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Rüber L, Gandolfi A, Foresti D, Paltrinieri L, Splendiani A, Seehausen O. Phylogenetic and biogeographic history of brook lampreys ( Lampetra: Petromyzontidae) in the river basins of the Adriatic Sea based on DNA barcode data. Ecol Evol 2023; 13:e10496. [PMID: 37674653 PMCID: PMC10477476 DOI: 10.1002/ece3.10496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023] Open
Abstract
The Adriatic brook lamprey, Lampetra zanandreai Vladykov 1955, was described from northeastern Italy. Its distribution is thought to include left tributaries of the River Po and the river basins of the Adriatic Sea from the River Po to the River Isonzo/Soča in Italy, Switzerland and Slovenia. It also shows a geographically isolated distribution in the Potenza River on the Adriatic slope in Central Italy. Lampetra from the Neretva River system in Croatia and Bosnia and Herzegovina and the Morača River system in Montenegro that were previously identified as L. zanandreai were recently described as a new species Lampetra soljani Tutman, Freyhof, Dulčić, Glamuzina & Geiger 2017 based on morphological data and a genetic distance between the two species of roughly 2.5% in the DNA barcoding gene cytochrome oxidase I (COI). Since DNA barcodes for L. zanandreai are only available for one population from the upper Po River in northwestern Italy, we generated additional COI nucleotide sequence data of this species from Switzerland, northeastern and central Italy comprising near topotypic material and obtained GenBank sequences of the species from Slovenia to better assess the evolutionary history of the two brook lamprey species in the river basins of the Adriatic Sea. Our data show a low sequence divergence of <1% between L. zanandreai from Switzerland, northeastern and central Italy and Slovenia and the Balkan species L. soljani. However, members of the population previously identified as 'L. zanandreai' from northwest Italy are genetically highly divergent from those of L. zanandreai and likely belong to an undescribed species, L. sp. 'upper Po'. The presence of a unique and highly divergent brook lamprey lineage in the upper Po River suggests that L. zanandreai and Lampetra sp. 'upper Po' may have evolved in separate paleo drainages during the formation of the modern Po Valley subsequent to marine inundations in the Pliocene.
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Affiliation(s)
- Lukas Rüber
- Naturhistorisches Museum BernBernSwitzerland
- Aquatic Ecology & EvolutionInstitute of Ecology and Evolution, University of BernBernSwitzerland
| | - Andrea Gandolfi
- Conservation Genomics Research UnitResearch and Innovation Centre ‐ Fondazione Edmund MachSan Michele all'Adige (TN)Italy
| | | | | | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'AmbienteUniversità Politecnica delle MarcheAnconaItaly
| | - Ole Seehausen
- Aquatic Ecology & EvolutionInstitute of Ecology and Evolution, University of BernBernSwitzerland
- Department of Fish Ecology and EvolutionEawag ‐ Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
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Zhang W, Hu Y, Zhang S, Shao J. Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex. Mol Phylogenet Evol 2023:107840. [PMID: 37279815 DOI: 10.1016/j.ympev.2023.107840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
Accurate species delimitation is the key to biodiversity conservation and is fundamental to most branches of biology. However, species delimitation remains challenging in those evolutionary radiations associated with mating system transition from outcrossing to self-fertilization, which have frequently occurred in angiosperms and are usually accompanied by rapid speciation. Here, using the Primula cicutariifolia complex as a case, we integrated molecular, morphological and reproductive isolation evidence to test and verify whether its outcrossing (distylous) and selfing (homostylous) populations have developed into independent evolutionary lineages. Phylogenetic trees based on whole plastomes and SNPs of the nuclear genome both indicated that the distylous and homostylous populations grouped into two different clades. Multispecies coalescent, gene flow and genetic structure analyses all supported such two clades as two different genetic entities. In morphology, as expected changes in selfing syndrome, homostylous populations have significantly fewer umbel layers and smaller flower and leaf sizes compared to distylous populations, and the variation range of some floral traits, such as corolla diameter and umbel layers, show obvious discontinuity. Furthermore, hand-pollinated hybridization between the two clades produced almost no seeds, indicating that well post-pollination reproductive isolation has been established between them. Therefore, the distylous and homostylous populations in this studied complex are two independent evolutionary lineages, and thus these distylous populations should be treated as a distinct species, here named Primula qiandaoensis W. Zhang & J.W. Shao sp. nov.. Our empirical study of the P. cicutariifolia complex highlights the importance of applying multiple lines of evidence, in particular genomic data, to delimit species in pervasive evolutionary plant radiations associated with mating system transition.
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Affiliation(s)
- Wei Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; College of Life Sciences, Anqing Normal University, Anqing 246011, Anhui, China
| | - Yingfeng Hu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Siyu Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; Provincial Key Laboratory of Conservation and Utilization of Biological Resources, Wuhu 241000, Anhui, China.
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Decanter N, Normand R, Souissi A, Labbé C, Edeline E, Evanno G. Sperm competition experiments reveal low prezygotic postmating isolation between parasitic and nonparasitic lamprey ecotypes. Ecol Evol 2023; 13:e9970. [PMID: 37021081 PMCID: PMC10067809 DOI: 10.1002/ece3.9970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
The role of postmating sexual selection as a potential reproductive barrier in speciation is not well understood. Here, we studied the effects of sperm competition and cryptic female choice as putative postmating barriers in two lamprey ecotypes with a partial reproductive isolation. The European river lamprey Lampetra fluviatilis is anadromous and parasitic of other fish species, whereas the brook lamprey Lampetra planeri is freshwater resident and nonparasitic. We measured sperm traits in both ecotypes and designed sperm competition experiments to test the occurrence of cryptic female choice. We also performed sperm competition experiments either at equal semen volume or equal sperm number to investigate the role of sperm velocity on fertilization success. We observed distinct sperm traits between ecotypes with a higher sperm concentration and a lower sperm velocity for L. planeri compared with L. fluviatilis. The outcomes of sperm competition reflected these differences in sperm traits, and there was no evidence for cryptic female choice irrespective of female ecotype. At equal semen volume, L. planeri males had a higher fertilization success than L. fluviatilis and vice versa at equal sperm number. Our results demonstrate that different sperm traits between ecotypes can influence the male reproductive success and thus gene flow between L. planeri and L. fluviatilis. However, postmating prezygotic barriers are absent and thus cannot explain the partial reproductive isolation between ecotypes.
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Affiliation(s)
- Nolwenn Decanter
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMERRennesFrance
| | - Romane Normand
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMERRennesFrance
| | - Ahmed Souissi
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMERRennesFrance
| | - Catherine Labbé
- INRAE, UMR1037 LPGP, Fish Physiology and GenomicsCampus de Beaulieu35000RennesFrance
| | - Eric Edeline
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMERRennesFrance
| | - Guillaume Evanno
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMERRennesFrance
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Phylogenetics and the Cenozoic radiation of lampreys. Curr Biol 2023; 33:397-404.e3. [PMID: 36586410 DOI: 10.1016/j.cub.2022.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 10/13/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
The development of a movable jaw is one of the most important transitions in the evolutionary history of animals.1 Jawed vertebrates rapidly diversified after appearing approximately 470 million years ago. Today, only lampreys and hagfishes represent the once dominant jawless grade2,3,4 and comprise less than 1% of living vertebrate species. Their relationship to other vertebrates ranks among the more contentious problems in animal phylogenetics.5,6,7,8,9,10,11,12 Further, the phylogenetic relationships within lampreys and hagfishes remain unclear,13,14,15 and the ages of their living lineages are largely unexplored.16,17 Because of their importance for the genomic and developmental changes that prefigured jawed vertebrate diversity,18,19,20,21 the evolutionary history of lampreys and hagfishes is a major frontier of organismal biology. Of these two clades, lampreys22 are more ecologically diverse, exhibiting freshwater, anadromous, and fully marine forms, as well as parasitic and nonparasitic species.23,24 Here, we present a new phylogeny and historical biogeographic reconstruction of all living lampreys. Whereas the early diversification of this clade tracks Pangaean fragmentation, lampreys also rapidly radiated in the northern hemisphere during the mid-Cretaceous and directly after the Cretaceous-Paleogene extinction. These radiations mirrored concurrent ones in other animals and plants and coincided with changes to lamprey ecology and feeding behavior. Our results suggest that 80% of living lamprey clades appeared in the last 20 million years of Earth history. Rather than gradually accumulating since the oldest stem-group forms appeared in the early Paleozoic, living lamprey biodiversity results from diversifications extending from the Cretaceous to present.
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Miller AK, Timoshevskaya N, Smith JJ, Gillum J, Sharif S, Clarke S, Baker C, Kitson J, Gemmell NJ, Alexander A. Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). J Hered 2022; 113:380-397. [PMID: 35439308 PMCID: PMC9308044 DOI: 10.1093/jhered/esac014] [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: 09/15/2021] [Accepted: 03/23/2022] [Indexed: 11/12/2022] Open
Abstract
Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.
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Affiliation(s)
- Allison K Miller
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Nataliya Timoshevskaya
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, Kentucky, 40506-0225 USA
| | - Joanne Gillum
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Saeed Sharif
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research Limited, PO Box 11 115, Hamilton 3251 New Zealand
| | - Jane Kitson
- Ngāi Tahu, Kitson Consulting Ltd, Invercargill/Waihopai, 9879, New Zealand
| | - Neil J Gemmell
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
| | - Alana Alexander
- Anatomy Department, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin, 9016, New Zealand
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Dong X, Yi W, Zheng C, Zhu X, Wang S, Xue H, Ye Z, Bu W. Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data. ZOOL SCR 2021. [DOI: 10.1111/zsc.12523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenbo Yi
- Department of Biology Xinzhou Teachers University Xinzhou China
| | - Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Shujing Wang
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Huaijun Xue
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
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Ajmani N, Yasmin T, Docker MF, Good SV. Transcriptomic analysis of gonadal development in parasitic and non-parasitic lampreys (Ichthyomyzon spp.), with a comparison of genomic resources in these non-model species. G3-GENES GENOMES GENETICS 2021; 11:6134134. [PMID: 33576778 PMCID: PMC8022942 DOI: 10.1093/g3journal/jkab030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
Lampreys are jawless fishes that diverged ∼550 million years ago from other vertebrates. Sequencing of the somatic and the germline genomes of the sea lamprey (Petromyzon marinus) in 2013 and 2018, respectively, has helped to improve our understanding of the genes and gene networks that control many aspects of lamprey development. However, little is known about the genetic basis of gonadal differentiation in lampreys, partly due to the prolonged period during which their gonads remain sexually indeterminate. We performed RNA-sequencing on gonadal samples from four chestnut lamprey (Ichthyomyzon castaneus) and six northern brook lamprey (I. fossor) to identify differentially expressed genes (DEG’s) and pathways associated with transcriptomic differences in: (1) larvae during early gonadal differentiation versus definitive females (i.e., with oocytes in the slow cytoplasmic growth phase); and (2) females versus definitive males undergoing spermatogonial proliferation. We compared the mapping percentages of these transcriptomes to the two available sea lamprey reference genomes and three annotation files (Ensembl and UCSC for the somatic genome and SIMRbase for the germline genome). We found that mapping the RNA-seq reads to the germline genome gave superior results and, using Trinotate, we provided new putative annotations for 8161 genes in the somatic assembly and 880 genes for the germline assembly. We identified >2000 DEG’s between stages and sexes, as well as biological pathways associated with each. Interestingly, some of the upregulated genes (e.g., DEG’s associated with spermiation) suggest that changes in gene expression can precede morphological changes by several months. In contrast, only 81 DEG’s were evident between the chestnut lamprey (that remains sexually immature during an extended post-metamorphic parasitic feeding phase) and the nonparasitic northern brook lamprey (that undergoes sexual maturation near the end of metamorphosis), but few replicates were available for comparable stages and sexes. This work lays the foundation for identifying and confirming the orthology and the function of genes involved in gonadal development in these and other lamprey species across more developmental stages.
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Affiliation(s)
- Nisha Ajmani
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
| | - Tamanna Yasmin
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
| | - Margaret F Docker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
| | - Sara V Good
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada.,Department of Biology, University of Winnipeg, Winnipeg, Canada
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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Naseka AM, Renaud CB. Morphology-based taxonomic re-assessment of the Arctic lamprey, Lethenteron camtschaticum (Tilesius, 1811) and taxonomic position of other members of the genus. Zookeys 2020; 991:1-67. [PMID: 33223898 PMCID: PMC7674401 DOI: 10.3897/zookeys.991.54938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/03/2020] [Indexed: 11/29/2022] Open
Abstract
The lamprey genus Lethenteron Creaser & Hubbs, 1922 is widespread across Eurasia and North America, but the number and distribution of its constituent species is not firmly established. After a morphological examination of extant type material of the currently recognized species and their synonyms, Lethenteronmitsukurii (Hatta, 1901) is resurrected with Le.matsubarai Vladykov & Kott, 1978 as its junior synonym. Amongst nonparasitic species Le.reissneri (Dybowski, 1869) and Le.mitsukurii are confirmed as present in Japan and the former is also present on Sakhalin. An in-depth study of large samples of nonparasitic lamprey adults from Japan and Sakhalin Island is needed to determine whether the lower trunk myomere (< 66) individuals from these areas represent one or more undescribed species, or Le.mitsukurii, or Le.reissneri, or a mixture of these three alternatives. The material from the Anadyr Estuary identified by Berg (1931, 1948) as Lampetrajaponicakessleri has been re-identified as Le.camtschaticum and there is no evidence that Le.kessleri occurs there. Lethenteronreissneri is reported from the Angara River system, Yenisei River drainage, Russia. Lethenteronalaskense Vladykov & Kott, 1978 is provisionally considered to be a junior synonym of Le.kessleri (Anikin, 1905). Petromyzonernstii Dybowski, 1872, Ammocoetesaureus Bean, 1881, Petromyzondentex Anikin, 1905, Lampetramitsukuriimajor Hatta, 1911, and Lampetrajaponicaseptentrionalis Berg, 1931 are junior synonyms of Petromyzonmarinuscamtschaticus Tilesius, 1811. A key is provided to adults of the six species recognized as belonging in the genus Lethenteron.
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Affiliation(s)
- Alexander M Naseka
- Naturhistorisches Museum Wien, Burgring 7, 1010 Vienna, Austria Naturhistorisches Museum Wien Vienna Austria
| | - Claude B Renaud
- Centre for Arctic Knowledge and Exploration, Research & Collections, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, ON K1P 6P4 Canada Canadian Museum of Nature Ottawa Canada
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Song YS, Bae SE, Kang JH, Park JY, Kim JK. Cryptic diversity in the inshore hagfish, Eptatretus burgeri (Myxinidae, Pisces) from the northwest Pacific. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3410-3414. [PMID: 33458189 PMCID: PMC7782252 DOI: 10.1080/23802359.2020.1823256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The fishery of inshore hagfish (Eptatretus burgeri) is particularly important from the perspective of the eel-skin leather industry in the northwest Pacific. In order to reveal the genetic diversity and population structure of E. burgeri in the northwest Pacific, we analyzed partial nucleotide sequences of three mitochondrial DNA regions (523 bp in COI, 712 bp in ND4 and 617 bp in Cytb) based on specimens collected from six locations in Korea and Japan. The genetic diversities of E. burgeri were higher in Korean locations compared to Japanese ones. AMOVA showed that E. burgeri was completely separated into two groups (group A: southern coast of Korea and western coast of Japan vs. group B: eastern coast of Japan). Furthermore, groups A and B were divided into each two lineages (lineage I: west southern coast of Korea, lineage II: east southern coast of Korea and western coast of Japan, lineage III and IV: eastern coast of Japan). Our molecular results suggest that these two groups and lineages of E. burgeri may be different evolutionary significant unit and management unit, respectively.
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Affiliation(s)
- Young Sun Song
- Department of Marine Biology, Pukyong National University, Busan, Korea
| | - Seung-Eun Bae
- Department of Marine Biology, Pukyong National University, Busan, Korea
| | - Jung-Ha Kang
- National Institute of Fisheries Science, Busan, Korea
| | | | - Jin-Koo Kim
- Department of Marine Biology, Pukyong National University, Busan, Korea
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11
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Balakirev ES, Kravchenko AY, Semenchenko AA. Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment. Genes (Basel) 2020; 11:E1071. [PMID: 32933022 PMCID: PMC7564937 DOI: 10.3390/genes11091071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/22/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.
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Affiliation(s)
- Evgeniy S. Balakirev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia;
- School of Biomedicine, Far Eastern Federal University, Vladivostok 690950, Russia
| | - Alexandra Yu. Kravchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia;
- Laboratory of Ecology and Evolutionary Biology of Aquatic Organisms, School of Natural Sciences, Far Eastern Federal University, Vladivostok 690950, Russia;
| | - Alexander A. Semenchenko
- Laboratory of Ecology and Evolutionary Biology of Aquatic Organisms, School of Natural Sciences, Far Eastern Federal University, Vladivostok 690950, Russia;
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De Cahsan B, Nagel R, Schedina IM, King JJ, Bianco PG, Tiedemann R, Ketmaier V. Phylogeography of the European brook lamprey (Lampetra planeri) and the European river lamprey (Lampetra fluviatilis) species pair based on mitochondrial data. JOURNAL OF FISH BIOLOGY 2020; 96:905-912. [PMID: 32039478 DOI: 10.1111/jfb.14279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 06/10/2023]
Abstract
The European river lamprey Lampetra fluviatilis and the European brook lamprey Lampetra planeri (Block 1784) are classified as a paired species, characterized by notably different life histories but morphological similarities. Previous work has further shown limited genetic differentiation between these two species at the mitochondrial DNA level. Here, we expand on this previous work, which focused on lamprey species from the Iberian Peninsula in the south and mainland Europe in the north, by sequencing three mitochondrial marker regions of Lampetra individuals from five river systems in Ireland and five in southern Italy. Our results corroborate the previously identified pattern of genetic diversity for the species pair. We also show significant genetic differentiation between Irish and mainland European lamprey populations, suggesting another ichthyogeographic district distinct from those previously defined. Finally, our results stress the importance of southern Italian L. planeri populations, which maintain several private alleles and notable genetic diversity.
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Affiliation(s)
- Binia De Cahsan
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Rebecca Nagel
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ina-Maria Schedina
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | | | - Ralph Tiedemann
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Valerio Ketmaier
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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13
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Pedraza-Marrón CDR, Silva R, Deeds J, Van Belleghem SM, Mastretta-Yanes A, Domínguez-Domínguez O, Rivero-Vega RA, Lutackas L, Murie D, Parkyn D, Bullock LH, Foss K, Ortiz-Zuazaga H, Narváez-Barandica J, Acero A, Gomes G, Betancur-R R. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Proc Biol Sci 2019; 286:20182924. [PMID: 30940064 PMCID: PMC6501682 DOI: 10.1098/rspb.2018.2924] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Abstract
Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species ( L. campechanus). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favour the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. Despite finding evidence of introgression in geographically neighbouring populations in northern South America, our genomic analyses strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.
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Affiliation(s)
| | - Raimundo Silva
- Instituto de Estudos Costeiros, Laboratório de Genética Aplicada, Campus Bragança, Alameda Leandro Ribeiro, S/N, Aldeia, 68600-000 Bragança, Pará, Brazil
| | - Jonathan Deeds
- USFDA Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740, USA
| | - Steven M. Van Belleghem
- Department of Biology, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, PR 00931, USA
| | - Alicia Mastretta-Yanes
- CONACYT Research Fellow – Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, México, Liga Periférico – Insurgentes Sur, No. 4903, 14010, México, DF, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, 58000, Morelia, Michoacán, México
| | - Rafael A. Rivero-Vega
- Department of Biology, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, PR 00931, USA
| | - Loretta Lutackas
- Department of Biology, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, PR 00931, USA
- North Carolina Wildlife Resources Commission, Raleigh, NC 27699-1700, USA
| | - Debra Murie
- University of Florida, School of Forest Resources and Conservation, Program of Fisheries and Aquatic Sciences, Gainesville, FL 32653, USA
| | - Daryl Parkyn
- University of Florida, School of Forest Resources and Conservation, Program of Fisheries and Aquatic Sciences, Gainesville, FL 32653, USA
| | - Lewis H. Bullock
- Florida Fish and Wildlife Research Institute, 100 8th Ave SE, St. Petersburg, FL 33701, USA
| | - Kristin Foss
- Florida Fish and Wildlife Conservation Commission, Farris Bryant Building, 620 S. Meridian St., Tallahassee, FL 32399-1600, USA
| | - Humberto Ortiz-Zuazaga
- Computer Science Department, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, PR 00931, USA
| | | | - Arturo Acero
- Universidad Nacional de Colombia Sede Caribe Cecimar, El Rodadero, Santa Marta, Colombia
| | - Grazielle Gomes
- Instituto de Estudos Costeiros, Laboratório de Genética Aplicada, Campus Bragança, Alameda Leandro Ribeiro, S/N, Aldeia, 68600-000 Bragança, Pará, Brazil
- Instituto de Estudos Costeiros, Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro, S/N, Aldeia, 68600-000 Bragança, Pará, Brazil
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Room 314, Norman, OK 73019, USA
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14
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Hume JB, Recknagel H, Bean CW, Adams CE, Mable BK. RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry. Mol Ecol 2018; 27:4572-4590. [PMID: 30252984 DOI: 10.1111/mec.14881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
Abstract
Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater-resident nonparasitic lampreys from anadromous-parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction-associated DNA sequencing), we found that a freshwater-parasitic ecotype was highly distinct from an anadromous-parasitic form (Qlake-P = 96.8%, Fst = 0.154), but that a freshwater-nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous-parasitic ecotype (Qanad-P = 37.7%), there is no evidence of introgression into the freshwater-parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater-parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post-glacial regions, followed by periods of extensive gene flow among such diverging populations.
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Affiliation(s)
- John B Hume
- Department of Fisheries and Wildlife, College of Agriculture & Natural Resources, Michigan State University, East Lansing, Michigan.,Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.,Scottish Natural Heritage, Clydebank, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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15
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Rougemont Q, Gagnaire PA, Perrier C, Genthon C, Besnard AL, Launey S, Evanno G. Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes. Mol Ecol 2016; 26:142-162. [PMID: 27105132 DOI: 10.1111/mec.13664] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/22/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating parallelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.
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Affiliation(s)
- Quentin Rougemont
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095, Montpellier, France.,Station Méditerranéenne de l'Environnement Littoral, Université de Montpellier, 2 Rue des Chantiers, F-34200, Sète, France
| | - Charles Perrier
- CEFE-CNRS, Centre D'Ecologie Fonctionnelle et Evolutive, Route de Mende, 34090, Montpellier, France
| | - Clémence Genthon
- Plateforme génomique INRA GenoToul Chemin de Borderouge - Auzeville, 31320, Castanet-Tolosan, France
| | - Anne-Laure Besnard
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Sophie Launey
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - Guillaume Evanno
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, 35042, Rennes, France.,Agrocampus Ouest, UMR ESE, 65 rue de Saint-Brieuc, 35042, Rennes, France
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16
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Rougemont Q, Roux C, Neuenschwander S, Goudet J, Launey S, Evanno G. Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations. PeerJ 2016; 4:e1910. [PMID: 27077007 PMCID: PMC4830234 DOI: 10.7717/peerj.1910] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/17/2016] [Indexed: 12/19/2022] Open
Abstract
Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey (L. planeri) show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.
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Affiliation(s)
- Quentin Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Camille Roux
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Vital-IT, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, Université de Lausanne, Lausanne, Switzerland
| | - Sophie Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
| | - Guillaume Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, Institut National de la Recherche Agronomique, Rennes, France
- UMR 985 Ecologie et Santé des Ecosystèmes, Agrocampus Ouest, Rennes, France
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17
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Mateus CS, Almeida PR, Mesquita N, Quintella BR, Alves MJ. European Lampreys: New Insights on Postglacial Colonization, Gene Flow and Speciation. PLoS One 2016; 11:e0148107. [PMID: 26871930 PMCID: PMC4752455 DOI: 10.1371/journal.pone.0148107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 01/13/2016] [Indexed: 01/26/2023] Open
Abstract
Ice ages are known to be the most dominant palaeoclimatic feature occurring on Earth, producing severe climatic oscillations and consequently shaping the distribution and the population structure of several species. Lampreys constitute excellent models to study the colonization of freshwater systems, as they commonly appear in pairs of closely related species of anadromous versus freshwater resident adults, thus having the ability to colonize new habitats, through the anadromous species, and establish freshwater resident derivates. We used 10 microsatellite loci to investigate the spatial structure, patterns of gene flow and migration routes of Lampetra populations in Europe. We sampled 11 populations including the migratory L. fluviatilis and four resident species, L. planeri, L. alavariensis, L. auremensis and L. lusitanica, the last three endemic to the Iberian Peninsula. In this southern glacial refugium almost all sampled populations represent a distinct genetic cluster, showing high levels of allopatric differentiation, reflecting long periods of isolation. As result of their more recent common ancestor, populations from northern Europe are less divergent among them, they are represented by fewer genetic clusters, and there is evidence of strong recent gene flow among populations. These previously glaciated areas from northern Europe may have been colonized from lampreys expanding out of the Iberian refugia. The pair L. fluviatilis/L. planeri is apparently at different stages of speciation in different locations, showing evidences of high reproductive isolation in the southern refugium, and low differentiation in the north.
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Affiliation(s)
- Catarina Sofia Mateus
- MARE – Centro de Ciências do Mar e do Ambiente, Universidade de Évora, Évora, Portugal
- Museu Nacional de História Natural e da Ciência & Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
| | - Pedro Raposo Almeida
- MARE – Centro de Ciências do Mar e do Ambiente, Universidade de Évora, Évora, Portugal
- Departamento de Biologia, Escola de Ciências e Tecnologia, Universidade Évora, Évora, Portugal
| | - Natacha Mesquita
- Museu Nacional de História Natural e da Ciência & Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | - Bernardo Ruivo Quintella
- MARE – Centro de Ciências do Mar e do Ambiente, Universidade de Évora, Évora, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Maria Judite Alves
- Museu Nacional de História Natural e da Ciência & Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
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18
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Abstract
Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.
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Affiliation(s)
- David W McCauley
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
| | - Margaret F Docker
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
| | - Steve Whyard
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
| | - Weiming Li
- David W. McCauley ( ) is affiliated with the Department of Biology at the University of Oklahoma, in Norman. Margaret F. Docker and Steve Whyard are affiliated with the Department of Biological Sciences at the University of Manitoba, in Winnipeg, Canada. Weiming Li is affiliated with the Department of Fisheries and Wildlife at Michigan State University, in East Lansing
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19
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Rougemont Q, Gaigher A, Lasne E, Côte J, Coke M, Besnard AL, Launey S, Evanno G. Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys. J Evol Biol 2015; 28:2248-63. [PMID: 26348652 DOI: 10.1111/jeb.12750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 01/10/2023]
Abstract
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here, we used a combination of mating trials, experimental crosses and population genetic analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (Lampetra planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size-assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically based divergent selection may explain these variable levels of divergence among sympatric population pairs, but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress towards speciation.
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Affiliation(s)
- Q Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - A Gaigher
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France.,Laboratory for Conservation Biology, Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - E Lasne
- Muséum National d'Histoire Naturelle, CRESCO, Dinard, France.,UMR CARRTEL, INRA, Thonon-les-Bains, France
| | - J Côte
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - M Coke
- Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique, INRA, Rennes, France
| | - A-L Besnard
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - S Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - G Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
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20
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Makhrov AA, Popov IY. Life forms of lampreys (Petromyzontidae) as a manifestation of intraspecific diversity of ontogenesis. Russ J Dev Biol 2015. [DOI: 10.1134/s1062360415040074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Bartels H, Docker MF, Krappe M, White MM, Wrede C, Potter IC. Variations in the presence of chloride cells in the gills of lampreys (Petromyzontiformes) and their evolutionary implications. JOURNAL OF FISH BIOLOGY 2015; 86:1421-1428. [PMID: 26023689 DOI: 10.1111/jfb.12633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although confined to fresh water, non-parasitic species of lampreys and the landlocked parasitic sea lamprey, all of which were derived relatively recently from an adromous ancestors, still develop chloride cells, whose function in their ancestors was for osmoregulation in marine waters during the adult parasitic phase. In contrast, such cells are not developed by the non-parasitic least brook lamprey Lampetra aepyptera, which has been separated from its ancestor for >2 million years, nor by the freshwater parasitic species of the genus Ichthyomyzon. The length of time that a non-parasitic species or landlocked parasitic form or species has spent in fresh water is thus considered the overriding factor determining whether chloride cells are developed by those lampreys.
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Affiliation(s)
- H Bartels
- Institut für Funktionelle und Angewandte Anatomie, Medizinische Hochschule Hannover, Germany
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22
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Bracken FSA, Hoelzel AR, Hume JB, Lucas MC. Contrasting population genetic structure among freshwater-resident and anadromous lampreys: the role of demographic history, differential dispersal and anthropogenic barriers to movement. Mol Ecol 2015; 24:1188-204. [PMID: 25689694 PMCID: PMC4413359 DOI: 10.1111/mec.13112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 11/30/2022]
Abstract
The tendency of many species to abandon migration remains a poorly understood aspect of evolutionary biology that may play an important role in promoting species radiation by both allopatric and sympatric mechanisms. Anadromy inherently offers an opportunity for the colonization of freshwater environments, and the shift from an anadromous to a wholly freshwater life history has occurred in many families of fishes. Freshwater-resident forms have arisen repeatedly among lampreys (within the Petromyzontidae and Mordaciidae), and there has been much debate as to whether anadromous lampreys, and their derived freshwater-resident analogues, constitute distinct species or are divergent ecotypes of polymorphic species. Samples of 543 European river lamprey Lampetra fluviatilis (mostly from anadromous populations) and freshwater European brook lamprey Lampetra planeri from across 18 sites, primarily in the British Isles, were investigated for 13 polymorphic microsatellite DNA loci, and 108 samples from six of these sites were sequenced for 829 bp of mitochondrial DNA (mtDNA). We found contrasting patterns of population structure for mtDNA and microsatellite DNA markers, such that low diversity and little structure were seen for all populations for mtDNA (consistent with a recent founder expansion event), while fine-scale structuring was evident for nuclear markers. Strong differentiation for microsatellite DNA loci was seen among freshwater-resident L. planeri populations and between L. fluviatilis and L. planeri in most cases, but little structure was evident among anadromous L. fluviatilis populations. We conclude that postglacial colonization founded multiple freshwater-resident populations with strong habitat fidelity and limited dispersal tendencies that became highly differentiated, a pattern that was likely intensified by anthropogenic barriers.
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Affiliation(s)
- Fiona S A Bracken
- School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK
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23
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Pereira AM, Doadrio I, Robalo JI, Almada VC. Different stocks of brook lamprey in Spain and their origin from Lampetra fluviatilis at two distinct times and places. JOURNAL OF FISH BIOLOGY 2014; 85:1793-1798. [PMID: 25257102 DOI: 10.1111/jfb.12513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 07/23/2014] [Indexed: 06/03/2023]
Abstract
Using the mitochondrial non-coding region I, it was shown that the two Spanish Lampetra planeri populations (Cares-Deva and Olabidea-Ugarana) correspond to different genetic units. The Cares-Deva population is probably a recent offshoot of Lampetra fluviatilis, being the Olabidea-Ugarana population less diverse and of older origin.
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Affiliation(s)
- A M Pereira
- Marine and Environmental Sciences Centre and Eco-Ethology Research Unit, ISPA-Instituto Universitário Rua Jardim do Tabaco 34 1149-041 Lisboa, Portugal
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24
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Knebelsberger T, Dunz AR, Neumann D, Geiger MF. Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding. Mol Ecol Resour 2014; 15:562-72. [PMID: 25186809 DOI: 10.1111/1755-0998.12322] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/15/2014] [Accepted: 08/20/2014] [Indexed: 11/30/2022]
Abstract
This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour-Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.
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Affiliation(s)
- Thomas Knebelsberger
- Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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Spice EK, Docker MF. Reduced fecundity in non-parasitic lampreys may not be due to heterochronic shift in ovarian differentiation. J Zool (1987) 2014. [DOI: 10.1111/jzo.12150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. K. Spice
- Department of Biological Sciences; University of Manitoba; Winnipeg MB Canada
| | - M. F. Docker
- Department of Biological Sciences; University of Manitoba; Winnipeg MB Canada
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Berner D, Moser D, Roesti M, Buescher H, Salzburger W. GENETIC ARCHITECTURE OF SKELETAL EVOLUTION IN EUROPEAN LAKE AND STREAM STICKLEBACK. Evolution 2014; 68:1792-805. [DOI: 10.1111/evo.12390] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/11/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Daniel Berner
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Dario Moser
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Heinz Buescher
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
| | - Walter Salzburger
- Zoological Institute; University of Basel; Vesalgasse 1, CH-4051 Basel Switzerland
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Faria R, Renaut S, Galindo J, Pinho C, Melo-Ferreira J, Melo M, Jones F, Salzburger W, Schluter D, Butlin R. Advances in Ecological Speciation: an integrative approach. Mol Ecol 2014; 23:513-21. [DOI: 10.1111/mec.12616] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/28/2013] [Accepted: 11/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
- IBE, Institute of Evolutionary Biology (UPF-CSIC); Universitat Pompeu Fabra. PRBB; Av. Doctor Aiguader N88 08003 Barcelona Spain
| | - Sebastien Renaut
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada V6T 1Z4
| | - Juan Galindo
- Departamento de Bioquímica, Xenética e Inmunoloxía; Facultade de Bioloxía; Universidade de Vigo; Campus Universitario 36310 Vigo Spain
| | - Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | - Martim Melo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio; Laboratório Associado; Universidade do Porto. Campus Agrário de Vairão; 4485-661 Vairão Portugal
| | - Felicity Jones
- Friedrich Miescher Laboratory of the Max Planck Society; Tuebingen 72070 Germany
| | - Walter Salzburger
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Dolph Schluter
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada V6T 1Z4
| | - Roger Butlin
- Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
- Sven Lovén Centre - Tjärnö; University of Gothenburg; S-452 96 Strömstad Sweden
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