1
|
Phylogeography of Sarmarutilus rubilio (Cypriniformes: Leuciscidae): Complex Genetic Structure, Clues to a New Cryptic Species and Further Insights into Roaches Phylogeny. Genes (Basel) 2022; 13:genes13061071. [PMID: 35741833 PMCID: PMC9222716 DOI: 10.3390/genes13061071] [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: 05/04/2022] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Italy hosts a large number of endemic freshwater fish species due to complex geological events which promoted genetic differentiation and allopatric speciation. Among them, the South European roach Sarmarutilus rubilio inhabits various freshwater environments in three different ichthyogeographic districts. We investigated the genetic diversity of S. rubilio using two different mitochondrial markers (COI and CR), aiming to define its relationship with other similar taxa from the Balkan area and, from a phylogeographic perspective, test the effects of past hydrogeological dynamics of Italian river basins on its genetic structure and demographic history. Our analysis highlighted a marked genetic divergence between S. rubilio and all other roach species and, among Italian samples, revealed the existence of three deeply divergent geographic haplogroups, named A, B and C. Haplogroup C likely corresponds to a new putative cryptic species and is located at the northern border of the South European roach range; haplogroup B is restricted to Southern Italy; and haplogroup A is widespread across the entire range and in some sites it is in co-occurrence with C or B. Their origin is probably related to the tectonic uplifting of the Apuan Alps in the north and of the Colli Albani Volcano in the south during the Pleistocene, which promoted isolation and vicariance followed by secondary contacts.
Collapse
|
2
|
Corral‐Lou A, Perea S, Perdices A, Doadrio I. Quaternary geomorphological and climatic changes associated with the diversification of Iberian freshwater fishes: The case of the genus
Cobitis
(Cypriniformes, Cobitidae). Ecol Evol 2022; 12:e8635. [PMID: 35261740 PMCID: PMC8888266 DOI: 10.1002/ece3.8635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
We studied the population genetic structure of Cobitis vettonica, an endangered freshwater fish species endemic to the Iberian Peninsula, in order to propose a biogeographic model of the responses of species to the multiple changes that occurred in the Iberian hydrological system during the Quaternary period. We also deciphered the relationship of C. vettonica with its sister species C. paludica, particularly in sympatric areas, and provide genetic information for conservation purposes. To achieve this goal, we analyzed both mitochondrial and nuclear data (the cytochrome b and the nuclear recombination activating 1 genes) and a battery of single‐nucleotide polymorphisms (SNPs) of 248 individuals of C. vettonica or C. paludica from 38 localities, including some sympatric ones, covering the entire distribution area of C. vettonica. We highlight the important role played by the hydrogeomorphological processes and climatic changes that occurred in the Iberian Peninsula during the Quaternary on both the population structure of C. vettonica and its relationship with its sister species C. paludica. Our results support the genetic introgression of populations at the eastern limit of the distribution of C. vettonica. Furthermore, we postulate genetic introgression in sympatric areas. Finally, we propose the establishment or expansion of four Operational Conservation Units (OCUs) for C. vettonica, and highlight the threat faced by its populations due to the low level of genetic diversity detected for some of its populations and genetic introgression with C. paludica, which could eventually displace C. vettonica, resulting in a loss of diversity in this species.
Collapse
Affiliation(s)
- Andrea Corral‐Lou
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
- Consultores en Biología de la Conservación S.L. Madrid Spain
| | - Silvia Perea
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
- Instituto de Biología Departamento de Zoología Universidad Nacional Autónoma de México Ciudad de México México
| | - Anabel Perdices
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| |
Collapse
|
3
|
Rossi AR, Petrosino G, Crescenzo S, Milana V, Talarico L, Martinoli M, Rakaj A, Lorenzoni M, Carosi A, Ciuffardi L, Tancioni L. Phylogeography and population structure of Squalius lucumonis: A baseline for conservation of an Italian endangered freshwater fish. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
4
|
Corral‐Lou A, Perea S, Aparicio E, Doadrio I. Phylogeography and species delineation of the genusPhoxinusRafinesque, 1820 (Actinopterygii: Leuciscidae) in the Iberian Peninsula. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12320] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andrea Corral‐Lou
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| | - Silvia Perea
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| | - Enric Aparicio
- Institute of Aquatic Ecology University of Girona Girona Spain
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| |
Collapse
|
5
|
Integrative study of population structure of Telestes dabar, the strictly endemic cyprinid species from the Dinaric karst on the Balkan Peninsula. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1302-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
6
|
Palandačić A, Naseka A, Ramler D, Ahnelt H. Contrasting morphology with molecular data: an approach to revision of species complexes based on the example of European Phoxinus (Cyprinidae). BMC Evol Biol 2017; 17:184. [PMID: 28793855 PMCID: PMC5549366 DOI: 10.1186/s12862-017-1032-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/02/2017] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European Phoxinus phoxinus species complex was used. RESULTS The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely P. ketmaieri, P. likai, and P. apollonicus. For three species (P. strandjae, P. strymonicus, P. morella), further investigation with increased data sampling was suggested, while two primary hypotheses, P. bigerri and P. colchicus, were supported as secondary species hypotheses. Finally, six of the primary species hypotheses (P. phoxinus, P. lumaireul, P. karsticus, P. septimanae, P. marsilii and P. csikii) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis. CONCLUSION The approach has proven useful for revision of species complexes, and the study can serve as an overview of the Phoxinus genus in Europe, as well as a solid basis for further work.
Collapse
Affiliation(s)
- Anja Palandačić
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria.
| | - Alexander Naseka
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
- Department of Ichthyology and Hydrobiology, Faculty for Biology and Soil, Saint Petersburg State University, 7/9 Universitetskaya nab, St. Petersburg, 199034, Russia
| | - David Ramler
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Harald Ahnelt
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| |
Collapse
|
7
|
Gouskov A, Vorburger C. Postglacial recolonizations, watershed crossings and human translocations shape the distribution of chub lineages around the Swiss Alps. BMC Evol Biol 2016; 16:185. [PMID: 27612944 PMCID: PMC5017123 DOI: 10.1186/s12862-016-0750-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/19/2016] [Indexed: 11/25/2022] Open
Abstract
Background Distributions of European fish species were shaped by glaciations and the geological history of river networks until human activities partially abrogated the restrictions of biogeographical regions. The nearby origins of the Rhine, Rhone, Danube and Po rivers in the Swiss Alps allow the examination of historical and human-influenced patterns in fish genetic structure over a small geographic scale. We investigated these patterns in the widespread European chub (Squalius cephalus) from the Rhone, Rhine and Danube catchments and its proposed southern sister species Italian chub (Squalius squalus) from the Po catchment. Results A phylogenetic tree constructed from mitochondrial Cytochrome b and COI sequences was consistent with earlier work in that it showed a separation of European chub and Italian chub, which was also reflected in microsatellite allele frequencies, morphological traits and shape differences quantified by geometric morphometrics. A new finding was that the predominant mitochondrial haplotype of European chub from the Rhine and Rhone catchments was also discovered in some individuals from Swiss populations of the Italian chub, presumably as a result of human translocation. Consistent with postglacial recolonizations from multiple refugia along the major rivers, the nuclear genetic structure of the European chub largely reflected drainage structure, but it was modified by watershed crossings between Rhine and Rhone near Lake Geneva as well as between Danube and Rhine near Lake Constance. Conclusion Our study adds new insights into the cyprinid colonization history of central Europe by showing that multiple processes shaped the distribution of different chub lineages around the Swiss Alps. Interestingly, we find evidence that cross-catchment migration has been mediated by unusual geological events such as drainage captures or watershed crossings facilitated by retreating glaciers, as well as evidence that human transport has interfered with the historical distribution of these fish (European chub haplotypes present in the Italian chub). The desirable preservation of evolutionarily distinct lineages will thus require the prevention of further translocations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0750-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexandre Gouskov
- Eawag, Aquatic Ecology Department, Überlandstrasse 133, P.O.Box 611, 8600, Dübendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092, Zürich, Switzerland
| | - Christoph Vorburger
- Eawag, Aquatic Ecology Department, Überlandstrasse 133, P.O.Box 611, 8600, Dübendorf, Switzerland. .,Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092, Zürich, Switzerland.
| |
Collapse
|
8
|
Palandačić A, Bravničar J, Zupančič P, Šanda R, Snoj A. Molecular data suggest a multispecies complex of Phoxinus (Cyprinidae) in the Western Balkan Peninsula. Mol Phylogenet Evol 2015; 92:118-23. [DOI: 10.1016/j.ympev.2015.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
|
9
|
Lucentini L, Chiesa S, Giannetto D, Pompei L, Natali M, Sala P, Volta P, Lorenzoni M, Fontaneto D. Integrative taxonomy does not support the occurrence of two species of the Squalius squalus complex (Actinopterygii, Cypriniformes, Cyprinidae) in Italy. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
10
|
Hinsinger DD, Gaudeul M, Couloux A, Bousquet J, Frascaria-Lacoste N. The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation. Mol Phylogenet Evol 2014; 77:223-37. [PMID: 24795215 DOI: 10.1016/j.ympev.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.
Collapse
Affiliation(s)
- Damien D Hinsinger
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France; Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 'Origine, Structure et Evolution de la Biodiversité', 16 rue Buffon, CP 39, F-75005 Paris, France.
| | - Arnaud Couloux
- Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Nathalie Frascaria-Lacoste
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France.
| |
Collapse
|
11
|
Barão KR, Gonçalves GL, Mielke OHH, Kronforst MR, Moreira GRP. Species boundaries inPhilaethriabutterflies: an integrative taxonomic analysis based on genitalia ultrastructure, wing geometric morphometrics, DNA sequences, and amplified fragment length polymorphisms. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Kim R. Barão
- PPG Biologia Animal; Departamento de Zoologia; Universidade Federal do Rio Grande do Sul; Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435 Porto Alegre RS 91501-970 Brazil
| | - Gislene L. Gonçalves
- PPG Genética e Biologia Molecular; Departamento de Genética; Universidade Federal do Rio Grande do Sul; Avenida Bento Gonçalves, 9500 Porto Alegre RS 91501-970 Brazil
- Instituto de Alta Investigación; Universidad de Tarapacá; Antofagasta 1520 Arica Chile
| | - Olaf H. H. Mielke
- Departamento de Zoologia; Universidade Federal do Paraná; Caixa Postal 19020 Curitiba PR 81531-980 Brazil
| | - Marcus R. Kronforst
- Department of Ecology and Evolution; University of Chicago; Chicago IL 60637 USA
| | - Gilson R. P. Moreira
- Departamento de Zoologia; Universidade Federal do Rio Grande do Sul; Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-970 Porto Alegre RS 91501-970 Brazil
| |
Collapse
|
12
|
Russo T, Scardi M, Cataudella S. Applications of self-organizing maps for ecomorphological investigations through early ontogeny of fish. PLoS One 2014; 9:e86646. [PMID: 24466185 PMCID: PMC3900585 DOI: 10.1371/journal.pone.0086646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
We propose a new graphical approach to the analysis of multi-temporal morphological and ecological data concerning the life history of fish, which can typically serves models in ecomorphological investigations because they often undergo significant ontogenetic changes. These changes can be very complex and difficult to describe, so that visualization, abstraction and interpretation of the underlying relationships are often impeded. Therefore, classic ecomorphological analyses of covariation between morphology and ecology, performed by means of multivariate techniques, may result in non-exhaustive models. The Self Organizing map (SOM) is a new, effective approach for pursuing this aim. In this paper, lateral outlines of larval stages of gilthead sea bream (Sparus aurata) and dusky grouper (Epinephelus marginatus) were recorded and broken down using by means of Elliptic Fourier Analysis (EFA). Gut contents of the same specimens were also collected and analyzed. Then, shape and trophic habits data were examined by SOM, which allows both a powerful visualization of shape changes and an easy comparison with trophic habit data, via their superimposition onto the trained SOM. Thus, the SOM provides a direct visual approach for matching morphological and ecological changes during fish ontogenesis. This method could be used as a tool to extract and investigate relationships between shape and other sinecological or environmental variables, which cannot be taken into account simultaneously using conventional statistical methods.
Collapse
Affiliation(s)
- Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, “Tor Vergata” University of Rome, Rome, Italy
- * E-mail:
| | - Michele Scardi
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, “Tor Vergata” University of Rome, Rome, Italy
| | - Stefano Cataudella
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, “Tor Vergata” University of Rome, Rome, Italy
| |
Collapse
|