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Wang C, Hu L, Song Y, Xie H, Yang L, Serekbol G, Huo B, Chen S. The Evolution of Three Schizothoracinae Species from Two Major River Systems in Northwest China Based on Otolith Morphology and Skeletal Structure. BIOLOGY 2024; 13:517. [PMID: 39056710 PMCID: PMC11274347 DOI: 10.3390/biology13070517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/28/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024]
Abstract
Schizothoracinae species are the largest group of Cypriniformes that readily adapt to the natural conditions of the Qinghai-Tibet Plateau. This group has habitat characteristics and distribution patterns centered on the Qinghai-Tibet Plateau. To study the evolution of three Schizothoracinae species in Northwest China, the evolutionary characteristics of these species were explored based on differences in otolith morphology and skeletal morphology. From 2020 to 2022, 138 samples (63 Aspiorhynchus laticeps, 35 Diptychus maculatus and 40 Schizothorax pseudaksaiensis) were collected from the Tarim River and Ili River, 6 basic morphological parameters of otoliths were measured and converted into 6 morphological factors and 7 morphological indices. A total of 77 Fourier transform coefficients of each otolith were selected The first three principal components accounted for 92.834% of the total variation in 13 otolith morphological indices of the three Schizothoracinae species, and the overall discrimination rate was 94.20%. According to the principal component analysis of 77 Fourier harmonic values of otoliths, the first 20 principal components explained 97.233% of the total variation, and the overall discrimination rate was 100%. The results of the cluster analysis directly reflected the relationships between related species. The differences in the bone morphology of the three Schizothoracinae species were particularly reflected in the number of whiskers, pharyngeal teeth and vertebrae, and there were also significant differences in the shapes of the sphenotic (SP), pterotic (PTE), preoperculum (PO), branchiostegal ray (BRA) and basibranchial (BB) bones. Their unique morphological and skeletal characteristics are closely related to geological changes and water system evolutionary trends. This study contributes to the understanding of species identification and the evolutionary status of plateau fishes, provides a reference for further evolutionary classification and for assessing the evolutionary mechanisms of plateau fishes, and provides a scientific basis for phylogeny and germplasm resource protection.
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Affiliation(s)
- Chengxin Wang
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China; (C.W.); (L.H.); (Y.S.); (H.X.); (L.Y.)
| | - Linghui Hu
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China; (C.W.); (L.H.); (Y.S.); (H.X.); (L.Y.)
| | - Yong Song
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China; (C.W.); (L.H.); (Y.S.); (H.X.); (L.Y.)
| | - Haoyang Xie
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China; (C.W.); (L.H.); (Y.S.); (H.X.); (L.Y.)
| | - Liting Yang
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China; (C.W.); (L.H.); (Y.S.); (H.X.); (L.Y.)
| | - Gulden Serekbol
- College of Animal Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China;
| | - Bin Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China;
| | - Shengao Chen
- College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, Alar 843300, China; (C.W.); (L.H.); (Y.S.); (H.X.); (L.Y.)
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Abdussamad EM, Toji T, Margaret AMR, Mini KG, Rajesh KM, Azeez PA, Ramar V, Retheesh TB, Abbas AM, Shihab I, George SM, Prathibha R, Gopalakrishnan A. Untangling the taxonomic ambiguities of the spotted seerfish Scomberomorus guttatus with the description of a new species from India. JOURNAL OF FISH BIOLOGY 2024; 104:662-680. [PMID: 37844010 DOI: 10.1111/jfb.15582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/24/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023]
Abstract
Scomberomorus guttatus has been subjected to a series of synonym assignations over the years. Its taxonomy has been mired with ambiguities due to the greater-than-average morphological variations observed in samples from different regions. An integrated taxonomic revision with molecular support indicated that the species that was thought to be a single entity, in reality, is a complex of three distinct species. They are morphologically distinct with respect to the body depth and elongation, cephalic morphometry, and meristic characteristics. Otolith morphometry and phylogenetic evidence further established the taxonomic divergence within the spotted seerfish complex. The phylogenetic characteristic as indicated by the mitochondrial Cytochrome c Oxidase subunit I (COI) sequence unveiled that S. guttatus had a high intraspecific divergence of 11.1% from its two identical congeners and a divergence of 2.34% between the congeners, indicating scope for categorizing them as separate species. Based on the morphological and molecular evidence, S. guttatus is redescribed; the senior synonym Scomberomorus leopardus is resurrected as a valid species; and a new species Scomberomorus avirostrus n. sp. is described with keys for species distinction.
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Affiliation(s)
| | - Thomas Toji
- ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | | | | | | | | | - Vinothkumar Ramar
- ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | | | | | - Ismail Shihab
- ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Sneha M George
- ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
| | - Rohith Prathibha
- ICAR-Central Marine Fisheries Research Institute (CMFRI), Kochi, India
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Neves J, Veríssimo A, Múrias Santos A, Garrido S. Comparing otolith shape descriptors for population structure inferences in a small pelagic fish, the European sardine Sardina pilchardus (Walbaum, 1792). JOURNAL OF FISH BIOLOGY 2023; 102:1219-1236. [PMID: 36880257 DOI: 10.1111/jfb.15369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/02/2023] [Indexed: 05/13/2023]
Abstract
Otolith shape analysis has been one of the most used approaches to study population structure in the past decades. Currently, two sets of shape descriptors are used to perform otolith shape analysis, namely, Elliptic Fourier descriptor (EFd), which focuses on the overall otolith shape differences, and Discrete Wavelet descriptor (DWd), which is sensible to local differences along the otolith contour. Here, the authors conducted a comparative analysis of the performance of both the descriptors in reconstructing the population structure and connectivity patterns in a small pelagic fish species with a wide geographical distribution and fast growth rate, the European sardine Sardina pilchardus (Walbaum, 1792), for the first time. A combination of each otolith shape descriptor and shape indices was explored using multivariate statistical methods. The two otolith shape descriptors showed similar, although limited, overall classification success associated with the population dynamic characteristics of the species. Both descriptors point to migration among adjacent areas, such as northern Atlantic locations, eastern Mediterranean and even across well-defined physical obstacles, such as the Strait of Gibraltar, among Atlantic and western Mediterranean locations. Both descriptors supported the division of the populations of Mediterranean waters into three main groups but slightly differed in the group limits of the Atlantic waters. A comparison of the present results with those from previous otolith shape analysis studies using EFd on a decadal time scale revealed differences in the population structure and connectivity patterns compared to the earlier period. These differences not only may be attributed to changes in environmental variables leading to changes in population dynamics but can also be the result of the sardine biomass sharp decrease that occurred in the past decade.
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Affiliation(s)
- João Neves
- Faculty of Sciences, University of Porto, Porto, Portugal
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
- Portuguese Institute for Sea and Atmosphere (IPMA), Lisbon, Portugal
| | - Ana Veríssimo
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - António Múrias Santos
- Faculty of Sciences, University of Porto, Porto, Portugal
- CIBIO - Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - Susana Garrido
- Portuguese Institute for Sea and Atmosphere (IPMA), Lisbon, Portugal
- Marine and Environmental Sciences Centre (MARE), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Zarei F, Esmaeili HR, Sadeghi R, Schliewen UK, Kovačić M, Abbasi K, Gholamhosseini A. An integrative insight into the diversity, distribution, and biogeography of the freshwater endemic clade of the Ponticola syrman group (Teleostei: Gobiidae) in the Caucasus biodiversity hotspot. Ecol Evol 2022; 12:e9300. [PMID: 36177146 PMCID: PMC9478520 DOI: 10.1002/ece3.9300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/12/2022] [Accepted: 08/25/2022] [Indexed: 11/06/2022] Open
Abstract
Freshwater habitats of the Caucasus biodiversity hotspot represent a center of endemism for the gobiid genus Ponticola Iljin, 1927. Hitherto, large-scale molecular studies, owing to restricted taxon and geographical sampling, have failed to give an elaborate picture of diversity and evolutionary history of these species. Here, to contribute to filling this gap, we assessed taxonomic diversity, phylogeography and evolutionary history for the south Caspian populations of Ponticola presently classified as P. iranicus and P. patimari, using an integrative taxonomic approach comprising an entire geographic range sampling, and analyses of mitochondrial DNA haplotypes, the head lateral line system, otolith shape, and meristic and morphometric variation. All freshwater samples of the P. syrman group belong to a monophyletic clade with two main subclades: a small subclade confined to the upper Sefidroud sub-basin including the type locality of P. iranicus and a large subclade with three geographically constrained haplogroups (Hg1, Hg2, and Hg3), comprising the rest of the distribution. Hg1 showed an eastern distribution including the type locality of P. patimari, while Hg2 and Hg3 are sister groups with central and western-central distributions, respectively. The freshwater clade diverged from P. syrman during the Tyurkyanian low stand (~150 m b.s.l. lasting ~0.1 Myr), while the divergence of P. iranicus and P. patimari and radiations within P. patimari took place during the Bakunian high stand (up to 50 m a.s.l. lasting ~378-480 kya). Species delimitation analyses indicated two distinct species, corresponding to each main subclade. Although the otolith shape and lateral line analyses did not reflect with phylogeographic pattern, PCA and DFA plots of meristic and morphometric data showed a clear separation of the two major subclades corresponding to P. iranicus and P. patimari, suggesting the presence of significant morphological variation meriting formal taxonomic recognition. Overall, our findings (i) reveal the presence of two freshwater endemic species in the P. syrman group, and pending further investigation, hypothesize the presence of a third cryptic species; (ii) revise and document a narrow distributional range and low diversity for P. iranicus, in contrast to a wider distributional range and high diversity for P. patimari; (iii) suggest that the climatic oscillations of the Pleistocene were associated with the cladogenesis within the P. syrman group; and (iv) allowed for the recognition of conservation units and proposition of management measures.
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Affiliation(s)
- Fatah Zarei
- Ichthyology and Molecular Systematics Research Laboratory, Department of Biology, College of SciencesShiraz UniversityShirazIran
| | - Hamid Reza Esmaeili
- Ichthyology and Molecular Systematics Research Laboratory, Department of Biology, College of SciencesShiraz UniversityShirazIran
| | - Reza Sadeghi
- Department of BiologyIslamic Azad UniversityBorujerdIran
| | - Ulrich K. Schliewen
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMünchenGermany
| | | | - Keyvan Abbasi
- Inland Waters Aquaculture Research Center, Iranian Fisheries Sciences Research InstituteAgricultural Research, Education and Extension OrganizationBandar AnzaliIran
| | - Ali Gholamhosseini
- Ichthyology and Molecular Systematics Research Laboratory, Department of Biology, College of SciencesShiraz UniversityShirazIran
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Kikuchi E, García S, da Costa PAS, Cardoso LG, Haimovici M. Discrimination of red porgy Pagrus pagrus (Sparidae) potential stocks in the south-western Atlantic by otolith shape analysis. JOURNAL OF FISH BIOLOGY 2021; 98:548-556. [PMID: 33111352 DOI: 10.1111/jfb.14598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Otolith shape analysis is a powerful method for fish stock identification. We compared the otolith shape of Pagrus pagrus (Linnaeus 1758) along with its distribution in four south-western Atlantic regions where it is commercially fished: Rio de Janeiro, Rio Grande do Sul in southern Brazil, the Argentine-Uruguayan Common Fishing Zone (UA) and the Argentinian Exclusive Fishing Zone (AR). Otolith shapes were compared by Elliptical Fourier and Wavelet coefficients among specimens in a size range with similar otoliths, morphometric parameters and ages. Four potential stocks were identified: one in the AR, a second along the UA which included specimens from southern Brazil with well-marked opaque bands in its otoliths (MRS), the third in southern Brazil with faint or absent opaque bands in its otoliths (FRS) and the fourth along Rio de Janeiro. The difference in the otolith shape among regions followed differences reported using other stock identification techniques. The similarity between otoliths from UA and MRS (ANOVA-like, P > 0.01) can be explained by seasonal short-range migrations. Otoliths shape differences between MRS and FRS (ANOVA-like, P < 0.01) suggest that P. pagrus does not form a homogeneous group in southern Brazil.
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Affiliation(s)
- Eidi Kikuchi
- Laboratório de Recursos Pesqueiros Demersais, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
- Programa de Pós-Graduação em Oceanografia Biológica, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Sebastían García
- Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), Mar del Plata, Argentina
| | - Paulo Alberto Silva da Costa
- Departamento de Ecologia e Recursos Marinhos, IBIO, Universidade Federal do Estado do Rio de Janeiro, UNIRIO, Rio de Janeiro, Brazil
| | - Luis Gustavo Cardoso
- Laboratório de Recursos Pesqueiros Demersais, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Manuel Haimovici
- Laboratório de Recursos Pesqueiros Demersais, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
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Afanasyev PK, Orlov AM, Rolsky AY. Otolith Shape Analysis as a Tool for Species Identification and Studying the Population Structure of Different Fish Species. BIOL BULL+ 2018. [DOI: 10.1134/s1062359017080027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Berg F, Almeland OW, Skadal J, Slotte A, Andersson L, Folkvord A. Genetic factors have a major effect on growth, number of vertebrae and otolith shape in Atlantic herring (Clupea harengus). PLoS One 2018; 13:e0190995. [PMID: 29324892 PMCID: PMC5764352 DOI: 10.1371/journal.pone.0190995] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/22/2017] [Indexed: 12/29/2022] Open
Abstract
Atlantic herring, Clupea harengus, have complex population structures. Mixing of populations is known, but the extent of connectivity is still unclear. Phenotypic plasticity results in divergent phenotypes in response to environmental factors. A marked salinity gradient occurs from Atlantic Ocean (salinity 35) into the Baltic Sea (salinity range 2-12). Herring from both habitats display phenotypic and genetic variability. To explore how genetic factors and salinity influence phenotypic traits like growth, number of vertebrae and otolith shape an experimental population consisting of Atlantic purebreds and Atlantic/Baltic F1 hybrids were incubated and co-reared at two different salinities, 16 and 35, for three years. The F1-generation was repeatedly sampled to evaluate temporal variation. A von Bertalanffy growth model indicated that reared Atlantic purebreds had a higher maximum length (26.2 cm) than Atlantic/Baltic hybrids (24.8 cm) at salinity 35, but not at salinity 16 (25.0 and 24.8 cm, respectively). In contrast, Atlantic/Baltic hybrids achieved larger size-at-age than the wild caught Baltic parental group. Mean vertebral counts and otolith aspect ratios were higher for reared Atlantic purebreds than Atlantic/Baltic hybrids, consistent with the differences between parental groups. There were no significant differences in vertebral counts and otolith aspect ratios between herring with the same genotype but raised in different salinities. A Canonical Analysis of Principal Coordinates was applied to analyze the variation in wavelet coefficients that described otolith shape. The first discriminating axis identified the differences between Atlantic purebreds and Atlantic/Baltic hybrids, while the second axis represented salinity differences. Assigning otoliths based on genetic groups (Atlantic purebreds vs. Atlantic/Baltic hybrids) yielded higher classification success (~90%) than based on salinities (16 vs. 35; ~60%). Our results demonstrate that otolith shape and vertebral counts have a significant genetic component and are therefore useful for studies on population dynamics and connectivity.
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Affiliation(s)
- Florian Berg
- University of Bergen, Department of Biology, Bergen, Norway
- Institute of Marine Research (IMR), Nordnes, Bergen, Norway
- * E-mail:
| | | | - Julie Skadal
- University of Bergen, Department of Biology, Bergen, Norway
| | - Aril Slotte
- Institute of Marine Research (IMR), Nordnes, Bergen, Norway
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Arild Folkvord
- University of Bergen, Department of Biology, Bergen, Norway
- Institute of Marine Research (IMR), Nordnes, Bergen, Norway
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Bacha M, Jeyid AM, Jaafour S, Yahyaoui A, Diop M, Amara R. Insights on stock structure of round sardinella Sardinella aurita off north-west Africa based on otolith shape analysis. JOURNAL OF FISH BIOLOGY 2016; 89:2153-2166. [PMID: 27506834 DOI: 10.1111/jfb.13117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
This study examines the geographic variability in otolith shape of round sardinella Sardinella aurita as a tool for stock discrimination. Fish were analysed from six sampling locations from Senegal to the Mediterranean coast of Morocco. A combination of otolith shape indices and elliptic Fourier descriptors was investigated by multivariate statistical procedures. Within the studied area, three distinct groups were identified with an overall correct classification of 78%. Group A: Nador (Alboran Sea), group B: Casablanca (northern Morocco) and group C: Senegalese-Mauritanian. The results of this study confirm the absence of an Atlantic Ocean-Mediterranean Sea transition for this species, the Gibraltar Strait acting as an efficient barrier for S. aurita population separation. Off north-west Africa, fish from northern Morocco form a single group which is clearly isolated from Senegalese-Mauritanian waters, confirming the existence of a distinct stock in this area. Among group C, some discontinuity exists and suggests the existence of a sedentary fraction of S. aurita in northern Mauritania (Arguin Bank). The results are discussed in relation to oceanographic features and physical barriers to dispersal and fish management strategy in the study area.
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Affiliation(s)
- M Bacha
- Université du Littoral Côte d'Opale, Laboratory of Oceanography and Geosciences, Wimereux, 62930, France.
| | - A M Jeyid
- Université du Littoral Côte d'Opale, Laboratory of Oceanography and Geosciences, Wimereux, 62930, France
- Institut Mauritanien de Recherches Océanographiques et des Pêches (IMROP), BP 22, Nouadhibou, Mauritania
| | - S Jaafour
- Université du Littoral Côte d'Opale, Laboratory of Oceanography and Geosciences, Wimereux, 62930, France
- Mohammed V University of Agdal, Laboratory of Zoology and General Biology, Rabat, Morocco
| | - A Yahyaoui
- Mohammed V University of Agdal, Laboratory of Zoology and General Biology, Rabat, Morocco
| | - M Diop
- Université du Littoral Côte d'Opale, Laboratory of Oceanography and Geosciences, Wimereux, 62930, France
- Laboratoire de Toxicologie et d'Hydrologie (LTH), UCAD, 5005, Dakar, Senegal
| | - R Amara
- Université du Littoral Côte d'Opale, Laboratory of Oceanography and Geosciences, Wimereux, 62930, France
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Otolith variation in Pacific herring (Clupea pallasii) reflects mitogenomic variation rather than the subspecies classification. Polar Biol 2016. [DOI: 10.1007/s00300-015-1882-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Libungan LA, Slotte A, Husebø Å, Godiksen JA, Pálsson S. Latitudinal Gradient in Otolith Shape among Local Populations of Atlantic Herring (Clupea harengus L.) in Norway. PLoS One 2015; 10:e0130847. [PMID: 26101885 PMCID: PMC4478005 DOI: 10.1371/journal.pone.0130847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 11/19/2022] Open
Abstract
Otolith shape analysis of Atlantic herring (Clupea harengus) in Norwegian waters shows significant differentiation among fjords and a latitudinal gradient along the coast where neighbouring populations are more similar to each other than to those sampled at larger distances. The otolith shape was obtained using quantitative shape analysis, the outlines were transformed with Wavelet and analysed with multivariate methods. The observed morphological differences are likely to reflect environmental differences but indicate low dispersal among the local herring populations. Otolith shape variation suggests also limited exchange between the local populations and their oceanic counterparts, which could be due to differences in spawning behaviour. Herring from the most northerly location (69°N) in Balsfjord, which is genetically more similar to Pacific herring (Clupea pallasii), differed in otolith shape from all the other populations. Our results suggest that the semi-enclosed systems, where the local populations live and breed, are efficient barriers for dispersal. Otolith shape can thus serve as a marker to identify the origin of herring along the coast of Norway.
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Affiliation(s)
- Lísa Anne Libungan
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Aril Slotte
- Institute of Marine Research, Bergen, Norway
- Hjort Centre for Marine Ecosystem Dynamics, Bergen, Norway
| | - Åse Husebø
- Institute of Marine Research, Bergen, Norway
| | - Jane A. Godiksen
- Institute of Marine Research, Bergen, Norway
- Hjort Centre for Marine Ecosystem Dynamics, Bergen, Norway
| | - Snæbjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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ShapeR: an R package to study otolith shape variation among fish populations. PLoS One 2015; 10:e0121102. [PMID: 25803855 PMCID: PMC4372608 DOI: 10.1371/journal.pone.0121102] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 02/09/2015] [Indexed: 11/19/2022] Open
Abstract
ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or Wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or Wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.
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