1
|
Vučić T, Drobnjaković M, Ajduković M, Bugarčić M, Wielstra B, Ivanović A, Cvijanović M. A staging table of Balkan crested newt embryonic development to serve as a baseline in evolutionary developmental studies. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38953174 DOI: 10.1002/jez.b.23269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
There is an increased interest in the evolution and development of newts from the genus Triturus because: (1) morphological differentiation among the nine constituent species largely corresponds to different ecological preferences, (2) hybridization between different species pairs has various evolutionary outcomes in terms of life history traits and morphology, and (3) the genus expresses a balanced lethal system that causes arrested growth and death of half of the embryos. These features provide natural experimental settings for molecular, morphological, and life-history studies. Therefore, we produce a staging table for the Balkan crested newt (T. ivanbureschi). We provide detailed descriptions of 34 embryonic stages based on easily observable and interpretable external morphological characters, to ensure reproducibility. Compared with previous staging tables for Triturus, we include a vastly increased sample size and provide high-resolution photographs in lateral, ventral, and dorsal view, complemented by videos of specific developmental periods, and accompanied by detailed explanations on how to delineate the specific stages. Our staging table will serve as a baseline in comparative studies on Triturus newts: an emerging model system in evolutionary and developmental studies.
Collapse
Affiliation(s)
- Tijana Vučić
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Marija Drobnjaković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maja Ajduković
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marko Bugarčić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ben Wielstra
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ana Ivanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
2
|
Kazilas C, Dufresnes C, France J, Kalaentzis K, Martínez-Solano I, de Visser MC, Arntzen JW, Wielstra B. Spatial genetic structure in European marbled newts revealed with target enrichment by sequence capture. Mol Phylogenet Evol 2024; 194:108043. [PMID: 38382821 DOI: 10.1016/j.ympev.2024.108043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/21/2023] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group because morphological data show geographical variation and because the Iberian Peninsula is a recognized center of speciation and intraspecific genetic diversity for all kinds of organisms, amphibians included. We use target enrichment by sequence capture to generate c. 7 k nuclear DNA markers. We observe limited genetic exchange between the species, which confirms their distinctiveness. Both species show substantial genetic structuring that is only in part mirrored by morphological variation. Genetically differentiated groups are found in the south (T. marmoratus) and west (T. pygmaeus) of the species ranges. Our observations highlight the position of the Iberian Peninsula as a hotspot for genetic differentiation.
Collapse
Affiliation(s)
- Christos Kazilas
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands.
| | - Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - James France
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Konstantinos Kalaentzis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Manon C de Visser
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands
| |
Collapse
|
3
|
Porretta D, Canestrelli D. The ecological importance of hybridization. Trends Ecol Evol 2023; 38:1097-1108. [PMID: 37620217 DOI: 10.1016/j.tree.2023.07.003] [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: 03/12/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Hybridization as an evolutionary process has been studied in depth over the past few decades. Research has focused on its role in shaping reproductive barriers, its adaptive value, and its genomic consequences. In contrast, our knowledge of ecological dimensions of hybridization is still in its infancy, despite hybridization being an inherently ecological interaction. Using examples from various organisms, we show that hybridization can affect and be affected by non-reproductive interactions, including predation, competition, parasitism, mutualism, commensalism, and organism-environment interactions, with significant implications for community structure and ecosystem functioning. However, since these dimensions of hybridization have mostly been revealed from studies designed to decipher other evolutionary processes, we argue that much of the eco-evolutionary importance of hybridization is yet to be discovered.
Collapse
Affiliation(s)
- Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, Italy.
| | | |
Collapse
|
4
|
Kalaentzis K, Arntzen JW, Avcı A, van den Berg V, Beukema W, France J, Olgun K, van Riemsdijk I, Üzüm N, de Visser MC, Wielstra B. Hybrid zone analysis confirms cryptic species of banded newt and does not support competitive displacement since secondary contact. Ecol Evol 2023; 13:e10442. [PMID: 37664506 PMCID: PMC10468612 DOI: 10.1002/ece3.10442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
When two putatively cryptic species meet in nature, hybrid zone analysis can be used to estimate the extent of gene flow between them. Two recently recognized cryptic species of banded newt (genus Ommatotriton) are suspected to meet in parapatry in Anatolia, but a formal hybrid zone analysis has never been conducted. We sample populations throughout the range, with a focus on the supposed contact zone, and genotype them for 31 nuclear DNA SNP markers and mtDNA. We determine the degree of genetic admixture, introgression, and niche overlap. We reveal an extremely narrow hybrid zone, suggesting strong selection against hybrids, in line with species status. The hybrid zone does not appear to be positioned at an ecological barrier, and there is significant niche overlap. Therefore, the hybrid zone is best classified as a tension zone, maintained by intrinsic selection against hybrids. While the two banded newt species can evidently backcross, we see negligible introgression and the pattern is symmetric, which we interpret as supporting the fact that the hybrid zone has been practically stationary since its origin (while extensive hybrid zone movement has been suggested in other newt genera in the region). Our study illustrates the use of hybrid zone analysis to test cryptic species status.
Collapse
Affiliation(s)
- Konstantinos Kalaentzis
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Hydrobiological Station of Rhodes, Hellenic Centre for Marine ResearchRhodesGreece
| | - Jan W. Arntzen
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Aziz Avcı
- Department of BiologyAydın Adnan Menderes UniversityAydınTurkey
| | - Victor van den Berg
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Wouter Beukema
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON)NijmegenThe Netherlands
| | - James France
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Kurtuluş Olgun
- Department of BiologyAydın Adnan Menderes UniversityAydınTurkey
| | - Isolde van Riemsdijk
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Plant Evolutionary EcologyInstitute of Evolution & Ecology, University of TübingenTübingenGermany
| | - Nazan Üzüm
- Department of BiologyAydın Adnan Menderes UniversityAydınTurkey
| | - Manon C. de Visser
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
- Naturalis Biodiversity CenterLeidenThe Netherlands
| |
Collapse
|
5
|
Maldonado-Coelho M, Dos Santos SS, Isler ML, Svensson-Coelho M, Sotelo-Muñoz M, Miyaki CY, Ricklefs RE, Blake JG. Evolutionary and Ecological Processes Underlying Geographic Variation in Innate Bird Songs. Am Nat 2023; 202:E31-E52. [PMID: 37531273 DOI: 10.1086/725016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
AbstractEcological and evolutionary processes underlying spatial variation in signals involved in mate recognition and reproductive isolation are crucial to understanding the causes of population divergence and speciation. Here, to test hypotheses concerning the causes of song divergence, we examine how songs of two sister species of Atlantic Forest suboscine birds with innate songs, the Pyriglena fire-eye antbirds, vary across their ranges. Specifically, we evaluated the influence of isolation by distance and introgressive hybridization, as well as morphological and environmental variation, on geographic variation in male songs. Analyses based on 496 male vocalizations from 63 locations across a 2,200-km latitudinal transect revealed clinal changes in the structure of songs and showed that introgressive hybridization increases both the variability and the homogenization of songs in the contact zone between the two species. We also found that isolation by distance, morphological constraints, the environment, and genetic introgression independently predicted song variation across geographic space. Our study shows the importance of an integrative approach that investigates the roles of distinct ecological and evolutionary processes that influence acoustic signal evolution.
Collapse
|
6
|
Bruni G, Chiocchio A, Nascetti G, Cimmaruta R. Different patterns of introgression in a three species hybrid zone among European cave salamanders. Ecol Evol 2023; 13:e10437. [PMID: 37636870 PMCID: PMC10447881 DOI: 10.1002/ece3.10437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/29/2023] Open
Abstract
Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, where hybrids backcross with parental populations leading to the spread of new alleles into the parental genomes. Whereas many hybrid zones have been reported in American Plethodontid salamanders, only a single hybrid zone has been documented in European plethodontids so far, which is located at the Apuan Alps in the Italian Peninsula. Here, we describe a previously unreported hybrid zone in the Northern Apennines involving all the three Plethodontid salamander species inhabiting the Italian Peninsula. We found 21 new Speleomantes sites of occurrence, from a hitherto unexplored area located at the boundaries between three Speleomantes species ranges. Using mitochondrial (Cytb and ND2 genes) and nuclear markers (two diagnostic SNPs at the NCX1 gene), we revealed a three-way contact zone where all the three mainland species hybridize: S. strinatii, S. ambrosii and S. italicus. We observed a strong mitonuclear discordance, with mitochondrial markers showing a conspicuous geographic pattern, while diagnostic nuclear SNPs coexisted in both the same populations and individuals, providing evidence of hybridization in many possible combinations. The introgression is asymmetric, with S. italicus mitogenome usually associated with S. a. ambrosii and, to a lesser extent, to S. strinatii nuclear alleles. This finding confirms that Plethodontid are a group of choice to investigate hybridization mechanisms and suggests that behavioural, genetic and ecological components may concur in determining the direction and extent of introgression.
Collapse
Affiliation(s)
| | - Andrea Chiocchio
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Giuseppe Nascetti
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| | - Roberta Cimmaruta
- Department of Ecological and Biological SciencesTuscia UniversityViterboItaly
| |
Collapse
|
7
|
Gaczorek TS, Marszałek M, Dudek K, Arntzen JW, Wielstra B, Babik W. Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones. Mol Ecol 2023; 32:867-880. [PMID: 36458894 PMCID: PMC10108261 DOI: 10.1111/mec.16804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/03/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognized pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or de novo mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six Triturus newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of Triturus species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.
Collapse
Affiliation(s)
- Tomasz S Gaczorek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Marzena Marszałek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| |
Collapse
|
8
|
Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution 2022; 76:899-914. [PMID: 35323995 PMCID: PMC9324800 DOI: 10.1111/evo.14462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.
Collapse
Affiliation(s)
- Susana Freitas
- Department of Ecology and EvolutionUniversity of LausanneLausanneCH‐1015Switzerland
| | - Anja Marie Westram
- IST AustriaKlosterneuburg3400Austria,Faculty of Biosciences and AquacultureNord UniversityBodøN‐8049Norway
| | - Tanja Schwander
- Department of Ecology and EvolutionUniversity of LausanneLausanneCH‐1015Switzerland
| | | | - Çetin Ilgaz
- Department of Biology, Faculty of ScienceDokuz Eylül Universityİzmir35400Turkey,Fauna and Flora Research CentreDokuz Eylül Universityİzmir35610Turkey
| | - Yusuf Kumlutas
- Department of Biology, Faculty of ScienceDokuz Eylül Universityİzmir35400Turkey,Fauna and Flora Research CentreDokuz Eylül Universityİzmir35610Turkey
| | - David James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIOUniversidade do PortoCampus de VairãoVairão4485–661Portugal
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIOUniversidade do PortoCampus de VairãoVairão4485–661Portugal,Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPorto4169‐007Portugal
| | - Roger K. Butlin
- Department of Animal and Plant SciencesThe University of SheffieldSheffieldS10 2TNUnited Kingdom,Department of Marine SciencesUniversity of GothenburgGothenburgSE‐40530Sweden
| |
Collapse
|
9
|
Aguillon SM, Rohwer VG. Revisiting a classic hybrid zone: Movement of the northern flicker hybrid zone in contemporary times. Evolution 2022; 76:1082-1090. [PMID: 35318662 DOI: 10.1111/evo.14474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 01/22/2023]
Abstract
Natural hybrid zones have provided important insights into the evolutionary process, and their geographic dynamics over time can help to disentangle the underlying biological processes that maintain them. Here, we leverage replicated sampling of an identical transect across the hybrid zone between yellow-shafted and red-shafted flickers in the Great Plains to assess its stability over ∼60 years (1955-1957 to 2016-2018). We identify a ∼73-km westward shift in the hybrid zone center toward the range of the red-shafted flicker, but find no associated changes in width over our sampling period. In fact, the hybrid zone remains remarkably narrow, suggesting some kind of selective pressure maintains the zone. By comparing to previous work in the same geographic region, it appears likely that the movement in the hybrid zone has occurred in the years since the early 1980s. This recent movement may be related to changes in climate or land management practices that have allowed westward movement of yellow-shafted flickers into the Great Plains.
Collapse
Affiliation(s)
- Stepfanie M Aguillon
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, 14850.,Current Address: Department of Biology, Stanford University, Stanford, California, 94305
| | - Vanya G Rohwer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853.,Cornell University Museum of Vertebrates, Ithaca, New York, 14850
| |
Collapse
|
10
|
Vučić T, Ivanović A, Ajduković M, Bajler N, Cvijanović M. The Reproductive Success of Triturus ivanbureschi × T. macedonicus F1 Hybrid Females (Amphibia: Salamandridae). Animals (Basel) 2022; 12:ani12040443. [PMID: 35203151 PMCID: PMC8868055 DOI: 10.3390/ani12040443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Two moderately related large-bodied newt species endemic to the Balkan Peninsula, the Balkan crested newt (Triturus ivanbureschi) and the Macedonian crested newt (T. macedonicus), coexist and hybridize in central Serbia. Many generations of mutual hybrid crossings and backcrossings with parental species shaped the genetic composition of hybrid populations. Natural populations have admixed nuclear DNA (nuDNA) of parental species and T. ivanbureschi mitochondrial DNA (mtDNA), which is usually maternally inherited. The mechanisms that direct gene flow and shape the first generations of hybrids could explain the formation of hybrid zones and their maintenance in nature. We followed and compared life history traits related to reproduction of the first generation of reciprocal hybrids obtained by experimental crossing. Our results suggested that possible incompatibilities between mitochondrial and nuclear genomes, which could lead to the exclusion of T. macedonicus mtDNA in natural populations, most likely act at later stages of development or subsequent hybrid generations. Results from this study add to the growing knowledge of Triturus hybrid biology and ecology, which is the baseline for conservation programs necessary to protect these highly endangered amphibians. Abstract Two large-bodied newt species, Triturus ivanbureschi and T. macedonicus, hybridize in nature across the Balkan Peninsula. Consequences of hybridization upon secondary contact of two species include species displacement and asymmetrical introgression of T. ivanbureschi mtDNA. We set an experimental reciprocal cross of parental species and obtained two genotypes of F1 hybrids (with T. ivanbureschi or T. macedonicus mtDNA). When hybrids attained sexual maturity, they were engaged in mutual crossings and backcrossing with parental species. We followed reproductive traits over two successive years. Our main aim was to explore the reproductive success of F1 females carrying different parental mtDNA. Additionally, we tested for differences in reproductive success within female genotypes depending on the crossing with various male genotypes (hybrids or parental species). Both female genotypes had similar oviposition periods, number of laid eggs and hatched larvae but different body and egg sizes. Overall reproductive success (percentage of egg-laying females and viability of embryos) was similar for both genotypes. The type of crossing led to some differences in reproductive success within female genotypes. The obtained results suggest that processes that led to exclusion of T. macedonicus mtDNA in natural populations may be related to the survival at postembryonic stages of F2 generation or reproductive barriers that emerged in subsequent hybrid generations.
Collapse
Affiliation(s)
- Tijana Vučić
- Faculty of Biology, Institute of Zoology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.I.); (N.B.)
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
- Correspondence: (T.V.); (M.C.)
| | - Ana Ivanović
- Faculty of Biology, Institute of Zoology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.I.); (N.B.)
| | - Maja Ajduković
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
| | - Nikola Bajler
- Faculty of Biology, Institute of Zoology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.I.); (N.B.)
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
- Correspondence: (T.V.); (M.C.)
| |
Collapse
|
11
|
Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
Collapse
Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| |
Collapse
|
12
|
Sequeira F, Arntzen JW, van Gulik D, Hajema S, Diaz RL, Wagt M, van Riemsdijk I. Genetic traces of hybrid zone movement across a fragmented habitat. J Evol Biol 2022; 35:400-412. [PMID: 35043504 DOI: 10.1111/jeb.13982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n=22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego river. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego river (n=6), or further northwards (n=8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego river valley. We noted the absence of significant linkage disequilibrium and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.
Collapse
Affiliation(s)
- Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Jan W Arntzen
- Institute of Biology, Leiden University, Leiden, The Netherlands.,Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Davy van Gulik
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Steven Hajema
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Ruben Lopez Diaz
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Mattijn Wagt
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Isolde van Riemsdijk
- Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands.,Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| |
Collapse
|
13
|
Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
Collapse
Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
| |
Collapse
|
14
|
van Riemsdijk I, Arntzen JW, Babik W, Bogaerts S, Franzen M, Kalaentzis K, Litvinchuk SN, Olgun K, Wijnands JWPM, Wielstra B. Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure. Mol Phylogenet Evol 2021; 167:107361. [PMID: 34775056 DOI: 10.1016/j.ympev.2021.107361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.
Collapse
Affiliation(s)
- Isolde van Riemsdijk
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands; Institute for Evolution and Ecology, Auf der Morgenstelle 5, D-72076, Tübingen University, Tübingen, Germany
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | | | - Michael Franzen
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Konstantinos Kalaentzis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 St. Petersburg, Russia
| | - Kurtuluş Olgun
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydın, Turkey
| | - Jan Willem P M Wijnands
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands.
| |
Collapse
|
15
|
Provenance and genetic diversity of the non-native geckos Phelsuma grandis Gray 1870 and Gekko gecko (Linnaeus 1758) in southern Florida, USA. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02463-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
16
|
Tominaga A, Matsui M, Matsui M. Structure and movement of the hybrid zone between two divergent lineages of the Japanese newt
Cynops pyrrhogaster
(Amphibia: Urodela) in central Japan. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | | |
Collapse
|
17
|
Pflugbeil G, Affenzeller M, Tribsch A, Comes HP. Primary hybrid zone formation in Tephroseris helenitis (Asteraceae), following postglacial range expansion along the central Northern Alps. Mol Ecol 2021; 30:1704-1720. [PMID: 33548078 PMCID: PMC8048512 DOI: 10.1111/mec.15832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/26/2022]
Abstract
Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental-selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid-Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate-driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species' postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long-term, west-to-east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.
Collapse
Affiliation(s)
- Georg Pflugbeil
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Andreas Tribsch
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| |
Collapse
|
18
|
Palomar G, Dudek K, Wielstra B, Jockusch EL, Vinkler M, Arntzen JW, Ficetola GF, Matsunami M, Waldman B, Těšický M, Zieliński P, Babik W. Molecular Evolution of Antigen-Processing Genes in Salamanders: Do They Coevolve with MHC Class I Genes? Genome Biol Evol 2021; 13:6121093. [PMID: 33501944 PMCID: PMC7883663 DOI: 10.1093/gbe/evaa259] [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] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Proteins encoded by antigen-processing genes (APGs) prepare antigens for presentation by the major histocompatibility complex class I (MHC I) molecules. Coevolution between APGs and MHC I genes has been proposed as the ancestral gnathostome condition. The hypothesis predicts a single highly expressed MHC I gene and tight linkage between APGs and MHC I. In addition, APGs should evolve under positive selection, a consequence of the adaptive evolution in MHC I. The presence of multiple highly expressed MHC I genes in some teleosts, birds, and urodeles appears incompatible with the coevolution hypothesis. Here, we use urodele amphibians to test two key expectations derived from the coevolution hypothesis: 1) the linkage between APGs and MHC I was studied in Lissotriton newts and 2) the evidence for adaptive evolution in APGs was assessed using 42 urodele species comprising 21 genera from seven families. We demonstrated that five APGs (PSMB8, PSMB9, TAP1, TAP2, and TAPBP) are tightly linked (<0.5 cM) to MHC I. Although all APGs showed some codons under episodic positive selection, we did not find a pervasive signal of positive selection expected under the coevolution hypothesis. Gene duplications, putative gene losses, and divergent allelic lineages detected in some APGs demonstrate considerable evolutionary dynamics of APGs in salamanders. Overall, our results indicate that if coevolution between APGs and MHC I occurred in urodeles, it would be more complex than envisaged in the original formulation of the hypothesis.
Collapse
Affiliation(s)
- Gemma Palomar
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, The Netherlands.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Elizabeth L Jockusch
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Gentile F Ficetola
- Department of Environmental Sciences and Policy, University of Milano, Italy.,Laboratoire d'Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes and Université Savoie Mont Blanc, Grenoble, France
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Bruce Waldman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA.,School of Biological Sciences, Seoul National University, South Korea
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
19
|
Abdelaziz M, Muñoz-Pajares AJ, Berbel M, García-Muñoz A, Gómez JM, Perfectti F. Asymmetric Reproductive Barriers and Gene Flow Promote the Rise of a Stable Hybrid Zone in the Mediterranean High Mountain. FRONTIERS IN PLANT SCIENCE 2021; 12:687094. [PMID: 34512685 PMCID: PMC8424041 DOI: 10.3389/fpls.2021.687094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/15/2021] [Indexed: 05/13/2023]
Abstract
Hybrid zones have the potential to shed light on evolutionary processes driving adaptation and speciation. Secondary contact hybrid zones are particularly powerful natural systems for studying the interaction between divergent genomes to understand the mode and rate at which reproductive isolation accumulates during speciation. We have studied a total of 720 plants belonging to five populations from two Erysimum (Brassicaceae) species presenting a contact zone in the Sierra Nevada mountains (SE Spain). The plants were phenotyped in 2007 and 2017, and most of them were genotyped the first year using 10 microsatellite markers. Plants coming from natural populations were grown in a common garden to evaluate the reproductive barriers between both species by means of controlled crosses. All the plants used for the field and greenhouse study were characterized by measuring traits related to plant size and flower size. We estimated the genetic molecular variances, the genetic differentiation, and the genetic structure by means of the F-statistic and Bayesian inference. We also estimated the amount of recent gene flow between populations. We found a narrow unimodal hybrid zone where the hybrid genotypes appear to have been maintained by significant levels of a unidirectional gene flow coming from parental populations and from weak reproductive isolation between them. Hybrid plants exhibited intermediate or vigorous phenotypes depending on the analyzed trait. The phenotypic differences between the hybrid and the parental plants were highly coherent between the field and controlled cross experiments and through time. The highly coherent results obtained by combining field, experimental, and genetic data demonstrate the existence of a stable and narrow unimodal hybrid zone between Erysimum mediohispanicum and Erysimum nevadense at the high elevation of the Sierra Nevada mountains.
Collapse
Affiliation(s)
- Mohamed Abdelaziz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- *Correspondence: Mohamed Abdelaziz
| | - A. Jesús Muñoz-Pajares
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Laboratório Associado, Plant Biology, Research Centre in Biodiversity and Genetic Resources, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade Do Porto, Campus Agrário de Vairão, Fornelo e Vairão, Portugal
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | - Modesto Berbel
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - Ana García-Muñoz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - José M. Gómez
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Almeria, Spain
| | - Francisco Perfectti
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| |
Collapse
|
20
|
Arntzen JW, López‐Delgado J, Riemsdijk I, Wielstra B. A genomic footprint of a moving hybrid zone in marbled newts. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jan W. Arntzen
- Naturalis Biodiversity Center Leiden The Netherlands
- Institute of Biology Leiden University Leiden The Netherlands
| | - Julia López‐Delgado
- Naturalis Biodiversity Center Leiden The Netherlands
- Institute of Biology Leiden University Leiden The Netherlands
| | - Isolde Riemsdijk
- Naturalis Biodiversity Center Leiden The Netherlands
- Institute of Biology Leiden University Leiden The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center Leiden The Netherlands
- Institute of Biology Leiden University Leiden The Netherlands
| |
Collapse
|
21
|
Dufresnes C, Probonas NM, Strachinis I. A reassessment of the diversity of green toads (Bufotes) in the circum-Aegean region. Integr Zool 2020; 16:420-428. [PMID: 32978888 DOI: 10.1111/1749-4877.12494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The dynamic biogeography of glacial refugia may cause complex patterns of genetic admixture between parapatric taxa, which in turn can mislead their systematics, diversity, and distributions. We investigated this issue for green toads (Bufotes) inhabiting the circum-Aegean region, a biodiversity hotspot of the Eastern Mediterranean. A previous phylogeographic study based on mitochondrial and microsatellite loci identified the hybrid zone between the European (viridis) and Anatolian (sitibundus) lineages of B. viridis all over the Balkan Peninsula, but subsequent range-wide genomic analyses (>1000 SNPs) located this transition in Turkey, a thousand kilometers eastwards. In order to clarify the diversity and taxonomy of the circum-Aegean populations, we reconciled these conflicting findings by integrating previous data with pure sitibundus individuals. Our results confirmed that the viridis/sitibundus hybrid zone extends in Western Anatolia, but that southeastern European populations feature cytonuclear discordances and a high and structured microsatellite diversity. This remarkable situation may stem from a massive geographic displacement of the hybrid zone during the last glacial fluctuations, an underappreciated yet seemingly common feature among the herpetofauna of the region. Our study thus contributes to the rising view that mitochondrial DNA can be a poor predictor of current phylogeographic structure, hence the need for genomic data, especially for narrowly distributed taxa. Finally, the analyses unambiguously support the distinction of a micro-endemic clade of green toads unique to some Cyclades islands, for which we provide a formal taxonomic description.
Collapse
Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | | | - Ilias Strachinis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Natural Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
22
|
Toyama KS, Crochet P, Leblois R. Sampling schemes and drift can bias admixture proportions inferred by
structure. Mol Ecol Resour 2020; 20:1769-1785. [DOI: 10.1111/1755-0998.13234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Ken S. Toyama
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
| | - Pierre‐André Crochet
- CEFE CNRS University of Montpellier Université Paul Valéry Montpellier 3 EPHE IRD Montpellier France
| | - Raphaël Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
| |
Collapse
|
23
|
Šmíd J, Douda J, Krak K, Mandák B. Analyses of Hybrid Viability across a Hybrid Zone between Two Alnus Species Using Microsatellites and cpDNA Markers. Genes (Basel) 2020; 11:E770. [PMID: 32659930 PMCID: PMC7397206 DOI: 10.3390/genes11070770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/09/2023] Open
Abstract
Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the variability of microsatellites and chloroplast DNA between these species and their putative hybrids to create an overall picture of the development of the hybrid zone and its predicted type. To elucidate the gene transfer within both species, the origins of individual ploidies and especially the role of triploid hybrids, a germination experiment was carried out linked with a flow cytometry study of the resulting seedlings. The tension zone model seems to offer the most adequate explanation of our observations, with selection against triploid hybrids and the spatial positioning of the hybrid zone. Despite selection against them, the triploid hybrids play an important role in the exchange of genes between the two species and therefore serve as a bridge for introgression. The presence of fertile triploids is essential for enriching the haplotype diversity between these species and for the development of new genetic lineages.
Collapse
Affiliation(s)
- Jan Šmíd
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic; (J.Š.); (J.D.); (K.K.)
| | - Jan Douda
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic; (J.Š.); (J.D.); (K.K.)
| | - Karol Krak
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic; (J.Š.); (J.D.); (K.K.)
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Bohumil Mandák
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha-Suchdol, Czech Republic; (J.Š.); (J.D.); (K.K.)
- Institute of Botany, Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| |
Collapse
|
24
|
Capblancq T, Després L, Mavárez J. Genetic, morphological and ecological variation across a sharp hybrid zone between two alpine butterfly species. Evol Appl 2020; 13:1435-1450. [PMID: 32684968 PMCID: PMC7359832 DOI: 10.1111/eva.12925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 11/26/2022] Open
Abstract
Identifying the mechanisms involved in the formation and maintenance of species is a central question in evolutionary biology, and distinguishing the selective drivers of populations' divergence from demographic processes is of particular interest to better understand the speciation process. Hybrid zones are recognized to provide ideal places to investigate the genetic architecture of speciation and to identify the mechanisms allowing diverging species to maintain their integrity in the face of gene flow. Here, we studied two alpine butterfly species, Coenonympha macromma and C. gardetta, which can be found flying together and hybridizing in narrow contact zones in the southern French Alps. We characterized the genomic composition of individuals, their morphology and their local habitat requirements, within and around a hybrid zone. Genetic diversity analysis at 794 SNPs revealed that all individuals within the hybrid zone were highly admixed, which was not the case outside the hybrid zone. Cline analysis showed that, despite ongoing hybridization, 56 out of 122 loci differentially fixed or nearly so between the two species were impermeable to introgression across the sharp hybrid zone (9 km wide). We also found concordance in cline position and width among genetic, morphological and environmental variation, suggesting a coupling of different reproductive barriers. Habitat characteristics such as the presence of trees and shrubs and the start of the growing season were strongly associated with the genetic variation, and we found evidence of divergence at genetic markers associated with morphology and physiology, putatively involved in visual or environmental reproductive isolation. We discuss the various behavioural and ecological factors that might interplay to maintain current levels of divergence and gene flow between this species pair.
Collapse
Affiliation(s)
- Thibaut Capblancq
- Laboratoire d’Écologie AlpineUMR UGA‐USMB‐CNRS 5553Université Grenoble AlpesGrenobleFrance
- Department of Plant BiologyUniversity of VermontBurlingtonVTUSA
| | - Laurence Després
- Laboratoire d’Écologie AlpineUMR UGA‐USMB‐CNRS 5553Université Grenoble AlpesGrenobleFrance
| | - Jesús Mavárez
- Laboratoire d’Écologie AlpineUMR UGA‐USMB‐CNRS 5553Université Grenoble AlpesGrenobleFrance
- Departamento de Ciencias Biológicas y AmbientalesUniversidad Jorge Tadeo LozanoBogotáColombia
| |
Collapse
|
25
|
McEntee JP, Burleigh JG, Singhal S. Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation. Am Nat 2020; 196:9-28. [PMID: 32552108 DOI: 10.1086/709109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.
Collapse
|
26
|
The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs. Sci Rep 2020; 10:5502. [PMID: 32218506 PMCID: PMC7099067 DOI: 10.1038/s41598-020-62382-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/11/2020] [Indexed: 01/13/2023] Open
Abstract
Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a trend that contacts zones resulting from post-glacial expansions and human translocations feature more extensive introgression than those established within refugial areas. Integrating the biogeographic history of incipient species, i.e. their age since first contact together with their genetic divergence, thus appears timely to draw sound evolutionary and taxonomic inferences from patterns of introgression across hybrid zones.
Collapse
|
27
|
İpekdal K, Burban C, Sauné L, Battisti A, Kerdelhué C. From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting. Ecol Evol 2020; 10:1623-1638. [PMID: 32076539 PMCID: PMC7029074 DOI: 10.1002/ece3.6018] [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: 06/28/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022] Open
Abstract
Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co-occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.
Collapse
Affiliation(s)
| | | | - Laure Sauné
- INRAE, CBGP (INRAE, CIRAD, RD, Montpellier Supagro, Univ. Montpellier)MontpellierFrance
| | | | - Carole Kerdelhué
- INRAE, CBGP (INRAE, CIRAD, RD, Montpellier Supagro, Univ. Montpellier)MontpellierFrance
| |
Collapse
|
28
|
Royer AM, Waite-Himmelwright J, Smith CI. Strong Selection Against Early Generation Hybrids in Joshua Tree Hybrid Zone Not Explained by Pollinators Alone. FRONTIERS IN PLANT SCIENCE 2020; 11:640. [PMID: 32528500 PMCID: PMC7264850 DOI: 10.3389/fpls.2020.00640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/24/2020] [Indexed: 05/07/2023]
Abstract
Coevolution frequently plays an important role in diversification, but the role of obligate pollination mutualisms in the maintenance of hybrid zones has rarely been investigated. Like most members of the genus Yucca, the two species of Joshua tree (Yucca brevifolia and Yucca jaegeriana) are involved in a tightly coevolved mutualism with yucca moths. There is strong evidence of a history of coevolution between Joshua trees and their moth pollinators. We use a geographic clines approach in the Joshua tree hybrid zone to ask if selection by the moths may currently contribute to maintaining separation between these species. We compare genomic, phenotypic, and pollinator frequency clines to test whether pollinators maintain the hybrid zone or follow it as passive participants. The results reveal dramatic overlapping genomic and pollinator clines, consistent with a narrow hybrid zone maintained by strong selection. Wider phenotypic clines and a chloroplast genomic cline displaced opposite the expected direction suggest that pollinators are not the main source of selection maintaining the hybrid zone. Rather, it seems that high levels of reproductive isolation, likely acting through multiple barriers and involving many parts of the genome, keep the hybrid zone narrow.
Collapse
Affiliation(s)
- Anne M. Royer
- Biology Department, The University of Scranton, Scranton, PA, United States
- *Correspondence: Anne M. Royer,
| | | | | |
Collapse
|
29
|
Menon M, Landguth E, Leal‐Saenz A, Bagley JC, Schoettle AW, Wehenkel C, Flores‐Renteria L, Cushman SA, Waring KM, Eckert AJ. Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow. Evol Appl 2020; 13:195-209. [PMID: 31892952 PMCID: PMC6935588 DOI: 10.1111/eva.12795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/20/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023] Open
Abstract
A lack of optimal gene combinations, as well as low levels of genetic diversity, is often associated with the formation of species range margins. Conservation efforts rely on predictive modelling using abiotic variables and assessments of genetic diversity to determine target species and populations for controlled breeding, germplasm conservation and assisted migration. Biotic factors such as interspecific competition and hybridization, however, are largely ignored, despite their prevalence across diverse taxa and their role as key evolutionary forces. Hybridization between species with well-developed barriers to reproductive isolation often results in the production of offspring with lower fitness. Generation of novel allelic combinations through hybridization, however, can also generate positive fitness consequences. Despite this possibility, hybridization-mediated introgression is often considered a threat to biodiversity as it can blur species boundaries. The contribution of hybridization towards increasing genetic diversity of populations at range margins has only recently gathered attention in conservation studies. We assessed the extent to which hybridization contributes towards range dynamics by tracking spatio-temporal changes in the central location of a hybrid zone between two recently diverged species of pines: Pinus strobiformis and P. flexilis. By comparing geographic cline centre estimates for global admixture coefficient with morphological traits associated with reproductive output, we demonstrate a northward shift in the hybrid zone. Using a combination of spatially explicit, individual-based simulations and linkage disequilibrium variance partitioning, we note a significant contribution of adaptive introgression towards this northward movement, despite the potential for differences in regional population size to aid hybrid zone movement. Overall, our study demonstrates that hybridization between recently diverged species can increase genetic diversity and generate novel allelic combinations. These novel combinations may allow range margin populations to track favourable climatic conditions or facilitate adaptive evolution to ongoing and future climate change.
Collapse
Affiliation(s)
- Mitra Menon
- Integrative Life SciencesVirginia Commonwealth UniversityRichmondVirginia
| | - Erin Landguth
- School of Public and Community Health SciencesUniversity of MontanaMissoulaMontana
| | - Alejandro Leal‐Saenz
- Programa Institucional de Doctorado en Ciencias Agropecuarias y ForestalesUniversidad Juárez del Estado de DurangoDurangoMexico
| | - Justin C. Bagley
- Department of BiologyVirginia Commonwealth UniversityRichmondVirginia
| | - Anna W. Schoettle
- Rocky Mountain Research StationUSDA Forest ServiceFort CollinsColorado
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la MaderaUniversidad Juarez del Estado de DurangoDurangoMexico
| | | | | | | | - Andrew J. Eckert
- Department of BiologyVirginia Commonwealth UniversityRichmondVirginia
| |
Collapse
|
30
|
Wong ELY, Nevado B, Osborne OG, Papadopulos AST, Bridle JR, Hiscock SJ, Filatov DA. Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna. Mol Ecol 2019; 29:394-412. [PMID: 31793091 DOI: 10.1111/mec.15319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.
Collapse
Affiliation(s)
- Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | |
Collapse
|
31
|
Arntzen JW. An amphibian species pushed out of Britain by a moving hybrid zone. Mol Ecol 2019; 28:5145-5154. [PMID: 31643124 PMCID: PMC6900066 DOI: 10.1111/mec.15285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023]
Abstract
Classical theory states that hybrid zones will be stable in troughs of low population density where dispersal is hampered. Yet, evidence for moving hybrid zones is mounting. One possible reason that moving zones have been underappreciated is that they may drive themselves into oblivion and with just the superseding species remaining, morphological and genetic signals of past species replacement may be difficult to appreciate. Using genetic data (32 diagnostic single nucleotide polymorphisms) from a clinal hybrid zone of the common toad (Bufo bufo) and the spined toad (Bufo spinosus) in France for comparison, alleles of the latter species were documented in common toads in the south of Great Britain, at frequencies in excess of 10%. Because long distance dispersal across the Channel is unlikely, the conclusion reached was that the continental toad hybrid zone which previously extended into Britain, moved southwards and extirpated B. spinosus. Species distribution models for the mid-Holocene and the present support that climate has locally changed in favour of B. bufo. The system bears resemblance with the demise of Homo neanderthalensis and the rise of Homo sapiens and provides an example that some paleoanthropologists demanded in support of a hominin "leaky replacement" scenario. The toad example is informative just because surviving pure B. spinosus and an extant slowly moving interspecific hybrid zone are available for comparison.
Collapse
|
32
|
van Riemsdijk I, Butlin RK, Wielstra B, Arntzen JW. Testing an hypothesis of hybrid zone movement for toads in France. Mol Ecol 2019; 28:1070-1083. [PMID: 30609055 DOI: 10.1111/mec.15005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/08/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
Collapse
Affiliation(s)
- Isolde van Riemsdijk
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ben Wielstra
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California
| | - Jan W Arntzen
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands
| |
Collapse
|
33
|
Sequeira F, Bessa-Silva A, Tarroso P, Sousa-Neves T, Vallinoto M, Gonçalves H, Martínez-Solano I. Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt. J Evol Biol 2019; 33:202-216. [PMID: 31677317 DOI: 10.1111/jeb.13562] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022]
Abstract
The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.
Collapse
Affiliation(s)
- Fernando Sequeira
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Pedro Tarroso
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Tiago Sousa-Neves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Pará, Brasil
| | - Marcelo Vallinoto
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Helena Gonçalves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Iñigo Martínez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC (MNCN-CSIC), Madrid, Spain
| |
Collapse
|
34
|
Mačát Z, Rulík M, Jablonski D, Reiter A, Jeřábková L, Rada S, Mikulíček P. Species-specific habitat preferences do not shape the structure of a crested newt hybrid zone ( Triturus cristatus x T. carnifex). Ecol Evol 2019; 9:12446-12458. [PMID: 31788189 PMCID: PMC6875670 DOI: 10.1002/ece3.5683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/31/2019] [Accepted: 09/04/2019] [Indexed: 11/08/2022] Open
Abstract
Reproductive isolation barriers maintain the integrity of species by preventing interspecific gene flow. They involve temporal, habitat or behavioral isolation acting before fertilization, and postzygotic isolation manifested as hybrid mortality or sterility. One of the approaches of how to study reproductive isolation barriers is through the analysis of hybrid zones. In this paper, we describe the structure of a hybrid zone between two crested newt species (Triturus cristatus and T. carnifex) in the southern part of the Czech Republic using morphological, microsatellite, and mitochondrial (mtDNA) markers. Specifically, we tested the hypothesis that the structure of the hybrid zone is maintained by species-specific habitat preferences. Comparing the genetic structure of populations with geographical and ecological parameters, we found that the hybrid zone was structured primarily geographically, with T. cristatus-like populations occurring in the northeast and T. carnifex-like populations in the southwest. Despite T. cristatus tending to occur in deeper ponds and T. carnifex on localities with more shading, the effect of both ecological parameters on the structure of the zone was minimal. Next, we corroborated that T. carnifex individuals and some hybrids possess mtDNA of T. dobrogicus, whose nuclear background was not detected in the studied hybrid zone. Hybridization between T. carnifex and T. dobrogicus (resulting in unidirectional mtDNA introgression) had to predate subsequent formation of the hybrid zone between T. cristatus and T. carnifex. Populations of crested newts in the southern part of the Czech Republic thus represent a genetic mosaic of nuclear and mitochondrial genomes of three species.
Collapse
Affiliation(s)
- Zdeněk Mačát
- Department of Ecology and Environmental SciencesPalacky UniversityOlomoucCzech Republic
| | - Martin Rulík
- Department of Ecology and Environmental SciencesPalacky UniversityOlomoucCzech Republic
| | | | | | - Lenka Jeřábková
- Nature Conservation Agency of the Czech RepublicPrahaCzech Republic
| | - Stanislav Rada
- Department of Ecology and Environmental SciencesPalacky UniversityOlomoucCzech Republic
| | | |
Collapse
|
35
|
Dudek K, Gaczorek TS, Zieliński P, Babik W. Massive introgression of major histocompatibility complex (MHC) genes in newt hybrid zones. Mol Ecol 2019; 28:4798-4810. [PMID: 31574568 DOI: 10.1111/mec.15254] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated European newts, Lissotriton montandoni and L. vulgaris, we demonstrated recent and ongoing MHC class I and II introgression in the Carpathian region. The extent of introgression correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded similarity between transects within species, implying pervasive introgression - a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.
Collapse
Affiliation(s)
- Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Tomasz S Gaczorek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
36
|
Zieliński P, Dudek K, Arntzen JW, Palomar G, Niedzicka M, Fijarczyk A, Liana M, Cogǎlniceanu D, Babik W. Differential introgression across newt hybrid zones: Evidence from replicated transects. Mol Ecol 2019; 28:4811-4824. [DOI: 10.1111/mec.15251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Zieliński
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | | | - Gemma Palomar
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Anna Fijarczyk
- Département de Biologie Faculté des Sciences et de génie Université Laval Québec QC Canada
| | | | - Dan Cogǎlniceanu
- Faculty of Natural Sciences and Agricultural Sciences University Ovidius Constanţa Constanţa Romania
| | - Wiesław Babik
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| |
Collapse
|
37
|
Wang S, Rohwer S, Delmore K, Irwin DE. Cross-decades stability of an avian hybrid zone. J Evol Biol 2019; 32:1242-1251. [PMID: 31430391 DOI: 10.1111/jeb.13524] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 01/04/2023]
Abstract
Hybrid zones are particularly valuable for understanding the evolution of partial reproductive isolation between differentiated populations. An increasing number of hybrid zones have been inferred to move over time, but in most such cases zone movement has not been tested with long-term genomic data. The hybrid zone between Townsend's Warblers (Setophaga townsendi) and Hermit Warblers (S. occidentalis) in the Washington Cascades was previously inferred to be moving from northern S. townsendi southwards towards S. occidentalis, based on plumage and behavioural patterns as well as a 2000-km genetic wake of hermit mitochondrial DNA (mtDNA) in coastal Townsend's Warblers. We directly tested whether hybrid zone position has changed over 2-3 decades by tracking plumage, mtDNA and nuclear genomic variation across the hybrid zone over two sampling periods (1987-94 and 2015-16). Surprisingly, there was no significant movement in genomic or plumage cline centres between the two time periods. Plumage cline widths were narrower than expected by neutral diffusion, consistent with a 'tension zone' model, in which selection against hybrids is balanced by movement of parental forms into the zone. Our results indicate that this hybrid zone is either stable in its location or moving at a rate that is not detectable over 2-3 decades. Despite considerable gene flow, the stable clines in multiple phenotypic and genotypic characters over decades suggest evolutionary stability of this young pair of sister species, allowing divergence to continue. We propose a novel biogeographic scenario to explain these patterns: rather than the hybrid zone having moved thousands of kilometres to its current position, inland Townsend's met coastal Hermit Warbler populations along a broad front of the British Columbia and Alaska coast and hybridization led to replacement of the Hermit Warbler plumage with Townsend's Warbler plumage patterns along this coastline. Hence, hybrid zones along British Columbia and Alaska moved only a short distance from the inland to the coast, whereas the Hermit Warbler phenotype appears stable in Washington and further south. This case provides an example of the complex biogeographic processes that have led to the distribution of current phenotypes within and among closely related species.
Collapse
Affiliation(s)
- Silu Wang
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Sievert Rohwer
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, USA
| | - Kira Delmore
- Department of Biology, Texas A & M, College Station, TX, USA
| | - Darren E Irwin
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
38
|
Dufresnes C, Mazepa G, Jablonski D, Sadek RA, Litvinchuk SN. A river runs through it: tree frog genomics supports the Dead Sea Rift as a rare phylogeographical break. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Phylogeographical breaks can be viewed as regional hotspots of diversity where the genetic integrity of incipient species is put to the test. We focus on an understudied species transition from the Middle East, namely the Dead Sea Rift in the Levant region, which presumably divided the tree frogs Hyla savignyi and H. felixarabica. Combining multilocus genetic analyses (mitochondrial DNA and RAD-sequencing) with ecological niche modelling, we test whether the rift effectively acts as a biogeographical barrier preventing this pair from admixing and merging. The answer is yes: despite weak signs of introgression, all parapatric populations were assigned to either species without cyto-nuclear discordance. Yet, the projected distributions under present and glacial conditions largely overlapped in the area, meaning their current parapatric ranges do not represent an ecological transition. Instead, we hypothesize that H. savignyi and H. felixarabica are maintained apart by limited opportunities for dispersal across the barren Jordan Valley, combined with advanced reproductive isolation. Therefore, the Dead Sea Rift may represent a rare phylogeographical break, and we encourage international efforts to assess its contribution to the rich biodiversity of the Middle East.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Laboratory for Conservation Biology, University of Lausanne, Lausanne, Switzerland
| | - Glib Mazepa
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Genetics, Evolutionary Biology, Norbyvägen, Uppsala, Sweden
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova, Mlynská dolina, Bratislava, Slovakia
| | - Riyad A Sadek
- Biology Department, American University of Beirut, Beirut, Lebanon
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, St. Petersburg, Russia
- Department of Zoology and Physiology, Dagestan State University, Makhachkala, Dagestan, Russia
| |
Collapse
|
39
|
Dufresnes C, Déjean T, Zumbach S, Schmidt BR, Fumagalli L, Ramseier P, Dubey S. Early detection and spatial monitoring of an emerging biological invasion by population genetics and environmental DNA metabarcoding. CONSERVATION SCIENCE AND PRACTICE 2019. [DOI: 10.1111/csp2.86] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Christophe Dufresnes
- Hintermann & Weber SA Montreux Switzerland
- Laboratory for Conservation Biology, Department of Ecology and EvolutionUniversity of Lausanne Lausanne Switzerland
| | | | | | - Benedikt R. Schmidt
- Info fauna—karch, UNiMail Neuchâtel Switzerland
- Institut für Evolutionsbiologie und UmweltwissenschaftenUniversität Zürich Zürich Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and EvolutionUniversity of Lausanne Lausanne Switzerland
| | | | - Sylvain Dubey
- Hintermann & Weber SA Montreux Switzerland
- Laboratory for Conservation Biology, Department of Ecology and EvolutionUniversity of Lausanne Lausanne Switzerland
- Agrosustain SA Nyon Switzerland
| |
Collapse
|
40
|
Dufresnes C, Strachinis I, Suriadna N, Mykytynets G, Cogălniceanu D, Székely P, Vukov T, Arntzen JW, Wielstra B, Lymberakis P, Geffen E, Gafny S, Kumlutaş Y, Ilgaz Ç, Candan K, Mizsei E, Szabolcs M, Kolenda K, Smirnov N, Géniez P, Lukanov S, Crochet PA, Dubey S, Perrin N, Litvinchuk SN, Denoël M. Phylogeography of a cryptic speciation continuum in Eurasian spadefoot toads (Pelobates). Mol Ecol 2019; 28:3257-3270. [PMID: 31254307 DOI: 10.1111/mec.15133] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/30/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
Cryptic phylogeographic diversifications provide unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecological and behavioural differentiation. Yet, to date very few comparative studies have been attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eurasian amphibians, the Pelobates spadefoot toads, by conducting multilocus (restriction site associated DNA sequencing and mitochondrial DNA) phylogenetic, phylogeographic and hybrid zone analyses. Within the P. syriacus complex, we discovered species-level cryptic divergences (>5 million years ago [My]) between populations distributed in the Near-East (hereafter P. syriacus sensu stricto [s.s.]) and southeastern Europe (hereafter P. balcanicus), each featuring deep intraspecific lineages. Altogether, we could scale hybridizability to divergence time along six different stages, spanning from sympatry without gene flow (P. fuscus and P. balcanicus, >10 My), parapatry with highly restricted hybridization (P. balcanicus and P. syriacus s.s., >5 My), narrow hybrid zones (~15 km) consistent with partial reproductive isolation (P. fuscus and P. vespertinus, ~3 My), to extensive admixture between Pleistocene and refugial lineages (≤2 My). This full spectrum empirically supports a gradual build up of reproductive barriers through time, reversible up until a threshold that we estimate at ~3 My. Hence, cryptic phylogeographic lineages may fade away or become reproductively isolated species simply depending on the time they persist in allopatry, and without definite ecomorphological divergence.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Hintermann & Weber SA, Montreux, Switzerland.,Laboratory for Conservation Biology, University of Lausanne, Lausanne, Switzerland
| | - Ilias Strachinis
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nataliia Suriadna
- Melitopol Insitute of Ecology and Social Technologies of University "Ukraine", Melitopol, Zaporizhia, Ukraine
| | | | - Dan Cogălniceanu
- Faculty of Natural Sciences and Agricultural Sciences, University Ovidius Constanţa, Constanţa, Romania
| | - Paul Székely
- Departamento de Ciencias Biológicas, EcoSs Lab, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Tanja Vukov
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Petros Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
| | - Eli Geffen
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Sarig Gafny
- School of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Kamil Candan
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, İzmir, Turkey.,Research and Application Center for Fauna and Flora, Dokuz Eylül University, Buca, İzmir, Turkey
| | - Edvárd Mizsei
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Márton Szabolcs
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Krzysztof Kolenda
- Department of Evolutionary Biology and Conservation of Vertebrates, Institute of Environmental Biology, University of Wrocław, Wrocław, Poland
| | - Nazar Smirnov
- Department of Nature, Chernivtsi Regional Museum, Chernivtsi, Ukraine
| | - Philippe Géniez
- CEFE, EPHE-PSL, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Simeon Lukanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Pierre-André Crochet
- CEFE, CNRS, University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Sylvain Dubey
- Hintermann & Weber SA, Montreux, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Agrosustain SA, Nyon, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.,Department of Zoology and Physiology, Dagestan State University, Makhachkala, Russia
| | - Mathieu Denoël
- Laboratory of Fish and Amphibian Ethology, Behavioural Biology Group, Freshwater and OCeanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
| |
Collapse
|
41
|
Billerman SM, Cicero C, Bowie RCK, Carling MD. Phenotypic and genetic introgression across a moving woodpecker hybrid zone. Mol Ecol 2019; 28:1692-1708. [DOI: 10.1111/mec.15043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Shawn M. Billerman
- Department of Zoology and Physiology University of Wyoming Laramie Wyoming
- Program in Ecology University of Wyoming Laramie Wyoming
| | - Carla Cicero
- Museum of Vertebrate Zoology University of California Berkeley California
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology University of California Berkeley California
- Department of Integrative Biology University of California Berkeley California
| | - Matthew D. Carling
- Department of Zoology and Physiology University of Wyoming Laramie Wyoming
- Program in Ecology University of Wyoming Laramie Wyoming
| |
Collapse
|
42
|
Wielstra B, McCartney-Melstad E, Arntzen J, Butlin R, Shaffer H. Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle. Mol Phylogenet Evol 2019; 133:120-127. [DOI: 10.1016/j.ympev.2018.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/30/2018] [Accepted: 12/30/2018] [Indexed: 11/29/2022]
|
43
|
Abstract
Ben Wielstra introduces Eurasian newts of the genus Triturus.
Collapse
Affiliation(s)
- Ben Wielstra
- Institute of Biology Leiden, Leiden University, 2300 RA Leiden, The Netherlands; Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands.
| |
Collapse
|
44
|
Goüy de Bellocq J, Wasimuddin, Ribas A, Bryja J, Piálek J, Baird SJE. Holobiont suture zones: Parasite evidence across the European house mouse hybrid zone. Mol Ecol 2018; 27:5214-5227. [PMID: 30427096 DOI: 10.1111/mec.14938] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 02/06/2023]
Abstract
Parasite hybrid zones resulting from host secondary contact have never been described in nature although parasite hybridization is well known and secondary contact should affect them similarly to free-living organisms. When host populations are isolated, diverge and recontact, intimate parasites (host specific, direct life cycle) carried during isolation will also meet and so may form parasite hybrid zones. If so, we hypothesize these should be narrower than the host's hybrid zone as shorter parasite generation time allows potentially higher divergence. We investigate multilocus genetics of two parasites across the European house mouse hybrid zone. We find each host taxon harbours its own parasite taxa. These also hybridize: Parasite hybrid zones are significantly narrower than the host's. Here, we show a host hybrid zone is a suture zone for a subset of its parasite community and highlight the potential of such systems as windows on the evolutionary processes of host-parasite interactions and recombinant pathogen emergence.
Collapse
Affiliation(s)
| | - Wasimuddin
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Alexis Ribas
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic.,Section of Parasitology, Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Josef Bryja
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jaroslav Piálek
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic
| | - Stuart J E Baird
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic
| |
Collapse
|
45
|
Dufresnes C, Mazepa G, Rodrigues N, Brelsford A, Litvinchuk SN, Sermier R, Lavanchy G, Betto-Colliard C, Blaser O, Borzée A, Cavoto E, Fabre G, Ghali K, Grossen C, Horn A, Leuenberger J, Phillips BC, Saunders PA, Savary R, Maddalena T, Stöck M, Dubey S, Canestrelli D, Jeffries DL. Genomic Evidence for Cryptic Speciation in Tree Frogs From the Apennine Peninsula, With Description of Hyla perrini sp. nov. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00144] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
46
|
Bisconti R, Porretta D, Arduino P, Nascetti G, Canestrelli D. Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy. Sci Rep 2018; 8:13187. [PMID: 30181603 PMCID: PMC6123427 DOI: 10.1038/s41598-018-31535-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/08/2018] [Indexed: 01/17/2023] Open
Abstract
Discordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. Recent population declines in central Italy partially erased the genetic imprints of past hybridization dynamics. However, the overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species' range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.
Collapse
Affiliation(s)
- Roberta Bisconti
- Tuscia University, Department of Ecological and Biological Sciences, Viterbo, 01100, Italy.
| | - Daniele Porretta
- University of Rome, "Sapienza", Department of Environmental Biology, Rome, 00185, Italy
| | - Paola Arduino
- Tuscia University, Department of Ecological and Biological Sciences, Viterbo, 01100, Italy
| | - Giuseppe Nascetti
- Tuscia University, Department of Ecological and Biological Sciences, Viterbo, 01100, Italy
| | - Daniele Canestrelli
- Tuscia University, Department of Ecological and Biological Sciences, Viterbo, 01100, Italy
| |
Collapse
|
47
|
Arntzen JW, Üzüm N, Ajduković MD, Ivanović A, Wielstra B. Absence of heterosis in hybrid crested newts. PeerJ 2018; 6:e5317. [PMID: 30065885 PMCID: PMC6063215 DOI: 10.7717/peerj.5317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/04/2018] [Indexed: 11/27/2022] Open
Abstract
Relationships between phylogenetic relatedness, hybrid zone spatial structure, the amount of interspecific gene flow and population demography were investigated, with the newt genus Triturus as a model system. In earlier work, a bimodal hybrid zone of two distantly related species combined low interspecific gene flow with hybrid sterility and heterosis was documented. Apart from that, a suite of unimodal hybrid zones in closely related Triturus showed more or less extensive introgressive hybridization with no evidence for heterosis. We here report on population demography and interspecific gene flow in two Triturus species (T. macedonicus and T. ivanbureschi in Serbia). These are two that are moderately related, engage in a heterogeneous uni-/bimodal hybrid zone and hence represent an intermediate situation. This study used 13 diagnostic nuclear genetic markers in a population at the species contact zone. This showed that all individuals were hybrids, with no parentals detected. Age, size and longevity and the estimated growth curves are not exceeding that of the parental species, so that we conclude the absence of heterosis in T. macedonicus-T. ivanbureschi. Observations across the genus support the hypothesis that fertile hybrids allocate resources to reproduction and infertile hybrids allocate resources to growth. Several Triturus species hybrid zones not yet studied allow the testing of this hypothesis.
Collapse
Affiliation(s)
| | - Nazan Üzüm
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, Aydin, Turkey
| | - Maja D. Ajduković
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Ana Ivanović
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| |
Collapse
|
48
|
Souissi A, Bonhomme F, Manchado M, Bahri-Sfar L, Gagnaire PA. Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.). Heredity (Edinb) 2018; 121:579-593. [PMID: 29713088 DOI: 10.1038/s41437-018-0079-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/12/2018] [Accepted: 03/10/2018] [Indexed: 11/09/2022] Open
Abstract
Investigating gene flow between closely related species and its variation across the genome is important to understand how reproductive barriers shape genome divergence before speciation is complete. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter gene exchange between species, leading to heterogeneous genome divergence. In the present study, genome-wide divergence and introgression patterns were investigated between two sole species, Solea senegalensis and Solea aegyptiaca, using restriction-associated DNA sequencing (RAD-Seq) to analyze samples taken from a transect spanning the hybrid zone. An integrative approach combining geographic and genomic clines methods with an analysis of individual locus introgression accounting for the demographic history of divergence was conducted. Our results showed that the two sole species have come into secondary contact postglacially, after experiencing a prolonged period (ca. 1.1 to 1.8 Myrs) of allopatric separation. Secondary contact resulted in the formation of a tension zone characterized by strong reproductive isolation, which only allowed introgression in a limited fraction of the genome. We found multiple evidence for a preferential direction of introgression in the S. aegyptiaca genetic background, indicating a possible recent or ongoing movement of the hybrid zone. Deviant introgression signals found in the opposite direction suggested that S. senegalensis could have possibly undergone adaptive introgression that has not yet spread throughout the entire species range. Our study thus illustrates the varied outcomes of genetic interactions between divergent gene pools that recently met after a long history of divergence.
Collapse
Affiliation(s)
- Ahmed Souissi
- Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France. .,CNRS-Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral, 34200, Sète, France. .,Faculté des Sciences de Tunis UR11ES08 Biologie intégrative et écologie évolutive et fonctionnelle des milieux aquatiques, Université de Tunis El Manar, 2092, Tunis, Tunisia.
| | - François Bonhomme
- Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.,CNRS-Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral, 34200, Sète, France
| | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500, El Puerto de Santa María, Cádiz, Spain
| | - Lilia Bahri-Sfar
- Faculté des Sciences de Tunis UR11ES08 Biologie intégrative et écologie évolutive et fonctionnelle des milieux aquatiques, Université de Tunis El Manar, 2092, Tunis, Tunisia
| | - Pierre-Alexandre Gagnaire
- Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.,CNRS-Institut des Sciences de l'Evolution, UMR5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral, 34200, Sète, France
| |
Collapse
|
49
|
Buddhachat K, Suwannapoom C. Phylogenetic relationships and genetic diversity of the Polypedates leucomystax complex in Thailand. PeerJ 2018; 6:e4263. [PMID: 29362696 PMCID: PMC5774300 DOI: 10.7717/peerj.4263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/23/2017] [Indexed: 11/20/2022] Open
Abstract
Taxonomic uncertainty of the Asian tree frog Polypedates leucomystax complex presents the challenging task of inferring its biogeographical history. Here, we describe its dispersion and the genetic relationships among different populations in Thailand, where we connect the population of the P. leucomystax complex of the Sunda Islands to the Indochina (mainland) population based on analyses of 266 sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Our maternal genealogy implies that there are four well-supported lineages in Thailand, consisting of Northern A (clade A: Polypedates sp.), Nan (clade B: P. cf. impresus), Southern (clade C: P. cf. leucomystax) and Northern D (clade D: P. cf. megacephalus), with Bayesian posterior probability >0.9. Phylogeny and haplotype networks indicate that clades A, B and D are sympatric. In contrast, clade C (P. cf. leucomystax) and clade D (P. cf. megacephalus) are genetically divergent due to the geographical barrier of the Isthmus of Kra, resulting in an allopatric distribution. Climatic conditions, in particular differences in rainfall on each side of the Isthmus of Kra, may play an important role in limiting the immigration of both clades. For the within-populations of either clades C or D, there was no significant correlation between geographic and genetic distance by the isolation-by-distance test, indicating intraspecific-dispersal of each clade. Population expansion occurred in clade C, whereas clade D showed a constant population. Taken together, the P. leucomystax complex in South East Asia may have diversified under climatic pressure, leading to allopatric and/or sympatric speciation.
Collapse
|
50
|
Wielstra B, Burke T, Butlin RK, Arntzen JW. A signature of dynamic biogeography: enclaves indicate past species replacement. Proc Biol Sci 2017; 284:20172014. [PMID: 29187631 PMCID: PMC5740283 DOI: 10.1098/rspb.2017.2014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future.
Collapse
Affiliation(s)
- B Wielstra
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Naturalis Biodiversity Center, PO Box 9517, Leiden, 2300 RA, The Netherlands
| | - T Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - R K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, Gothenburg 405 30, Sweden
| | - J W Arntzen
- Naturalis Biodiversity Center, PO Box 9517, Leiden, 2300 RA, The Netherlands
| |
Collapse
|