMC8984805 DOI: 10.1098/rspb.2021.2738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Molecular-based analysis has become a fundamental tool to understand the role of Quaternary glacial episodes. In the Magellan Province in southern South America, ice covering during the last glacial maximum (20 ka) radically altered the landscape/seascape, speciation rates and distribution of species. For the notothenioid fishes of the genus Harpagifer, in the area are described two nominal species. Nevertheless, this genus recently colonized South America from Antarctica, providing a short time for speciation processes. Combining DNA sequences and genotyping-by-sequencing SNPs, we evaluated the role of Quaternary glaciations over the patterns of genetic structure in Harpagifer across its distribution in the Magellan Province. DNA sequences showed low phylogeographic structure, with shared and dominant haplotypes between nominal species, suggesting a single evolutionary unit. SNPs identified contrastingly two groups in Patagonia and a third well-differentiated group in the Falkland/Malvinas Islands with limited and asymmetric gene flow. Linking the information of different markers allowed us to infer the relevance of postglacial colonization mediated by the general oceanographic circulation patterns. Contrasting rough- and fine-scale genetic patterns highlights the relevance of combined methodologies for species delimitation, which, depending on the question to be addressed, allows discrimination among phylogeographic structure, discarding incipient speciation, and contemporary spatial differentiation processes.
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Affiliation(s)
- N I Segovia
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.,Instituto Milenio en Socio-ecología Costera (SECOS), Coquimbo, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
| | - C A González-Wevar
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile.,Instituto de Ciencias Marinas y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.,Centro de Investigación en Dinámicas de Ecosistemas de Altas Latitudes (Fondap IDEAL), Universidad Austral de Chile
| | - J Naretto
- Costa Humboldt, Puerto Varas, Los Lagos, Chile
| | - S Rosenfeld
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Laboratorio de Ecosistemas Antárticos y sub-Antárticos, Universidad de Magallanes, Chile
| | - P Brickle
- South Atlantic Environmental Research Institute (SAERI), PO Box 609, Stanley Cottage, Port Stanley, Falkland Islands, UK
| | - M Hüne
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Centro de Investigación para la Conservación de los Ecosistemas Australes (ICEA), Punta Arenas, Chile
| | - V Bernal
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
| | - P A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.,Instituto Milenio en Socio-ecología Costera (SECOS), Coquimbo, Chile
| | - E Poulin
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile. Las Palmeras 3425, Ñuñoa, Santiago, Chile.,Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MI-BASE), Valdivia, Chile
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5
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Rocha RM, Teixeira JA, Barros RCD. Genetic diversity in the Diplosoma listerianum complex (Ascidiacea: Didemnidae) from the Western Atlantic. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1988003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rosana M. Rocha
- Zoology Department, Universidade Federal do Paraná, CP 19020, Curitiba 81531-980, Brazil
| | - Joyce Ana Teixeira
- Zoology Department, Universidade Federal do Paraná, CP 19020, Curitiba 81531-980, Brazil
| | - Rodolfo Corrêa de Barros
- Parasitology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Rua Padre Camargo, 280, Curitiba 80060-240, Brazil
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6
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An elongated COI fragment to discriminate botryllid species and as an improved ascidian DNA barcode. Sci Rep 2021; 11:4078. [PMID: 33603059 PMCID: PMC7892571 DOI: 10.1038/s41598-021-83127-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
Botryllids are colonial ascidians widely studied for their potential invasiveness and as model organisms, however the morphological description and discrimination of these species is very problematic, leading to frequent specimen misidentifications. To facilitate species discrimination and detection of cryptic/new species, we developed new barcoding primers for the amplification of a COI fragment of about 860 bp (860-COI), which is an extension of the common Folmer's barcode region. Our 860-COI was successfully amplified in 177 worldwide-sampled botryllid colonies. Combined with morphological analyses, 860-COI allowed not only discriminating known species, but also identifying undescribed and cryptic species, resurrecting old species currently in synonymy, and proposing the assignment of clade D of the model organism Botryllus schlosseri to Botryllus renierii. Importantly, within clade A of B. schlosseri, 860-COI recognized at least two candidate species against only one recognized by the Folmer's fragment, underlining the need of further genetic investigations on this clade. This result also suggests that the 860-COI could have a greater ability to diagnose cryptic/new species than the Folmer's fragment at very short evolutionary distances, such as those observed within clade A. Finally, our new primers simplify the amplification of 860-COI even in non-botryllid ascidians, suggesting their wider usefulness in ascidians.
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7
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Segovia NI, González-Wevar CA, Haye PA. Signatures of local adaptation in the spatial genetic structure of the ascidian Pyura chilensis along the southeast Pacific coast. Sci Rep 2020; 10:14098. [PMID: 32839518 PMCID: PMC7445245 DOI: 10.1038/s41598-020-70798-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022] Open
Abstract
The highly heterogeneous Humboldt Current System (HCS) and the 30°S transition zone on the southeast Pacific coast, represent an ideal scenario to test the influence of the environment on the spatial genomic structure in marine near-shore benthic organisms. In this study, we used seascape genomic tools to evaluate the genetic structure of the commercially important ascidian Pyura chilensis, a species that exhibits a low larval transport potential but high anthropogenic dispersal. A recent study in this species recorded significant genetic differentiation across a transition zone around 30°S in putatively adaptive SNPs, but not in neutral ones, suggesting an important role of environmental heterogeneity in driving genetic structure. Here, we aim to understand genomic-oceanographic associations in P. chilensis along the Southeastern Pacific coast using two combined seascape genomic approaches. Using 149 individuals from five locations along the HCS, a total of 2,902 SNPs were obtained by Genotyping-By-Sequencing, of which 29–585 were putatively adaptive loci, depending on the method used for detection. In adaptive loci, spatial genetic structure was better correlated with environmental differences along the study area (mainly to Sea Surface Temperature, upwelling-associated variables and productivity) than to the geographic distance between sites. Additionally, results consistently showed the presence of two groups, located north and south of 30°S, which suggest that local adaptation processes seem to allow the maintenance of genomic differentiation and the spatial genomic structure of the species across the 30°S biogeographic transition zone of the Humboldt Current System, overriding the homogenizing effects of gene flow.
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Affiliation(s)
- Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.,Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología Y Biodiversidad IEB, Universidad de Chile, Santiago, Chile
| | - Claudio A González-Wevar
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología Y Biodiversidad IEB, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Marinas Y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP de Investigaciones en Dinámica de Ecosistemas de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
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8
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Hudson J, Johannesson K, McQuaid CD, Rius M. Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate. Evol Appl 2020; 13:600-612. [PMID: 32431738 PMCID: PMC7045719 DOI: 10.1111/eva.12893] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/30/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping-by-sequencing to study both native and introduced ranges of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.
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Affiliation(s)
- Jamie Hudson
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
| | - Kerstin Johannesson
- Department of Marine SciencesTjärnö Marine LaboratoryUniversity of GothenburgStrömstadSweden
| | - Christopher D. McQuaid
- Department of Zoology and EntomologyCoastal Research GroupRhodes UniversityGrahamstownSouth Africa
| | - Marc Rius
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
- Department of ZoologyCentre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgAuckland ParkSouth Africa
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9
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Morales‐González S, Giles EC, Quesada‐Calderón S, Saenz‐Agudelo P. Fine-scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific. Ecol Evol 2019; 9:9855-9868. [PMID: 31534699 PMCID: PMC6745665 DOI: 10.1002/ece3.5526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine-scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine-scale genetic patterns among localities.
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Affiliation(s)
- Sarai Morales‐González
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Magister en Ciencias Mención GenéticaEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Emily C. Giles
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Doctorado en Ciencias Mención Ecología y EvoluciónEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Suany Quesada‐Calderón
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Doctorado en Ciencias Mención Ecología y EvoluciónEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
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10
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Haye PA, Segovia NI, Varela AI, Rojas R, Rivadeneira MM, Thiel M. Genetic and morphological divergence at a biogeographic break in the beach-dwelling brooder Excirolana hirsuticauda Menzies (Crustacea, Peracarida). BMC Evol Biol 2019; 19:118. [PMID: 31185884 PMCID: PMC6560899 DOI: 10.1186/s12862-019-1442-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND There is a biogeographic break located at 30°S in the southeast Pacific, in a coastal area of strong environmental discontinuities. Several marine benthic taxa with restricted dispersal have a coincident phylogeographic break at 30°S, indicating that genetic structure is moulded by life history traits that limit gene flow and thereby promote divergence and speciation. In order to evaluate intraspecific divergence at this biogeographic break, we investigated the genetic and morphological variation of the directly developing beach isopod Excirolana hirsuticauda along 1900 km of the southeast Pacific coast, across 30°S. RESULTS The COI sequences and microsatellite data both identified a strong discontinuity between populations of E. hirsuticauda to the north and south of 30°S, and a second weaker phylogeographic break at approximately 35°S. The three genetic groups were evidenced by different past demographic and genetic diversity signatures, and were also clearly distinguished with microsatellite data clustering. The COI sequences established that the genetic divergence of E. hirsuticauda at 30°S started earlier than divergence at 35°. Additionally, the three groups have different past demographic signatures, with probable demographic expansion occurring earlier in the southern group (south of 35°S), associated with Pleistocene interglacial periods. Interestingly, body length, multivariate morphometric analyses, and the morphology of a fertilization-related morphological character in males, the appendix masculina, reinforced the three genetic groups detected with genetic data. CONCLUSIONS The degree of divergence of COI sequences, microsatellite data, and morphology was concordant and showed two geographic areas in which divergence was promoted at differing historical periods. Variation in the appendix masculina of males has probably promoted reproductive isolation. This variation together with gene flow restrictions promoted by life history traits, small body size, oceanographic discontinuities and sandy-beach habitat continuity, likely influenced species divergence at 30°S in the southeast Pacific coast. The degree of genetic and morphological differentiation of populations to the north and south of 30°S suggests that E. hirsuticauda harbours intraspecific divergence consistent with reproductive isolation and an advanced stage of speciation. The speciation process within E. hirsuticauda has been shaped by both restrictions to gene flow and a prezygotic reproductive barrier.
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Affiliation(s)
- Pilar A. Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
| | - Nicolás I. Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
| | - Andrea I. Varela
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Universidad Católica del Norte, Coquimbo, Chile
| | - Rodrigo Rojas
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
| | - Marcelo M. Rivadeneira
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
| | - Martin Thiel
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Universidad Católica del Norte, Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
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11
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Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis. Sci Rep 2017; 7:44559. [PMID: 28300177 PMCID: PMC5353582 DOI: 10.1038/srep44559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/09/2017] [Indexed: 12/15/2022] Open
Abstract
Marine benthic organisms inhabit a heterogeneous environment in which connectivity between populations occurs mainly through dispersive larval stages, while local selective pressures acting on early life history stages lead to non-random mortality, shaping adaptive genetic structure. In order to test the influence of local adaptation and neutral processes in a marine benthic species with low dispersal, in this study we used Genotyping by Sequencing technology to compare the neutral and putatively selected signals (neutral and outlier loci, respectively) in SNPs scattered throughout the genome in six local populations of the commercially exploited ascidian Pyura chilensis along the southeast Pacific coast (24°–42°S). This species is sessile as an adult, has a short-lived larval stage, and may also be dispersed by artificial transport as biofouling. We found that the main signal in neutral loci was a highly divergent lineage present at 39°S, and a subjacent signal that indicated a separation at 30°S (north/south), widely reported in the area. North/south separation was the main signal in outlier loci, and the linage divergence at 39°S was subjacent. We conclude that the geographic structure of the genetic diversity of outlier and neutral loci was established by different strengths of environmental, historical and anthropogenic factors.
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12
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Guo B, Wares JP. Large-scale gene flow in the barnacle Jehlius cirratus and contrasts with other broadly-distributed taxa along the Chilean coast. PeerJ 2017; 5:e2971. [PMID: 28194316 PMCID: PMC5299995 DOI: 10.7717/peerj.2971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/09/2017] [Indexed: 11/25/2022] Open
Abstract
We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3,000 km of the linear range of this species, there is only slight regional structure indicated, with overall Φ CT of 0.036 (p < 0.001) yet no support for isolation by distance. While these results suggest greater structure than previous studies of J. cirratus had indicated, the pattern of diversity is still far more subtle than in other similarly-distributed species with similar larval and life history traits. We compare these data and results with recent findings in four other intertidal species that have planktotrophic larvae. There are no clear patterns among these taxa that can be associated with intertidal depth or other known life history traits.
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Affiliation(s)
- Baoying Guo
- College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - John P. Wares
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, USA
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Hu ZM, Li JJ, Sun ZM, Oak JH, Zhang J, Fresia P, Grant WS, Duan DL. Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific. Mol Ecol 2016; 24:5020-33. [PMID: 26334439 DOI: 10.1111/mec.13367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 02/01/2023]
Abstract
A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene-late Miocene (c. 4.5-7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.
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Affiliation(s)
- Zi-Min Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jing-Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Min Sun
- Laboratory of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jung-Hyun Oak
- Department of Oceanography, Pusan National University, Pusan, 609-735, Korea
| | - Jie Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pablo Fresia
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, Uruguay
| | - W Stewart Grant
- Alaska Department of Fish and Game, Anchorage, AK, 99518, USA
| | - De-Lin Duan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
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Haye PA, Gallardo-Escárate C. Transcriptome characterization of the ascidian Pyura chilensis using 454-pyrosequencing data from two distant localities on the southeast Pacific. Mar Genomics 2014; 20:19-22. [PMID: 25526667 DOI: 10.1016/j.margen.2014.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 11/30/2022]
Abstract
This study describes the results from transcriptomes sequenced by 454-pyrosequencing from two populations separated by 10° of latitude of the endemic tunicate Pyura chilensis. Most transcripts were assembled in 43,972 contigs with an average length of 842 nucleotides. De novo assembly revealed that less than 30% of the contigs were annotated to Gene Ontology terms. A total of 71,662 single nucleotide polymorphisms (SNPs) were detected in 14,712 contigs. In silico differential expression of contigs annotated for SNPs revealed several genes differentially expressed in individuals collected from both populations. The present genomic resource will provide the basis to perform functional genomics on the species via the localization of genomic markers that can aid in determining levels of local adaptation, overall genetic structure and the genetic assessment of restocking programs for this species.
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Affiliation(s)
- Pilar A Haye
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile; Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile.
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, University of Concepción, Concepción, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
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Haye PA, Segovia NI, Muñoz-Herrera NC, Gálvez FE, Martínez A, Meynard A, Pardo-Gandarillas MC, Poulin E, Faugeron S. Phylogeographic structure in benthic marine invertebrates of the southeast Pacific coast of Chile with differing dispersal potential. PLoS One 2014; 9:e88613. [PMID: 24586356 PMCID: PMC3929388 DOI: 10.1371/journal.pone.0088613] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 01/15/2014] [Indexed: 11/18/2022] Open
Abstract
The role of dispersal potential on phylogeographic structure, evidenced by the degree of genetic structure and the presence of coincident genetic and biogeographic breaks, was evaluated in a macrogeographic comparative approach along the north-central coast of Chile, across the biogeographic transition zone at 30°S. Using 2,217 partial sequences of the mitochondrial Cytochrome Oxidase I gene of eight benthic invertebrate species along ca. 2,600 km of coast, we contrasted dispersal potential with genetic structure and determined the concordance between genetic divergence between biogeographic regions and the biogeographic transition zone at 30°S. Genetic diversity and differentiation highly differed between species with high and low dispersal potential. Dispersal potential, sometimes together with biogeographic region, was the factor that best explained the genetic structure of the eight species. The three low dispersal species, and one species assigned to the high dispersal category, had a phylogeographic discontinuity coincident with the biogeographic transition zone at 30°S. Furthermore, coalescent analyses based on the isolation-with-migration model validate that the split between biogeographic regions north and south of 30°S has a historic origin. The signatures of the historic break in high dispersers is parsimoniously explained by the homogenizing effects of gene flow that have erased the genetic signatures, if ever existed, in high dispersers. Of the four species with structure across the break, only two had significant albeit very low levels of asymmetric migration across the transition zone. Historic processes have led to the current biogeographic and phylogeographic structure of marine species with limited dispersal along the north-central coast of Chile, with a strong lasting impact in their genetic structure.
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Affiliation(s)
- Pilar A. Haye
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte & Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Nicolás I. Segovia
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte & Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
| | - Natalia C. Muñoz-Herrera
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte & Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Francisca E. Gálvez
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte & Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
| | - Andrea Martínez
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
| | - Andrés Meynard
- Centro de Conservación Marina, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María C. Pardo-Gandarillas
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
- Centro de Conservación Marina, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
| | - Sylvain Faugeron
- Centro de Conservación Marina, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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