1
|
Reier S, Kruckenhauser L, Snoj A, Trontelj P, Palandačić A. The minnow Phoxinus lumaireul (Leuciscidae) shifts the Adriatic-Black Sea basin divide in the north-western Dinaric Karst region. ECOHYDROLOGY : ECOSYSTEMS, LAND AND WATER PROCESS INTERACTIONS, ECOHYDROGEOMORPHOLOGY 2022; 15:e2449. [PMID: 36245897 PMCID: PMC9539529 DOI: 10.1002/eco.2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/25/2022] [Accepted: 06/26/2022] [Indexed: 06/16/2023]
Abstract
Karst landscapes are characterized by intermittent and sinking streams. The most common method used to study underground hydrological connections in karst is tracing tests. However, a more biologically oriented approach has been suggested: analysis of the genetic structure of aquatic organisms. Biological tracers can be sought among trogloxenes, that is, surface species that occasionally enter caves and groundwater. One such example is the fish genus Phoxinus, which exhibits high genetic diversity and complex phylogeography in the Balkan Peninsula. In the north-western Dinaric Karst, the complex hydrological network was digitalized in 2020. Contemporaneously, Phoxinus lumaireul populations in the Slovenian Dinaric Karst were intensively sampled and analysed for fragments of two mitochondrial genes and one nuclear gene. The derived phylogeographic structure and data on hydrological connections were compared to evaluate support for three alternative scenarios: The genetic structure (1) is a consequence of the ongoing geneflow through underground connections, (2) reflects a previous hydrological network or (3) is an outcome of anthropogenic translocations. The results suggest that the first two scenarios seem to have played a major role, while the third has not had profound effects on the genetic composition. Comparison between the genetic structure of Slovenian Dinaric Karst sampling sites and that of hydrologically isolated reference sampling sites indicated a greater genetic connectivity in the former. Moreover, the range of Adriatic (1a) and Black Sea (1c) haplotypes does not correspond to the Adriatic-Black Sea basin divide but is shifted northwards.
Collapse
Affiliation(s)
- Susanne Reier
- First Zoological DepartmentNatural History Museum ViennaViennaAustria
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Luise Kruckenhauser
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
- Central Research LaboratoriesNatural History Museum ViennaViennaAustria
| | - Aleš Snoj
- Department of Animal Science, Biotechnical FacultyUniversity of LjubljanaDomžaleSlovenia
| | - Peter Trontelj
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Anja Palandačić
- First Zoological DepartmentNatural History Museum ViennaViennaAustria
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| |
Collapse
|
2
|
Buj I, Knjaz M, Ćaleta M, Marčić Z, Ivić L, Onorato L, Šanda R, Vukić J, Horvatić S, Zanella D, Mustafić P. Phylogeographic pattern, genetic diversity, and evolutionary history of the enigmatic freshwater fish species
Aulopyge huegelii
(Actinopterygii: Cyprinidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivana Buj
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Mia Knjaz
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Marko Ćaleta
- Faculty of Teacher Education University of Zagreb Zagreb Croatia
| | - Zoran Marčić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Lucija Ivić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Lucija Onorato
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | | | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Sven Horvatić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Davor Zanella
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Perica Mustafić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| |
Collapse
|
3
|
Mazungula DN, Chakona A. An integrative taxonomic review of the Natal mountain catfish, Amphilius natalensis Boulenger 1917 (Siluriformes, Amphiliidae), with description of four new species. JOURNAL OF FISH BIOLOGY 2021; 99:219-239. [PMID: 33635552 DOI: 10.1111/jfb.14714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
An integrative taxonomic analysis combining mitochondrial cytochrome oxidase subunit I sequences, morphology, colour pattern and two species delimitation approaches revealed the existence of five lineages within the Natal mountain catfish, Amphilius natalensis, in southern Africa. These lineages are separated by substantial genetic divergences (1.6%-9.46%), and they can be consistently distinguished from one another based on a combination of morphology and colour pattern differences. Additionally, the lineages are allopatrically distributed and confined to isolated river systems draining discrete mountain ranges, which makes gene flow among them unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other four lineages represent new species to science which are described as Amphilius zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zambezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov., endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an updated identification key for the mountain catfishes of southern Africa is provided.
Collapse
Affiliation(s)
- Daniel Nkosinathi Mazungula
- National Research Foundation - South African Institute for Aquatic Biodiversity, Makhanda (Grahamstown), South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda (Grahamstown), South Africa
| | - Albert Chakona
- National Research Foundation - South African Institute for Aquatic Biodiversity, Makhanda (Grahamstown), South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda (Grahamstown), South Africa
| |
Collapse
|
4
|
Widayanti R, Kusumaastuti KA, Novi JM, Adani FK, Gultom CRP, Prastiti AD, Nugroho HA, Pakpahan S. Genetic variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene. Vet World 2021; 14:751-757. [PMID: 33935423 PMCID: PMC8076454 DOI: 10.14202/vetworld.2021.751-757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial 12S ribosomal RNA (rRNA) gene. Materials and Methods: In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial 12S rRNA gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The 12S rRNA sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships. Results: In total, 178 variation sites in the 12S rRNA gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08. Conclusion: Indonesian catfish were divided into four clades based on the 12S rRNA gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with Hemibagrus nemurus, the catfish EM was grouped with Mystus vittatus, the catfish BSBJ was grouped with Pangasius pangasius, and the catfish PD and BF were grouped with Netuma thalassina.
Collapse
Affiliation(s)
- Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ken Ayik Kusumaastuti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Joana Martha Novi
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Khairuna Adani
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Catrine Relia Patrecia Gultom
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayuning Devina Prastiti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Herjuno Ari Nugroho
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46, Cibinong, West Java, Indonesia
| | - Suhendra Pakpahan
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Jakarta-Bogor KM 46, Cibinong, West Java, Indonesia
| |
Collapse
|
5
|
Megarani DV, Nugroho HA, Andarini ZP, Surbakti YDRBR, Widayanti R. Genetic characterization and phylogenetic study of Indonesian indigenous catfish based on mitochondrial cytochrome B gene. Vet World 2020; 13:96-103. [PMID: 32158157 PMCID: PMC7020122 DOI: 10.14202/vetworld.2020.96-103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022] Open
Abstract
Aims This study aimed to determine the genetic characterization and phylogenetic structure of Indonesian indigenous catfish using cytochrome B (Cyt B) sequences. Materials and Methods The genomes of 26 catfishes caught from nine rivers from nine different geographical locations around Indonesia were analyzed. The tissue isolation method was used to isolate the total genome of the fishes. Furthermore, polymerase chain reaction was done to amplify the mtDNA Cyt B using the CytBF and CytBR primers. Following sequencing, the analysis of genetic variation and the phylogenetic relationship was performed using MEGA version X software. Results Cyt B gene sequencing attained a total of 1139 nucleotides encrypting 379 amino acids for all samples. The ClustalW alignment program using MEGA X software revealed 395 substituted nucleotides, which then translated into 63 amino acid variation sites among all 26 samples. No amino acids in catfish BB were different compared to catfish PM, MP, and KR2,3. Catfish MS had one modified amino acid; KR1 and KS had two different amino acids; BF had 38 different amino acids; EM had 31 different amino acids; and BSBJ had 26 different amino acids compared to catfish BB. The most significant alteration of amino acids was between catfish EM and BF (49 amino acids). Conclusion Indonesian catfish were divided into five clades based on the Cyt B gene. Samples KR and MP (Sumatra); MS and BB (Kalimantan); and PM (Java) were clustered with Hemibagrus nemurus and Hemibagrus wyckioides (Bagridae family). Samples from Kalimantan (KS) and one sample of KR (KR1) from Sumatra were clustered with Sperata seenghala and Hemibagrus spilopterus (Bagridae family). Samples from Java (BSBJ) were clustered with Pseudolais pleurotaenia (Pangasiidae family). Samples EM (Java) were together with Mystus cavasius (Bagridae family). Samples from West Papua were clustered with Potamosilurus latirostris (Ariidae family).
Collapse
Affiliation(s)
- Dorothea Vera Megarani
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Herjuno Ari Nugroho
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, West Java, Indonesia
| | - Zahrah Prawita Andarini
- Veterinary Medicine Undergraduate Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yura Dwi Risa B R Surbakti
- Veterinary Medicine Undergraduate Program, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| |
Collapse
|
6
|
Buj I, Marčić Z, Čavlović K, Ćaleta M, Tutman P, Zanella D, Duplić A, Raguž L, Ivić L, Horvatić S, Mustafić P. Multilocus phylogenetic analysis helps to untangle the taxonomic puzzle of chubs (genus Squalius: Cypriniformes: Actinopteri) in the Adriatic basin of Croatia and Bosnia and Herzegovina. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractFish of the genus Squalius inhabit various freshwater habitats across Europe and Asia, with a particularly high diversity in the Mediterranean area, but the taxonomic status of many populations is still a matter of debate. This study aims to resolve the taxonomic uncertainties of chubs distributed in the Adriatic basin of Croatia and Bosnia and Herzegovina. Phylogenetic reconstruction based on the mitochondrial gene for cytochrome b and two nuclear genes, the recombination activating gene 1 and the rhodopsin gene, reveal high diversity of chubs in the investigated area. Two evolutionary independent groups are revealed: the first comprising the species Squalius illyricus, S. microlepis, S. svallize, S. tenellus and S. zrmanjae, and a second group corresponding with S. squalus. Genetic distinctiveness of species belonging to different groups is high due to their divergence that began in the Middle Miocene. In addition to allopatric speciation as the main force of divergence of Adriatic Squalius species, several instances of natural hybridizations were detected, contributing to the observed diversity. A comparison of phylogenetic scenarios using Bayesian factors corroborated the molecular basis for recognition of six Squalius species in the Adriatic basin, while Squalius janae is confirmed to be a junior synonym of S. squalus.
Collapse
Affiliation(s)
- Ivana Buj
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Zoran Marčić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kristina Čavlović
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Ćaleta
- Faculty of Teacher Education, University of Zagreb, Zagreb, Croatia
| | - Pero Tutman
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Davor Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Aljoša Duplić
- Croatian Agency for Environment and Nature, Zagreb, Croatia
| | - Lucija Raguž
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Lucija Ivić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sven Horvatić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Perica Mustafić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
7
|
Widayanti R, Haryanto A, Artama WT, Pakpahan S. Genetic variation and phylogenetic analysis of Indonesian indigenous catfish based on mitochondrial cytochrome oxidase subunit III gene. Vet World 2019; 12:896-900. [PMID: 31440011 PMCID: PMC6661475 DOI: 10.14202/vetworld.2019.896-900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/09/2019] [Indexed: 11/16/2022] Open
Abstract
Aim This study aimed to analyze the genetic variation and phylogenetic reconstruction of Indonesian indigenous catfish using mitochondrial cytochrome oxidase subunit III sequences. Materials and Methods A total of 19 samples of catfish were collected from seven rivers (Elo [EM], Progo [PM], Kampar [KR], Musi [MP], Mahakam [MS], Kapuas [KS], and Bengawan Solo [BSBJ]) in five different geographical locations in Indonesia. The genome was isolated from the tissue. Mitochondrial DNA cytochrome oxidase subunit III was amplified using polymerase chain reaction (PCR) with CO3F and CO3R primers. The PCR products were sequenced and continued to analyze genetic variation and phylogenetic relationship using MEGA version 7.0 software. Results Cytochrome c oxidase (COX)-III gene sequencing obtained 784 nucleotides encoding 261 amino acids. Sequenced COX-III gene fragments were aligned along with other catfish from Genbank using ClustalW program and genetic diversity among species was analyzed using the MEGA Version 7.0 software. Among all samples, there were substitution mutations at 78 nucleotide sites, and there were 14 variations in amino acids. Catfish from PM, KR, MP, and KS had the same amino acids as Hemibagrus nemurus (KJ573466.1), while EM catfish had eight different amino acids and catfishBSBJhad 12 different amino acids. Conclusion Indonesian catfish divided into four clades. BBSJ Catfish were grouped with Pangasianodon gigas, EM catfish were grouped with Mystus rhegma, and KS catfish were grouped with Hemibagrus spilopterus, while catfish MS, KR, PM, andMP were grouped with H. nemurus.
Collapse
Affiliation(s)
- Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Aris Haryanto
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Wayan Tunas Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta, Indonesia
| | - Suhendra Pakpahan
- Biology Study Program, Faculty of Biotechnology, Duta Wacana Christian University, Yogyakarta, Indonesia
| |
Collapse
|
8
|
Hnátková E, Triantaphyllidis C, Ozouf-Costaz C, Lukáš Choleva, Majtánová Z, Bohlen J, Ráb P. Karyotype and chromosomal characteristics of rDNA of Cobitisstrumicae Karaman, 1955 (Teleostei, Cobitidae) from Lake Volvi, Greece. COMPARATIVE CYTOGENETICS 2018; 12:483-491. [PMID: 30498563 PMCID: PMC6251958 DOI: 10.3897/compcytogen.v12i4.28068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/26/2018] [Indexed: 10/05/2023]
Abstract
The karyotype of Greek cobitid fish Cobitisstrumicae Karaman, 1955, from Lake Volvi, Greece, a representative of one of its two major intraspecific phylogenetic lineages, was analysed by means of sequential Giemsa-staining, C-banding, silver-staining, CMA3 fluorescence banding and also by in situ hybridization (FISH) with rDNA probe. The diploid chromosome number was 2n = 50, karyotype composed of 10 pairs of metacentric to submetacentric and 15 pairs of subtelocentric to acrocentric chromosomes. The nucleolus organizer regions (NORs) as revealed by Ag- and CMA3 staining and FISH were situated in the telomeric region of the fourth submetacentric chromosome pair. The chromosomes contained very low content of C-positive heterochromatin. No heteromorphic sex chromosomes were detected. This first karyotype report for any species of lineage Bicanestrinia Băcescu, 1962 shows a simple karyotype dominated by acrocentric chromosomes and possessing single NOR-bearing chromosome pair. Cytotaxonomic implications of this finding for the taxonomy of the genus Cobitis Linnaeus, 1758 are further discussed.
Collapse
Affiliation(s)
- Eva Hnátková
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Kamýcká 129, Czech RepublicCzech University of Life SciencesPragueCzech Republic
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Costas Triantaphyllidis
- Department of Genetics, Development and Molecular Biology, Faculty of Sciences, School of Biology, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, GreeceAristotle University of ThessalonikiThessalonikiGreece
| | - Catherine Ozouf-Costaz
- Institut de Biologie Paris Seine, UMR 7138 “Evolution”, Sorbonne Universités, Case 5, 7 quai St Bernard, 75952 Paris cedex 05, Paris, FranceSorbonne UniversitésParisFrance
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Joerg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| |
Collapse
|
9
|
Christodoulou MD, Battey NH, Culham A. Can you make morphometrics work when you know the right answer? Pick and mix approaches for apple identification. PLoS One 2018; 13:e0205357. [PMID: 30321222 PMCID: PMC6188776 DOI: 10.1371/journal.pone.0205357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/24/2018] [Indexed: 11/19/2022] Open
Abstract
Morphological classification of living things has challenged science for several centuries and has led to a wide range of objective morphometric approaches in data gathering and analysis. In this paper we explore those methods using apple cultivars, a model biological system in which discrete groups are pre-defined but in which there is a high level of overall morphological similarity. The effectiveness of morphometric techniques in discovering the groups is evaluated using statistical learning tools. No one technique proved optimal in classification on every occasion, linear morphometric techniques slightly out-performing geometric (72.6% accuracy on test set versus 66.7%). The combined use of these techniques with post-hoc knowledge of their individual successes with particular cultivars achieves a notably higher classification accuracy (77.8%). From this we conclude that even with pre-determined discrete categories, a range of approaches is needed where those categories are intrinsically similar to each other, and we raise the question of whether in studies where potentially continuous natural variation is being categorised the level of match between categories is routinely set too high.
Collapse
Affiliation(s)
- Maria D. Christodoulou
- University of Reading Herbarium, Harborne Building, School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Nicholas Hugh Battey
- School of Biological Sciences, University of Reading, Whiteknights Reading, United Kingdom
| | - Alastair Culham
- University of Reading Herbarium, Harborne Building, School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
- * E-mail:
| |
Collapse
|
10
|
Perdices A, Ozeren CS, Erkakan F, Freyhof J. Diversity of spined loaches from Asia Minor in a phylogenetic context (Teleostei: Cobitidae). PLoS One 2018; 13:e0205678. [PMID: 30308027 PMCID: PMC6181420 DOI: 10.1371/journal.pone.0205678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/29/2018] [Indexed: 11/19/2022] Open
Abstract
Accurate determination of species diversity in areas of high endemicity, particularly those lacking comprehensive systematic knowledge, represents a challenge for both taxonomists and conservationists. This need is particularly evident in areas greatly affected by anthropogenic disturbances such as the Eastern Mediterranean and its freshwater environments. To improve our knowledge of Eastern Mediterranean freshwater fishes, we phylogenetically studied Western Palearctic Cobitis species, focusing on those found in Turkey. Overall, our results provide a robust framework to assess the number of species of Cobitis. Phylogenetic reconstructions based on mitochondrial (cyt b) and nuclear (RAG1) sequences show seven major clades (Clades 1-7) grouping all Western Palearctic Cobitis species, except C. melanoleuca. In general, each major clade comprises Cobitis species that inhabit geographically close areas and have similar secondary sexual characters. Multiple divergent lineages were identified in our analyses, some of which were highly divergent such as the ones inhabiting Turkish freshwaters. Moreover, in some analyses, several of the identified lineages were incongruent with a priori defined species. Furthermore, our analyses identified eight potentially new candidate species, six that had been suggested in previous studies and two that are reported here for the first time. Our results reveal Turkey as the area with the greatest diversity of spined loaches in the Mediterranean.
Collapse
Affiliation(s)
- Anabel Perdices
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- * E-mail:
| | - Cevher S. Ozeren
- Department of Biology, Faculty of Science, University of Ankara, Ankara, Turkey
| | - Füsun Erkakan
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe Campus, Ankara, Turkey
| | - Jörg Freyhof
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| |
Collapse
|
11
|
Betancourt-Resendes I, Pérez-Rodríguez R, Domínguez-Domínguez O. Speciation of silverside Chirostoma attenuatum
(Pisces: Atheriniformes) in Central Mexico. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Isaí Betancourt-Resendes
- Programa Institucional de Doctorado en Ciencias Biológicas; Facultad de Biología; Universidad Michoacana de San Nicolás de Hidalgo; Morelia Michoacán México
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática; Facultad de Biología; Universidad Michoacana de San Nicolás de Hidalgo; Morelia Michoacán México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática; Facultad de Biología; Universidad Michoacana de San Nicolás de Hidalgo; Morelia Michoacán México
| |
Collapse
|
12
|
Tutman P, Buj I, Ćaleta M, Hamzić A, KorjeniĆ E, Adrović A, Glamuzina B. Status and distribution of spined loaches (Cobitidae) and stone loaches (Nemacheilidae) in Bosnia and Herzegovina. FOLIA ZOOLOGICA 2017. [DOI: 10.25225/fozo.v66.i4.a2.2017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Pero Tutman
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - Ivana Buj
- University of Zagreb, Faculty of Science, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Marko Ćaleta
- University of Zagreb, Faculty of Teacher Education, Savska cesta 77, 10000 Zagreb, Croatia
| | - Adem Hamzić
- University of Sarajevo, Faculty of Science, Zmaja od Bosne 33–35, 71000 Sarajevo, Bosnia and Herzegovina;,
| | - Enad KorjeniĆ
- University of Sarajevo, Faculty of Science, Zmaja od Bosne 33–35, 71000 Sarajevo, Bosnia and Herzegovina;,
| | - Avdul Adrović
- University of Tuzla, Faculty of Science, Univerzitetska 4, 75000 Tuzla, Bosnia and Herzegovina
| | - Branko Glamuzina
- University of Dubrovnik, Department for Aquaculture, Ćira Carića 4, 20000 Dubrovnik, Croatia
| |
Collapse
|
13
|
Patil TS, Tamboli AS, Patil SM, Bhosale AR, Govindwar SP, Muley DV. Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae). C R Biol 2016; 339:364-70. [PMID: 27427438 DOI: 10.1016/j.crvi.2016.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/24/2016] [Accepted: 06/03/2016] [Indexed: 11/15/2022]
Abstract
Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution.
Collapse
|
14
|
Nakajima J. Cobitis takenoi sp. n. (Cypriniformes, Cobitidae): a new spined loach from Honshu Island, Japan. Zookeys 2016:119-28. [PMID: 27103876 PMCID: PMC4829672 DOI: 10.3897/zookeys.568.7733] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/27/2016] [Indexed: 11/25/2022] Open
Abstract
A new species of spined loach, Cobitistakenoisp. n., is described based on the holotype and ten paratypes collected from Tango District, Honshu Island, Japan. The new species is distinguished by a combination of the following character states: 1) the lamina circularis at the base of the pectoral fin in adult male having a simple roundish plate form; 2) a narrowing of the upper segments of the first branched ray of the pectoral fin; 3) a short maxillary barbel whose length equals diameter of the eye; 4) 14 prepelvic myotomes, and 5) L3 and L5 well developed, forming longitudinal obvious stripes in males during the spawning season.
Collapse
Affiliation(s)
- Jun Nakajima
- Fukuoka Institute of Health and Environmental Sciences, Mukaizano 39, Dazaifu, Fukuoka 818-0135, Japan
| |
Collapse
|
15
|
Previšić A, Gelemanović A, Urbanič G, Ternjej I. Cryptic diversity in the Western Balkan endemic copepod: Four species in one? Mol Phylogenet Evol 2016; 100:124-134. [PMID: 27063254 DOI: 10.1016/j.ympev.2016.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 10/22/2022]
Abstract
We use mitochondrial (mtCOI) and nuclear (nH3) sequence data to investigate differentiation of Eudiaptomus hadzici, a freshwater copepod endemic to the Western Balkans. E. hadzici has a disjunct distribution and morphological differences were observed at regional scale. In the current study 6 out of 7 known populations are included. We applied several species delimiting approaches, distance based methods (K2P p-distance and Automatic Barcode Gap Discovery, ABGD) using the mtCOI, Bayesian phylogeny and the Bayesian method implemented in bPTP and BPP programs using the concatenated sequences of both genes. Phylogenetic and species delimitation analyses all suggest that the nominal species E. hadzici consists of four isolated, cryptic evolutionary lineages in the Western Balkans. Each of the four lineages inhabits a single lake or a group of lakes in close proximity. They exhibit major differences in secondary sexual characters, e.g. right antennule in males. Denticulation of spine on 13th segment is substantially distinct among the four lineages, having different number and shape of tooth-like protrusions. Gene flow and dispersal are restricted to very small spatial scale, but with local differences, implying that diverse historical and contemporary processes are operating at small spatial scales in E. hadzici. In order to further examine spatial and temporal diversification patterns, we constructed a dated species tree analysis using (*)BEAST. Due to lack of reliable calibration points and taxa specific evolutionary rates, two evolutionary rates were applied and the faster one (2.6% myr) seems more plausible considering the geological history of the region. The divergence of E. hadzici lineages is dated from Early Miocene onwards with geographically close lineages diverging more recently, Late Miocene to Pleistocene and Pleistocene, respectively. Overall, our findings shed light on cryptic genetic complexity of endemics in one of European biodiversity hotspots. Moreover, this study represents one further example of integrative taxonomy, linking DNA methodology and classical taxonomy based on morphology. Therefore, it lays groundwork for future taxonomy and biogeography of freshwater microcrustaceans in the region.
Collapse
Affiliation(s)
- Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia.
| | - Andrea Gelemanović
- School of Medicine, University of Split, Šoltanska 2, 21000 Split, Croatia
| | - Gorazd Urbanič
- Institute for Water of the Republic of Slovenia, Hajdrihova 28 c, 1000 Ljubljana, Slovenia
| | - Ivančica Ternjej
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| |
Collapse
|
16
|
Stierandová S, Vukić J, Vasil’eva ED, Zogaris S, Shumka S, Halačka K, Vetešník L, Švátora M, Nowak M, Stefanov T, Koščo J, Mendel J. A multilocus assessment of nuclear and mitochondrial sequence data elucidates phylogenetic relationships among European spirlins (Alburnoides, Cyprinidae). Mol Phylogenet Evol 2016; 94:479-491. [DOI: 10.1016/j.ympev.2015.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 01/12/2023]
|
17
|
Buj I, Šanda R, Marčić Z, Ćaleta M, Mrakovčić M. Sexual dimorphism of five Cobitis species (Cypriniformes, Actinopterygii) in the Adriatic watershed. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i2.a2.2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ivana Buj
- Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Radek Šanda
- National Museum, Václavské náměstí 68, 115 79 Prague 1, Czech Republic
| | - Zoran Marčić
- Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Marko Ćaleta
- Faculty of Teacher Education, University of Zagreb, Savska cesta 77, 10000 Zagreb, Croatia
| | - Milorad Mrakovčić
- Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| |
Collapse
|
18
|
Buj I, Ćaleta M, Marčić Z, Šanda R, Vukić J, Mrakovčić M. Different Histories, Different Destinies‒Impact of Evolutionary History and Population Genetic Structure on Extinction Risk of the Adriatic Spined Loaches (Genus Cobitis; Cypriniformes, Actinopterygii). PLoS One 2015; 10:e0131580. [PMID: 26176227 PMCID: PMC4503428 DOI: 10.1371/journal.pone.0131580] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/03/2015] [Indexed: 11/17/2022] Open
Abstract
The region of Balkans is often considered as an ichthyologic "hot spot", with a great number of species and high portion of endemics living in fresh waters in a relatively small area. The Adriatic watershed in Croatia and Herzegovina is inhabited by six spined loach species (genus Cobitis) whose extinction risk estimations were based solely on their extent of occurrence (and/or area of occupancy) and its fragmentation, and conservation proposals do not consider diversity below species level. In this investigation we employed molecular genetic methods to describe present genetic structure of the Adriatic spined loaches and reveal their demographic history. The divergence of the Adriatic lineages inside the genus Cobitis started in Miocene and lasted until Pleistocene epoch. Geological events responsible for shaping recent diversity of spined loaches in the Adriatic basin are: the Dinarid Mountains upwelling, the evolution of Dinaric Lake system, local tectonic activity, river connections during glaciations and differences in sea level. Even though all the investigated species inhabit karstic rivers located in the same geographic area and that were subject of similar geological events, the results obtained reveal great differences in their genetic diversity and structure and point out the necessity of different conservation measures to ensure their future viability. High level of genetic polymorphism is characteristic for species located more to the south. Two species comprised of more than one population have completely different intraspecific structure; populations of C. illyrica are genetically distinct and represent separate evolutionary significant units, whereas intraspecific structure of C. narentana corresponds to metapopulational pattern. Without population genetic data, evolutionary significant units could be easily misidentified. Furthermore, the obtained results affirm that population genetic measurements are able to detect differences among closely located and related species and estimate extinction risk even more accurately than currently applied IUCN criteria.
Collapse
Affiliation(s)
- Ivana Buj
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Ćaleta
- Faculty of Teacher education, University of Zagreb, Zagreb, Croatia
| | - Zoran Marčić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Jasna Vukić
- Department of Ecology, Charles University, Prague, Czech Republic
| | - Milorad Mrakovčić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
19
|
Zanella LN, DeFaveri J, Zanella D, Merilä J, Šanda R, Mrakovčić M. Does predation drive morphological differentiation among Adriatic populations of the three-spined stickleback? Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda N. Zanella
- Department of Zoology; Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
| | - Jacquelin DeFaveri
- Ecological Genetic Research Unit; Department of Biological Sciences; University of Helsinki; PO Box 65 FI-00014 Helsinki Finland
| | - Davor Zanella
- Department of Zoology; Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
| | - Juha Merilä
- Ecological Genetic Research Unit; Department of Biological Sciences; University of Helsinki; PO Box 65 FI-00014 Helsinki Finland
| | - Radek Šanda
- Department of Zoology; National Museum; Václavské nám. 68 11579 Praha 1 Czech Republic
| | - Milorad Mrakovčić
- Department of Zoology; Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
| |
Collapse
|