1
|
Zhang S, Lin M, Liu J, Chen J, Liu D, Zhao J, Yao M. A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing. BMC Ecol Evol 2022; 22:117. [PMID: 36241967 PMCID: PMC9569074 DOI: 10.1186/s12862-022-02072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022] Open
Abstract
Background The successful establishment of a species population following a single introduction of a few individuals to a non-native area has been limited. Nevertheless, the oriental fire-bellied toad (Bombina orientalis) population in Beijing is purportedly descended from a single introduction of about 200 individuals translocated from Yantai, Shandong Province, China, in 1927. Results To resolve the introduction process and to understand the genetic consequences since that introduction approximately 90 years ago, we investigated the population’s genetic diversity and structure using 261 toads from Beijing and two native Shandong populations and inferred the species’ introduction history using simulation-based approaches. Analysis of mitochondrial DNA (mtDNA) sequences showed the two haplotypes found in Beijing nested within Yantai haplotypes, thus corroborating the historical record of the translocation source. The mtDNA and 11 nuclear microsatellite markers revealed both considerably lower genetic diversity in Beijing than in the source population and strong genetic differentiation between them. Although the current census population in Beijing may be in the range of a few thousand, the effective population size was estimated at only 20–57. Simulations also suggest that this population may have descended from 40–60 founders. Conclusions The Beijing population’s genetic patterns were consistent with the consequences of a severe bottleneck during introduction followed by genetic drift. The introduction trajectory constructed for this B. orientalis population reveals the genetic footprints of a small population sustained in isolation for nearly a century. Our results provide an intriguing example of establishment success from limited founders and may inform ex situ conservation efforts as well as the management of biological invasions. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02072-z.
Collapse
Affiliation(s)
- Shan Zhang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| | - Meixi Lin
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.19006.3e0000 0000 9632 6718Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Jiawei Liu
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.170205.10000 0004 1936 7822Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Jiangce Chen
- grid.63054.340000 0001 0860 4915Mechanical Engineering Department, University of Connecticut, Storrs, CT 06269 USA
| | - Dong Liu
- grid.263817.90000 0004 1773 1790Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Jindong Zhao
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| | - Meng Yao
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| |
Collapse
|
2
|
Jin L, Liao WB, Merilä J. Genomic evidence for adaptive differentiation among
Microhyla fissipes
populations: Implications for conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme Faculty of Biological and Environmental Sciences FI‐00014 University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity School Biological Sciences The University of Hong KongHong Kong SAR
| |
Collapse
|
3
|
Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution. Animals (Basel) 2021; 11:ani11051429. [PMID: 34067517 PMCID: PMC8156418 DOI: 10.3390/ani11051429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Habitat isolation and loss are significant factors that lead to the decline of wildlife populations worldwide, and habitat loss further leads to the shrinkage of populations, which increases the risk of inbreeding and the genetic decline of the populations. To explore the independent evolutionary characteristics of different populations, this study analyzed the genetic disparity of the introduced oriental fire-bellied toad in Beijing from a source population in Shandong Province. The results show that, despite originating from a small artificially introduced population, the toads in the Beijing region have maintained a moderate genetic diversity after 90 years of independent evolution, indicating that this species has a high capacity for survival and adaptation. Abstract Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.
Collapse
|
4
|
Zampiglia M, Bisconti R, Maiorano L, Aloise G, Siclari A, Pellegrino F, Martino G, Pezzarossa A, Chiocchio A, Martino C, Nascetti G, Canestrelli D. Drilling Down Hotspots of Intraspecific Diversity to Bring Them Into On-Ground Conservation of Threatened Species. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00205] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
5
|
Cayuela H, Léna JP, Lengagne T, Kaufmann B, Mondy N, Konecny L, Dumet A, Vienney A, Joly P. Relatedness predicts male mating success in a pond-breeding amphibian. Anim Behav 2017. [DOI: 10.1016/j.anbehav.2017.05.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
6
|
Nürnberger B, Lohse K, Fijarczyk A, Szymura JM, Blaxter ML. Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses. Evolution 2016; 70:1803-18. [PMID: 27282112 PMCID: PMC5129456 DOI: 10.1111/evo.12978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 05/18/2016] [Accepted: 05/27/2016] [Indexed: 12/26/2022]
Abstract
Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.
Collapse
Affiliation(s)
- Beate Nürnberger
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom. .,Current Address: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Anna Fijarczyk
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom.,Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.,Current Address: Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Mark L Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| |
Collapse
|
7
|
Guo B, Lu D, Liao WB, Merilä J. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toadBufo andrewsi. Mol Ecol 2016; 25:3884-900. [PMID: 27289071 DOI: 10.1111/mec.13722] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/02/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Di Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Wen Bo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education); China West Normal University; Nanchong 637009 China
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| |
Collapse
|
8
|
Plantamp C, Salort K, Gibert P, Dumet A, Mialdea G, Mondy N, Voituron Y. All or nothing: Survival, reproduction and oxidative balance in Spotted Wing Drosophila (Drosophila suzukii) in response to cold. JOURNAL OF INSECT PHYSIOLOGY 2016; 89:28-36. [PMID: 27040270 DOI: 10.1016/j.jinsphys.2016.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/23/2016] [Accepted: 03/31/2016] [Indexed: 06/05/2023]
Abstract
Winter severity and overwintering capacity are key ecological factors in successful invasions, especially in ectotherms. The integration of physiological approaches into the study of invasion processes is emerging and promising. Physiological information describes the mechanisms underlying observed survival and reproductive capacities, and it can be used to predict an organism's response to environmental perturbations such as cold temperatures. We investigated the effects of various cold treatments on life history and physiological traits of an invasive pest species, Drosophila suzukii, such as survival, fertility and oxidative balance. This species, a native of temperate Asian areas, is known to survive where cold temperatures are particularly harsh and has been recently introduced into Europe and North America. We found that cold treatments had a strong impact on adult survival but no effect on female's fertility. Although only minor changes were observed after cold treatment on studied physiological traits, a strong sex-based difference was observed in both survival and physiological markers (antioxidant defences and oxidative markers). Females exhibited higher survival, reduced oxidative defences, less damage to nucleic acids, and more damage to lipids. These results suggest that D. suzukii relies on a pathway other than oxidative balance to resist cold injury. Altogether, our results provide information concerning the mechanisms of successful invasion by D. suzukii. These findings may assist in the development of population models that predict the current and future geographic ranges of this species.
Collapse
Affiliation(s)
- Christophe Plantamp
- Université de Lyon, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Université Claude Bernard, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France.
| | - Katleen Salort
- Université de Lyon, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Université Claude Bernard, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France; Université de Lyon, UMR 5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, Université Claude Bernard, ENTPE, CNRS, 6 rue Raphaël Dubois, F-69622 Villeurbanne, France
| | - Patricia Gibert
- Université de Lyon, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Université Claude Bernard, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Adeline Dumet
- Université de Lyon, UMR 5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, Université Claude Bernard, ENTPE, CNRS, 6 rue Raphaël Dubois, F-69622 Villeurbanne, France
| | - Gladys Mialdea
- Université de Lyon, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Université Claude Bernard, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Nathalie Mondy
- Université de Lyon, UMR 5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, Université Claude Bernard, ENTPE, CNRS, 6 rue Raphaël Dubois, F-69622 Villeurbanne, France
| | - Yann Voituron
- Université de Lyon, UMR 5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, Université Claude Bernard, ENTPE, CNRS, 6 rue Raphaël Dubois, F-69622 Villeurbanne, France
| |
Collapse
|
9
|
Ancient, but not recent, population declines have had a genetic impact on alpine yellow-bellied toad populations, suggesting potential for complete recovery. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0818-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
10
|
Hartel T, Nemes S, Mara G. BREEDING PHENOLOGY AND SPATIO-TEMPORAL DYNAMICS OF POND USE BY THE YELLOW-BELLIED TOAD (BOMBINA VARIEGATA) POPULATION: THE IMPORTANCE OF POND AVAILABILITY AND DURATION. ACTA ACUST UNITED AC 2012. [DOI: 10.1080/13921657.2007.10512816] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tibor Hartel
- a Mircea Eliade College , Str. 1. Decembrie 1918 nr. 31, 545400 , Sighişoara , Romania
| | - Szilárd Nemes
- b School of Mathematical Sciences, University of Gothenburg , SE-41296 , Göteborg , Sweden
| | - Gyöngyvér Mara
- c Sapientia Hungarian University of Transylvania, Department of Technical and Nature Sciences , Pţa. Libertăţii 1, 530104 , Miercurea-Ciuc , Romania
| |
Collapse
|
11
|
PRUNIER J, KAUFMANN B, GROLET O, PICARD D, POMPANON F, JOLY P. Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (
Ichthyosaura alpestris
). Mol Ecol Resour 2012; 12:524-31. [DOI: 10.1111/j.1755-0998.2012.03116.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. PRUNIER
- Ecosphère, 3bis rue des Remises, 94100 Saint Maur des Fossés, France
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| | - B. KAUFMANN
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| | - O. GROLET
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| | - D. PICARD
- Université d’Angers, Laboratoire d’Etudes Environnementales des Systèmes Anthropisés, 2 Boulevard Lavoisier, 49045 Angers Cedex 01, France
| | - F. POMPANON
- Université Joseph Fourier, Laboratoire d’Ecologie Alpine, CNRS, UMR 5553, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
| | - P. JOLY
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| |
Collapse
|
12
|
Cano JM, Li MH, Laurila A, Vilkki J, Merilä J. First-generation linkage map for the common frog Rana temporaria reveals sex-linkage group. Heredity (Edinb) 2011; 107:530-6. [PMID: 21587305 DOI: 10.1038/hdy.2011.39] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The common frog (Rana temporaria) has become a model species in the fields of ecology and evolutionary biology. However, lack of genomic resources has been limiting utility of this species for detailed evolutionary genetic studies. Using a set of 107 informative microsatellite markers genotyped in a large full-sib family (800 F1 offspring), we created the first linkage map for this species. This partial map-distributed over 15 linkage groups-has a total length of 1698.8 cM. In line with the fact that males are the heterogametic sex in this species and a reduction of recombination is expected, we observed a lower recombination rate in the males (map length: 1371.5 cM) as compared with females (2089.8 cM). Furthermore, three loci previously documented to be sex-linked (that is, carrying male-specific alleles) in adults from the wild mapped to the same linkage group. The linkage map described in this study is one of the densest ones available for amphibians. The discovery of a sex linkage group in Rana temporaria, as well as other regions with strongly reduced male recombination rates, should help to uncover the genetic underpinnings of the sex-determination system in this species. As the number of linkage groups found (n=15) is quite close to the actual number of chromosomes (n=13), the map should provide a useful resource for further evolutionary, ecological and conservation genetic work in this and other closely related species.
Collapse
Affiliation(s)
- J M Cano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland.
| | | | | | | | | |
Collapse
|
13
|
Lalouette L, Kaufmann B, Konecny L, Renault D, Douady CJ. Characterization and PCR multiplexing of 14 new polymorphic microsatellite loci for the invasive subantarctic carabid Merizodus soledadinus (Coleoptera: Carabidae). CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9105-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Danancher D, Cellot B, Dolédec S, Reynaud D. Isolation and characterization of the first eight microsatellite loci in Gammarus fossarum (Crustacea, Amphipoda) and cross-amplification in Gammarus pulex and Gammarus orinos. Mol Ecol Resour 2009; 9:1418-21. [PMID: 21564925 DOI: 10.1111/j.1755-0998.2009.02662.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We characterized the first microsatellite markers for Gammarus fossarum. Eight loci gave satisfactory amplification patterns in two stream populations (Southern France) with number of alleles ranging from 2 to 10 and expected heterozygosity from 0.076 to 0.857. We performed cross-amplification in two closely related gammarid species, Gammarus pulex and Gammarus orinos. Among the eight tested microsatellite loci, four correctly amplified in G. pulex and three in G. orinos.
Collapse
Affiliation(s)
- Delphine Danancher
- UMR CNRS 5023-Université Lyon 1, 43 Boulevard du 11 Novembre 1918, F-69622 Villeurbanne Cedex, France
| | | | | | | |
Collapse
|
15
|
Pabijan M, Spolsky C, Uzzell T, Szymura JM. Comparative analysis of mitochondrial genomes in Bombina (Anura; Bombinatoridae). J Mol Evol 2008; 67:246-56. [PMID: 18696031 DOI: 10.1007/s00239-008-9123-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 05/08/2008] [Accepted: 05/09/2008] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genomes of two basal anurans, Bombina bombina and B. variegata (Anura; Bombinatoridae), were sequenced. The gene order of their mitochondrial DNA (mtDNA) is identical to that of canonical vertebrate mtDNA. In contrast, we show that there are structural differences in regulatory regions and protein coding genes between the mtDNA of these two closely related species. Corrected sequence divergence between the mtDNA of B. bombina and B. variegata amounts to 8.7% (2.3% divergence in amino acids). Comparisons with two East Asian congeners show that the control region contains two repeat regions, LV1 and LV2, present in all species except for B. bombina, in which LV2 has been secondarily lost. The rRNAs and tRNAs are characterized by low nucleotide divergence. The protein coding genes are considerably more disparate, although functional constraint is high but variable among genes, as evidenced by dN/dS ratios. A mtDNA phylogeny established the distribution of autapomorphic nonsynonomous substitutions in the mitogenomes of B. bombina and B. variegata. Nine of 98 nonsynonomous substitutions led to radical amino acid replacements that may alter mitochondrial protein function. Most radical substitutions were found in ND2, ND4, or ND5, encoding mitochondrial subunits of complex I of the electron transport system. The extensive divergence between the mitogenomes of B. bombina and B. variegata is discussed in terms of its possible role in impeding gene flow in natural hybrid zones between these two species.
Collapse
Affiliation(s)
- Maciej Pabijan
- Department of Comparative Anatomy, Jagiellonian University, Ingardena 6, 30-060, Krakow, Poland.
| | | | | | | |
Collapse
|
16
|
Di Candia MR, Routman EJ. Cytonuclear discordance across a leopard frog contact zone. Mol Phylogenet Evol 2007; 45:564-75. [PMID: 17689987 DOI: 10.1016/j.ympev.2007.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 11/17/2022]
Abstract
We conducted a genetic analysis of the extent of hybridization within and outside a contact zone between two North American leopard frogs, Rana blairi and Rana pipiens by comparing distribution patterns of mitochondrial and nuclear haplotypes. The contact zone, located between South Dakota, Nebraska, and Iowa, USA, was previously examined using morphological data in the 1970s, leading to the conclusion that hybridization was rare between R. pipiens and R. blairi. Our genetic analysis of 51 populations (611 samples) shows strong cytonuclear discordance. Mitochondrial-haplotype distribution matches the same pattern as the documented species spatial distributions based on morphology. However, the geographic distribution of the nuclear haplotypes reveals asymmetrical swamping of the R. pipiens nuclear haplotypes by R. blairi haplotypes. Phylogenetic analyses of both mitochondrial and nuclear markers provide strong evidence for the presence of R. blairi-R. pipiens introgression for the nuclear marker. A pattern of mitochondrial isolation with nuclear introgression is extremely unusual, and predicted to occur much less often than the reverse.
Collapse
Affiliation(s)
- M Rita Di Candia
- San Francisco State University, Department of Biology, 1600 Holloway Avenue, San Francisco, CA 94132, USA
| | | |
Collapse
|
17
|
HOFMAN SEBASTIAN, SZYMURA JACEKM. Limited mitochondrial DNA introgression in a Bombina hybrid zone. Biol J Linn Soc Lond 2007. [DOI: 10.1111/j.1095-8312.2007.00795.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
Yanchukov A, Hofman S, Szymura JM, Mezhzherin SV, Morozov‐Leonov SY, Barton NH, Nürnberger B. HYBRIDIZATION OFBOMBINA BOMBINAANDB. VARIEGATA(ANURA, DISCOGLOSSIDAE) AT A SHARP ECOTONE IN WESTERN UKRAINE: COMPARISONS ACROSS TRANSECTS AND OVER TIME. Evolution 2007. [DOI: 10.1111/j.0014-3820.2006.tb01139.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexey Yanchukov
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, B. Khmelnitzkogo Str. 15, 01601 Kiev, Ukraine
- Department of Comparative Anatomy, Jagiellonian University, Ingardena 6,30–0601 Kraków, Poland
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland
- Department Biologie II, Ludwig‐Maximilians‐Universität München, Grosshaderner Str. 2, 82152 Planegg‐Martinsried, Germany
| | - Sebastian Hofman
- Department of Comparative Anatomy, Jagiellonian University, Ingardena 6,30–0601 Kraków, Poland
| | - Jacek M. Szymura
- Department of Comparative Anatomy, Jagiellonian University, Ingardena 6,30–0601 Kraków, Poland
| | - Sergey V. Mezhzherin
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, B. Khmelnitzkogo Str. 15, 01601 Kiev, Ukraine
| | - Sviatoslav Y. Morozov‐Leonov
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, B. Khmelnitzkogo Str. 15, 01601 Kiev, Ukraine
| | - Nicholas H. Barton
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, Scotland
| | - Beate Nürnberger
- Department Biologie II, Ludwig‐Maximilians‐Universität München, Grosshaderner Str. 2, 82152 Planegg‐Martinsried, Germany
| |
Collapse
|
19
|
Britch SC, Swartout EJ, Hampton DD, Draney ML, Chu J, Marshall JL, Howard DJ. Genetic architecture of conspecific sperm precedence in Allonemobius fasciatus and A. socius. Genetics 2007; 176:1209-22. [PMID: 17435237 PMCID: PMC1894585 DOI: 10.1534/genetics.106.064949] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of barriers to gene exchange is centrally important to speciation. We used the crickets Allonemobius fasciatus and A. socius to investigate the genetic architecture of conspecific sperm precedence (CSP), a postinsemination prezygotic reproductive barrier. With amplified fragment-length polymorphism (AFLP) markers and controlled crosses we constructed linkage maps and estimated positions of QTL associated with CSP. The majority of QTL have low to moderate effects, although a few QTL exist in A. socius with large effects, and the numbers of QTL are comparable to numbers of genes accounting for species differences in other studies. The QTL are spread across many unlinked markers, yet QTL placed with linked markers are on a small number of linkage groups that could reflect the role of the large Allonemobius sex chromosome in prezygotic isolation. Although many QTL had positive effects on conspecific sperm utilization several QTL also exerted negative effects, which could be explained by intraspecific sexual conflict, sperm competition, or epistasis of introgressed genes on novel backgrounds. One unexpected outcome was that A. socius CSP alleles have a stronger effect than those from A. fasciatus in hybrid females, causing hybrids to behave like A. socius with regard to sperm utilization. Implications of this asymmetry in the Allonemobius hybrid zone are discussed.
Collapse
Affiliation(s)
- Seth C Britch
- Department of Biology, New Mexico State University, Las Cruces, New Mexico 88003, USA.
| | | | | | | | | | | | | |
Collapse
|
20
|
Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity (Edinb) 2007; 100:158-70. [PMID: 17314923 DOI: 10.1038/sj.hdy.6800937] [Citation(s) in RCA: 380] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A central challenge in evolutionary biology is to identify genes underlying ecologically important traits and describe the fitness consequences of naturally occurring variation at these loci. To address this goal, several novel approaches have been developed, including 'population genomics,' where a large number of molecular markers are scored in individuals from different environments with the goal of identifying markers showing unusual patterns of variation, potentially due to selection at linked sites. Such approaches are appealing because of (1) the increasing ease of generating large numbers of genetic markers, (2) the ability to scan the genome without measuring phenotypes and (3) the simplicity of sampling individuals without knowledge of their breeding history. Although such approaches are inherently applicable to non-model systems, to date these studies have been limited in their ability to uncover functionally relevant genes. By contrast, quantitative genetics has a rich history, and more recently, quantitative trait locus (QTL) mapping has had some success in identifying genes underlying ecologically relevant variation even in novel systems. QTL mapping, however, requires (1) genetic markers that specifically differentiate parental forms, (2) a focus on a particular measurable phenotype and (3) controlled breeding and maintenance of large numbers of progeny. Here we present current advances and suggest future directions that take advantage of population genomics and quantitative genetic approaches - in both model and non-model systems. Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation.
Collapse
Affiliation(s)
- J R Stinchcombe
- Department of Ecology and Evolutionary Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
| | | |
Collapse
|
21
|
HAUSWALDT JS, SCHRÖDER C, TIEDEMANN R. Nine new tetranucleotide microsatellite markers for the fire-bellied toad (Bombina bombina). ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01516.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
STUCKAS H, TIEDEMANN R. Eight new microsatellite loci for the critically endangered fire-bellied toad Bombina bombina and their cross-species applicability among anurans. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2005.01171.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
23
|
Yanchukov A, Hofman S, Szymura JM, Mezhzherin SV, Morozov-Leonov SY, Barton NH, Nürnberger B. HYBRIDIZATION OF BOMBINA BOMBINA AND B. VARIEGATA (ANURA, DISCOGLOSSIDAE) AT A SHARP ECOTONE IN WESTERN UKRAINE: COMPARISONS ACROSS TRANSECTS AND OVER TIME. Evolution 2006. [DOI: 10.1554/04-739.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
24
|
Nürnberger B, Barton NH, Kruuk LEB, Vines TH. Mating patterns in a hybrid zone of fire-bellied toads (Bombina): inferences from adult and full-sib genotypes. Heredity (Edinb) 2004; 94:247-57. [PMID: 15536484 DOI: 10.1038/sj.hdy.6800607] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy-Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.
Collapse
Affiliation(s)
- B Nürnberger
- Department Biologie II, Ludwig-Maximilians-Universität München, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany.
| | | | | | | |
Collapse
|