1
|
Karpiński L, Gorring P, Hilszczański J, Szczepański WT, Plewa R, Łoś K, Cognato AI. Integrative taxonomy tests possible hybridisation between Central Asian cerambycids (Coleoptera). ZOOL SCR 2022. [DOI: 10.1111/zsc.12570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lech Karpiński
- Museum and Institute of Zoology Polish Academy of Sciences Warsaw Poland
| | - Patrick Gorring
- Department of Entomology Michigan State University East Lansing USA
- Department of Organismic and Evolutionary Biology Harvard University Cambridge USA
| | - Jacek Hilszczański
- Department of Forest Protection Forest Research Institute Sękocin Stary Poland
| | | | - Radosław Plewa
- Department of Forest Protection Forest Research Institute Sękocin Stary Poland
| | | | | |
Collapse
|
2
|
Horta P, Raposeira H, Baños A, Ibáñez C, Razgour O, Rebelo H, Juste J. Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats. Sci Rep 2022; 12:11695. [PMID: 35803997 PMCID: PMC9270368 DOI: 10.1038/s41598-022-15412-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Cryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.
Collapse
Affiliation(s)
- Pedro Horta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal. .,OII - Observatório Inovação Investigação, Seia, Portugal. .,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Helena Raposeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.,OII - Observatório Inovação Investigação, Seia, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | | | - Carlos Ibáñez
- Departmento de Ecología Evolutiva, Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain.,CIBER de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
| | | | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,ESS, Polytechnic Institute of Setúbal, Setúbal, Portugal, Campus do IPS - Estefanilha, 2910-761 Setúbal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Javier Juste
- Departmento de Ecología Evolutiva, Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain.,CIBER de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
| |
Collapse
|
3
|
Congrains C, Zucchi RA, de Brito RA. Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of neotropical true fruit flies (Anastrepha: Tephritidae). Mol Phylogenet Evol 2021; 162:107200. [PMID: 33984467 DOI: 10.1016/j.ympev.2021.107200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 01/30/2021] [Accepted: 05/03/2021] [Indexed: 01/08/2023]
Abstract
New sequencing techniques have allowed us to explore the variation on thousands of genes and elucidate evolutionary relationships of lineages even in complex scenarios, such as when there is rapid diversification. That seems to be the case of species in the genus Anastrepha, which shows great species diversity that has been divided into 21 species groups, several of which show wide geographical distribution. The fraterculus group has several economically important species and it is also an outstanding model for speciation studies, since it includes several lineages that have diverged recently possibly in the presence of interspecific gene flow. Our main goal is to test whether we can infer phylogenetic relationships of recently diverged taxa with gene flow, such as what is expected for the fraterculus group and determine whether certain genes remain informative even in this complex scenario. An analysis of thousands of orthologous genes derived from transcriptome datasets of 10 different lineages across the genus, including some of the economically most important pests, revealed signals of incomplete lineage sorting, vestiges of ancestral introgression between more distant lineages and ongoing gene flow between closely related lineages. Though these patterns affect the phylogenetic signal, the phylogenomic inferences consistently show that the morphologically identified species here investigated are in different evolutionary lineages, with the sole exception involving Brazilian lineages of A. fraterculus, which has been suggested to be a complex assembly of cryptic species. A tree space analysis suggested that genes with greater phylogenetic resolution have evolved under similar selection pressures and are more resilient to intraspecific gene flow, which would make it more likely that these genomic regions may be useful for identifying fraterculus group lineages. Our findings help establish relationships among the most important Anastrepha species groups, as well as bring further data to indicate that the diversification of fraterculus group lineages, and even other lineages in the genus Anastrepha, has been strongly influenced by interspecific gene flow.
Collapse
Affiliation(s)
- Carlos Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
| | - Roberto A Zucchi
- Escola Superior de Agricultura "Luiz de Queiroz" - ESALQ, Universidade de São Paulo - USP, Piracicaba, SP, Brazil
| | - Reinaldo A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| |
Collapse
|
4
|
Scriber JM. Assessing ecological and physiological costs of melanism in North American Papilio glaucus females: two decades of dark morph frequency declines. INSECT SCIENCE 2020; 27:583-612. [PMID: 30456932 PMCID: PMC7277061 DOI: 10.1111/1744-7917.12653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/11/2018] [Accepted: 09/17/2018] [Indexed: 06/09/2023]
Abstract
Polymorphisms for melanic form of insects may provide various selective advantages. However, melanic alleles may have significant/subtle pleiotrophic "costs." Several potential pleiotrophic effects of the W (=Y)-linked melanism gene in Papilio glaucus L. (Lepidoptera) showed no costs for melanic versus yellow in adult size, oviposition preferences, fecundity, egg viability, larval survival/growth rates, cold stress tolerance, or postdiapause emergence times. Sexual selection (males choosing yellow rather than mimetic dark females) had been suggested to provide a balanced polymorphism in P. glaucus, but spermatophore counts in wild females and direct field tethering studies of size-matched pairs of virgin females (dark and yellow), show that male preferences are random or frequency-dependent from Florida to Michigan, providing no yellow counter-advantages. Recent frequency declines of dark (melanic/mimetic) females in P. glaucus populations are shown in several major populations from Florida (27.3°N latitude) to Ohio (38.5° N). Summer temperatures have increased significantly at all these locations during this time (1999-2018), but whether dark morphs may be more vulnerable (in any stage) to such climate warming remains to be determined. Additional potential reasons for the frequency declines in mimetic females are discussed: (i) genetic introgression of Z-linked melanism suppressor genes from P. canadensis (R & J) and the hybrid species, P. appalachiensis (Pavulaan & Wright), (ii) differential developmental incompatibilities, or Haldane effects, known to occur in hybrids, (iii) selection against intermediately melanic ("dusty") females (with the W-linked melanic gene, b+) which higher temperatures can cause.
Collapse
Affiliation(s)
- J. Mark Scriber
- Department of EntomologyMichigan State UniversityEast LansingMichiganUSA
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| |
Collapse
|
5
|
Zhang W, Leon-Ricardo BX, van Schooten B, Van Belleghem SM, Counterman BA, McMillan WO, Kronforst MR, Papa R. Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation. Genome Biol Evol 2019; 11:2963-2975. [PMID: 31518398 PMCID: PMC6821300 DOI: 10.1093/gbe/evz202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
Butterfly eyes are complex organs that are composed of a diversity of proteins and they play a central role in visual signaling and ultimately, speciation, and adaptation. Here, we utilized the whole eye transcriptome to obtain a more holistic view of the evolution of the butterfly eye while accounting for speciation events that co-occur with ancient hybridization. We sequenced and assembled transcriptomes from adult female eyes of eight species representing all major clades of the Heliconius genus and an additional outgroup species, Dryas iulia. We identified 4,042 orthologous genes shared across all transcriptome data sets and constructed a transcriptome-wide phylogeny, which revealed topological discordance with the mitochondrial phylogenetic tree in the Heliconius pupal mating clade. We then estimated introgression among lineages using additional genome data and found evidence for ancient hybridization leading to the common ancestor of Heliconius hortense and Heliconius clysonymus. We estimated the Ka/Ks ratio for each orthologous cluster and performed further tests to demonstrate genes showing evidence of adaptive protein evolution. Furthermore, we characterized patterns of expression for a subset of these positively selected orthologs using qRT-PCR. Taken together, we identified candidate eye genes that show signatures of adaptive molecular evolution and provide evidence of their expression divergence between species, tissues, and sexes. Our results demonstrate: 1) greater evolutionary changes in younger Heliconius lineages, that is, more positively selected genes in the cydno-melpomene-hecale group as opposed to the sara-hortense-erato group, and 2) suggest an ancient hybridization leading to speciation among Heliconius pupal-mating species.
Collapse
Affiliation(s)
- Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Life Sciences, Peking University, Beijing, China
- Department of Ecology and Evolution, University of Chicago
| | | | - Bas van Schooten
- Department of Biology, University of Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico
| | | | | | | | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico
| |
Collapse
|
6
|
Cong Q, Grishin NV. Comparative analysis of swallowtail transcriptomes suggests molecular determinants for speciation and adaptation. Genome 2018; 61:843-855. [PMID: 30365901 PMCID: PMC8934176 DOI: 10.1139/gen-2018-0084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genetic determinants of speciation in closely related species are poorly understood. We sequenced and analyzed transcriptomes of swallowtail butterflies Heraclides cresphontes (northeastern species) and Heraclides rumiko (southwestern species), a pair of mostly allopatric sister species whose distribution ranges overlap narrowly in central Texas. We found that the two swallowtails confidently differ (FST > 0.5 for both species) in about 5% of genes, similarly to the divergence in another pair of swallowtail species Pterourus glaucus (southern species) and Pterourus canadensis (northern species). The same genes tend to diverge in both species pairs, suggesting similar speciation paths in Heraclides and Pterourus. The most significant differences for both species pairs were found in the circadian clock genes that were conserved within each species and diverged strongly between species (P-value < 0.01 and FST > 0.7). This divergence implied that adaptations to different climates and photoperiod at different latitudes or differences in mating behavior, including mating time and copulation duration, may be possible factors in ecological or behavioral-based speciation. Finally, we suggest several nuclear DNA regions that consistently and prominently differ between the sister swallowtail species as nuclear barcodes for swallowtail identification, with the best barcode being an exon from the protein TIMELESS.
Collapse
Affiliation(s)
- Qian Cong
- a Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Nick V Grishin
- a Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
- b Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA
| |
Collapse
|
7
|
Ottenburghs J, Megens HJ, Kraus RHS, van Hooft P, van Wieren SE, Crooijmans RPMA, Ydenberg RC, Groenen MAM, Prins HHT. A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol Biol 2017; 17:201. [PMID: 28830337 PMCID: PMC5568201 DOI: 10.1186/s12862-017-1048-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1048-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jente Ottenburghs
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Robert H S Kraus
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg, 1D-78315, Radolfzell, Germany.,Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Sipke E van Wieren
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Ronald C Ydenberg
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.,Centre for Wildlife Ecology, Simon Fraser University, V5A 1S6, Burnaby, BC, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Herbert H T Prins
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| |
Collapse
|
8
|
Ryan SF, Fontaine MC, Scriber JM, Pfrender ME, O'Neil ST, Hellmann JJ. Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient. Mol Ecol 2017; 26:4725-4742. [DOI: 10.1111/mec.14236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 06/12/2017] [Accepted: 06/19/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Sean F. Ryan
- USDA ARS Gainesville FL USA
- Department of Biological Sciences University of Notre Dame South Bend IN USA
| | - Michael C. Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen AG Groningen The Netherlands
| | - J. Mark Scriber
- Department of Entomology Michigan State University East Lansing MI USA
- McGuire Center for Lepidoptera and Diversity University of Florida Gainesville FL USA
| | - Michael E. Pfrender
- Department of Biological Sciences University of Notre Dame South Bend IN USA
- Environmental Change Initiative University of Notre Dame South Bend IN USA
| | - Shawn T. O'Neil
- Department of Biological Sciences University of Notre Dame South Bend IN USA
- Center for Genome Research and Biocomputing Oregon State University Corvallis OR USA
| | - Jessica J. Hellmann
- Department of Biological Sciences University of Notre Dame South Bend IN USA
- Institute on the Environment and Department of Ecology, Evolution and Behavior University of Minnesota St. Paul MN USA
| |
Collapse
|
9
|
Mao X, Tsagkogeorga G, Bailey SE, Rossiter SJ. Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Sebastian E. Bailey
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| |
Collapse
|
10
|
Timmermans MJTN, Thompson MJ, Collins S, Vogler AP. Independent evolution of sexual dimorphism and female-limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas). Mol Ecol 2017; 26:1273-1284. [PMID: 28100020 DOI: 10.1111/mec.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 12/09/2016] [Accepted: 01/03/2017] [Indexed: 11/29/2022]
Abstract
Several species of swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and nonmimetic. The evolution of such sex-limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a nonmimetic, sexually dimorphic stage has been proposed for two closely related sexually dimorphic species: Papilio phorcas, a nonmimetic species with two female forms, and Papilio dardanus, a female-limited polymorphic mimetic species. Their close relationship indicates that female-limited polymorphism could be a shared derived character of the two species. Here, we present a phylogenomic analysis of the dardanus group using 3964 nuclear loci and whole mitochondrial genomes, showing that they are not sister species and thus that the sexually dimorphic state has arisen independently in the two species. Nonhomology of the female polymorphism in both species is supported by population genetic analysis of engrailed, the presumed mimicry switch locus in P. dardanus. McDonald-Kreitman tests performed on SNPs in engrailed showed the signature of balancing selection in a polymorphic population of P. dardanus, but not in monomorphic populations, nor in the nonmimetic P. phorcas. Hence, the wing polymorphism does not balance polymorphisms in engrailed in P. phorcas. Equally, unlike in P. dardanus, none of the SNPs in P. phorcas engrailed were associated with either female morph. We conclude that sexual dimorphism due to female polymorphism evolved independently in both species from monomorphic, nonmimetic states. While sexual selection may drive male-female dimorphism in nonmimetic species, in mimetic Papilios, natural selection for protection from predators in females is an alternative route to sexual dimorphism.
Collapse
Affiliation(s)
- M J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - M J Thompson
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.,Department of Zoology, Cambridge University, Downing Street, Cambridge, CB2 3EJ, UK
| | - S Collins
- ABRI, PO Box 14308, Westlands, 0800, Nairobi, Kenya
| | - A P Vogler
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| |
Collapse
|
11
|
Zhang W, Dasmahapatra KK, Mallet J, Moreira GRP, Kronforst MR. Genome-wide introgression among distantly related Heliconius butterfly species. Genome Biol 2016; 17:25. [PMID: 26921238 PMCID: PMC4769579 DOI: 10.1186/s13059-016-0889-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/28/2016] [Indexed: 12/30/2022] Open
Abstract
Background Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. Results We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Conclusions Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0889-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
| | | | - James Mallet
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Gilson R P Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
| |
Collapse
|
12
|
Arias CF, Van Belleghem S, McMillan WO. Genomics at the evolving species boundary. CURRENT OPINION IN INSECT SCIENCE 2016; 13:7-15. [PMID: 27436548 DOI: 10.1016/j.cois.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/07/2015] [Indexed: 06/06/2023]
Abstract
Molecular studies on hybridization date back to Dobzhansky who compared chromosomal banding patterns to determine if interspecific gene flow occurred in nature [1]. Now, the advent of high-throughput sequencing provides increasingly fine insights into genomic differentiation between incipient taxa that are changing our view of adaptation and speciation and the links between the two. Empirical data from hybridizing taxa demonstrate highly heterogeneous patterns of genomic differentiation. Although underlining reasons for this heterogeneity are complex, studies of hybridizing taxa offers some of the best insights into the regions of the genome under divergent selection and the role these regions play in species boundaries. The challenge moving forward is to develop a better theoretical framework that fully leverages these powerful natural experiments.
Collapse
Affiliation(s)
- Carlos F Arias
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama; Biology Program, Faculty of Natural Science and Mathematics, Universidad del Rosario, Carrera 24 # 63c-69, Bogotá 111221, Colombia
| | - Steven Van Belleghem
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom; Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, Panama.
| |
Collapse
|
13
|
Zhang L, Wu W, Yan HF, Ge XJ. Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales. Evol Bioinform Online 2016; 11:81-91. [PMID: 26819541 PMCID: PMC4718149 DOI: 10.4137/ebo.s22448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.
Collapse
Affiliation(s)
- Lu Zhang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
14
|
Cong Q, Grishin NV. The complete mitochondrial genome of Lerema accius and its phylogenetic implications. PeerJ 2016; 4:e1546. [PMID: 26788426 PMCID: PMC4715447 DOI: 10.7717/peerj.1546] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/09/2015] [Indexed: 11/23/2022] Open
Abstract
Butterflies and moths (Lepidoptera) are becoming model organisms for genetics and evolutionary biology. Decoding the Lepidoptera genomes, both nuclear and mitochondrial, is an essential step in these studies. Here we describe a protocol to assemble mitogenomes from Next Generation Sequencing reads obtained through whole-genome sequencing and report the 15,338 bp mitogenome of Lerema accius. The mitogenome is AT-rich and encodes 13 proteins, 22 transfer-RNAs, and two ribosomal-RNAs, with a gene order typical for Lepidoptera mitogenomes. A phylogenetic study based on the protein sequences using both Bayesian Inference and Maximum Likelihood methods consistently place Lerema accius with other grass skippers (Hesperiinae).
Collapse
Affiliation(s)
- Qian Cong
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center , Dallas, TX , United States
| | - Nick V Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States; Howard Hughes Medical Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|
15
|
Dupuis JR, Sperling FAH. Repeated Reticulate Evolution in North American Papilio machaon Group Swallowtail Butterflies. PLoS One 2015; 10:e0141882. [PMID: 26517268 PMCID: PMC4627828 DOI: 10.1371/journal.pone.0141882] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 10/14/2015] [Indexed: 01/07/2023] Open
Abstract
Hybridization between distinct populations or species is increasingly recognized as an important process for generating biodiversity. However, the interaction between hybridization and speciation is complex, and the diverse evolutionary outcomes of hybridization are difficult to differentiate. Here we characterize potential hybridization in a species group of swallowtail butterflies using microsatellites, DNA sequences, and morphology, and assess whether adaptive introgression or homoploid hybrid speciation was the primary process leading to each putative hybrid lineage. Four geographically separated hybrid populations were identified in the Papilio machaon species group. One distinct mitochondrial DNA clade from P. machaon was fixed in three hybrid taxa (P. brevicauda, P. joanae, and P. m. kahli), while one hybrid swarm (P. zelicaon x machaon) exhibited this hybrid mtDNA clade as well as widespread parental mtDNA haplotypes from both parental species. Microsatellite markers and morphology showed variable admixture and intermediacy, ranging from signatures of prolonged differential introgression from the paternal species (P. polyxenes/P. zelicaon) to current gene flow with both parental species. Divergences of the hybrid lineages dated to early- to mid-Pleistocene, suggesting that repeated glaciations and subsequent range shifts of parental species, particularly P. machaon hudsonianus, facilitated initial hybridization. Although each lineage is distinct, P. joanae is the only taxon with sufficient evidence (ecological separation from parental species) to define it as a homoploid hybrid species. The repetition of hybridization in this group provides a valuable foundation for future research on hybridization, and these results emphasize the potential for hybridization to drive speciation in diverse ways.
Collapse
Affiliation(s)
- Julian R. Dupuis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
16
|
The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications. Meta Gene 2015; 5:68-83. [PMID: 26106582 PMCID: PMC4475787 DOI: 10.1016/j.mgene.2015.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/19/2015] [Accepted: 05/11/2015] [Indexed: 11/21/2022] Open
Abstract
Due to the intriguing morphology, lifecycle, and diversity of butterflies and moths, Lepidoptera are emerging as model organisms for the study of genetics, evolution and speciation. The progress of these studies relies on decoding Lepidoptera genomes, both nuclear and mitochondrial. Here we describe a protocol to obtain mitogenomes from Next Generation Sequencing reads performed for whole-genome sequencing and report the complete mitogenome of Papilio (Pterourus) glaucus. The circular mitogenome is 15,306 bp in length and rich in A and T. It contains 13 protein-coding genes (PCGs), 22 transfer-RNA-coding genes (tRNA), and 2 ribosomal-RNA-coding genes (rRNA), with a gene order typical for mitogenomes of Lepidoptera. We performed phylogenetic analyses based on PCG and RNA-coding genes or protein sequences using Bayesian Inference and Maximum Likelihood methods. The phylogenetic trees consistently show that among species with available mitogenomes Papilio glaucus is the closest to Papilio (Agehana) maraho from Asia.
Collapse
|
17
|
Šíchová J, Voleníková A, Dincă V, Nguyen P, Vila R, Sahara K, Marec F. Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies. BMC Evol Biol 2015; 15:89. [PMID: 25981157 PMCID: PMC4436027 DOI: 10.1186/s12862-015-0375-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/07/2015] [Indexed: 11/26/2022] Open
Abstract
Background Chromosomal rearrangements have the potential to limit the rate and pattern of gene flow within and between species and thus play a direct role in promoting and maintaining speciation. Wood white butterflies of the genus Leptidea are excellent models to study the role of chromosome rearrangements in speciation because they show karyotype variability not only among but also within species. In this work, we investigated genome architecture of three cryptic Leptidea species (L. juvernica, L. sinapis and L. reali) by standard and molecular cytogenetic techniques in order to reveal causes of the karyotype variability. Results Chromosome numbers ranged from 2n = 85 to 91 in L. juvernica and 2n = 69 to 73 in L. sinapis (both from Czech populations) to 2n = 51 to 55 in L. reali (Spanish population). We observed significant differences in chromosome numbers and localization of cytogenetic markers (rDNA and H3 histone genes) within the offspring of individual females. Using FISH with the (TTAGG)n telomeric probe we also documented the presence of multiple chromosome fusions and/or fissions and other complex rearrangements. Thus, the intraspecific karyotype variability is likely due to irregular chromosome segregation of multivalent meiotic configurations. The analysis of female meiotic chromosomes by GISH and CGH revealed multiple sex chromosomes: W1W2W3Z1Z2Z3Z4 in L. juvernica, W1W2W3Z1Z2Z3 in L. sinapis and W1W2W3W4Z1Z2Z3Z4 in L. reali. Conclusions Our results suggest a dynamic karyotype evolution and point to the role of chromosomal rearrangements in the speciation of Leptidea butterflies. Moreover, our study revealed a curious sex determination system with 3–4 W and 3–4 Z chromosomes, which is unique in the Lepidoptera and which could also have played a role in the speciation process of the three Leptidea species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0375-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jindra Šíchová
- Institute of Entomology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Anna Voleníková
- Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Vlad Dincă
- Biodiversity Institute of Ontario, University of Guelph, N1G 2W1, Guelph, ON, Canada. .,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu-Fabra), 08003, Barcelona, Spain.
| | - Petr Nguyen
- Institute of Entomology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu-Fabra), 08003, Barcelona, Spain.
| | - Ken Sahara
- Laboratory of Applied Entomology, Faculty of Agriculture, Iwate University, Morioka, 020-8550, Japan.
| | - František Marec
- Institute of Entomology, Biology Centre CAS, 370 05, České Budějovice, Czech Republic. .,Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| |
Collapse
|
18
|
Kozak KM, Wahlberg N, Neild AFE, Dasmahapatra KK, Mallet J, Jiggins CD. Multilocus species trees show the recent adaptive radiation of the mimetic heliconius butterflies. Syst Biol 2015; 64:505-24. [PMID: 25634098 PMCID: PMC4395847 DOI: 10.1093/sysbio/syv007] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 01/23/2015] [Indexed: 11/25/2022] Open
Abstract
Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach failed to reflect the underlying variation in the history of individual loci. However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Neotropics over the past 23 myr, or changes caused by diversity-dependent effects on the rate of diversification. We find that the rate of diversification has increased on the branch leading to the presently most species-rich genus Heliconius, but the change occurred gradually and cannot be unequivocally attributed to a specific environmental driver. Our study provides comprehensive comparison of philosophically distinct species tree reconstruction methods and provides insights into the diversification of an important insect radiation in the most biodiverse region of the planet.
Collapse
Affiliation(s)
- Krzysztof M Kozak
- Butterfly Genetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, UK; Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland; Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biology, University of York, YO10 5DD Heslington, York, UK; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Niklas Wahlberg
- Butterfly Genetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, UK; Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland; Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biology, University of York, YO10 5DD Heslington, York, UK; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Andrew F E Neild
- Butterfly Genetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, UK; Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland; Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biology, University of York, YO10 5DD Heslington, York, UK; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kanchon K Dasmahapatra
- Butterfly Genetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, UK; Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland; Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biology, University of York, YO10 5DD Heslington, York, UK; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - James Mallet
- Butterfly Genetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, UK; Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland; Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biology, University of York, YO10 5DD Heslington, York, UK; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chris D Jiggins
- Butterfly Genetics Group, Department of Zoology, University of Cambridge, CB2 3EJ Cambridge, UK; Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland; Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biology, University of York, YO10 5DD Heslington, York, UK; and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
19
|
Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense. Cell Rep 2015; 10:910-919. [PMID: 25683714 PMCID: PMC8935626 DOI: 10.1016/j.celrep.2015.01.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/19/2014] [Accepted: 01/09/2015] [Indexed: 12/30/2022] Open
Abstract
Predicting phenotype from genotype represents the epitome of biological questions. Comparative genomics of appropriate model organisms holds the promise of making it possible. However, the high heterozygosity of many Eukaryotes currently prohibits assembling their genomes. Here, we report the 376 Mb genome sequence of Papilio glaucus (Pgl), the first sequenced genome from the Papilionidae family. We obtained the genome from a wild-caught specimen using a cost-effective strategy that overcomes the high (2%) heterozygosity problem. Comparative analyses suggest the molecular bases of various phenotypic traits, including terpene production in the Papilionidae-specific organ, osmeterium. Comparison of Pgl and Papilio canadensis transcriptomes reveals mutation hotspots (4% genes) associated with their divergence: four key circadian clock proteins are enriched in inter-species mutations and likely responsible for the difference in pupal diapause. Finally, the Pgl genome confirms Papilio appalachiensis as a hybrid of Pgl and Pca, but suggests it inherited 3/4 of its genes from Pca. The swallowtail butterfly has attracted broad attention from people. Now, Cong et al. present the genome of the Eastern Tiger Swallowtail obtained with a protocol that works for highly heterozygous genomes. Comparative analyses provide insights to caterpillar chemical defense, winter sleep of pupae, speciation mechanisms, and hybrid species.
Collapse
|
20
|
Shiraiwa K, Cong Q, Grishin NV. A new Heraclides swallowtail (Lepidoptera, Papilionidae) from North America is recognized by the pattern on its neck. Zookeys 2014; 468:85-135. [PMID: 25610342 PMCID: PMC4296521 DOI: 10.3897/zookeys.468.8565] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/04/2014] [Indexed: 11/12/2022] Open
Abstract
Heraclidesrumiko Shiraiwa & Grishin, sp. n. is described from southwestern United States, Mexico, and Central America (type locality: USA, Texas, Duval County). It is closely allied to Heraclidescresphontes (Cramer, 1777) and the two species are sympatric in central Texas. The new species is diagnosed by male genitalia and exhibits a nearly 3% difference from Heraclidescresphontes in the COI DNA barcode sequence of mitochondrial DNA. The two Heraclides species can usually be told apart by the shape and size of yellow spots on the neck, by the wing shape, and the details of wing patterns. "Western Giant Swallowtail" is proposed as the English name for Heraclidesrumiko. To stabilize nomenclature, neotype for Papiliocresphontes Cramer, 1777, an eastern United States species, is designated from Brooklyn, New York, USA; and lectotype for Papiliothoas Linnaeus, 1771 is designated from Suriname. We sequenced DNA barcodes and ID tags of nearly 400 Papilionini specimens completing coverage of all Heraclides species. Comparative analyses of DNA barcodes, genitalia, and facies suggest that Heraclidesoviedo (Gundlach, 1866), reinstated status, is a species-level taxon rather than a subspecies of Heraclidesthoas (Linnaeus, 1771); and Heraclidespallas (G. Gray, [1853]), reinstated status, with its subspecies HeraclidesPapiliobajaensis (J. Brown & Faulkner, 1992), comb. n., and Heraclidesanchicayaensis Constantino, Le Crom & Salazar, 2002, stat. n., are not conspecific with Heraclidesastyalus (Godart, 1819).
Collapse
Affiliation(s)
| | - Qian Cong
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA 75390-9050
| | - Nick V. Grishin
- Howard Hughes Medical Institute
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA 75390-9050
| |
Collapse
|
21
|
Timmermans MJTN, Baxter SW, Clark R, Heckel DG, Vogel H, Collins S, Papanicolaou A, Fukova I, Joron M, Thompson MJ, Jiggins CD, ffrench-Constant RH, Vogler AP. Comparative genomics of the mimicry switch in Papilio dardanus. Proc Biol Sci 2014; 281:rspb.2014.0465. [PMID: 24920480 PMCID: PMC4071540 DOI: 10.1098/rspb.2014.0465] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The African Mocker Swallowtail, Papilio dardanus, is a textbook example in evolutionary genetics. Classical breeding experiments have shown that wing pattern variation in this polymorphic Batesian mimic is determined by the polyallelic H locus that controls a set of distinct mimetic phenotypes. Using bacterial artificial chromosome (BAC) sequencing, recombination analyses and comparative genomics, we show that H co-segregates with an interval of less than 500 kb that is collinear with two other Lepidoptera genomes and contains 24 genes, including the transcription factor genes engrailed (en) and invected (inv). H is located in a region of conserved gene order, which argues against any role for genomic translocations in the evolution of a hypothesized multi-gene mimicry locus. Natural populations of P. dardanus show significant associations of specific morphs with single nucleotide polymorphisms (SNPs), centred on en. In addition, SNP variation in the H region reveals evidence of non-neutral molecular evolution in the en gene alone. We find evidence for a duplication potentially driving physical constraints on recombination in the lamborni morph. Absence of perfect linkage disequilibrium between different genes in the other morphs suggests that H is limited to nucleotide positions in the regulatory and coding regions of en. Our results therefore support the hypothesis that a single gene underlies wing pattern variation in P. dardanus.
Collapse
Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Science, Natural History Museum London, London SW7 5BD, UK Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Simon W Baxter
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Rebecca Clark
- Department of Life Science, Natural History Museum London, London SW7 5BD, UK Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - David G Heckel
- Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena 07745, Germany
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Beutenberg Campus, Jena 07745, Germany
| | - Steve Collins
- African Butterfly Research Institute, 0800 Westlands, Nairobi 14308, Kenya
| | - Alexie Papanicolaou
- School of Biosciences, University of Exeter, Cornwall Campus, Daphne du Maurier Building, Penryn TR10 9EZ, UK CSIRO Ecosystem Sciences, Black Mountain Laboratories, Canberra 2601, Australia
| | - Iva Fukova
- School of Biosciences, University of Exeter, Cornwall Campus, Daphne du Maurier Building, Penryn TR10 9EZ, UK
| | - Mathieu Joron
- Muséum National d'Histoire Naturelle, CNRS UMR 7205, CP50, 45 Rue Buffon, Paris 75005, France
| | - Martin J Thompson
- Department of Life Science, Natural History Museum London, London SW7 5BD, UK Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Richard H ffrench-Constant
- School of Biosciences, University of Exeter, Cornwall Campus, Daphne du Maurier Building, Penryn TR10 9EZ, UK
| | - Alfried P Vogler
- Department of Life Science, Natural History Museum London, London SW7 5BD, UK Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| |
Collapse
|
22
|
Kunte K, Zhang W, Tenger-Trolander A, Palmer DH, Martin A, Reed RD, Mullen SP, Kronforst MR. doublesex is a mimicry supergene. Nature 2014; 507:229-32. [PMID: 24598547 DOI: 10.1038/nature13112] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/30/2014] [Indexed: 12/30/2022]
Abstract
One of the most striking examples of sexual dimorphism is sex-limited mimicry in butterflies, a phenomenon in which one sex--usually the female--mimics a toxic model species, whereas the other sex displays a different wing pattern. Sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio, in which it is often associated with female mimetic polymorphism. In multiple polymorphic species, the entire wing pattern phenotype is controlled by a single Mendelian 'supergene'. Although theoretical work has explored the evolutionary dynamics of supergene mimicry, there are almost no empirical data that address the critical issue of what a mimicry supergene actually is at a functional level. Using an integrative approach combining genetic and association mapping, transcriptome and genome sequencing, and gene expression analyses, we show that a single gene, doublesex, controls supergene mimicry in Papilio polytes. This is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci. Analysis of gene expression and DNA sequence variation indicates that isoform expression differences contribute to the functional differences between dsx mimicry alleles, and protein sequence evolution may also have a role. Our results combine elements from different hypotheses for the identity of supergenes, showing that a single gene can switch the entire wing pattern among mimicry phenotypes but may require multiple, tightly linked mutations to do so.
Collapse
Affiliation(s)
- K Kunte
- 1] National Center for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India [2]
| | - W Zhang
- 1] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA [2]
| | - A Tenger-Trolander
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - D H Palmer
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - A Martin
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - R D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - S P Mullen
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - M R Kronforst
- 1] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA [2] Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
23
|
Adaptations to "Thermal Time" Constraints in Papilio: Latitudinal and Local Size Clines Differ in Response to Regional Climate Change. INSECTS 2014; 5:199-226. [PMID: 26462585 PMCID: PMC4592633 DOI: 10.3390/insects5010199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/20/2013] [Accepted: 01/08/2014] [Indexed: 11/17/2022]
Abstract
Adaptations to "thermal time" (=Degree-day) constraints on developmental rates and voltinism for North American tiger swallowtail butterflies involve most life stages, and at higher latitudes include: smaller pupae/adults; larger eggs; oviposition on most nutritious larval host plants; earlier spring adult emergences; faster larval growth and shorter molting durations at lower temperatures. Here we report on forewing sizes through 30 years for both the northern univoltine P. canadensis (with obligate diapause) from the Great Lakes historical hybrid zone northward to central Alaska (65° N latitude), and the multivoltine, P. glaucus from this hybrid zone southward to central Florida (27° N latitude). Despite recent climate warming, no increases in mean forewing lengths of P. glaucus were observed at any major collection location (FL to MI) from the 1980s to 2013 across this long latitudinal transect (which reflects the "converse of Bergmann's size Rule", with smaller females at higher latitudes). Unlike lower latitudes, the Alaska, Ontonogon, and Chippewa/Mackinac locations (for P. canadensis) showed no significant increases in D-day accumulations, which could explain lack of size change in these northernmost locations. As a result of 3-4 decades of empirical data from major collection sites across these latitudinal clines of North America, a general "voltinism/size/D-day" model is presented, which more closely predicts female size based on D-day accumulations, than does latitude. However, local "climatic cold pockets" in northern Michigan and Wisconsin historically appeared to exert especially strong size constraints on female forewing lengths, but forewing lengths quickly increased with local summer warming during the recent decade, especially near the warming edges of the cold pockets. Results of fine-scale analyses of these "cold pockets" are in contrast to non-significant changes for other Papilio populations seen across the latitudinal transect for P. glaucus and P. canadensis in general, highlighting the importance of scale in adaptations to climate change. Furthermore, we also show that rapid size increases in cold pocket P. canadensis females with recent summer warming are more likely to result from phenotypic plasticity than genotypic introgression from P. glaucus, which does increase size in late-flight hybrids and P. appalachiensis.
Collapse
|
24
|
Scriber JM. Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes. INSECTS 2013; 5:1-61. [PMID: 26462579 PMCID: PMC4592632 DOI: 10.3390/insects5010001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/04/2013] [Accepted: 12/06/2013] [Indexed: 01/11/2023]
Abstract
Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.
Collapse
Affiliation(s)
- Jon Mark Scriber
- Department of Entomology, Michigan State University, East Lansing, Michigan, MI 48824, USA.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|