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Messerschmid TFE, Abrahamczyk S, Bañares-Baudet Á, Brilhante MA, Eggli U, Hühn P, Kadereit JW, dos Santos P, de Vos JM, Kadereit G. Inter- and intra-island speciation and their morphological and ecological correlates in Aeonium (Crassulaceae), a species-rich Macaronesian radiation. ANNALS OF BOTANY 2023; 131:697-721. [PMID: 36821492 PMCID: PMC10147336 DOI: 10.1093/aob/mcad033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/22/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The most species-rich and ecologically diverse plant radiation on the Canary Islands is the Aeonium alliance (Crassulaceae). In island radiations like this, speciation can take place either within islands or following dispersal between islands. Aiming at quantifying intra- and inter-island speciation events in the evolution of Aeonium, and exploring their consequences, we hypothesized that (1) intra-island diversification resulted in stronger ecological divergence of sister lineages, and that (2) taxa on islands with a longer history of habitation by Aeonium show stronger ecological differentiation and produce fewer natural hybrids. METHODS We studied the biogeographical and ecological setting of diversification processes in Aeonium with a fully sampled and dated phylogeny inferred using a ddRADseq approach. Ancestral areas and biogeographical events were reconstructed in BioGeoBEARS. Eleven morphological characters and three habitat characteristics were taken into account to quantify the morphological and ecological divergence between sister lineages. A co-occurrence matrix of all Aeonium taxa is presented to assess the spatial separation of taxa on each island. KEY RESULTS We found intra- and inter-island diversification events in almost equal numbers. In lineages that diversified within single islands, morphological and ecological divergence was more pronounced than in lineages derived from inter-island diversification, but only the difference in morphological divergence was significant. Those islands with the longest history of habitation by Aeonium had the lowest percentages of co-occurring and hybridizing taxon pairs compared with islands where Aeonium arrived later. CONCLUSIONS Our findings illustrate the importance of both inter- and intra-island speciation, the latter of which is potentially sympatric speciation. Speciation on the same island entailed significantly higher levels of morphological divergence compared with inter-island speciation, but ecological divergence was not significantly different. Longer periods of shared island habitation resulted in the evolution of a higher degree of spatial separation and stronger reproductive barriers.
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Affiliation(s)
- Thibaud F E Messerschmid
- Botanischer Garten München-Nymphenburg, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, 80638 München, Germany
| | - Stefan Abrahamczyk
- Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
- Abteilung Botanik, Staatliches Museum für Naturkunde Stuttgart, 70191 Stuttgart, Germany
| | - Ángel Bañares-Baudet
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, E-38200 La Laguna, Tenerife, Spain
| | - Miguel A Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1340-017 Lisboa, Portugal
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich/Grün Stadt Zürich, 8002 Zürich, Switzerland
| | - Philipp Hühn
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Patrícia dos Santos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) and Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Department of Environmental Sciences – Botany, University of Basel, 4056 Basel, Switzerland
| | - Jurriaan M de Vos
- Department of Environmental Sciences – Botany, University of Basel, 4056 Basel, Switzerland
| | - Gudrun Kadereit
- Botanischer Garten München-Nymphenburg, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, 80638 München, Germany
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Mort ME, Kerbs BR, Kelly JK, Silva LB, Moura M, de Sequeira MM, Santos-Guerra A, Schaefer H, Alfredo Reyes-Betancort J, Caujapé-Castells J, Crawford DJ. Multiplexed shotgun genotyping (MSG) data resolve phylogenetic relationships within and among archipelagos in Macaronesian Tolpis. AMERICAN JOURNAL OF BOTANY 2022; 109:952-965. [PMID: 35608078 DOI: 10.1002/ajb2.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Plants endemic to oceanic archipelagos are suitable for studying evolution, being isolated on substrates of different ages. Evolution has been recent, rendering traditionally employed sequences insufficiently variable for resolving relationships. This study includes sampling in the genus Tolpis (Asteraceae) from the Azores, Madeira, and Cape Verde, and expands upon an earlier study demonstrating the efficacy of multiplexed shotgun genotyping (MSG) for resolving relationships in Canarian Tolpis. METHODS Genomic libraries for 90 accessions of Tolpis and two from the outgroup were generated for genotyping individuals using MSG. Loci were de novo assembled with iPyrad, which clusters MSG loci within and between samples. A maximum likelihood phylogeny was generated with RAxML. Ancestral area reconstruction was inferred using R package BioGeoBEARS. RESULTS MSG data recovered a highly resolved phylogeny from population to inter-archipelago levels. Ancestral area reconstruction provided biogeographic hypotheses for the radiation of Macaronesian Tolpis. CONCLUSIONS Four major clades were resolved. The Madeiran endemic T. macrorhiza is sister to other Tolpis. Species from the Canaries, Cape Verdes, and the continent are sister to T. succulenta from Madeira, which has a sister subclade of Azorean populations composed of T. succulenta and T. azorica. Population-level resolution suggests unrecognized taxa on several archipelagos. Ancestral reconstruction suggests initial dispersal from the continent to Madeira, with dispersal to the Azores, then dispersal from Madeira to the Canary Islands, with both subsequent dispersal to the Cape Verdes and back-dispersal to the continent. Single-island radiations and inter-island dispersal are implicated in divergence in Macaronesian Tolpis.
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Affiliation(s)
- Mark E Mort
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Benjamin R Kerbs
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Lurdes Borges Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Universidade dos Açores, Rua da Mãe de Deus 13 A, 9501-801, Ponta Delgada, Açores, Portugal
| | - Mónica Moura
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, Universidade dos Açores, Rua da Mãe de Deus 13 A, 9501-801, Ponta Delgada, Açores, Portugal
| | - Miguel Menezes de Sequeira
- Madeira Botanical Group, Faculty of Life Sciences, Campus Universitário da Penteada, University of Madeira, 9020-105, Funchal, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-81, Ponta Delgada, Portugal
| | - Arnoldo Santos-Guerra
- Calle Guaidil 16, Urbanización Tamarco, Tegueste, Tenerife, Canary Islands, 38280, Spain
| | - Hanno Schaefer
- Department of Life Science Systems, Plant Biodiversity Research, Technical University of Munich, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - J Alfredo Reyes-Betancort
- Unidad de Botánica Aplicada, Instituto Canario de Investigaciones Agrarias, Jardín de Aclimatación de La Orotava, Puerto de La Cruz, Santa Cruz de Tenerife, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario "Viera y Clavijo"-Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino al Palmeral 15, Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
| | - Daniel J Crawford
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
- Department of Ecology & Evolutionary Biology, and the Biodiversity Institute, University of Kansas, Lawrence, Kansas, 66045-7534, USA
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Knope ML, Bellinger MR, Datlof EM, Gallaher TJ, Johnson MA. Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics. J Hered 2021; 111:119-137. [PMID: 31953949 DOI: 10.1093/jhered/esz066] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022] Open
Abstract
Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76-1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67-80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.
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Affiliation(s)
- Matthew L Knope
- Department of Biology, University of Hawai'i at Hilo, Hilo, HI
| | | | - Erin M Datlof
- Department of Biology, University of Hawai'i at Hilo, Hilo, HI
| | - Timothy J Gallaher
- Department of Biology, University of Washington, Seattle, WA.,Bernice Pauahi Bishop Museum, Honolulu, HI
| | - Melissa A Johnson
- USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI
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Carine M. Mastering the difficulties presented by the peculiarities of island life. A commentary on: 'Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequence data'. ANNALS OF BOTANY 2021; 127:iii-iv. [PMID: 33755052 PMCID: PMC8052920 DOI: 10.1093/aob/mcab025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article comments on: Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090
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Affiliation(s)
- Mark Carine
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Conservation in the face of hybridisation: genome-wide study to evaluate taxonomic delimitation and conservation status of a threatened orchid species. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01325-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Kerbs B, Crawford DJ, White G, Moura M, Borges Silva L, Schaefer H, Brown K, Mort ME, Kelly JK. How rapidly do self-compatible populations evolve selfing? Mating system estimation within recently evolved self-compatible populations of Azorean Tolpis succulenta (Asteraceae). Ecol Evol 2020; 10:13990-13999. [PMID: 33391697 PMCID: PMC7771160 DOI: 10.1002/ece3.6992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
Genome-wide genotyping and Bayesian inference method (BORICE) were employed to estimate outcrossing rates and paternity in two small plant populations of Tolpis succulenta (Asteraceae) on Graciosa island in the Azores. These two known extant populations of T. succulenta on Graciosa have recently evolved self-compatibility. Despite the expectation that selfing would occur at an appreciable rate (self-incompatible populations of the same species show low but nonzero selfing), high outcrossing was found in progeny arrays from maternal plants in both populations. This is inconsistent with an immediate transition to high selfing following the breakdown of a genetic incompatibility system. This finding is surprising given the small population sizes and the recent colonization of an island from self-incompatible colonists of T. succulenta from another island in the Azores, and a potential paucity of pollinators, all factors selecting for selfing through reproductive assurance. The self-compatible lineage(s) likely have high inbreeding depression (ID) that effectively halts the evolution of increased selfing, but this remains to be determined. Like their progeny, all maternal plants in both populations are fully outbred, which is consistent with but not proof of high ID. High multiple paternity was found in both populations, which may be due in part to the abundant pollinators observed during the flowering season.
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Affiliation(s)
- Benjamin Kerbs
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKSUSA
| | - Daniel J. Crawford
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Griffin White
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- ETH ZurichFunctional Genomics Center ZurichZurichSwitzerland
| | - Mónica Moura
- InBIO Laboratório Associado, Pólo dos AçoresFaculdade de Ciências TecnoclogiaCIBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade dos AçoresPonta DelgadaPortugal
| | - Lurdes Borges Silva
- InBIO Laboratório Associado, Pólo dos AçoresFaculdade de Ciências TecnoclogiaCIBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade dos AçoresPonta DelgadaPortugal
| | - Hanno Schaefer
- Department of Ecology and Ecosystem ManagementPlant Biodiversity ResearchTechnical University of MunichFreisingGermany
| | - Keely Brown
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKSUSA
| | - Mark E. Mort
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKSUSA
| | - John K. Kelly
- Department of Ecology & Evolutionary BiologyUniversity of KansasLawrenceKSUSA
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White OW, Reyes-Betancort JA, Chapman MA, Carine MA. Geographical isolation, habitat shifts and hybridisation in the diversification of the Macaronesian endemic genus Argyranthemum (Asteraceae). THE NEW PHYTOLOGIST 2020; 228:1953-1971. [PMID: 33006142 DOI: 10.1111/nph.16980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Inferring the processes responsible for the rich endemic diversity of oceanic island floras is important for our understanding of plant evolution and setting practical conservation priorities. This requires an accurate knowledge of phylogenetic relationships, which have often been difficult to resolve due to a lack of genetic variation. We employed genotyping-by-sequencing (GBS) to investigate how geographical isolation, habitat shifts, and hybridisation have contributed to the evolution of diversity observed in Argyranthemum Webb (Asteraceae), the largest genus of flowering plants endemic to the Macaronesian archipelagos. Species relationships were resolved, and biogeographical stochastic mapping identified intra-island speciation as the most frequent biogeographic process underlying diversification, contrary to the prevailing view in Argyranthemum and the Canary Islands. D-statistics revealed significant evidence of hybridisation between lineages co-occurring on the same island, however there was little support for the hypothesis that hybridisation may be responsible for the occurrence of nonmonophyletic multi-island endemic (MIE) species. Geographic isolation, habitat shifts and hybridisation have all contributed to the diversification of Argyranthemum, with intra-island speciation found to be more frequent than previously thought. Morphological convergence is also proposed to explain the occurrence of nonmonophyletic MIE species. This study reveals greater complexity in the evolutionary processes generating Macaronesian endemic diversity.
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Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - J Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Oratava, Instituto Canario de Investigaciones Agrarias - ICIA), C/ Retama 2, Puerto de la Cruz, Tenerife, 38400, Spain
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Gibson MJS, Crawford DJ, Holder MT, Mort ME, Kerbs B, de Sequeira MM, Kelly JK. Genome-wide genotyping estimates mating system parameters and paternity in the island species Tolpis succulenta. AMERICAN JOURNAL OF BOTANY 2020; 107:1189-1197. [PMID: 32864742 DOI: 10.1002/ajb2.1515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
PREMISE The mating system has profound consequences, not only for ecology and evolution, but also for the conservation of threatened or endangered species. Unfortunately, small populations are difficult to study owing to limits on sample size and genetic marker diversity. Here, we estimated mating system parameters in three small populations of an island plant using genomic genotyping. Although self-incompatible (SI) species are known to often set some self-seed, little is known about how "leaky SI" affects selfing rates in nature or the role that multiple paternity plays in small populations. METHODS We generalized the BORICE mating system program to determine the siring pattern within maternal families. We applied this algorithm to maternal families from three populations of Tolpis succulenta from Madeira Island and genotyped the progeny using RADseq. We applied BORICE to estimate each individual offspring as outcrossed or selfed, the paternity of each outcrossed offspring, and the level of inbreeding of each maternal plant. RESULTS Despite a functional self-incompatibility system, these data establish T. succulenta as a pseudo-self-compatible (PSC) species. Two of 75 offspring were strongly indicated as products of self-fertilization. Despite selfing, all adult maternal plants were fully outbred. There was high differentiation among and low variation within populations, consistent with a history of genetic isolation of these small populations. There were generally multiple sires per maternal family. Twenty-two percent of sib contrasts (between outcrossed offspring within maternal families) shared the same sire. CONCLUSIONS Genome-wide genotyping, combined with appropriate analytical methods, enables estimation of mating system and multiple paternity in small populations. These data address questions about the evolution of reproductive traits and the conservation of threatened populations.
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Affiliation(s)
- Matthew J S Gibson
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA
| | - Daniel J Crawford
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045-7534, USA
| | - Mark T Holder
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045-7534, USA
| | - Mark E Mort
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA
| | - Benjamin Kerbs
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA
| | - Miguel Menezes de Sequeira
- Madeira Botanical Group, Faculty of Life Sciences, University of Madeira, Campus Universitário da Penteada, 9020-105, Funchal, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores, 9501-81, Ponta Delgada, Portugal
| | - John K Kelly
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7534, USA
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Halbritter DA, Storer CG, Kawahara AY, Daniels JC. Phylogeography and population genetics of pine butterflies: Sky islands increase genetic divergence. Ecol Evol 2019; 9:13389-13401. [PMID: 31871652 PMCID: PMC6912906 DOI: 10.1002/ece3.5793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/05/2022] Open
Abstract
The sky islands of southeastern Arizona (AZ) mark a major transition zone between tropical and temperate biota and are considered a neglected biodiversity hotspot. Dispersal ability and host plant specificity are thought to impact the history and diversity of insect populations across the sky islands. We aimed to investigate the population structure and phylogeography of two pine-feeding pierid butterflies, the pine white (Neophasia menapia) and the Mexican pine white (Neophasia terlooii), restricted to these "islands" at this transition zone. Given their dependence on pines as the larval hosts, we hypothesized that habitat connectivity affects population structure and is at least in part responsible for their allopatry. We sampled DNA from freshly collected butterflies from 17 sites in the sky islands and adjacent high-elevation habitats and sequenced these samples using ddRADSeq. Up to 15,399 SNPs were discovered and analyzed in population genetic and phylogenetic contexts with Stacks and pyRAD pipelines. Low genetic differentiation in N. menapia suggests that it is panmictic. Conversely, there is strong evidence for population structure within N. terlooii. Each sky island likely contains a population of N. terlooii, and clustering is hierarchical, with populations on proximal mountains being more related to each other. The N. menapia habitat, which is largely contiguous, facilitates panmixia, while the N. terlooii habitat, restricted to the higher elevations on each sky island, creates distinct population structure. Phylogenetic results corroborate those from population genetic analyses. The historical climate-driven fluxes in forest habitat connectivity have implications for understanding the biodiversity of fragmented habitats.
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Affiliation(s)
- Dale A. Halbritter
- Entomology and Nematology DepartmentUniversity of FloridaGainesvilleFLUSA
- Present address:
USDA‐ARS Invasive Plant Research Laboratory3225 College AveFort LauderdaleFL33314USA
| | - Caroline G. Storer
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Jaret C. Daniels
- Entomology and Nematology DepartmentUniversity of FloridaGainesvilleFLUSA
- McGuire Center for Lepidoptera and BiodiversityFlorida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
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Restructuring of the 'Macaronesia' biogeographic unit: A marine multi-taxon biogeographical approach. Sci Rep 2019; 9:15792. [PMID: 31690834 PMCID: PMC6831653 DOI: 10.1038/s41598-019-51786-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/03/2019] [Indexed: 01/10/2023] Open
Abstract
The Azores, Madeira, Selvagens, Canary Islands and Cabo Verde are commonly united under the term “Macaronesia”. This study investigates the coherency and validity of Macaronesia as a biogeographic unit using six marine groups with very different dispersal abilities: coastal fishes, echinoderms, gastropod molluscs, brachyuran decapod crustaceans, polychaete annelids, and macroalgae. We found no support for the current concept of Macaronesia as a coherent marine biogeographic unit. All marine groups studied suggest the exclusion of Cabo Verde from the remaining Macaronesian archipelagos and thus, Cabo Verde should be given the status of a biogeographic subprovince within the West African Transition province. We propose to redefine the Lusitanian biogeographical province, in which we include four ecoregions: the South European Atlantic Shelf, the Saharan Upwelling, the Azores, and a new ecoregion herein named Webbnesia, which comprises the archipelagos of Madeira, Selvagens and the Canary Islands.
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Romeiras MM, Pena AR, Menezes T, Vasconcelos R, Monteiro F, Paulo OS, Moura M. Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity. Int J Mol Sci 2019; 20:E2782. [PMID: 31174340 PMCID: PMC6600550 DOI: 10.3390/ijms20112782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/16/2019] [Accepted: 06/04/2019] [Indexed: 12/22/2022] Open
Abstract
Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.
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Affiliation(s)
- Maria M Romeiras
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Ana Rita Pena
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Tiago Menezes
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
| | - Raquel Vasconcelos
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Filipa Monteiro
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal.
| | - Mónica Moura
- CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos Açores, 9501-855 Ponta Delgada, Azores, Portugal.
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Wagner ND, Gramlich S, Hörandl E. RAD sequencing resolved phylogenetic relationships in European shrub willows ( Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs. Ecol Evol 2018; 8:8243-8255. [PMID: 30250699 PMCID: PMC6145212 DOI: 10.1002/ece3.4360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 01/03/2023] Open
Abstract
The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic-alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.
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Affiliation(s)
- Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)University of GoettingenGöttingenGermany
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13
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Takayama K, Crawford DJ, López-Sepúlveda P, Greimler J, Stuessy TF. Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago. JOURNAL OF PLANT RESEARCH 2018. [PMID: 29536201 PMCID: PMC6404664 DOI: 10.1007/s10265-018-1023-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Adaptive radiation is a common evolutionary phenomenon in oceanic islands. From one successful immigrant population, dispersal into different island environments and directional selection can rapidly yield a series of morphologically distinct species, each adapted to its own particular environment. Not all island immigrants, however, follow this evolutionary pathway. Others successfully arrive and establish viable populations, but they remain in the same ecological zone and only slowly diverge over millions of years. This transformational speciation, or anagenesis, is also common in oceanic archipelagos. The critical question is why do some groups radiate adaptively and others not? The Juan Fernández Islands contain 105 endemic taxa of angiosperms, 49% of which have originated by adaptive radiation (cladogenesis) and 51% by anagenesis, hence providing an opportunity to examine characteristics of taxa that have undergone both types of speciation in the same general island environment. Life form, dispersal mode, and total number of species in progenitors (genera) of endemic angiosperms in the archipelago were investigated from literature sources and compared with modes of speciation (cladogenesis vs. anagenesis). It is suggested that immigrants tending to undergo adaptive radiation are herbaceous perennial herbs, with leaky self-incompatible breeding systems, good intra-island dispersal capabilities, and flexible structural and physiological systems. Perhaps more importantly, the progenitors of adaptively radiated groups in islands are those that have already been successful in adaptations to different environments in source areas, and which have also undergone eco-geographic speciation. Evolutionary success via adaptive radiation in oceanic islands, therefore, is less a novel feature of island lineages but rather a continuation of tendency for successful adaptive speciation in lineages of continental source regions.
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Affiliation(s)
- Koji Takayama
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Daniel J. Crawford
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, KS 60045 USA
| | | | - Josef Greimler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Tod F. Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
- Herbarium and Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212 USA
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14
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Koseva B, Crawford DJ, Brown K, Mort ME, Kelly JK. The genetic breakdown of sporophytic self-incompatibility in Tolpis coronopifolia (Asteraceae). THE NEW PHYTOLOGIST 2017; 216:1256-1267. [PMID: 28892151 PMCID: PMC5675808 DOI: 10.1111/nph.14759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/14/2017] [Indexed: 05/31/2023]
Abstract
Angiosperm diversity has been shaped by mating system evolution, with the most common transition from outcrossing to self-fertilizing. To investigate the genetic basis of this transition, we performed crosses between two species endemic to the Canary Islands, the self-compatible (SC) species Tolpis coronopifolia and its self-incompatible (SI) relative Tolpis santosii. We scored self-compatibility as self-seed set of recombinant plants within two F2 populations. To map and genetically characterize the breakdown of SI, we built a draft genome sequence of T. coronopifolia, genotyped F2 plants using multiplexed shotgun genotyping (MSG), and located MSG markers to the genome sequence. We identified a single quantitative trait locus (QTL) that explains nearly all variation in self-seed set in both F2 populations. To identify putative causal genetic variants within the QTL, we performed transcriptome sequencing on mature floral tissue from both SI and SC species, constructed a transcriptome for each species, and then located each predicted transcript to the T. coronopifolia genome sequence. We annotated each predicted gene within the QTL and found two strong candidates for SI breakdown. Each gene has a coding sequence insertion/deletion mutation within the SC species that produces a truncated protein. Homologs of each gene have been implicated in pollen development, pollen germination, and pollen tube growth in other species.
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Affiliation(s)
- Boryana Koseva
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Daniel J. Crawford
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Keely Brown
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Mark E. Mort
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7534, USA
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
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15
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Menezes T, Romeiras MM, de Sequeira MM, Moura M. Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia. Ecol Evol 2017; 8:88-108. [PMID: 29321854 PMCID: PMC5756848 DOI: 10.1002/ece3.3640] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 09/30/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022] Open
Abstract
Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages. We sequenced the ITS region and six cpDNA markers (atpB, matK, petD, rbcL, trnL-F, and psbA-trnH) from 10 Campanulaceae species, including seven endemic species in Macaronesia. The phylogeny of these taxa was reconstructed using maximum parsimony, maximum likelihood, and Bayesian inference. To study the relationships within each lineage, haplotype networks were calculated using NeighborNet and TCS algorithms. Moreover, data were combined with fossil information to construct time-calibrated trees for the Macaronesian Campanulaceae species. The phylogenetic analyses are largely congruent with current taxon circumscriptions, and all the endemic genera formed monophyletic clades, namely Azorina in Azores; Musschia in Madeira; and Campanula in Cape Verde. The Azorina clade and the Cape Verde endemic Campanula may share a common ancestor in North Africa, and the divergence was dated ca. 12.3 million years ago (Mya). The divergence of the Musschia clade began in the Pliocene ca. 3.4 Mya. Moreover, several examples of intraspecific variation were revealed among the native species with a clear geographic structured patterns, suggesting that cryptic diversity might exist within the native Macaronesian Campanulaceae when compared to the close mainland taxa (e.g., Campanula erinus, Trachelium caeruleum), but additional studies are needed to support the molecular data. This study highlights the power of combining data (e.g., phylogeny and divergence times, with species distribution data) for testing diversification hypotheses within the unique Macaronesian flora, providing useful information for future conservation efforts.
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Affiliation(s)
- Tiago Menezes
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory Faculdade de Ciências e Tecnologia Universidade dos Açores Ponta Delgada Azores Portugal
| | - Maria M Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF) Instituto Superior de Agronomia Universidade de Lisboa Lisbon Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Miguel M de Sequeira
- Madeira Botanical Group Faculdade de Ciências da Vida Universidade de Madeira Alto da PenteadaFunchal Madeira Portugal
| | - Mónica Moura
- CIBIO Research Centre in Biodiversity and Genetic Resources InBIO Associate Laboratory Faculdade de Ciências e Tecnologia Universidade dos Açores Ponta Delgada Azores Portugal
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16
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Kerbs B, Ressler J, Kelly JK, Mort ME, Santos-Guerra A, Gibson MJS, Caujapé-Castells J, Crawford DJ. The potential role of hybridization in diversification and speciation in an insular plant lineage: insights from synthetic interspecific hybrids. AOB PLANTS 2017; 9:plx043. [PMID: 29225761 PMCID: PMC5714139 DOI: 10.1093/aobpla/plx043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 08/25/2017] [Indexed: 05/17/2023]
Abstract
Hybridization is recognized as an important process in plant evolution, and this may be particularly true for island plants where several biotic and abiotic factors facilitate interspecific hybridization. Although rarely done, experimental studies could provide insights into the potential of natural hybridization to generate diversity when species come into contact in the dynamic island setting. The potential of hybridization to generate morphological variation was analysed within and among 12 families (inbred lines) of an F4 hybrid generation between two species of Tolpis endemic to the Canary Islands. Combinations of characters not seen in the parents were present in hybrids. Several floral and vegetative characters were transgressive relative to their parents. Morphometric studies of floral, vegetative and fruit characters revealed that several F4 families were phenotypically distinct from other families, and from their parents. The study demonstrates that morphologically distinct pollen-fertile lines, potentially worthy of taxonomic recognition if occurring in nature, can be generated in four generations. The ability of the hybrid lines to set self-seed would reduce gene flow among the lines, and among the hybrids and their parental species. Selfing would also facilitate the fixation of characters within each of the lines. Overall, the results show the considerable potential of hybridization for generating diversity and distinct phenotypes in island lineages.
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Affiliation(s)
- Benjamin Kerbs
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Jacob Ressler
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - John K Kelly
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Mark E Mort
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USA
| | - Arnoldo Santos-Guerra
- Calle Guaidil 16, Urbanización Tamarco, 38280 Tegueste, Tenerife, Canary Islands, Spain
| | | | - Juli Caujapé-Castells
- Jardín Botánico 13 Canario “Viera y Clavijo”-Unidad Asociada al CSIC (Cabildo de Gran Canaria), Camino del palmeral 14 15 (Tafira Alta), 35017 Las Palmas de Gran Canaria, Spain
| | - Daniel J Crawford
- Department of Ecology & Evolutionary Biology, and the Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7534, USA
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17
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Grewe F, Huang JP, Leavitt SD, Lumbsch HT. Reference-based RADseq resolves robust relationships among closely related species of lichen-forming fungi using metagenomic DNA. Sci Rep 2017; 7:9884. [PMID: 28852019 PMCID: PMC5575168 DOI: 10.1038/s41598-017-09906-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/31/2017] [Indexed: 01/13/2023] Open
Abstract
Despite increasing availability of phylogenomic datasets, strategies to generate genome-scale data from organisms involved in symbiotic relationships remains challenging. Restriction site-associated DNA sequencing (RADseq) can effectively generated reduced representation genomic loci. However, when using metagenomic DNA from inseparable symbiotic organisms, RADseq loci may belong to any number of the organisms involved in these intimate associations. In this study, we explored the potential for a reference-based RADseq approach to generate data for lichen-forming fungi from metagenomic DNA extracted from intact lichens. We simulated RAD data from draft genomes of closely related lichenized fungi to test if RADseq can reconstruct robust evolutionary relationships. Subsequently, we generated empirical RADseq data from metagenomic lichen DNA, with RADseq loci mapped back to a reference genome to exclude loci from other lichen symbionts that are represented in metagenomic libraries. In all cases, phylogenetic reconstructions using RADseq loci recovered diversification histories consistent with a previous study based on more comprehensive genome sampling. Furthermore, RADseq loci were found to resolve relationships among closely related species, which were otherwise indistinguishable using a phylogenetic species recognition criterion. Our studies revealed that a modified, reference-based RADseq approach can successfully be implemented to generate symbiont-specific phylogenomic data from metagenomic reads.
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Affiliation(s)
- Felix Grewe
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA.
| | - Jen-Pen Huang
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA
| | - Steven D Leavitt
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA.,Department of Biology & M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - H Thorsten Lumbsch
- Integrative Research Center, Science and Education, Field Museum of Natural History, 1400S Lake Shore Drive, Chicago, IL, 60605, USA
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18
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Vargas OM, Ortiz EM, Simpson BB. Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium). THE NEW PHYTOLOGIST 2017; 214:1736-1750. [PMID: 28333396 DOI: 10.1111/nph.14530] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 02/19/2017] [Indexed: 05/21/2023]
Abstract
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
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Affiliation(s)
- Oscar M Vargas
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University Ave, Ann Arbor, MI, 48109, USA
| | - Edgardo M Ortiz
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Beryl B Simpson
- Integrative Biology and Plant Resources Center, The University of Texas at Austin, Austin, TX, 78712, USA
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19
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Archibald JK, Cook J, Anderson B, Johnson SD, Mort ME. A reassessment of the phylogeny and circumscription of Zaluzianskya (Scrophulariaceae). Mol Phylogenet Evol 2017; 112:194-208. [PMID: 28411161 DOI: 10.1016/j.ympev.2017.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/26/2017] [Accepted: 04/10/2017] [Indexed: 10/19/2022]
Abstract
The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of floral and ecological traits. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. We present molecular data suggesting that this genus requires expansion via incorporation of species from other genera and recognition of unnamed cryptic species. This study advances prior molecular phylogenies of the southern African genus through the addition of DNA regions and 51 populations that had not previously been sampled in a published phylogeny. A total of 82 species of Zaluzianskya and related genera are included, adding 48 to those previously sampled. Results are presented from analyses of five DNA regions, including nuclear ITS and four rapidly evolving chloroplast regions (trnL-trnF, rpl16, rps16, and trnS-trnfM). Our primary finding is that the genus Phyllopodium is polyphyletic as currently circumscribed, with some species placed within Zaluzianskya and others grouping with Polycarena, indicating the need for further phylogenetic work on these genera. Preliminary support for the incorporation of Reyemia into Zaluzianskya is reinforced here by the first molecular analysis to include both species of Reyemia and a strong sampling of species across Zaluzianskya and major clades of tribe Limoselleae. The two disjunct, tropical African species of Zaluzianskya are also confirmed as members of this genus. Finally, a broad sampling of 21 populations of Z. microsiphon establishes their phylogenetic division into two to five separate lineages. Hybridization, coevolution, and cryptic speciation may each play a role in the evolution of Z. microsiphon. Further resolution within a clade comprising sections Nycterinia and Macrocalyx is needed to better understand their relationships.
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Affiliation(s)
- Jenny K Archibald
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | | | - Bruce Anderson
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Steven D Johnson
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Mark E Mort
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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20
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Gruenstaeudl M, Carstens BC, Santos-Guerra A, Jansen RK. Statistical hybrid detection and the inference of ancestral distribution areas in Tolpis (Asteraceae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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White OW, Doo B, Carine MA, Chapman MA. Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600050. [PMID: 27610280 PMCID: PMC5001862 DOI: 10.3732/apps.1600050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Oceanic islands offer unparalleled opportunities to investigate evolutionary processes such as adaptation and speciation. However, few genomic resources are available for oceanic island endemics. In this study, we publish transcriptome sequences from three Macaronesian endemic plant species (Argyranthemum broussonetii [Asteraceae], Descurainia bourgaeana [Brassicaceae], and Echium wildpretii [Boraginaceae]) that are representative of lineages that have radiated in the region. In addition, the utility of transcriptome data for marker development is demonstrated. METHODS AND RESULTS Transcriptomes from the three plant species were sequenced, assembled, and annotated. Between 1972 and 2282 simple sequence repeats (SSRs) were identified for each taxon. Primers were designed and tested for 30 of the candidate SSRs identified in Argyranthemum, of which 12 amplified well across three species and eight were polymorphic. CONCLUSIONS We demonstrate here that a single transcriptome sequence is sufficient to identify hundreds of polymorphic SSR markers. The SSRs are applicable to a wide range of questions relating to the evolution of island lineages.
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Affiliation(s)
- Oliver W. White
- Plants Division, Natural History Museum, London SW7 5BD, United Kingdom
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Bethany Doo
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Mark A. Carine
- Plants Division, Natural History Museum, London SW7 5BD, United Kingdom
| | - Mark A. Chapman
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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22
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Wessinger CA, Freeman CC, Mort ME, Rausher MD, Hileman LC. Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon. AMERICAN JOURNAL OF BOTANY 2016; 103:912-22. [PMID: 27208359 PMCID: PMC10874106 DOI: 10.3732/ajb.1500519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Evolutionary radiations provide opportunities to examine large-scale patterns in diversification and character evolution, yet are often recalcitrant to phylogenetic resolution due to rapid speciation events. The plant genus Penstemon has been difficult to resolve using Sanger sequence-based markers, leading to the hypothesis that it represents a recent North American radiation. The current study demonstrates the utility of multiplexed shotgun genotyping (MSG), a style of restriction site-associated DNA sequencing (RADseq), to infer phylogenetic relationships within a subset of species in this genus and provide insight into evolutionary patterns. METHODS We sampled genomic DNA, primarily from herbarium material, and subjected it to MSG library preparation and Illumina sequencing. The resultant sequencing reads were clustered into homologous loci, aligned, and concatenated into data matrices that differed according to clustering similarity and amount of missing data. We performed phylogenetic analyses on these matrices using maximum likelihood (RAxML) and a species tree approach (SVDquartets). KEY RESULTS MSG data provide a highly resolved estimate of species relationships within Penstemon. While most species relationships were highly supported, the position of certain taxa remains ambiguous, suggesting that increased taxonomic sampling or additional methodologies may be required. The data confirm that evolutionary shifts from hymenopteran- to hummingbird-adapted flowers have occurred independently many times. CONCLUSIONS This study demonstrates that phylogenomic approaches yielding thousands of variable sites can greatly improve species-level resolution of recent and rapid radiations. Similar to other studies, we found that less conservative similarity and missing data thresholds resulted in more highly supported topologies.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA
| | - Craig C Freeman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA R.L. McGregor Herbarium and Kansas Biological Survey, University of Kansas, Lawrence, Kansas 66047 USA
| | - Mark E Mort
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA
| | - Mark D Rausher
- Department of Biology, Duke University, Box 90338 Durham, North Carolina 27708 USA
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045 USA
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