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Wenzell KE, McDonnell AJ, Wickett NJ, Fant JB, Skogen KA. Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja. AMERICAN JOURNAL OF BOTANY 2021; 108:1270-1288. [PMID: 34289081 DOI: 10.1002/ajb2.1700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population-level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. METHODS Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. RESULTS We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. CONCLUSIONS Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco-evolutionary paths.
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Affiliation(s)
- Katherine E Wenzell
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Angela J McDonnell
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Norman J Wickett
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Jeremie B Fant
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Krissa A Skogen
- Program in Plant Biology and Conservation, Northwestern University, O.T. Hogan Hall, Room 6-140B, 2205 Tech Drive, Evanston, IL, 60208, USA
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, 60022, USA
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152
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Pillon Y, Hopkins HCF, Maurin O, Epitawalage N, Bradford J, Rogers ZS, Baker WJ, Forest F. Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments. AMERICAN JOURNAL OF BOTANY 2021; 108:1181-1200. [PMID: 34278558 PMCID: PMC8361763 DOI: 10.1002/ajb2.1688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
PREMISE Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long-range disjunctions. METHODS We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. RESULTS We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well-resolved genus-level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. CONCLUSIONS The current distribution of Cunoniaceae is best explained by long-distance dispersal with a few possible cases of Australasian-American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia.
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Affiliation(s)
- Yohan Pillon
- LSTMIRDINRAE, CIRADInstitut AgroUniv. MontpellierMontpellierFrance
| | | | | | | | | | - Zachary S. Rogers
- New Mexico State UniversityBox 30003MSC 3‐ILas CrucesNM88003‐8003USA
| | | | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3AEUK
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153
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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154
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Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K. HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311441. [PMID: 34336402 PMCID: PMC8312746 DOI: 10.1002/aps3.11441] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/28/2021] [Indexed: 05/24/2023]
Abstract
PREMISE Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. METHODS We used Angiosperms353 target capture data for Nepenthes, including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid samples were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. RESULTS All known Nepenthes hybrids and nine additional samples had high levels of heterozygous sites, had reads associated with multiple divergent clades, and were phased into accessions resembling divergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. DISCUSSION HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.
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Affiliation(s)
- Lars Nauheimer
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Nicholas Weigner
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Elizabeth Joyce
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Centre for Tropical Environmental Sustainability ScienceJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
| | - Charles Clarke
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- Cairns Botanic GardensCollins AvenueEdge HillQueensland4870Australia
| | - Katharina Nargar
- Australian Tropical HerbariumJames Cook UniversityMcGregor RoadSmithfieldQueensland4878Australia
- National Research Collections AustraliaCommonwealth Industrial and Scientific Research Organisation (CSIRO)GPO Box 1700CanberraAustralian Capital Territory2601Australia
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155
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Thomas SK, Liu X, Du Z, Dong Y, Cummings A, Pokorny L, Xiang Q(J, Leebens‐Mack JH. Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set. AMERICAN JOURNAL OF BOTANY 2021; 108:1112-1121. [PMID: 34263456 PMCID: PMC8361741 DOI: 10.1002/ajb2.1696] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 05/12/2021] [Indexed: 05/08/2023]
Abstract
PREMISE Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales. METHODS Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae. RESULTS We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL-III, a method statistically consistent with the multispecies coalescent model. CONCLUSIONS The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae-Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.
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Affiliation(s)
- Shawn K. Thomas
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Division of Biological SciencesUniversity of MissouriColumbiaMO65203USA
| | - Xiang Liu
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
- SyngentaResearch Triangle ParkNC27709USA
| | - Zhi‐Yuan Du
- Wuhan Botanical GardenThe Chinese Academy of SciencesWuhanHubei430074China
| | - Yibo Dong
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
- Global Health Infectious Disease ResearchCollege of Public HealthUniversity of South FloridaTampaFL33612USA
| | - Amanda Cummings
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondLondonTW9 3AEUK
- Computational/Systems Biology and Genomics ProgramCentre for Plant Biotechnology and GenomicsUPM‐INIA‐CSICPozuelo de Alarcón (Madrid)28223Spain
| | - Qui‐Yun (Jenny) Xiang
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNC27695USA
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156
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Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, McDonnell A, Pokorny L, Tate JA, Wicke S, Wickett NJ. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. AMERICAN JOURNAL OF BOTANY 2021; 108:1059-1065. [PMID: 34293179 DOI: 10.1002/ajb2.1703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Angela McDonnell
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Susann Wicke
- Plant Evolutionary Biology, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Plant Systematics and Biodiversity, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
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157
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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. AMERICAN JOURNAL OF BOTANY 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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158
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Ottenlips MV, Mansfield DH, Buerki S, Feist MAE, Downie SR, Dodsworth S, Forest F, Plunkett GM, Smith JF. Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex. AMERICAN JOURNAL OF BOTANY 2021; 108:1217-1233. [PMID: 34105148 PMCID: PMC8362113 DOI: 10.1002/ajb2.1676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/26/2021] [Indexed: 05/29/2023]
Abstract
PREMISE Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.
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Affiliation(s)
| | | | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
| | | | - Stephen R. Downie
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Steven Dodsworth
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
- School of Life SciencesUniversity of BedfordshireLutonLU1 3JUUK
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
| | - Gregory M. Plunkett
- Cullman Program for Molecular SystematicsNew York Botanical Garden2900 Southern BoulevardBronxNY10458USA
| | - James F. Smith
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
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159
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. AMERICAN JOURNAL OF BOTANY 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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160
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McDonnell AJ, Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, Pokorny L, Tate J, Wicke S, Wickett NJ. Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311443. [PMID: 34336400 PMCID: PMC8312743 DOI: 10.1002/aps3.11443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 05/30/2023]
Affiliation(s)
- Angela J. McDonnell
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
| | | | - Steven Dodsworth
- School of Life SciencesUniversity of BedfordshireUniversity SquareLutonLU1 3JUUnited Kingdom
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Sean W. Graham
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIA‐CSIC28223Pozuelo de Alarcón (Madrid)Spain
| | - Jennifer Tate
- School of Fundamental SciencesMassey UniversityPalmerston North4442New Zealand
| | - Susann Wicke
- Plant Evolutionary BiologyInstitute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
- Plant Systematics and BiodiversityInstitute for BiologyHumboldt‐Universität zu BerlinBerlinGermany
| | - Norman J. Wickett
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
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Slimp M, Williams LD, Hale H, Johnson MG. On the potential of Angiosperms353 for population genomic studies. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311419. [PMID: 34336401 PMCID: PMC8312745 DOI: 10.1002/aps3.11419] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 05/11/2023]
Abstract
PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)-typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.
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Affiliation(s)
- Madeline Slimp
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Lindsay D. Williams
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Haley Hale
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
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162
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Zuntini AR, Frankel LP, Pokorny L, Forest F, Baker WJ. A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. AMERICAN JOURNAL OF BOTANY 2021; 108:1066-1086. [PMID: 34278560 DOI: 10.1002/ajb2.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. CONCLUSIONS We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.
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Affiliation(s)
| | - Lorna P Frankel
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Faculty of Life and Environmental Sciences, University of Southampton Highfield Campus, Southampton, SO17 1BJ, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
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Siniscalchi CM, Hidalgo O, Palazzesi L, Pellicer J, Pokorny L, Maurin O, Leitch IJ, Forest F, Baker WJ, Mandel JR. Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311422. [PMID: 34336403 PMCID: PMC8312747 DOI: 10.1002/aps3.11422] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses. METHODS We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. RESULTS Our results show that the Compositae1061 kit provides an average of 721 loci, with 9-46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. DISCUSSION Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
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Affiliation(s)
- Carolina M. Siniscalchi
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
| | - Oriane Hidalgo
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Luis Palazzesi
- División PaleobotánicaMuseo Argentino de Ciencias NaturalesCONICETBuenos AiresC1405DJRArgentina
| | - Jaume Pellicer
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Present address:
Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIAPozuelo de Alarcón (Madrid)28223Spain
| | - Olivier Maurin
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Felix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | | | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Maurin O, Anest A, Bellot S, Biffin E, Brewer G, Charles-Dominique T, Cowan RS, Dodsworth S, Epitawalage N, Gallego B, Giaretta A, Goldenberg R, Gonçalves DJP, Graham S, Hoch P, Mazine F, Low YW, McGinnie C, Michelangeli FA, Morris S, Penneys DS, Pérez Escobar OA, Pillon Y, Pokorny L, Shimizu G, Staggemeier VG, Thornhill AH, Tomlinson KW, Turner IM, Vasconcelos T, Wilson PG, Zuntini AR, Baker WJ, Forest F, Lucas E. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. AMERICAN JOURNAL OF BOTANY 2021; 108:1087-1111. [PMID: 34297852 DOI: 10.1002/ajb2.1699] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
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Affiliation(s)
- Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Artemis Anest
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Edward Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Tristan Charles-Dominique
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil
| | - Renato Goldenberg
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | | | - Peter Hoch
- Missouri Botanical Garden, St. Louis, MO, 63110, USA
| | - Fiorella Mazine
- Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil
| | - Yee Wen Low
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | | | - Fabián A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | | | - Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Gustavo Shimizu
- Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil
| | - Andrew H Thornhill
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Ian M Turner
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Peter G Wilson
- Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Eve Lucas
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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165
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Doyle JJ. Defining coalescent genes: Theory meets practice in organelle phylogenomics. Syst Biol 2021; 71:476-489. [PMID: 34191012 DOI: 10.1093/sysbio/syab053] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.
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Affiliation(s)
- Jeff J Doyle
- Plant Biology Section, Plant Breeding & Genetics Section, and L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
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166
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Phylogenomic reconstruction addressing the Peltigeralean backbone (Lecanoromycetes, Ascomycota). FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00476-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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167
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Zhou W, Soghigian J, Xiang QYJ. A New Pipeline for Removing Paralogs in Target Enrichment Data. Syst Biol 2021; 71:410-425. [PMID: 34146111 PMCID: PMC8974407 DOI: 10.1093/sysbio/syab044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 06/04/2021] [Accepted: 06/12/2021] [Indexed: 12/30/2022] Open
Abstract
Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing
method that has been increasingly used for phylogenomic studies. Unfortunately, current
widely used pipelines for analysis of target enrichment data do not have a vigorous
procedure to remove paralogs in target enrichment data. In this study, we develop a
pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs
from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and
the entire pipeline applies criteria in both sequence similarity and heterozygous sites at
each locus in the identification of paralogs. Users may adjust the thresholds of sequence
identity and heterozygous sites to identify and remove paralogs according to the level of
phylogenetic divergence of their group of interest. The new pipeline also removes highly
polymorphic sites attributed to errors in sequence assembly and gappy regions in the
alignment. We demonstrated the value of the new pipeline using empirical data generated
from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea
(Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales).
Comparisons of data sets showed that the PPD identified many more putative paralogs than
the popular method HybPiper. Comparisons of tree topologies and divergence times showed
evident differences between data from HybPiper and data from our new PPD pipeline. We
further evaluated the accuracy and error rates of PPD by BLAST mapping of putative
paralogous and orthologous sequences to a reference genome sequence of Castanea
mollissima. Compared to HybPiper alone, PPD identified substantially more
paralogous gene sequences that mapped to multiple regions of the reference genome (31
genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper,
paralogous genes identified by both pipelines can be removed resulting in the construction
of more robust orthologous gene data sets for phylogenomic and divergence time analyses.
Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353
probe set for elucidating species relationships within a genus, and argues for the
importance of additional steps to filter paralogous genes and poorly aligned regions
(e.g., as occur through assembly errors), such as our new PPD pipeline described in this
study. [Angiosperms353; Castanea; divergence time;
Hamamelis; Hyb-Seq, paralogs, phylogenomics.]
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Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27965, USA
| | - John Soghigian
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27965, USA
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27965, USA
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168
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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169
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Introgression is widespread in the radiation of carnivorous Nepenthes pitcher plants. Mol Phylogenet Evol 2021; 163:107214. [PMID: 34052438 DOI: 10.1016/j.ympev.2021.107214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/14/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022]
Abstract
Introgression and hybridization are important processes in plant evolution, but they are difficult to study from a phylogenetic perspective, because they conflict with the bifurcating evolutionary history typically depicted in phylogenetic models. The role of hybridization in plant evolution is best documented in the form of allo-polyploidizations. In contrast, homoploid hybridization and introgression are less explored, although they may be crucial in adaptive radiations. Here we employ genome-wide data (ddRAD-seq, transcriptomes) to investigate the evolutionary history of Nepenthes, a radiation of c. 160 species of iconic carnivorous plants mainly from tropical Asia. Our data indicates that the main radiation is only c. 5 million years old, and confirms previous bifurcating phylogenies. However, due to a greatly expanded number of loci, we were able test for the first time the long-standing hypotheses of introgression and historical hybridization. The genus presents one very clear case of organellar capture between two distantly related but sympatric groups. Furthermore, all Nepenthes species show introgression signals in their nuclear genomes, as uncovered by a general survey of ABBA-BABA-like statistics. The ancestor of the rapid main radiation shows ancestry from two deeply diverged lineages, as indicated by phylogenetic network analyses. All major clades of the main radiation show further introgression both within and between each other, as suggested by admixture graphs. Our study supports the hypothesis that rapid adaptive radiations are hotspots of introgression in the tree of life, and highlights the need to consider non-treelike processes in evolutionary studies of Nepenthes in particular.
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170
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Grace OM, Pérez-Escobar OA, Lucas EJ, Vorontsova MS, Lewis GP, Walker BE, Lohmann LG, Knapp S, Wilkie P, Sarkinen T, Darbyshire I, Lughadha EN, Monro A, Woudstra Y, Demissew S, Muasya AM, Díaz S, Baker WJ, Antonelli A. Botanical Monography in the Anthropocene. TRENDS IN PLANT SCIENCE 2021; 26:433-441. [PMID: 33579621 DOI: 10.1016/j.tplants.2020.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs - comprehensive systematic treatments of a family or genus - have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.
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Affiliation(s)
| | | | | | | | | | | | - Lúcia G Lohmann
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, 05508-900, São Paulo, Brazil
| | - Sandra Knapp
- Department of Botany, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Peter Wilkie
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LP, UK
| | - Tiina Sarkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LP, UK
| | | | | | | | - Yannick Woudstra
- Royal Botanic Gardens, Kew, TW9 3AE, UK; Natural History Museum of Denmark, University of Copenhagen, Gothersgade 130, Copenhagen 1153, Denmark
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, National Herbarium, College of Natural Sciences, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7700, South Africa
| | - Sandra Díaz
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC) and FCEFyN, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000 Córdoba, Argentina
| | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 41319 Gothenburg, Sweden; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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171
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Cvetković T, Areces-Berazain F, Hinsinger DD, Thomas DC, Wieringa JJ, Ganesan SK, Strijk JS. Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l. G3-GENES GENOMES GENETICS 2021; 11:6248091. [PMID: 33892500 PMCID: PMC8496235 DOI: 10.1093/g3journal/jkab136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/11/2021] [Indexed: 11/22/2022]
Abstract
Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Despite numerous phylogenetic analyses employing multiple markers, relationships between several of its nine subfamilies, particularly within the largest lineage /Malvadendrina, remain unclear. In this study, we attempted to resolve the relationships within the major clades of Malvaceae s.l. using plastid genomes of 48 accessions representing all subfamilies. Maximum likelihood and Bayesian analyses recovered a fully resolved and well-supported topology confirming the split of the family into /Byttneriina (/Grewioideae +/Byttnerioideae) and /Malvadendrina. Within /Malvadendrina, /Helicteroideae occupied the earliest branching position, followed by /Sterculioideae, /Brownlowioideae, /Tiliodeae, and /Dombeyoideae formed a clade sister to /Malvatheca (/Malvoideae +/Bombacoideae), a grouping morphologically supported by the lack of androgynophore. Results from dating analyses suggest that all subfamilies originated during hot or warm phases in the Late Cretaceous to Paleocene. This study presents a well-supported phylogenetic framework for Malvaceae s.l. that will aid downstream revisions and evolutionary studies of this economically important plant family.
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Affiliation(s)
- Tijana Cvetković
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.,Biodiversity Genomics Team, Guangxi University, Daxuedonglu 100, Nanning, Guangxi, 530005, China
| | - Fabiola Areces-Berazain
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Herbarium UPRRP, Department of Biology, University of Puerto Rico, San Juan PR 00925-2537, United States of America
| | - Damien D Hinsinger
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000 Evry, France
| | - Daniel C Thomas
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
| | - Santhana K Ganesan
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Joeri S Strijk
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam
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172
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Amarasinghe P, Joshi S, Page N, Wijedasa LS, Merello M, Kathriarachchi H, Stone RD, Judd W, Kodandaramaiah U, Cellinese N. Evolution and biogeography of Memecylon. AMERICAN JOURNAL OF BOTANY 2021; 108:628-646. [PMID: 33745129 DOI: 10.1002/ajb2.1624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The woody plant group Memecylon (Melastomataceae) is a large clade occupying diverse forest habitats in the Old World tropics and exhibiting high regional endemism. Its phylogenetic relationships have been previously studied using ribosomal DNA with extensive sampling from Africa and Madagascar. However, divergence times, biogeography, and character evolution of Memecylon remain uninvestigated. We present a phylogenomic analysis of Memecylon to provide a broad evolutionary perspective of this clade. METHODS One hundred supercontigs of 67 Memecylon taxa were harvested from target enrichment. The data were subjected to coalescent and concatenated phylogenetic analyses. A timeline was provided for Memecylon evolution using fossils and secondary calibration. The calibrated Memecylon phylogeny was used to elucidate its biogeography and ancestral character states. RESULTS Relationships recovered by the phylogenomic analyses are strongly supported in both maximum likelihood and coalescent-based species trees. Memecylon is inferred to have originated in Africa in the Eocene and subsequently dispersed predominantly eastward via long-distance dispersal (LDD), although a reverse dispersal from South Asia westward to the Seychelles was postulated. Morphological data exhibited high levels of homoplasy, but also showed that several vegetative and reproductive characters were phylogenetically informative. CONCLUSIONS The current distribution of Memecylon appears to be the result of multiple ancestral LDD events. Our results demonstrate the importance of the combined effect of geographic and paleoclimatic factors in shaping the distribution of this group in the Old World tropics. Memecylon includes a number of evolutionarily derived morphological features that contribute to diversity within the clade.
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Affiliation(s)
- Prabha Amarasinghe
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Sneha Joshi
- Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | | | - Lahiru S Wijedasa
- Integrated Tropical Peat Research Program, NUS Environmental Research Institute (NERI), National University of Singapore, Singapore, 117411
- ConservationLinks Pvt. Ltd., 100 Commonwealth Crescent, no. 08-80, Singapore, 140100
| | | | | | | | - Walter Judd
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | | | - Nico Cellinese
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
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173
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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174
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New genetic markers for Sapotaceae phylogenomics: More than 600 nuclear genes applicable from family to population levels. Mol Phylogenet Evol 2021; 160:107123. [PMID: 33610647 DOI: 10.1016/j.ympev.2021.107123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 12/30/2022]
Abstract
Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.
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175
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Peakall R, Wong DCJ, Phillips RD, Ruibal M, Eyles R, Rodriguez-Delgado C, Linde CC. A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids. Mol Ecol Resour 2021; 21:1118-1140. [PMID: 33453072 DOI: 10.1111/1755-0998.13327] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 11/30/2022]
Abstract
With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative de novo and reference-guided assembly, before target sequence extraction, annotation and alignment, and application of a homology-aware k-mer block phylogenomic approach, prior to maximum likelihood and coalescence-based phylogenetic inference. Our evaluation considered 87 taxa in two test data sets: 67 samples spanning the tribe, and 72 samples involving 24 closely related Caladenia species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1-5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous k-mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customized multitiered sequence capture strategy, in combination with promising yet underutilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.
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Affiliation(s)
- Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ryan D Phillips
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Vic., Australia
| | - Monica Ruibal
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rodney Eyles
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Claudia Rodriguez-Delgado
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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176
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Folk RA, Kates HR, LaFrance R, Soltis DE, Soltis PS, Guralnick RP. High-throughput methods for efficiently building massive phylogenies from natural history collections. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11410. [PMID: 33680581 PMCID: PMC7910806 DOI: 10.1002/aps3.11410] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/20/2020] [Indexed: 05/10/2023]
Abstract
PREMISE Large phylogenetic data sets have often been restricted to small numbers of loci from GenBank, and a vetted sampling-to-sequencing phylogenomic protocol scaling to thousands of species is not yet available. Here, we report a high-throughput collections-based approach that empowers researchers to explore more branches of the tree of life with numerous loci. METHODS We developed an integrated Specimen-to-Laboratory Information Management System (SLIMS), connecting sampling and wet lab efforts with progress tracking at each stage. Using unique identifiers encoded in QR codes and a taxonomic database, a research team can sample herbarium specimens, efficiently record the sampling event, and capture specimen images. After sampling in herbaria, images are uploaded to a citizen science platform for metadata generation, and tissue samples are moved through a simple, high-throughput, plate-based herbarium DNA extraction and sequencing protocol. RESULTS We applied this sampling-to-sequencing workflow to ~15,000 species, producing for the first time a data set with ~50% taxonomic representation of the "nitrogen-fixing clade" of angiosperms. DISCUSSION The approach we present is appropriate at any taxonomic scale and is extensible to other collection types. The widespread use of large-scale sampling strategies repositions herbaria as accessible but largely untapped resources for broad taxonomic sampling with thousands of species.
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Affiliation(s)
- Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippiUSA
| | - Heather R. Kates
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Raphael LaFrance
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
- Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
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177
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Liu L, Zhang Y, Li P. Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data. PLANT DIVERSITY 2021; 43:43-53. [PMID: 33778224 PMCID: PMC7987720 DOI: 10.1016/j.pld.2020.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 06/02/2023]
Abstract
Celtis is a Cannabaceae genus of 60-70 species of trees, or rarely shrubs, commonly known as hackberries. This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals. Although previous studies have identified its phylogenetic position, interspecific relationships within Celtis remain unclear. In this study, we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources. The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp, with a typical angiosperm quadripartite structure, and encoded a total of 132 genes with 20 duplicated in the IRs. Comparative analyses showed that plastome content and structure were relatively conserved. Whole plastomes showed no signs of gene loss, translocations, inversions, or genome rearrangement. Six plastid hotspot regions (trnH-psbA, psbA-trnK, trnG-trnR, psbC-trnS, cemA-petA and rps8-rpl14), 4097 polymorphic nuclear SSRs, as well as 62 low or single-copy gene fragments were identified within Celtis. Moreover, the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C. biondii as sister to the ((((C. koraiensis, C. sinensis), C. tetrandra), C. julianae), C. cerasifera) clade. These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny, population genetics, and conservation biology.
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Affiliation(s)
- Luxian Liu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475000, China
| | - Yonghua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
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178
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Ogutcen E, Christe C, Nishii K, Salamin N, Möller M, Perret M. Phylogenomics of Gesneriaceae using targeted capture of nuclear genes. Mol Phylogenet Evol 2021; 157:107068. [PMID: 33422648 DOI: 10.1016/j.ympev.2021.107068] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023]
Abstract
Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperms-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group.
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Affiliation(s)
- Ezgi Ogutcen
- Conservatoire et Jardin botaniques de la Ville de Genève and Department of Botany and Plant Biology, University of Geneva, 1292 Chambésy, Switzerland
| | - Camille Christe
- Conservatoire et Jardin botaniques de la Ville de Genève and Department of Botany and Plant Biology, University of Geneva, 1292 Chambésy, Switzerland
| | - Kanae Nishii
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK; Kanagawa University, 2946, Tsuchiya, Hiratsuka-shi, Kanagawa 259-1293, Japan
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Mathieu Perret
- Conservatoire et Jardin botaniques de la Ville de Genève and Department of Botany and Plant Biology, University of Geneva, 1292 Chambésy, Switzerland.
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179
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Herzog SA, Latvis M. Examining the utility of DNA barcodes for the identification of tallgrass prairie flora. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11405. [PMID: 33552747 PMCID: PMC7845766 DOI: 10.1002/aps3.11405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
PREMISE The tallgrass prairies of North America are one of the most threatened ecosystems in the world, making efficient species identification essential for understanding and managing diversity. Here, we assess DNA barcoding with high-throughput sequencing as a method for rapid plant species identification. METHODS Using herbarium collections representing the tallgrass prairie flora of Oak Lake Field Station, South Dakota, USA, we amplified and examined four common nuclear and plastid barcode regions (ITS, matK, psbA-trnH, and rbcL), individually and in combination, to test their success in identifying samples to family, genus, and species levels using BLAST searches of three databases of varying size. RESULTS Concatenated barcodes increased performance, although none were significantly different than single-region barcodes. The plastid region psbA-trnH performed significantly more poorly than the others, while barcodes containing ITS performed best. Database size significantly affected identification success at all three taxonomic levels. Confident species-level identification ranged from 8-44% for the global database, 13-56% for the regional database, and 21-80% for the sampled species database, depending on the barcode used. DISCUSSION Barcoding was generally successful in identifying tallgrass prairie genera and families, but was of limited use in species-level identifications. Database size was an important factor in successful plant identification. We discuss future directions and considerations for improving the performance of DNA barcoding in tallgrass prairies.
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Affiliation(s)
- Sarah A. Herzog
- Department of Natural Resource ManagementSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
- C. A. Taylor HerbariumSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
| | - Maribeth Latvis
- Department of Natural Resource ManagementSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
- C. A. Taylor HerbariumSouth Dakota State University1390 College AvenueBrookingsSouth Dakota57007USA
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180
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Breinholt JW, Carey SB, Tiley GP, Davis EC, Endara L, McDaniel SF, Neves LG, Sessa EB, von Konrat M, Chantanaorrapint S, Fawcett S, Ickert‐Bond SM, Labiak PH, Larraín J, Lehnert M, Lewis LR, Nagalingum NS, Patel N, Rensing SA, Testo W, Vasco A, Villarreal JC, Williams EW, Burleigh JG. A target enrichment probe set for resolving the flagellate land plant tree of life. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11406. [PMID: 33552748 PMCID: PMC7845764 DOI: 10.1002/aps3.11406] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/05/2020] [Indexed: 05/08/2023]
Abstract
PREMISE New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. RESULTS Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.
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Affiliation(s)
- Jesse W. Breinholt
- RAPiD GenomicsGainesvilleFloridaUSA
- Intermountain HealthcareIntermountain Precision GenomicsSaint GeorgeUtahUSA
| | - Sarah B. Carey
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
| | - George P. Tiley
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
| | | | - Lorena Endara
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
| | | | | | - Emily B. Sessa
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
| | - Matt von Konrat
- Department of Research and EducationThe Field MuseumChicagoIllinoisUSA
| | | | - Susan Fawcett
- Pringle HerbariumDepartment of Plant BiologyUniversity of VermontBurlingtonVermontUSA
| | - Stefanie M. Ickert‐Bond
- Department of Wildlife and Biology and UA Museum of the NorthUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Paulo H. Labiak
- Departamento de BotânicaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Juan Larraín
- Instituto de BiologíaPontificia Universidad Católica de ValparaísoValparaísoChile
| | - Marcus Lehnert
- Department of Geobotany and Botanical GardenHerbarium, Martin Luther University Halle‐WittenbergHalleGermany
| | - Lily R. Lewis
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
| | | | - Nikisha Patel
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | | | - Weston Testo
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
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181
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Breinholt JW, Carey SB, Tiley GP, Davis EC, Endara L, McDaniel SF, Neves LG, Sessa EB, von Konrat M, Chantanaorrapint S, Fawcett S, Ickert-Bond SM, Labiak PH, Larraín J, Lehnert M, Lewis LR, Nagalingum NS, Patel N, Rensing SA, Testo W, Vasco A, Villarreal JC, Williams EW, Burleigh JG. A target enrichment probe set for resolving the flagellate land plant tree of life. APPLICATIONS IN PLANT SCIENCES 2021. [PMID: 33552748 DOI: 10.1101/2020.05.29.124081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. RESULTS Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.
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Affiliation(s)
- Jesse W Breinholt
- RAPiD Genomics Gainesville Florida USA
- Intermountain Healthcare Intermountain Precision Genomics Saint George Utah USA
| | - Sarah B Carey
- Department of Biology University of Florida Gainesville Florida USA
| | - George P Tiley
- Department of Biology University of Florida Gainesville Florida USA
- Department of Biology Duke University Durham North Carolina USA
| | | | - Lorena Endara
- Department of Biology University of Florida Gainesville Florida USA
| | | | | | - Emily B Sessa
- Department of Biology University of Florida Gainesville Florida USA
| | - Matt von Konrat
- Department of Research and Education The Field Museum Chicago Illinois USA
| | | | - Susan Fawcett
- Pringle Herbarium Department of Plant Biology University of Vermont Burlington Vermont USA
| | - Stefanie M Ickert-Bond
- Department of Wildlife and Biology and UA Museum of the North University of Alaska Fairbanks Fairbanks Alaska USA
| | - Paulo H Labiak
- Departamento de Botânica Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Juan Larraín
- Instituto de Biología Pontificia Universidad Católica de Valparaíso Valparaíso Chile
| | - Marcus Lehnert
- Department of Geobotany and Botanical Garden Herbarium, Martin Luther University Halle-Wittenberg Halle Germany
| | - Lily R Lewis
- Department of Biology University of Florida Gainesville Florida USA
| | | | - Nikisha Patel
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
| | | | - Weston Testo
- Department of Biology University of Florida Gainesville Florida USA
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182
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Schneider JV, Paule J, Jungcurt T, Cardoso D, Amorim AM, Berberich T, Zizka G. Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:638650. [PMID: 33613613 PMCID: PMC7890083 DOI: 10.3389/fpls.2021.638650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family's backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family's species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
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Affiliation(s)
- Julio V. Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Entomology III, Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Tanja Jungcurt
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - André Márcio Amorim
- Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
- Herbário André Maurício Vieira de Carvalho, CEPEC, CEPLAC, Itabuna, Brazil
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Lab-Center, Frankfurt am Main, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- *Correspondence: Georg Zizka, ;
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183
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Kandziora M, Sklenář P, Kolář F, Schmickl R. How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example. FRONTIERS IN PLANT SCIENCE 2021; 12:765719. [PMID: 35069621 PMCID: PMC8777076 DOI: 10.3389/fpls.2021.765719] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/22/2021] [Indexed: 05/17/2023]
Abstract
A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.
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Affiliation(s)
- Martha Kandziora
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Martha Kandziora,
| | - Petr Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
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184
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Grewe F, Ametrano C, Widhelm TJ, Leavitt S, Distefano I, Polyiam W, Pizarro D, Wedin M, Crespo A, Divakar PK, Lumbsch HT. Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota). IMA Fungus 2020; 11:27. [PMID: 33317627 PMCID: PMC7734834 DOI: 10.1186/s43008-020-00051-x] [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: 08/24/2020] [Accepted: 11/29/2020] [Indexed: 11/10/2022] Open
Abstract
Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.
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Affiliation(s)
- Felix Grewe
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA.
| | - Claudio Ametrano
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Todd J Widhelm
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Steven Leavitt
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, UT, USA
| | - Isabel Distefano
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
| | - Wetchasart Polyiam
- Lichen Research Unit, Biology Department, Faculty of Science, Ramkhamhaeng University, Ramkhamhaeng 24 Road, Bangkok, 10240, Thailand
| | - David Pizarro
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Ana Crespo
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pradeep K Divakar
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - H Thorsten Lumbsch
- Science & Education, The Grainger Bioinformatics Center, Negaunee Integrative Research Center, Gantz Family Collections Center, and Pritzker Laboratory for Molecular Systematics, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, USA
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185
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Koenen EJ, Kidner C, de Souza ÉR, Simon MF, Iganci JR, Nicholls JA, Brown GK, de Queiroz LP, Luckow M, Lewis GP, Pennington RT, Hughes CE. Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. AMERICAN JOURNAL OF BOTANY 2020; 107:1710-1735. [PMID: 33253423 PMCID: PMC7839790 DOI: 10.1002/ajb2.1568] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Catherine Kidner
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
| | - Élvia R. de Souza
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e BiotecnologiaParque Estação Biológica (PqEB)Avenida W5 norte70770‐917BrasíliaBrazil
| | - João R. Iganci
- Instituto de BiologiaUniversidade Federal de PelotasCampus Universitário Capão do LeãoTravessa André Dreyfus s/nCapão do Leão96010‐900Rio Grande do SulBrazil
| | - James A. Nicholls
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Australian National Insect CollectionCSIROClunies Ross StActonACT 2601Australia
| | - Gillian K. Brown
- Queensland HerbariumBrisbane Botanic GardensMount Coot‐tha, Mt Coot‐tha RoadToowong4066QueenslandAustralia
| | - Luciano P. de Queiroz
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Melissa Luckow
- L.H. Bailey HortoriumDepartment of Plant BiologyCornell University412 Mann Library BuildingIthacaNew York14853USA
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology DepartmentRoyal Botanic GardensKew, RichmondSurreyTW9 3AEUK
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
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186
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Straub SCK, Boutte J, Fishbein M, Livshultz T. Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11400. [PMID: 33304663 PMCID: PMC7705337 DOI: 10.1002/aps3.11400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/12/2020] [Indexed: 05/07/2023]
Abstract
PREMISE Apocynaceae is the 10th largest flowering plant family and a focus for study of plant-insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non-model taxa, such as Apocynaceae. METHODS Transcriptomes were used to design probes for targeted sequencing of putatively single-copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny. RESULTS From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent-based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genus Apocynum. Intraspecific comparison of Elytropus chilensis individuals revealed numerous single-nucleotide polymorphisms with potential for use in population-level studies. DISCUSSION Community use of this Hyb-Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
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Affiliation(s)
- Shannon C. K. Straub
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Julien Boutte
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Mark Fishbein
- Department of Plant Biology, Ecology, and EvolutionOklahoma State University301 Physical SciencesStillwaterOklahoma74078USA
| | - Tatyana Livshultz
- Department of Biodiversity, Earth, and Environmental Sciences and the Academy of Natural SciencesDrexel University1900 Benjamin Franklin ParkwayPhiladelphiaPennsylvania19103USA
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187
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Gardner EM, Johnson MG, Pereira JT, Puad ASA, Arifiani D, Sahromi , Wickett NJ, Zerega NJC. Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Syst Biol 2020; 70:syaa073. [PMID: 32970819 PMCID: PMC8048387 DOI: 10.1093/sysbio/syaa073] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
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Affiliation(s)
- Elliot M Gardner
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., Evanston, IL 60208, USA
- The Morton Arboretum, 4100 IL-53, Lisle, IL 60532, USA
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Florida International University, Institute of Environment, 11200 SW 8th Street, OE 148 Miami, Florida 33199, USA
| | - Matthew G Johnson
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Texas Tech University, Department of Biological Sciences, 2901 Main Street, Lubbock, TX 79409-3131, USA
| | - Joan T Pereira
- Forest Research Centre, Sabah Forestry Department, P.O. Box 1407, 90715 Sandakan, Sabah, Malaysia
| | - Aida Shafreena Ahmad Puad
- Faculty of Resource Science & Technology, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak 94300, Malaysia
| | - Deby Arifiani
- Herbarium Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Jawa Barat, Indonesia
| | - Sahromi
- Center for Plant Conservation Botanic Gardens, Indonesian Institute Of Sciences, Bogor, Jawa Barat, Indonesia Elliot M. Gardner and Matthew G. Johnson are co-first authors
| | - Norman J Wickett
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., Evanston, IL 60208, USA
| | - Nyree J C Zerega
- Chicago Botanic Garden, Negaunee Institute for Plant Conservation Science and Action, 1000 Lake Cook Road, Glencoe, IL 60022, USA
- Northwestern University, Plant Biology and Conservation Program, 2205 Tech Dr., Evanston, IL 60208, USA
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188
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Draper FC, Baker TR, Baraloto C, Chave J, Costa F, Martin RE, Pennington RT, Vicentini A, Asner GP. Quantifying Tropical Plant Diversity Requires an Integrated Technological Approach. Trends Ecol Evol 2020; 35:1100-1109. [PMID: 32912632 DOI: 10.1016/j.tree.2020.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Tropical biomes are the most diverse plant communities on Earth, and quantifying this diversity at large spatial scales is vital for many purposes. As macroecological approaches proliferate, the taxonomic uncertainties in species occurrence data are easily neglected and can lead to spurious findings in downstream analyses. Here, we argue that technological approaches offer potential solutions, but there is no single silver bullet to resolve uncertainty in plant biodiversity quantification. Instead, we propose the use of artificial intelligence (AI) approaches to build a data-driven framework that integrates several data sources - including spectroscopy, DNA sequences, image recognition, and morphological data. Such a framework would provide a foundation for improving species identification in macroecological analyses while simultaneously improving the taxonomic process of species delimitation.
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Affiliation(s)
- Frederick C Draper
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA; School of Geography, University of Leeds, Leeds, UK.
| | | | - Christopher Baraloto
- Institute of Environment, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Jerome Chave
- Laboratoire Evolution et Diversité Biologique (EDB) CNRS/UPS, Toulouse, France
| | - Flavia Costa
- Instituto Nacional de Pesquisas da Amazônia - INPA, Manaus, Brazil
| | - Roberta E Martin
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA
| | - R Toby Pennington
- Department of Geography, University of Exeter, Exeter, UK; Royal Botanic Garden, Edinburgh, UK
| | | | - Gregory P Asner
- Center for Global Discovery and Conservation Science, Arizona State University, Tempe, AZ, USA
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189
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Ma ZY, Nie ZL, Ren C, Liu XQ, Zimmer EA, Wen J. Phylogenomic relationships and character evolution of the grape family (Vitaceae). Mol Phylogenet Evol 2020; 154:106948. [PMID: 32866616 DOI: 10.1016/j.ympev.2020.106948] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/02/2020] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
Abstract
The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.
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Affiliation(s)
- Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA.
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190
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Rønsted N, Grace OM, Carine MA. Editorial: Integrative and Translational Uses of Herbarium Collections Across Time, Space, and Species. FRONTIERS IN PLANT SCIENCE 2020; 11:1319. [PMID: 32973855 PMCID: PMC7472523 DOI: 10.3389/fpls.2020.01319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/11/2020] [Indexed: 06/01/2023]
Affiliation(s)
- Nina Rønsted
- Science and Conservation, National Tropical Botanical Garden, Kalaheo, HI, United States
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Olwen M. Grace
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Mark A. Carine
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
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191
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Valderrama E, Sass C, Pinilla-Vargas M, Skinner D, Maas PJM, Maas-van de Kamer H, Landis JB, Guan CJ, Specht CD. Unraveling the Spiraling Radiation: A Phylogenomic Analysis of Neotropical Costus L. FRONTIERS IN PLANT SCIENCE 2020; 11:1195. [PMID: 32922414 PMCID: PMC7456938 DOI: 10.3389/fpls.2020.01195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/23/2020] [Indexed: 06/01/2023]
Abstract
The family of pantropical spiral gingers (Costaceae Nakai; c. 125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (c. 72 Neotropical species, c. 30 African, c. 23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L. (c. 57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical Costus species using a targeted enrichment approach. Baits were designed to capture conserved elements' variable at the species level using available genomic sequences of Costus species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.
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Affiliation(s)
- Eugenio Valderrama
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Chodon Sass
- The University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Maria Pinilla-Vargas
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | | | - Paul J. M. Maas
- Section Botany, Naturalis Biodiversity Center, Leiden, Netherlands
| | | | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Clarice J. Guan
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
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192
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Barrett CF. Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. PeerJ 2020; 8:e9315. [PMID: 32587799 PMCID: PMC7304433 DOI: 10.7717/peerj.9315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
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193
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Stull GW, Soltis PS, Soltis DE, Gitzendanner MA, Smith SA. Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. AMERICAN JOURNAL OF BOTANY 2020; 107:790-805. [PMID: 32406108 DOI: 10.1002/ajb2.1468] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
PREMISE Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. METHODS We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. RESULTS We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications. CONCLUSIONS Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.
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Affiliation(s)
- Gregory W Stull
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
- Department of Botany, Smithsonian Institution, Washington, D.C., 20013, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
| | | | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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194
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Jantzen JR, Amarasinghe P, Folk RA, Reginato M, Michelangeli FA, Soltis DE, Cellinese N, Soltis PS. A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11345. [PMID: 32477841 PMCID: PMC7249273 DOI: 10.1002/aps3.11345] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/20/2019] [Indexed: 05/21/2023]
Abstract
PREMISE Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae). METHODS We present a two-tiered pipeline. First, we identified putatively SCN loci using MarkerMiner and transcriptomes from distantly related species in Melastomataceae. Published loci and genes of functional significance were then added (384 total loci). Second, using HybPiper, we retrieved 689 homologous template sequences for these loci using genome-skimming data from within the focal clades. RESULTS We sequenced 193 loci common to Memecylon and Tibouchina. Probes designed from 56 template sequences successfully targeted sequences in both clades. Probes designed from genome-skimming data within a focal clade were more successful than probes designed from other sources. DISCUSSION Our pipeline successfully identified and targeted SCN loci in Memecylon and Tibouchina, enabling phylogenomic studies in both clades and potentially across Melastomataceae. This pipeline could be easily applied to other clades with few genomic resources.
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Affiliation(s)
- Johanna R. Jantzen
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Prabha Amarasinghe
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityStarkvilleMississippi39762USA
| | - Marcelo Reginato
- Institute of Systematic BotanyThe New York Botanical GardenBronxNew York10458USA
- Universidade Federal do Rio Grande do SulPorto AlegreRio Grande do Sul90040‐060Brazil
| | | | - Douglas E. Soltis
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Nico Cellinese
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
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195
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Kistler L, Bieker VC, Martin MD, Pedersen MW, Ramos Madrigal J, Wales N. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:605-629. [PMID: 32119793 DOI: 10.1146/annurev-arplant-081519-035837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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196
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Hale H, Gardner EM, Viruel J, Pokorny L, Johnson MG. Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11337. [PMID: 32351798 PMCID: PMC7186906 DOI: 10.1002/aps3.11337] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 05/19/2023]
Abstract
The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low-cost sequencing in non-model plant systems.
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Affiliation(s)
- Haley Hale
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Elliot M. Gardner
- The Morton ArboretumLisleIllinois60532USA
- Department of BiologyCase Western Reserve UniversityClevelandOhio44106USA
- Singapore Botanic GardensNational Parks Board1 Cluny Road259569Singapore
| | - Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Lisa Pokorny
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
- Present address:
Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIA28223Pozuelo de Alarcón (Madrid)Spain
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
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197
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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198
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Abstract
An increasing number of automobiles have led to a serious shortage of parking spaces and a serious imbalance of parking supply and demand. The best way to solve these problems is to achieve the reasonable planning and classify management of car parks, guide the intelligent parking, and then promote its marketization and industrialization. Therefore, we aim to adopt clustering method to classify car parks. Owing to the time series characteristics of car park data, a time series clustering framework, including preprocessing, distance measurement, clustering and evaluation, is first developed for classifying car parks. Then, in view of the randomness of existing clustering models, a new time series clustering model based on dynamic time warping (DTW) is proposed, which contains distance radius calculation, obtaining density of the neighbor area, k centers initialization, and clustering. Finally, some UCR datasets and data of 27 car parks are employed to evaluate the performance of the models and results show that the proposed model performs obviously better results than those clustering models based on Euclidean distance (ED) and traditional clustering models based on DTW.
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199
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Murphy B, Forest F, Barraclough T, Rosindell J, Bellot S, Cowan R, Golos M, Jebb M, Cheek M. A phylogenomic analysis of Nepenthes (Nepenthaceae). Mol Phylogenet Evol 2020; 144:106668. [DOI: 10.1016/j.ympev.2019.106668] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
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200
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Moore G, Tessler M, Cunningham SW, Betancourt J, Harbert R. Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA. Ecol Evol 2020; 10:2530-2544. [PMID: 32184999 PMCID: PMC7069311 DOI: 10.1002/ece3.6082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/11/2020] [Accepted: 01/15/2020] [Indexed: 12/14/2022] Open
Abstract
Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.
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Affiliation(s)
- Grace Moore
- Smith CollegeNorthamptonMassachusetts
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | - Michael Tessler
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | - Seth W. Cunningham
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
| | | | - Robert Harbert
- Sackler Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew York
- Stonehill CollegeEastonMassachusetts
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