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Bogár K, Stanivuk J, Géczi A, Fazekas GL, Kovács B, Lázár B, Molnár M, Ardó L, Ljubobratović U, Kovács G, Péter D, Várkonyi E, Káldy J. Investigation of Sexes and Fertility Potential of Female Russian Sturgeon ( Acipenser gueldenstaedtii) and Male American Paddlefish ( Polyodon spathula) Hybrids. Life (Basel) 2024; 14:818. [PMID: 39063572 PMCID: PMC11277912 DOI: 10.3390/life14070818] [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: 04/30/2024] [Revised: 06/16/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
In the present study, 10 allotriploid (3nALT) and 10 allopentaploid (5nALP) six-month-old hybrid fish and two 3nALT and four 5nALP 40-month-old hybrid fish, which resulted by crossing female Russian sturgeon Acipenser gueldenstaedtii (Brandt and Ratzeberg, 1833) and male American paddlefish Polyodon spathula (Walbaum, 1792), were investigated. It was revealed that six-month-old 3nALT and 5nALP hybrids initially had "undifferentiated" gonads, while in the 40-month-old hybrids, only testes were observed in one case of 3nALT and one case of 5nALP hybrids. The testis of 3nALT hybrids was partially developed with spermatogonia, while the testis of one 5nALP hybrid was in the second developmental stage with low spermatogonia density. We could not determine gonad differentiation in any of the cases when the hybrid individuals had the W sex chromosome. We concluded that the gonad differentiation of these interfamilial hybrids follows a similar pattern to interspecific hybrids of different ploidy parent species of the family Acipenseridae, which is consistent with the classical Haldane's rule. However, it cannot be excluded that the testis of this/these hybrid(s) may produce fertile sperm after sexual maturity, depending on additional genetic, hormonal and environmental factors, and further research is required for its evaluation.
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Affiliation(s)
- Katalin Bogár
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Jelena Stanivuk
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Aliz Géczi
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Georgina Lea Fazekas
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Balázs Kovács
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary; (B.K.); (D.P.)
| | - Bence Lázár
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, H-2100 Gödöllő, Hungary; (B.L.); (E.V.)
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Mariann Molnár
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, H-2100 Gödöllő, Hungary; (B.L.); (E.V.)
| | - László Ardó
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
| | - Uroš Ljubobratović
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
| | - Gyula Kovács
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
| | - Dániel Péter
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary; (B.K.); (D.P.)
| | - Eszter Várkonyi
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, H-2100 Gödöllő, Hungary; (B.L.); (E.V.)
| | - Jenő Káldy
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
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Dufresnes C, Monod-Broca B, Bellati A, Canestrelli D, Ambu J, Wielstra B, Dubey S, Crochet PA, Denoël M, Jablonski D. Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions. GLOBAL CHANGE BIOLOGY 2024; 30:e17180. [PMID: 38465701 DOI: 10.1111/gcb.17180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research (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
| | - Benjamin Monod-Broca
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Johanna Ambu
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sylvain Dubey
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), FOCUS, University of Liège, Liège, Belgium
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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Leal JL, Milesi P, Salojärvi J, Lascoux M. Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences. Syst Biol 2023; 72:372-390. [PMID: 36932679 PMCID: PMC10275558 DOI: 10.1093/sysbio/syad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 10/14/2022] [Accepted: 03/10/2023] [Indexed: 03/19/2023] Open
Abstract
Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.].
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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Multiplexed ISSR Genotyping by Sequencing (MIG-Seq). Methods Mol Biol 2023; 2638:403-414. [PMID: 36781659 DOI: 10.1007/978-1-0716-3024-2_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.
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Tricou T, Tannier E, de Vienne DM. Ghost lineages can invalidate or even reverse findings regarding gene flow. PLoS Biol 2022; 20:e3001776. [PMID: 36103518 PMCID: PMC9473628 DOI: 10.1371/journal.pbio.3001776] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.
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Affiliation(s)
- Théo Tricou
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
| | - Eric Tannier
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
- INRIA Grenoble Rhône-Alpes, F-38334 Montbonnot, France
| | - Damien M. de Vienne
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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Tricou T, Tannier E, de Vienne DM. Ghost Lineages Highly Influence the Interpretation of Introgression Tests. Syst Biol 2022; 71:1147-1158. [PMID: 35169846 PMCID: PMC9366450 DOI: 10.1093/sysbio/syac011] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 02/01/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Most species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression, and admixture, are therefore likely to involve "ghosts," that is extinct, unknown, or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario. [ABBA-BABA; D-statistic; gene flow; ghost lineage; introgression; simulation.].
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Affiliation(s)
- Théo Tricou
- Laboratoire de Biométrie et Biologie Évolutive UMR5558, Univ Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Eric Tannier
- Laboratoire de Biométrie et Biologie Évolutive UMR5558, Univ Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France
- Inria, Centre de Recherche de Lyon, F-69603 Villeurbanne, France
| | - Damien M de Vienne
- Laboratoire de Biométrie et Biologie Évolutive UMR5558, Univ Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France
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Dufresnes C, Crochet PA. Sex chromosomes as supergenes of speciation: why amphibians defy the rules? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210202. [PMID: 35694748 PMCID: PMC9189495 DOI: 10.1098/rstb.2021.0202] [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] [Indexed: 12/14/2022] Open
Abstract
As reflected by the two rules of speciation (Haldane's rule and the large X-/Z-effect), sex chromosomes are expected to behave like supergenes of speciation: they recombine only in one sex (XX females or ZZ males), supposedly recruit sexually antagonistic genes and evolve faster than autosomes, which can all contribute to pre-zygotic and post-zygotic isolation. While this has been mainly studied in organisms with conserved sex-determining systems and highly differentiated (heteromorphic) sex chromosomes like mammals, birds and some insects, these expectations are less clear in organismal groups where sex chromosomes repeatedly change and remain mostly homomorphic, like amphibians. In this article, we review the proposed roles of sex-linked genes in isolating nascent lineages throughout the speciation continuum and discuss their support in amphibians given current knowledge of sex chromosome evolution and speciation modes. Given their frequent recombination and lack of differentiation, we argue that amphibian sex chromosomes are not expected to become supergenes of speciation, which is reflected by the rarity of empirical studies consistent with a 'large sex chromosome effect' in frogs and toads. The diversity of sex chromosome systems in amphibians has a high potential to disentangle the evolutionary mechanisms responsible for the emergence of sex-linked speciation genes in other organisms. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, People's Republic of China
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Dedukh D, Riumin S, Kolenda K, Chmielewska M, Rozenblut-Kościsty B, Kaźmierczak M, Ogielska M, Krasikova A. Maintenance of pure hybridogenetic water frog populations: Genotypic variability in progeny of diploid and triploid parents. PLoS One 2022; 17:e0268574. [PMID: 35793279 PMCID: PMC9258834 DOI: 10.1371/journal.pone.0268574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
An intriguing outcome of hybridisation is the emergence of clonally and hemiclonally reproducing hybrids, that can sustain, reproduce, and lead to the emergence of polyploid forms. However, the maintenance of diploid and polyploid hybrid complexes in natural populations remains unresolved. We selected water frogs from the Pelophylax esculentus complex to study how diploid and triploid hybrids, which reproduce hemiclonally via hybridogenesis, are maintained in natural populations. During gametogenesis in diploid hybrids, one of the parental genomes is eliminated, and the remaining genome is endoreplicated. In triploid hybrids, the single-copy genome is typically eliminated, while genome endoreplication does not occur. To investigate how diploid and triploid hybrid frogs reproduce in populations without parental species, we crossed these hybrid animals from two separate pure hybrid populations located in Poland. Using cytogenetic analysis of tadpoles that emerged from the crosses, we established which gametes were produced by parental hybrids. The majority of hybrid females and hybrid males produced one type of gamete with the P. ridibundus genome. However, in both studied populations, approximately half of the diploid and triploid hybrids simultaneously produced gametes with different genome compositions and ploidy levels, specifically, the P. ridibundus and P. lessonae genomes, as well as diploid gametes with genomes of both parental species. Triploid hybrid males and females mostly produced haploid gametes with the P. lessonae genome; however, gametes with the P. ridibundus genome have also been observed. These results suggest that not all hybrids follow the classical hybridogenetic reproduction program and reveal a significant level of alterations in the gametogenesis pathways. In addition, we found a variable survival rate of particular progeny genotypes when we crossed hybrid females with different males suggesting the important role of postzygotic barriers on the maintenance of pure hybrid systems. We suggest that the observed variability in produced gametes and the different survival rate of the progeny with certain genotypes is crucial for the existence of pure hybrid systems.
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Affiliation(s)
- Dmitrij Dedukh
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Sergey Riumin
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Raisa Gorbacheva Мemorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First St. Petersburg State Medical University, Saint-Petersburg, Russia
| | - Krzysztof Kolenda
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Magdalena Chmielewska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Beata Rozenblut-Kościsty
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Mikołaj Kaźmierczak
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Maria Ogielska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Alla Krasikova
- Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, Russia
- * E-mail:
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Kumari G, Roopa Lavanya G, Shanmugavadivel PS, Singh Y, Singh P, Patidar B, Madhavan L, Gupta S, Singh NP, Pratap A. Genetic diversity and population genetic structure analysis of an extensive collection of wild and cultivated Vigna accessions. Mol Genet Genomics 2021; 296:1337-1353. [PMID: 34611751 DOI: 10.1007/s00438-021-01825-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Vigna is a large, pan-tropic and highly variable group of the legumes family which is known for its > 10 cultivated species having significant commercial value for their nutritious grains and multifarious uses. The wild vignas are considered a reservoir of numerous useful traits which can be deployed for introgression of resistance to biotic and abiotic stresses, seed quality and enhanced survival capability in extreme environments. Nonetheless, for their effective utilization through introgression breeding information on their genetic diversity, population structure and crossability is imperative. Keeping this in view, the present experiment was undertaken with 119 accessions including 99 wild Vigna accessions belonging to 19 species and 18 cultivated genotypes of Vigna and 2 of Phaseolus. Total 102 polymorphic SSRs were deployed to characterize the material at molecular level which produced 1758 alleles. The genotypes were grouped into four major clusters which were further sub-divided in nine sub-clusters. Interestingly, all cultivated species shared a single cluster while no such similarities were observed for the wild accessions as these were distributed in different groups of sub-clusters. The co-dominant allelic data of 114 accessions were then utilized for obtaining status of the accessions and their hybrid forms. The model-based population structure analysis categorized 114 accessions of Vigna into 6 genetically distinct sub-populations (K = 6) following admixture-model based simulation with varying levels of admixture. 91 (79.82%) accessions resembled their hierarchy and 23 (20.18%) accessions were observed as the admixture forms. Maximum number of accessions (25) were grouped in sub-population (SP) 6 and the least accessions were grouped in SP3 and SP5 (11 each). The population genetic structure, therefore, supported genetic diversity analysis and provided an insight into the genetic lineage of these species which will help in effective use of germplasm for development of cultivars following selective prebreeding activities.
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Affiliation(s)
- Gita Kumari
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - G Roopa Lavanya
- Sam Higginbottom University of Agricultural Technology and Sciences, Prayagraj, UP, 211 008, India
| | | | - Yogendra Singh
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Parikshit Singh
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Bharat Patidar
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Latha Madhavan
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Thrissur, Kerala, 680654, India
| | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - N P Singh
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| | - Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India.
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Barrios-Leal DY, Menezes RST, Ribeiro JV, Bizzo L, Melo de Sene F, Neves-da-Rocha J, Manfrin MH. A holocenic and dynamic hybrid zone between two cactophilic Drosophila species in a coastal lowland plain of the Brazilian Atlantic Forest. J Evol Biol 2021; 34:1737-1751. [PMID: 34538008 DOI: 10.1111/jeb.13934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 11/30/2022]
Abstract
Hybridization and introgression are processes that contribute to shaping biological diversity. The factors promoting the formation of these processes are multiples but poorly explored in a biogeographical and ecological context. In the southeast coastal plain of the Brazilian Atlantic Forest, a hybrid zone was described between two closely related cactophilic species, Drosophila antonietae and D. serido. Here, we revisited and analysed specimens from this hybrid zone to evaluate its temporal and spatial dynamic. We examined allopatric and sympatric populations of the flies using independent sources of data such as mitochondrial and nuclear sequences, microsatellite loci, morphometrics of wings and male genitalia, and climatic niche models. We also verified the emergence of the flies from necrotic tissues of collected cacti to verify the role of host association for the population dynamics. Our results support the existence of a hybrid zone due to secondary contact and limited to the localities where the two species are currently in contact. Furthermore, we detected asymmetric bidirectional introgression and the maintenance of the species integrity, ecological association and morphological characters, suggesting selection and limited introgression. Considering our paleomodels, probably this hybrid zone is recent and the contact occurred during the Holocene to the present day, favoured by range expansion of their populations due to expansion of open and dry areas in eastern South America during palaeoclimatic and geomorphological events.
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Affiliation(s)
- Dora Yovana Barrios-Leal
- Pós-Graduação, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - João Victor Ribeiro
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Luiz Bizzo
- UNIVALI - Universidade do Vale do Itajaí, Itajaí, Santa Catarina, Brazil.,Centro Universitário - Católica de Santa Catarina, Jaraguá do Sul, Santa Catarina, Brazil
| | - Fabio Melo de Sene
- Pós-Graduação, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - João Neves-da-Rocha
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Maura Helena Manfrin
- Pós-Graduação, Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
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11
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Stöck M, Dedukh D, Reifová R, Lamatsch DK, Starostová Z, Janko K. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200103. [PMID: 34304588 PMCID: PMC8310718 DOI: 10.1098/rstb.2020.0103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Dunja K. Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
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12
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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation. IMA Fungus 2021; 12:16. [PMID: 34193315 PMCID: PMC8246709 DOI: 10.1186/s43008-021-00068-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/23/2021] [Indexed: 02/06/2023] Open
Abstract
The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
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13
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Marsit S, Hénault M, Charron G, Fijarczyk A, Landry CR. The neutral rate of whole-genome duplication varies among yeast species and their hybrids. Nat Commun 2021; 12:3126. [PMID: 34035259 PMCID: PMC8149824 DOI: 10.1038/s41467-021-23231-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/19/2021] [Indexed: 11/09/2022] Open
Abstract
Hybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD may allow hybrids to thrive by increasing fitness, restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. Here we show, by measuring the spontaneous rate of WGD of more than 1300 yeast crosses evolved under relaxed selection, that some genotypes or combinations of genotypes are more prone to WGD, including some hybrids between closely related species. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.
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Affiliation(s)
- S Marsit
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada.
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada.
| | - M Hénault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada
| | - G Charron
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - A Fijarczyk
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada
| | - C R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Université Laval, Québec, QC, Canada.
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC, Canada.
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14
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Guo X, Mandáková T, Trachtová K, Özüdoğru B, Liu J, Lysak MA. Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe. Mol Biol Evol 2021; 38:1695-1714. [PMID: 33331908 PMCID: PMC8097306 DOI: 10.1093/molbev/msaa327] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (∼60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.
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Affiliation(s)
- Xinyi Guo
- CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karolína Trachtová
- CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, Beytepe, Ankara, Turkey
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Martin A Lysak
- CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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15
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Matute DR, Cooper BS. Comparative studies on speciation: 30 years since Coyne and Orr. Evolution 2021; 75:764-778. [PMID: 33491225 PMCID: PMC8247902 DOI: 10.1111/evo.14181] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/28/2022]
Abstract
Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.
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Affiliation(s)
- Daniel R. Matute
- Biology DepartmentUniversity of North CarolinaChapel HillNorth Carolina27510
| | - Brandon S. Cooper
- Division of Biological SciencesUniversity of MontanaMissoulaMontana59812
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16
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Parker VT, Rodriguez CY, Wechsler G, Vasey MC. Allopatry, hybridization, and reproductive isolation in Arctostaphylos. AMERICAN JOURNAL OF BOTANY 2020; 107:1798-1814. [PMID: 33274449 DOI: 10.1002/ajb2.1576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Hybridization plays a key role in introgressive adaptation, speciation, and adaptive radiation as a source of evolutionary innovation. Hybridization is considered common in Arctostaphylos, yet species boundaries are retained in stands containing multiple species. Arctostaphylos contains diploids and tetraploids, and recent phylogenies indicate two clades; we hypothesize combinations of these traits limit or promote hybridization rates. METHODS We statistically analyzed co-occurrence patterns of species by clade membership and ploidy level from 87 random 0.1 ha plots. We sampled multiple sites to analyze for percent hybridization based on morphology. Finally, phenophases were analyzed by scoring herbarium sheets for a large number of taxa from both clades as well as tetraploids, and second, surveying three field sites over two years for divergence in phenological stages between co-occurring taxa. RESULTS Most taxa in Arctostaphylos are allopatric relative to other congenerics. When two taxa co-occur, the patterns are a diploid with a tetraploid, or two diploids from different clades. When three taxa co-occur, the pattern is two diploids from different clades and a tetraploid. Field and herbarium data both indicate flowering phenology is displaced between diploids from the two clades; one of the diploid clades and tetraploids overlap considerably. CONCLUSIONS The two deep clades in Arctostaphylos are genetically distant, with hybrids rare or non-existent when taxa co-occur. Reproductive isolation between clades is enhanced by displaced flowering phenology for co-occurring species. Within clades, taxa appear to have few reproductive barriers other than an allopatric distribution or different ploidy levels.
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Affiliation(s)
- V Thomas Parker
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
| | - Christina Y Rodriguez
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
| | - Gail Wechsler
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
| | - Michael C Vasey
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
- San Francisco Bay National Estuarine Research Reserve, Estuary & Ocean Science Center, San Francisco State University, Romberg Tiburon Campus, 3150 Paradise Drive, Tiburon, California, 94920, USA
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17
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Molina WF, Costa GWWF, Cunha IMC, Bertollo LAC, Ezaz T, Liehr T, Cioffi MB. Molecular Cytogenetic Analysis in Freshwater Prawns of the Genus Macrobrachium (Crustacea: Decapoda: Palaemonidae). Int J Mol Sci 2020; 21:ijms21072599. [PMID: 32283616 PMCID: PMC7178241 DOI: 10.3390/ijms21072599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/18/2023] Open
Abstract
Freshwater prawns of the genus Macrobrachium are one of the important components of circumtropical marine, estuarine, and freshwater environments. They have been extensively exploited for human consumption for many years. More than 250 species reflect the evolutionary success of this highly diversified group, with a complex and challenging taxonomy due to morphological variations and vast geographical distribution. Although genetic approaches have been used to clarify phylogenetic and taxonomic aspects of Macrobrachium species, cytogenetic information is still very scarce and mostly focused on chromosome number and morphology. Here, we present chromosome data for three species from the Neotropical region, M. carcinus,M. acanthurus, and M. amazonicum, and one species from the Oriental region, M. rosenbergii. Using conventional cytogenetic approaches and chromosome mapping of repetitive DNAs by fluorescence in situ hybridization (FISH), we identified numerical diversification of the diploid set, within and between both zoogeographic regions. These included M. acanthurus and M. amazonicum sharing diploid chromosomes of 98, while M. carcinus has 94, and M. rosenbergii has 118 chromosomes. Argentophilic sites are also variable in number, but they occur in a much higher number than 18S rDNA, representing two to 10 sites within the study species. Microsatellites repeat motifs are also abundant in the chromosomes, with a co-localization and uniform distribution along the chromosome arms, but completely absent in the AT-rich centromeric regions. As a whole, our study suggests that the 2n divergence was followed by a considerable rDNA diversification. The abundance of the exceptional amount of microsatellite sequences in the chromosomes also suggests that they are essential components of the Macrobrachium genome and, therefore, maintained as a shared feature by the species, the reason for which is yet unknown.
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Affiliation(s)
- Wagner F. Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Gideão W. W. F. Costa
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Inailson M. C. Cunha
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59078970, Brazil; (W.F.M.); (G.W.W.F.C.); (I.M.C.C.)
| | - Luiz A. C. Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil; (L.A.C.B.); (M.B.C.)
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia;
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 7747 Jena, Germany
- Correspondence:
| | - Marcelo B. Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP C.P. 676, Brazil; (L.A.C.B.); (M.B.C.)
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18
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Keuler R, Garretson A, Saunders T, Erickson RJ, St Andre N, Grewe F, Smith H, Lumbsch HT, Huang JP, St Clair LL, Leavitt SD. Genome-scale data reveal the role of hybridization in lichen-forming fungi. Sci Rep 2020; 10:1497. [PMID: 32001749 PMCID: PMC6992703 DOI: 10.1038/s41598-020-58279-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Advancements in molecular genetics have revealed that hybridization may be common among plants, animals, and fungi, playing a role in evolutionary dynamics and speciation. While hybridization has been well-documented in pathogenic fungi, the effects of these processes on speciation in fungal lineages with different life histories and ecological niches are largely unexplored. Here we investigated the potential influence of hybridization on the emergence of morphologically and reproductively distinct asexual lichens. We focused on vagrant forms (growing obligately unattached to substrates) within a clade of rock-dwelling, sexually reproducing species in the Rhizoplaca melanophthalma (Lecanoraceae, Ascomycota) species complex. We used phylogenomic data from both mitochondrial and nuclear genomes to infer evolutionary relationships and potential patterns of introgression. We observed multiple instances of discordance between the mitochondrial and nuclear trees, including the clade comprising the asexual vagrant species R. arbuscula, R. haydenii, R. idahoensis, and a closely related rock-dwelling lineage. Despite well-supported phylogenies, we recovered strong evidence of a reticulated evolutionary history using a network approach that incorporates both incomplete lineage sorting and hybridization. These data suggest that the rock-dwelling western North American subalpine endemic R. shushanii is potentially the result of a hybrid speciation event, and introgression may have also played a role in other taxa, including vagrant species R. arbuscula, R. haydenii and R. idahoensis. We discuss the potential roles of hybridization in terms of generating asexuality and novel morphological traits in lichens. Furthermore, our results highlight the need for additional study of reticulate phylogenies when investigating species boundaries and evolutionary history, even in cases with well-supported topologies inferred from genome-scale data.
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Affiliation(s)
- Rachel Keuler
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Alexis Garretson
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Theresa Saunders
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Robert J Erickson
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Nathan St Andre
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - Felix Grewe
- Grainger Bioinformatics Center, Science & Education, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Hayden Smith
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center, Science & Education, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, 128 Academia Rd, Section 2, Nankang District, Taipei, 11529, Taiwan
| | - Larry L St Clair
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA
- M. L. Bean Life Science Museum, Brigham Young University, 1115 MLBM, Provo, UT, 84602, USA
| | - Steven D Leavitt
- Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT, 84602, USA.
- M. L. Bean Life Science Museum, Brigham Young University, 1115 MLBM, Provo, UT, 84602, USA.
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19
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Bartoš O, Röslein J, Kotusz J, Paces J, Pekárik L, Petrtýl M, Halačka K, Štefková Kašparová E, Mendel J, Boroń A, Juchno D, Leska A, Jablonska O, Benes V, Šídová M, Janko K. The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids. Mol Biol Evol 2020; 36:1902-1920. [PMID: 31077330 PMCID: PMC6735777 DOI: 10.1093/molbev/msz114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hybridization and polyploidization are important evolutionary processes whose impacts range from the alteration of gene expression and phenotypic variation to the triggering of asexual reproduction. We investigated fishes of the Cobitis taenia-elongatoides hybrid complex, which allowed us to disentangle the direct effects of both processes, due to the co-occurrence of parental species with their diploid and triploid hybrids. Employing morphological, ecological, and RNAseq approaches, we investigated the molecular determinants of hybrid and polyploid forms. In contrast with other studies, hybridization and polyploidy induced relatively very little transgressivity. Instead, Cobitis hybrids appeared intermediate with a clear effect of genomic dosing when triploids expressed higher similarity to the parent contributing two genome sets. This dosage effect was symmetric in the germline (oocyte gene expression), interestingly though, we observed an overall bias toward C. taenia in somatic tissues and traits. At the level of individual genes, expression-level dominance vastly prevailed over additivity or transgressivity. Also, trans-regulation of gene expression was less efficient in diploid hybrids than in triploids, where the expression modulation of homoeologs derived from the "haploid" parent was stronger than those derived from the "diploid" parent. Our findings suggest that the apparent intermediacy of hybrid phenotypes results from the combination of individual genes with dominant expression rather than from simple additivity. The efficiency of cross-talk between trans-regulatory elements further appears dosage dependent. Important effects of polyploidization may thus stem from changes in relative concentrations of trans-regulatory elements and their binding sites between hybridizing genomes. Links between gene regulation and asexuality are discussed.
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Affiliation(s)
- Oldřich Bartoš
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Röslein
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Paces
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Institute of Molecular Genetics, Laboratory of Genomics and Bioinformatics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Pekárik
- Plant Science and Biodiversity Center, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia.,Faculty of Education, Trnava University, Trnava, Slovakia
| | - Miloslav Petrtýl
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Štefková Kašparová
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Mendel
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alicja Boroń
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Leska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Olga Jablonska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Monika Šídová
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Vestec, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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20
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Matute DR, Comeault AA, Earley E, Serrato-Capuchina A, Peede D, Monroy-Eklund A, Huang W, Jones CD, Mackay TFC, Coyne JA. Rapid and Predictable Evolution of Admixed Populations Between Two Drosophila Species Pairs. Genetics 2020; 214:211-230. [PMID: 31767631 PMCID: PMC6944414 DOI: 10.1534/genetics.119.302685] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for over 20 generations. We assessed morphological, behavioral, and fitness-related traits from each replicate population periodically, and sequenced genomic DNA from the populations at generation 20. For both pairs of species, species-specific traits and their genomes regressed to those of the continental species. A few alleles from the island species persisted, but they tended to be proportionally rare among all sites in the genome and were rarely fixed within the populations. This paucity of alleles from the island species was particularly pronounced on the X-chromosome. These results indicate that nearly all foreign genes were quickly eliminated after hybridization and that selection against the minor species genome might be similar across experimental replicates.
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Affiliation(s)
- Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Aaron A Comeault
- School of Natural Sciences, Bangor University, Wales, UK LL57 2EN
| | - Eric Earley
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | | | - David Peede
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Anaïs Monroy-Eklund
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Wen Huang
- Program in Genetics and Department of Biological Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Corbin D Jones
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Trudy F C Mackay
- Program in Genetics and Department of Biological Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Jerry A Coyne
- Ecology and Evolution, University of Chicago, Illinois 60637
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21
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Dufresnes C, Mazepa G, Jablonski D, Oliveira RC, Wenseleers T, Shabanov DA, Auer M, Ernst R, Koch C, Ramírez-Chaves HE, Mulder KP, Simonov E, Tiutenko A, Kryvokhyzha D, Wennekes PL, Zinenko OI, Korshunov OV, Al-Johany AM, Peregontsev EA, Masroor R, Betto-Colliard C, Denoël M, Borkin LJ, Skorinov DV, Pasynkova RA, Mazanaeva LF, Rosanov JM, Dubey S, Litvinchuk S. Fifteen shades of green: The evolution of Bufotes toads revisited. Mol Phylogenet Evol 2019; 141:106615. [DOI: 10.1016/j.ympev.2019.106615] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 09/10/2019] [Indexed: 01/01/2023]
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22
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Wagner F, Ott T, Zimmer C, Reichhart V, Vogt R, Oberprieler C. 'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae). THE NEW PHYTOLOGIST 2019; 223:2039-2053. [PMID: 30851196 DOI: 10.1111/nph.15784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.
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Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Claudia Zimmer
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Verena Reichhart
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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23
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Marques DA, Meier JI, Seehausen O. A Combinatorial View on Speciation and Adaptive Radiation. Trends Ecol Evol 2019; 34:531-544. [DOI: 10.1016/j.tree.2019.02.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 01/28/2023]
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24
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MacGuigan DJ, Near TJ. Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae). Syst Biol 2019; 68:329-346. [PMID: 30395332 DOI: 10.1093/sysbio/syy074] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022] Open
Abstract
Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study, we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of approximately 30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression between Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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25
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Coppi A, Lastrucci L, Ferretti G, Viciani D. A phylogenetic study of two recently described endemic species of the Saxifraga granulata group from the central-north Mediterranean region (Italy) and their position in the context of the series Saxifraga (Saxifragaceae). SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1492997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Andrea Coppi
- Department of Biology, University of Florence, via G. La Pira 4, I-50121 Florence, Italy
| | - Lorenzo Lastrucci
- Department of Biology, University of Florence, via G. La Pira 4, I-50121 Florence, Italy
| | - Giulio Ferretti
- Department of Biology, University of Florence, via G. La Pira 4, I-50121 Florence, Italy
| | - Daniele Viciani
- Department of Biology, University of Florence, via G. La Pira 4, I-50121 Florence, Italy
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26
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Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation. Proc Natl Acad Sci U S A 2018; 115:9761-9766. [PMID: 30209213 PMCID: PMC6166845 DOI: 10.1073/pnas.1809685115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hybridization can promote speciation, and examples of putative hybrid species have now been identified across the tree of life. However, we still know little about the conditions that are most conducive to hybrid speciation. We have used experimental evolution in fruit flies (Drosophila) to show that both the genetic difference between hybridizing species and the number of hybridizing species affect the probability that hybrids evolve reproductive isolation from their parental species. Our results provide a systematic test of factors that affect homoploid hybrid speciation. Biologists will now be able to test the predictions that our experiments outline in naturally hybridizing species. These types of data hold the potential to greatly increase our understanding of hybridization’s role in generating biodiversity. Hybridization is often maladaptive and in some instances has led to the loss of biodiversity. However, hybridization can also promote speciation, such as during homoploid hybrid speciation, thereby generating biodiversity. Despite examples of homoploid hybrid species, the importance of hybridization as a speciation mechanism is still widely debated, and we lack a general understanding of the conditions most likely to generate homoploid hybrid species. Here we show that the level of genetic divergence between hybridizing species has a large effect on the probability that their hybrids evolve reproductive isolation. We find that populations of hybrids formed by parental species with intermediate levels of divergence were more likely to mate assortatively, and discriminate against their parental species, than those generated from weakly or strongly diverged parental species. Reproductive isolation was also found between hybrid populations, suggesting differential sorting of parental traits across populations. Finally, hybrid populations derived from three species were more likely to evolve reproductive isolation than those derived from two species, supporting arguments that hybridization-supplied genetic diversity can lead to the evolution of novel “adaptive systems” and promote speciation. Our results illustrate when we expect hybridization and admixture to promote hybrid speciation. Whether homoploid hybrid speciation is a common speciation mechanism in general remains an outstanding empirical question.
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27
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Betto-Colliard C, Hofmann S, Sermier R, Perrin N, Stöck M. Profound genetic divergence and asymmetric parental genome contributions as hallmarks of hybrid speciation in polyploid toads. Proc Biol Sci 2018; 285:rspb.2017.2667. [PMID: 29436499 PMCID: PMC5829204 DOI: 10.1098/rspb.2017.2667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/17/2018] [Indexed: 01/19/2023] Open
Abstract
The evolutionary causes and consequences of allopolyploidization, an exceptional pathway to instant hybrid speciation, are poorly investigated in animals. In particular, when and why hybrid polyploids versus diploids are produced, and constraints on sources of paternal and maternal ancestors, remain underexplored. Using the Palearctic green toad radiation (including bisexually reproducing species of three ploidy levels) as model, we generate a range-wide multi-locus phylogeny of 15 taxa and present four new insights: (i) at least five (up to seven) distinct allotriploid and allotetraploid taxa have evolved in the Pleistocene; (ii) all maternal and paternal ancestors of hybrid polyploids stem from two deeply diverged nuclear clades (6 Mya, 3.1-9.6 Mya), with distinctly greater divergence than the parental species of diploid hybrids found at secondary contact zones; (iii) allotriploid taxa possess two conspecific genomes and a deeply diverged allospecific one, suggesting that genomic imbalance and divergence are causal for their partly clonal reproductive mode; (iv) maternal versus paternal genome contributions exhibit asymmetry, with the maternal nuclear (and mitochondrial) genome of polyploids always coming from the same clade, and the paternal genome from the other. We compare our findings with similar patterns in diploid/polyploid vertebrates, and suggest deep ancestral divergence as a precondition for successful allopolyploidization.
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Affiliation(s)
- Caroline Betto-Colliard
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Sylvia Hofmann
- Department of Conservation Biology, UFZ Helmholtz-Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany
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28
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Meleshko O, Stenøien HK, Speed JDM, Flatberg KI, Kyrkjeeide MO, Hassel K. Is interspecific gene flow and speciation in peatmosses ( Sphagnum) constrained by phylogenetic relationship and life-history traits? LINDBERGIA 2018. [DOI: 10.25227/linbg.01107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Olena Meleshko
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Hans K. Stenøien
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - James D. M. Speed
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Kjell I. Flatberg
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | | | - Kristian Hassel
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
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29
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Boecklen WJ. Topology of syngameons. Ecol Evol 2017; 7:10486-10491. [PMID: 29299231 PMCID: PMC5743628 DOI: 10.1002/ece3.3507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/27/2017] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
Syngameons are sets of species linked by interspecific hybridization. Common observations regarding the structure of syngameons are that hybridization propensity is not uniform across species and that patterns of hybridization are dominated by a few species. I use computer simulations to test these claims in naturally occurring syngameons selected from the literature and from personal observation. Natural syngameons, especially those involving plants, typically exhibit nonrandom structure: The first three order statistics for the number of hybrid partners and the variance in the number of hybrid partners are larger than chance alone would predict. The structure of two insect syngameons examined is not significantly different from random. To test a hypothesis that variation in hybridization propensity across species in natural syngameons is simply an artifact of hybridization opportunity, I examine the structure of four artificial syngameons (fertility relationships) produced by full diallel crosses. Three of four artificial syngameons exhibit nonrandom structure, as the observed variation in number of successful crosses is larger than chance alone would predict. In general, there are no significant results involving the order statistics. Finally, I discuss biogeographic, ecological, and phylogenetic hypotheses for variation in hybridization propensity across species in natural syngameons.
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30
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Zhu F, Schlupp I, Tiedemann R. Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors. PLoS One 2016; 11:e0156209. [PMID: 27249369 PMCID: PMC4889153 DOI: 10.1371/journal.pone.0156209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 05/06/2016] [Indexed: 11/19/2022] Open
Abstract
The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish-two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.
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Affiliation(s)
- Fangjun Zhu
- University of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ingo Schlupp
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Ralph Tiedemann
- University of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail:
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31
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Woodhams MD, Lockhart PJ, Holland BR. Simulating and Summarizing Sources of Gene Tree Incongruence. Genome Biol Evol 2016; 8:1299-315. [PMID: 27017528 PMCID: PMC4898792 DOI: 10.1093/gbe/evw065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting.
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Affiliation(s)
- Michael D Woodhams
- Discipline of Mathematics, School of Physical Sciences, University of Tasmania, Hobart, Australia
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Barbara R Holland
- Discipline of Mathematics, School of Physical Sciences, University of Tasmania, Hobart, Australia
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32
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Záveská E, Fér T, Šída O, Marhold K, Leong-Škorničková J. Hybridization among distantly related species: Examples from the polyploid genus Curcuma (Zingiberaceae). Mol Phylogenet Evol 2016; 100:303-321. [PMID: 27090448 DOI: 10.1016/j.ympev.2016.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 01/17/2023]
Abstract
Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma, based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA (DCS, GAPDH, GLOBOSA3, LEAFY, ITS) and four non-coding cpDNA regions (trnL-trnF, trnT-trnL, psbA-trnH and matK), analysed as a single locus, were employed to construct a species tree and hybrid species trees using (*)BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma, which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida, C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin.
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Affiliation(s)
- Eliška Záveská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Tomáš Fér
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Otakar Šída
- Department of Botany, National Museum in Prague, Prague, Czech Republic
| | - Karol Marhold
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
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Barker MS, Arrigo N, Baniaga AE, Li Z, Levin DA. On the relative abundance of autopolyploids and allopolyploids. THE NEW PHYTOLOGIST 2016; 210:391-8. [PMID: 26439879 DOI: 10.1111/nph.13698] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Anthony E Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Donald A Levin
- Section of Integrative Biology, University of Texas, Austin, TX, 78713, USA
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Matthews A, Emelianova K, Hatimy AA, Chester M, Pellicer J, Ahmad KS, Guignard MS, Rouhan G, Soltis DE, Soltis PS, Leitch IJ, Leitch AR, Mavrodiev EV, Buggs RJA. 250 years of hybridization between two biennial herb species without speciation. AOB PLANTS 2015; 7:plv081. [PMID: 26187604 PMCID: PMC4571729 DOI: 10.1093/aobpla/plv081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/04/2015] [Indexed: 05/23/2023]
Abstract
Hybridization between plant species can generate novel morphological diversity and lead to speciation at homoploid or polyploid levels. Hybrids between biennial herbs Tragopogon pratensis and T. porrifolius have been studied in experimental and natural populations for over 250 years. Here we examine their current status in natural populations in southeast England. All hybrids found were diploid; they tended to grow taller and with more buds than their parental species; many showed partial fertility; a few showed evidence of backcrossing. However, we found no evidence to suggest that the hybrids are establishing as a new species, nor can we find literature documenting speciation of these hybrids elsewhere. This lack of speciation despite at least 250 years of hybridization contrasts with the fact that both parental species have formed new allopolyploid species through hybridization with another diploid, T. dubius. Understanding why hybrids often do not speciate, despite repeated opportunities, would enhance our understanding of both the evolutionary process and risk assessments of invasive species.
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Affiliation(s)
- Andrew Matthews
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK Present address: Division of Ecology and Evolution, Imperial College London, Silwood Park Campus, Ascot, UK
| | - Katie Emelianova
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Abubakar A Hatimy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael Chester
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Department of Plant Science, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Khawaja Shafique Ahmad
- Lab of Plant Taxonomy, Department of Botany, University of Agriculture, Faisalabad 38040, Pakistan
| | - Maité S Guignard
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Germinal Rouhan
- Museum national d'Histoire naturelle, UMR CNRS 7205, Herbier National, CP3916 rue Buffon, F-75231 Paris, France
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Evgeny V Mavrodiev
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Sánchez-Guillén RA, Córdoba-Aguilar A, Hansson B, Ott J, Wellenreuther M. Evolutionary consequences of climate-induced range shifts in insects. Biol Rev Camb Philos Soc 2015; 91:1050-1064. [PMID: 26150047 DOI: 10.1111/brv.12204] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 05/28/2015] [Accepted: 06/05/2015] [Indexed: 01/30/2023]
Abstract
Range shifts can rapidly create new areas of geographic overlap between formerly allopatric taxa and evidence is accumulating that this can affect species persistence. We review the emerging literature on the short- and long-term consequences of these geographic range shifts. Specifically, we focus on the evolutionary consequences of novel species interactions in newly created sympatric areas by describing the potential (i) short-term processes acting on reproductive barriers between species and (ii) long-term consequences of range shifts on the stability of hybrid zones, introgression and ultimately speciation and extinction rates. Subsequently, we (iii) review the empirical literature on insects to evaluate which processes have been studied, and (iv) outline some areas that deserve increased attention in the future, namely the genomics of hybridisation and introgression, our ability to forecast range shifts and the impending threat from insect vectors and pests on biodiversity, human health and crop production. Our review shows that species interactions in de novo sympatric areas can be manifold, sometimes increasing and sometimes decreasing species diversity. A key issue that emerges is that climate-induced hybridisations in insects are much more widespread than anticipated and that rising temperatures and increased anthropogenic disturbances are accelerating the process of species mixing. The existing evidence only shows the tip of the iceberg and we are likely to see many more cases of species mixing following range shifts in the near future.
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Affiliation(s)
- Rosa A Sánchez-Guillén
- Department of Biology, Lund University, Lund, 223 62, Sweden. .,Departamento de Ecología Evolutiva, Instituto of Ecología, Universidad Nacional Autónoma de México, 70 275, Mexico D.F., Mexico.
| | - Alex Córdoba-Aguilar
- Departamento de Ecología Evolutiva, Instituto of Ecología, Universidad Nacional Autónoma de México, 70 275, Mexico D.F., Mexico
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Jürgen Ott
- L.U.P.O. GmbH, 67705, Trippstadt, Germany
| | - Maren Wellenreuther
- Department of Biology, Lund University, Lund, 223 62, Sweden.,Plant and Food Research, Nelson, 7043, New Zealand
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Dedukh D, Litvinchuk S, Rosanov J, Mazepa G, Saifitdinova A, Shabanov D, Krasikova A. Optional Endoreplication and Selective Elimination of Parental Genomes during Oogenesis in Diploid and Triploid Hybrid European Water Frogs. PLoS One 2015; 10:e0123304. [PMID: 25894314 PMCID: PMC4403867 DOI: 10.1371/journal.pone.0123304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/03/2015] [Indexed: 11/25/2022] Open
Abstract
Incompatibilities between parental genomes decrease viability of interspecific hybrids; however, deviations from canonical gametogenesis such as genome endoreplication and elimination can rescue hybrid organisms. To evaluate frequency and regularity of genome elimination and endoreplication during gametogenesis in hybrid animals with different ploidy, we examined genome composition in oocytes of di- and triploid hybrid frogs of the Pelophylax esculentus complex. Obtained results allowed us to suggest that during oogenesis the endoreplication involves all genomes occurring before the selective genome elimination. We accepted the hypothesis that only elimination of one copied genome occurs premeiotically in most of triploid hybrid females. At the same time, we rejected the hypothesis stating that the genome of parental species hybrid frogs co-exist with is always eliminated during oogenesis in diploid hybrids. Diploid hybrid frogs demonstrate an enlarged frequency of deviations in oogenesis comparatively to triploid hybrids. Typical for hybrid frogs deviations in gametogenesis increase variability of produced gametes and provide a mechanism for appearance of different forms of hybrids.
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Affiliation(s)
- Dmitry Dedukh
- Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Spartak Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Juriy Rosanov
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Glib Mazepa
- Department of Ecology and Genetic, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- V.N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | | | | | - Alla Krasikova
- Saint-Petersburg State University, Saint-Petersburg, Russia
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37
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Betto-Colliard C, Sermier R, Litvinchuk S, Perrin N, Stöck M. Origin and genome evolution of polyploid green toads in Central Asia: evidence from microsatellite markers. Heredity (Edinb) 2015; 114:300-8. [PMID: 25370211 PMCID: PMC4815583 DOI: 10.1038/hdy.2014.100] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 09/10/2014] [Accepted: 09/22/2014] [Indexed: 02/08/2023] Open
Abstract
Polyploidization, which is expected to trigger major genomic reorganizations, occurs much less commonly in animals than in plants, possibly because of constraints imposed by sex-determination systems. We investigated the origins and consequences of allopolyploidization in Palearctic green toads (Bufo viridis subgroup) from Central Asia, with three ploidy levels and different modes of genome transmission (sexual versus clonal), to (i) establish a topology for the reticulate phylogeny in a species-rich radiation involving several closely related lineages and (ii) explore processes of genomic reorganization that may follow polyploidization. Sibship analyses based on 30 cross-amplifying microsatellite markers substantiated the maternal origins and revealed the paternal origins and relationships of subgenomes in allopolyploids. Analyses of the synteny of linkage groups identified three markers affected by translocation events, which occurred only within the paternally inherited subgenomes of allopolyploid toads and exclusively affected the linkage group that determines sex in several diploid species of the green toad radiation. Recombination rates did not differ between diploid and polyploid toad species, and were overall much reduced in males, independent of linkage group and ploidy levels. Clonally transmitted subgenomes in allotriploid toads provided support for strong genetic drift, presumably resulting from recombination arrest. The Palearctic green toad radiation seems to offer unique opportunities to investigate the consequences of polyploidization and clonal transmission on the dynamics of genomes in vertebrates.
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Affiliation(s)
- C Betto-Colliard
- Department of Ecology and Evolution, Biophore Building University of Lausanne, Lausanne, Switzerland
| | - R Sermier
- Department of Ecology and Evolution, Biophore Building University of Lausanne, Lausanne, Switzerland
| | - S Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - N Perrin
- Department of Ecology and Evolution, Biophore Building University of Lausanne, Lausanne, Switzerland
| | - M Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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38
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Buggs RJA, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE. The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0354. [PMID: 24958927 DOI: 10.1098/rstb.2013.0354] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb's phrasing of this issue and the more contemporary framework of cis- versus trans-regulation of duplicate gene expression in allopolyploid plants.
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Affiliation(s)
- Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA 50011, USA
| | - Jeffrey J Doyle
- L. H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, OR 97202, USA
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Grabowski PP, Morris GP, Casler MD, Borevitz JO. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass. Mol Ecol 2014; 23:4059-73. [PMID: 24962137 PMCID: PMC4142443 DOI: 10.1111/mec.12845] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 01/09/2023]
Abstract
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.
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Affiliation(s)
- Paul P Grabowski
- U.S. Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA; Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
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40
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Lashermes P, Combes MC, Hueber Y, Severac D, Dereeper A. Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:674-85. [PMID: 24628823 DOI: 10.1111/tpj.12505] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 05/27/2023]
Abstract
Allopolyploidization is widespread and has played a major role in flowering plant diversification. Genomic changes are common consequences of allopolyploidization, but their mechanisms of occurrence and dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen as a model to investigate genetic changes in allopolyploid using an approach that exploits next-generation sequencing technologies. Genes affected by putative homoeolog loss were inferred by comparing the numbers of single-nucleotide polymorphisms detected using RNA-seq in individual accessions of C. arabica, and between accessions of its two diploid progenitor species for common sequence positions. Their physical locations were investigated and clusters of genes exhibiting homoeolog loss were identified. To validate these results, genome sequencing data were generated from one accession of C. arabica and further analyzed. Genomic rearrangements involving homoeologous exchanges appear to occur in C. arabica and to be a major source of genetic diversity. At least 5% of the C. arabica genes were inferred to have undergone homoeolog loss. The detection of a large number of homoeologous exchange events (HEEs) shared by all accessions of C. arabica strongly reinforces the assumption of a single allopolyploidization event. Furthermore, HEEs were specific to one or a few accessions, suggesting that HEE accumulates gradually. Our results provide evidence for the important role of HEE in allopolyploid genome evolution.
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Affiliation(s)
- Philippe Lashermes
- IRD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
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Cohen H, Fait A, Tel-Zur N. Morphological, cytological and metabolic consequences of autopolyploidization in Hylocereus (Cactaceae) species. BMC PLANT BIOLOGY 2013; 13:173. [PMID: 24188386 PMCID: PMC3831760 DOI: 10.1186/1471-2229-13-173] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/26/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Genome doubling may have multi-level effects on the morphology, viability and physiology of polyploids compared to diploids. We studied the changes associated with autopolyploidization in two systems of somatic newly induced polyploids, diploid-autotetraploid and triploid-autohexaploid, belonging to the genus Hylocereus (Cactaceae). Stomata, fruits, seeds, embryos, and pollen were studied. Fruit pulp and seeds were subjected to metabolite profiling using established gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography (UPLC) Q-TOF-MS/MS (time of flight)-protocols. RESULTS Autopolyploid lines produced lower numbers of tetrads, larger pollen grains with lower viability, larger stomata with lower density, and smaller fruits with lower seed numbers and decreased seed viability. The abundance of sugars was lower in the fruits and seeds of the two duplicated lines than in their donor lines, accompanied by increased contents of amino acids, tricarboxylic acid (TCA) cycle intermediates, organic acids and flavonoids. Betacyanins, the major fruit pigments in diploid and triploid donors, decreased following genome doubling. Both autopolyploid Hylocereus lines thus exhibited unfavorable changes, with the outcome being more dramatic in the autohexaploid than in the autotetraploid line. CONCLUSION Induced autotetraploid and autohexaploid lines exhibited morphological and cytological characteristics that differed from those of their donor plants and that were accompanied by significant metabolic alterations. It is suggested that a developmental arrest occurs in the fruits of the autohexaploid line, since their pericarp shows a greater abundance of acids and of reduced sugars. We conclude that genome doubling does not necessarily confer a fitness advantage and that the extent of alterations induced by autopolyploidization depends on the genetic background of the donor genotype.
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Affiliation(s)
- Hagai Cohen
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Beer-Sheva 84990, Israel
| | - Aaron Fait
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Beer-Sheva 84990, Israel
| | - Noemi Tel-Zur
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, Beer-Sheva 84990, Israel
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Moraes AP, Chinaglia M, Palma-Silva C, Pinheiro F. Interploidy hybridization in sympatric zones: the formation of Epidendrum fulgens × E. puniceoluteum hybrids (Epidendroideae, Orchidaceae). Ecol Evol 2013; 3:3824-37. [PMID: 24198942 PMCID: PMC3810877 DOI: 10.1002/ece3.752] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 07/25/2013] [Accepted: 08/12/2013] [Indexed: 11/11/2022] Open
Abstract
Interspecific hybridization is a primary cause of extensive morphological and chromosomal variation and plays an important role in plant species diversification. However, the role of interploidal hybridization in the formation of hybrid swarms is less clear. Epidendrum encompasses wide variation in chromosome number and lacks strong premating barriers, making the genus a good model for clarifying the role of chromosomes in postzygotic barriers in interploidal hybrids. In this sense, hybrids from the interploidal sympatric zone between E. fulgens (2n = 2x = 24) and E. puniceoluteum (2n = 4x = 56) were analyzed using cytogenetic techniques to elucidate the formation and establishment of interploidal hybrids. Hybrids were not a uniform group: two chromosome numbers were observed, with the variation being a consequence of severe hybrid meiotic abnormalities and backcrossing with E. puniceoluteum. The hybrids were triploids (2n = 3x = 38 and 40) and despite the occurrence of enormous meiotic problems associated with triploidy, the hybrids were able to backcross, producing successful hybrid individuals with broad ecological distributions. In spite of the nonpolyploidization of the hybrid, its formation is a long-term evolutionary process rather than a product of a recent disturbance, and considering other sympatric zones in Epidendrum, these events could be recurrent.
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Affiliation(s)
- Ana P Moraes
- Laboratório de Biossistemática e Evolução de Plantas, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas/UNICAMP Campinas, São Paulo, Brasil ; Programa de Pós Graduação em Evolução e Diversidade, Universidade Federal do ABC/UFABC Santo André, São Paulo, Brasil
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Kwun HJ, Kim JK. Molecular phylogeny and new classification of the genera Eulophias and Zoarchias (PISCES, Zoarcoidei). Mol Phylogenet Evol 2013; 69:787-95. [PMID: 23845463 DOI: 10.1016/j.ympev.2013.06.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 06/22/2013] [Accepted: 06/28/2013] [Indexed: 12/12/2022]
Abstract
Morphological and osteological studies of the Zoarcoidei group have previously been undertaken, but the group (especially the genera Eulophias and Zoarchias) still remains enigmatic. Therefore, we conducted molecular phylogenetic studies on the two genera Eulophias and Zoarchias using two mitochondrial (16S rRNA and COI) and two nuclear genes (RAG2 and RNF213). Our phylogenetic analysis supported the monophyly of the suborder level of the Zoarcoidei, but rejected the previous morphology- and osteology-based classification hypotheses regarding the two genera. Conflict between mtDNA and nDNA phylogenies within the genus Eulophias implies that the genus shows a complicated relationship such as hybridization in the process of the evolutionary history. The genetic distances between the Eulophias (or Zoarchias) and other Zoarcoidei spp. were the greatest, showing different family-level affiliations. In addition, the mtDNA topology showed the two genera were clearly separated from each other as well as from the families Stichaeidae and Zoarcidae. Considering the new molecular phylogeny, we suggest a new classification for the two genera: (1) Eulophias belongs to a new family named as the Eulophiidae; (2) Zoarchias belongs to the family Neozoarcidae (sensu Radchenko et al., 2012b) rather than to Stichaeidae and Zoarcidae.
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Affiliation(s)
- Hyuck Joon Kwun
- Department of Marine Biology, Pukyong National University, 599-1 Daeyeon 3-Dong, Nam-gu, Busan 608-737, Republic of Korea.
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44
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Hegarty M, Coate J, Sherman-Broyles S, Abbott R, Hiscock S, Doyle J. Lessons from natural and artificial polyploids in higher plants. Cytogenet Genome Res 2013; 140:204-25. [PMID: 23816545 DOI: 10.1159/000353361] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy in higher plants is a major source of genetic novelty upon which selection may act to drive evolution, as evidenced by the widespread success of polyploid species in the wild. However, research into the effects of polyploidy can be confounded by the entanglement of several processes: genome duplication, hybridisation (allopolyploidy is frequent in plants) and subsequent evolution. The discovery of the chemical agent colchicine, which can be used to produce artificial polyploids on demand, has enabled scientists to unravel these threads and understand the complex genomic changes involved in each. We present here an overview of lessons learnt from studies of natural and artificial polyploids, and from comparisons between the 2, covering basic cellular and metabolic consequences through to alterations in epigenetic gene regulation, together with 2 in-depth case studies in Senecio and Glycine. See also the sister article focusing on animals by Arai and Fujimoto in this themed issue.
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Affiliation(s)
- M Hegarty
- IBERS, Aberystwyth University, Aberystwyth, UK. ayh @ aber.ac.uk
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Weiss-Schneeweiss H, Emadzade K, Jang TS, Schneeweiss G. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res 2013; 140:137-50. [PMID: 23796571 PMCID: PMC3859924 DOI: 10.1159/000351727] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
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Affiliation(s)
- H. Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - K. Emadzade
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - T.-S. Jang
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - G.M. Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
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Rentsch JD, Leebens-Mack J. Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae, Asparagaceae). Ecol Evol 2012; 2:2213-22. [PMID: 23139880 PMCID: PMC3488672 DOI: 10.1002/ece3.328] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 06/05/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
There is a growing appreciation for the importance of hybrid speciation in angiosperm evolution. Here, we show that Yucca gloriosa (Asparagaceae: Agavoideae) is the product of intersectional hybridization between Y. aloifolia and Y. filamentosa. These species, all named by Carl Linnaeus, exist in sympatry along the southeastern Atlantic coast of the United States. Yucca gloriosa was found to share a chloroplast haplotype with Y. aloifolia in all populations sampled. In contrast, nuclear gene-based microsatellite markers in Y. gloriosa are shared with both parents. The hybrid origin of Y. gloriosa is supported by multilocus analyses of the nuclear microsatellite markers including principal coordinates analysis (PCO), maximum-likelihood hybrid index scoring (HINDEX), and Bayesian cluster analysis (STRUCTURE). The putative parental species share only one allele at a single locus, suggesting there is little to no introgressive gene flow occurring between these species and Y. gloriosa. At the same time, diagnostic markers are segregating in Y. gloriosa populations. Lack of variation in the chloroplast of Y. aloifolia, the putative maternal parent, makes it difficult to rule out multiple hybrid origins of Y. gloriosa, but allelic variation at nuclear loci can be explained by a single hybrid origin of Y. gloriosa. Overall, these data provide strong support for the homoploid hybrid origin of Y. gloriosa.
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Affiliation(s)
- Jeremy D Rentsch
- Department of Plant Biology, University of Georgia Athens, Georgia, 30602
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Balakirev ES, Krupnova TN, Ayala FJ. DNA variation in the phenotypically-diverse brown alga Saccharina japonica. BMC PLANT BIOLOGY 2012; 12:108. [PMID: 22784095 PMCID: PMC3490969 DOI: 10.1186/1471-2229-12-108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 06/21/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. RESULTS The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. CONCLUSION Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Science, Vladivostok, 690059, Russia
| | - Tatiana N Krupnova
- Pacific Research Fisheries Centre (TINRO-Centre), Vladivostok, 690600, Russia
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
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Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:104. [PMID: 22748145 PMCID: PMC3509404 DOI: 10.1186/1471-2148-12-104] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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Zhang YX, Zeng CX, Li DZ. Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. Mol Phylogenet Evol 2012; 63:777-97. [PMID: 22415014 DOI: 10.1016/j.ympev.2012.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
The monophyly of tribe Arundinarieae (the temperate woody bamboos) has been unequivocally recovered in previous molecular phylogenetic studies. In a recent phylogenetic study, 10 major lineages in Arundinarieae were resolved based on eight non-coding plastid regions, which conflicted significantly with morphological classifications both at the subtribal and generic levels. Nevertheless, relationships among and within the 10 lineages remain unclear. In order to further unravel the evolutionary history of Arundinarieae, we used the nuclear GBSSI gene sequences along with those of eight plastid regions for phylogenetic reconstruction, with an emphasis on Chinese species. The results of the plastid analyses agreed with previous studies, whereas 13 primary clades revealed in the GBSSI phylogeny were better resolved at the generic level than the plastid phylogeny. Our analyses also revealed many inconsistencies between the plastid DNA and the nuclear GBSSI trees. These results implied that the nuclear genome and the plastid genome had different evolutionary trajectories. The patterns of incongruence suggested that lack of informative characters, incomplete lineage sorting, and/or hybridization (introgression) could be the causes. Seven putative hybrid species were hypothesized, four of which are discussed in detail on the basis of topological incongruence, chromosome numbers, morphology, and distribution patterns, and those taxa probably resulted from homoploid hybrid speciation. Overall, our study indicates that the tribe Arundinarieae has undergone a complex evolution.
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Affiliation(s)
- Yu-Xiao Zhang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming, Yunnan 650201, PR China
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Govindarajulu R, Hughes CE, Bailey CD. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation. AMERICAN JOURNAL OF BOTANY 2011; 98:2049-2063. [PMID: 22123714 DOI: 10.3732/ajb.1100259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. METHODS Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. RESULTS Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. CONCLUSIONS Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.
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