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Jabłońska A, Navarro N, Laffont R, Wattier R, Pešić V, Zawal A, Vukić J, Grabowski M. An integrative approach challenges species hypotheses and provides hints for evolutionary history of two Mediterranean freshwater palaemonid shrimps (Decapoda: Caridea). THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1953624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- A. Jabłońska
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - N. Navarro
- EPHE, PSL University, Paris, France
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - R. Laffont
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - R. Wattier
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - V. Pešić
- Department of Biology, University of Montenegro, Podgorica, Montenegro
| | - A. Zawal
- Department of Invertebrate Zoology and Limnology, Center of Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland
| | - J. Vukić
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M. Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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2
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Fruciano C, Schmidt D, Ramírez Sanchez MM, Morek W, Avila Valle Z, Talijančić I, Pecoraro C, Schermann Legionnet A. Tissue preservation can affect geometric morphometric analyses: a case study using fish body shape. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Abstract
In geometric morphometrics, the extent of variation attributable to non-biological causes (i.e. measurement error) is sometimes overlooked. The effects of this variation on downstream statistical analyses are also largely unknown. In particular, it is unclear whether specimen preservation induces substantial variation in shape and whether such variation affects downstream statistical inference. Using a combination of empirical fish body shape data and realistic simulations, we show that preservation introduces substantial artefactual variation and significant non-random error (i.e. bias). Most changes in shape occur when fresh fish are frozen and thawed, whereas a smaller change in shape is observed when frozen and thawed fish are fixed in formalin and transferred to ethanol. Surprisingly, we also show that, in our case, preservation produces only minor effects on three downstream analyses of shape variation: classification using canonical variate analysis, permutation tests of differences in means and computations of differences in mean shape between groups. Even mixing of differently preserved specimens has a relatively small effect on downstream analyses. However, we suggest that mixing fish with different preservation should still be avoided and discuss the conditions in which this practice might be justified.
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Affiliation(s)
- Carmelo Fruciano
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Dominik Schmidt
- Department of Modeling and Systems Analysis, Hochschule Geisenheim University, Geisenheim, Germany
| | - Marcia Maria Ramírez Sanchez
- Laboratorio de Biometría y Biología Pesquera, Facultad de Estudios Superiores Zaragoza, UNAM, Mexico City, Mexico
| | - Witold Morek
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - Zamira Avila Valle
- Laboratorio de Biometría y Biología Pesquera, Facultad de Estudios Superiores Zaragoza, UNAM, Mexico City, Mexico
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3
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Evans KM, Williams KL, Westneat MW. Do Coral Reefs Promote Morphological Diversification? Exploration of Habitat Effects on Labrid Pharyngeal Jaw Evolution in the Era of Big Data. Integr Comp Biol 2019; 59:696-704. [DOI: 10.1093/icb/icz103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Coral reefs are complex marine habitats that have been hypothesized to facilitate functional specialization and increased rates of functional and morphological evolution. Wrasses (Labridae: Percomorpha) in particular, have diversified extensively in these coral reef environments and have evolved adaptations to further exploit reef-specific resources. Prior studies have found that reef-dwelling wrasses exhibit higher rates of functional evolution, leading to higher functional variation than in non-reef dwelling wrasses. Here, we examine this hypothesis in the lower pharyngeal tooth plate of 134 species of reef and non-reef-associated labrid fishes using high-resolution morphological data in the form of micro-computed tomography scans and employing three-dimensional geometric morphometrics to quantify shape differences. We find that reef-dwelling wrasses do not differ from non-reef-associated wrasses in morphological disparity or rates of shape evolution. However, we find that some reef-associated species (e.g., parrotfishes and tubelips) exhibit elevated rates of pharyngeal jaw shape evolution and have colonized unique regions of morphospace. These results suggest that while coral reef association may provide the opportunity for specialization and morphological diversification, species must still be able to capitalize on the ecological opportunities to invade novel niche space, and that these novel invasions may prompt rapid rates of morphological evolution in the associated traits that allow them to capitalize on new resources.
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Affiliation(s)
- Kory M Evans
- Department of Fisheries Wildlife and Conservation Biology, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul, MN 55108, USA
| | - Keiffer L Williams
- Department of Fisheries Wildlife and Conservation Biology, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, St. Paul, MN 55108, USA
| | - Mark W Westneat
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
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Raffini F, Fruciano C, Meyer A. Morphological and genetic correlates in the left–right asymmetric scale-eating cichlid fish of Lake Tanganyika. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
- International Max Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse, Konstanz, Germany
- International Max Planck Research School (IMPRS) for Organismal Biology, University of Konstanz, Konstanz, Germany
- Radcliffe Institute for Advance Study, Harvard University, Cambridge, MA, USA
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5
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Fruciano C, Franchini P, Kovacova V, Elmer KR, Henning F, Meyer A. Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish. Nat Commun 2016; 7:12736. [PMID: 27597183 PMCID: PMC5025864 DOI: 10.1038/ncomms12736] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 07/28/2016] [Indexed: 01/03/2023] Open
Abstract
Our understanding of how biological diversity arises is limited, especially in the case of speciation in the face of gene flow. Here we investigate the genomic basis of adaptive traits, focusing on a sympatrically diverging species pair of crater lake cichlid fishes. We identify the main quantitative trait loci (QTL) for two eco-morphological traits: body shape and pharyngeal jaw morphology. These traits diverge in parallel between benthic and limnetic species in the repeated adaptive radiations of this and other fish lineages. Remarkably, a single chromosomal region contains the highest effect size QTL for both traits. Transcriptomic data show that the QTL regions contain genes putatively under selection. Independent population genomic data corroborate QTL regions as areas of high differentiation between the sympatric sister species. Our results provide empirical support for current theoretical models that emphasize the importance of genetic linkage and pleiotropy in facilitating rapid divergence in sympatry.
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Affiliation(s)
- Carmelo Fruciano
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Paolo Franchini
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Viera Kovacova
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Department for Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Kathryn R Elmer
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.,Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow G12 8QQ, UK
| | - Frederico Henning
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie and Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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6
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Raffini F, Fruciano C, Franchini P, Meyer A. Towards understanding the genetic basis of mouth asymmetry in the scale-eating cichlidPerissodus microlepis. Mol Ecol 2016; 26:77-91. [DOI: 10.1111/mec.13699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology; Max-Planck-Institut für Ornithologie; Am Obstberg 1 78315 Radolfzell Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie; Department of Biology; University of Konstanz; Universitätsstrasse 10 78464 Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology; Max-Planck-Institut für Ornithologie; Am Obstberg 1 78315 Radolfzell Germany
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Fruciano C, Franchini P, Raffini F, Fan S, Meyer A. Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus. Ecol Evol 2016; 6:4102-14. [PMID: 27516867 PMCID: PMC4877357 DOI: 10.1002/ece3.2184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 04/18/2016] [Accepted: 04/22/2016] [Indexed: 12/14/2022] Open
Abstract
Established empirical cases of sympatric speciation are scarce, although there is an increasing consensus that sympatric speciation might be more common than previously thought. Midas cichlid fish are one of the few substantiated cases of sympatric speciation, and they formed repeated radiations in crater lakes. In contrast, in the same environment, such radiation patterns have not been observed in other species of cichlids and other families of fish. We analyze morphological and genetic variation in a cichlid species (Archocentrus centrarchus) that co-inhabits several crater lakes with the Midas species complex. In particular, we analyze variation in body and pharyngeal jaw shape (two ecologically important traits in sympatrically divergent Midas cichlids) and relate that to genetic variation in mitochondrial control region and microsatellites. Using these four datasets, we analyze variation between and within two Nicaraguan lakes: a crater lake where multiple Midas cichlids have been described and a lake where the source population lives. We do not observe any within-lake clustering consistent across morphological traits and genetic markers, suggesting the absence of sympatric divergence in A. centrarchus. Genetic differentiation between lakes was low and morphological divergence absent. Such morphological similarity between lakes is found not only in average morphology, but also when analyzing covariation between traits and degree of morphospace occupation. A combined analysis of the mitochondrial control region in A. centrarchus and Midas cichlids suggests that a difference between lineages in the timing of crater lake colonization cannot be invoked as an explanation for the difference in their levels of diversification. In light of our results, A. centrarchus represents the ideal candidate to study the genomic differences between these two lineages that might explain why some lineages are more likely to speciate and diverge in sympatry than others.
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Affiliation(s)
- Carmelo Fruciano
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 1078457 Konstanz Germany; School of Earth, Environmental & Biological Sciences Queensland University of Technology Brisbane Qld 4000 Australia
| | - Paolo Franchini
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Francesca Raffini
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 1078457 Konstanz Germany; International Max Planck Research School (IMPRS) for Organismal Biology Max-Planck-Institut für Ornithologie Am Obstberg 178315 Radolfzell Germany
| | - Shaohua Fan
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Department of Biology Chair of Zoology and Evolutionary Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
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QUINTELA FERNANDOM, FORNEL RODRIGO, FREITAS THALESR. Geographic variation in skull shape of the water rat Scapteromys tumidus (Cricetidae, Sigmodontinae): isolation-by-distance plus environmental and geographic barrier effects? ACTA ACUST UNITED AC 2016; 88 Suppl 1:451-66. [DOI: 10.1590/0001-3765201620140631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/30/2015] [Indexed: 11/22/2022]
Abstract
ABSTRACT The geographic variation in skull size and shape of the swamp rat Scapteromys tumidus was examined in samples from eight geographic clusters in almost of its distribution in southern Brazil and Uruguay. For analysis we used two-dimensional geometric morphometric methods for dorsal, ventral and lateral views of the skull. The geometric descriptors showed no significant differences in skull size between geographic clusters, while differences in shape were highly significant. We found a significant and moderate correlation between geographic and morphological distances, corroborating the isolation-by-distance model. Samples from the Rio Grande do Sul central coastal plain were the most differentiated, segregating completely from all other samples in canonical variate analysis for the dorsal view. The most visible variable regions in skull were the zygomatic arch (mainly the squamosal root of zygomatic) and the lateral braincase borders. Once correlation between geographic and morphological distances were not strong, it is possible that other factors (environmental heterogeneity and/or geographic barriers) may are acting in S. tumidus skull differentiation.
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Affiliation(s)
| | - RODRIGO FORNEL
- Universidade Regional Integrada do Alto Uruguai e das Missões, Brazil
| | - THALES R.O. FREITAS
- Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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9
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Measurement error in geometric morphometrics. Dev Genes Evol 2016; 226:139-58. [DOI: 10.1007/s00427-016-0537-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/28/2015] [Indexed: 10/22/2022]
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10
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Schmieder DA, Benítez HA, Borissov IM, Fruciano C. Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches. PLoS One 2015; 10:e0127043. [PMID: 25965335 PMCID: PMC4428882 DOI: 10.1371/journal.pone.0127043] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/11/2015] [Indexed: 11/19/2022] Open
Abstract
External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species--in this case European horseshoe bats (Rhinolophidae, Chiroptera)--based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern.
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Affiliation(s)
- Daniela A. Schmieder
- Sensory Ecology Group, Max Planck Institute for Ornithology, Seewiesen, Germany
- Conservation Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Hugo A. Benítez
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Ivailo M. Borissov
- Sensory Ecology Group, Max Planck Institute for Ornithology, Seewiesen, Germany
- Department of Zoology, University of Tel Aviv, Tel Aviv, Israel
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Biological, Zoological and Environmental Sciences, University of Catania, Catania, Italy
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Gunter HM, Fan S, Xiong F, Franchini P, Fruciano C, Meyer A. Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Mol Ecol 2013; 22:4516-31. [PMID: 23952004 DOI: 10.1111/mec.12417] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/25/2013] [Accepted: 05/28/2013] [Indexed: 11/29/2022]
Abstract
Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genes-markers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.
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Affiliation(s)
- Helen M Gunter
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457, Konstanz, Germany
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FRUCIANO CARMELO, TIGANO CONCETTA, FERRITO VENERA. Geographical and morphological variation within and between colour phases inCoris julis(L. 1758), a protogynous marine fish. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01700.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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