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Chen JT, Lidén M, Huang XH, Zhang L, Zhang XJ, Kuang TH, Landis JB, Wang D, Deng T, Sun H. An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2138-2156. [PMID: 37119474 DOI: 10.1111/jipb.13499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/25/2023] [Indexed: 06/19/2023]
Abstract
The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent "series". Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five "series", 25 sections and one "series" are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.
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Affiliation(s)
- Jun-Tong Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Magnus Lidén
- Evolutionary Biology Centre, Systematic Biology, Uppsala University, Uppsala, 75236, Sweden
| | - Xian-Han Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Liang Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xin-Jian Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian-Hui Kuang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Dong Wang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Lesica P, Lavin M. Will molecular phylogenetics help decrease nomenclatural instability? AMERICAN JOURNAL OF BOTANY 2023; 110:e16219. [PMID: 37561649 DOI: 10.1002/ajb2.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 08/12/2023]
Affiliation(s)
- Peter Lesica
- Division of Biological Sciences, University of Montana, Missoula, 59812, Montana, USA
| | - Matt Lavin
- Plant Sciences and Plant Pathology Department, Montana State University, Bozeman, 59717, Montana, USA
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Hong Z, Peng D, Tembrock LR, Liao X, Xu D, Liu X, Wu Z. Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales. Commun Biol 2023; 6:587. [PMID: 37264116 DOI: 10.1038/s42003-023-04980-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/25/2023] [Indexed: 06/03/2023] Open
Abstract
Sandalwood is one of the most expensive woods in the world and is well known for its long-lasting and distinctive aroma. In our study, chromosome-level genome assemblies for two sandalwood species (Santalum album and Santalum yasi) were constructed by integrating NGS short reads, RNA-seq, and Hi-C libraries with PacBio HiFi long reads. The S. album and S. yasi genomes were both assembled into 10 pseudochromosomes with a length of 229.59 Mb and 232.64 Mb, containing 21,673 and 22,816 predicted genes and a repeat content of 28.93% and 29.54% of the total genomes, respectively. Further analyses resolved a Santalum-specific whole-genome triplication event after divergence from ancestors of the Santalales lineage Malania, yet due to dramatic differences in transposon content, the Santalum genomes were only one-sixth the size of the Malania oleifera genome. Examination of RNA-seq data revealed a suite of genes that are differentially expressed in haustoria and might be involved in host hemiparasite interactions. The two genomes presented here not only provide an important comparative dataset for studying genome evolution in early diverging eudicots and hemiparasitic plants but will also hasten the application of conservation genomics for a lineage of trees recovering from decades of overexploitation.
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Affiliation(s)
- Zhou Hong
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, 510520, Guangzhou, China
| | - Dan Peng
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, 518120, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, 518120, Shenzhen, China
| | - Daping Xu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, 510520, Guangzhou, China
| | - Xiaojing Liu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, 510520, Guangzhou, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, 518120, Shenzhen, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518124, Shenzhen, China.
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Campos M, Kelley E, Gravendeel B, Médail F, Maarten Christenhusz JM, Fay MF, Catalán P, Leitch IJ, Forest F, Wilkin P, Viruel J. Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae). ANNALS OF BOTANY 2023; 131:635-654. [PMID: 36681900 PMCID: PMC10147332 DOI: 10.1093/aob/mcad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/23/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade) and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data. METHODS We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches. KEY RESULTS Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patterns were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis. CONCLUSIONS We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communis sensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communis sensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.
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Affiliation(s)
- Miguel Campos
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Plant Biology and Ecology, University of Seville, 41012, Spain
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain
| | - Emma Kelley
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden 2333 CR, The Netherlands
- Radboud Institute for Biological and Environmental Sciences, RIBES 6500 GL, Nijmegen, The Netherlands
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Écologie marine et continentale (IMBE), Aix Marseille University, Avignon University, CNRS, IRD, Campus Aix, Technopôle de l’Environnement Arbois-Méditerranée, F-13545 Aix-en-Provence cedex 4, France
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Pilar Catalán
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza 50018, Spain
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
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Kantor A, Kučera J, Šlenker M, Breidy J, Dönmez AA, Marhold K, Slovák M, Svitok M, Zozomová-Lihová J. Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials. ANNALS OF BOTANY 2023; 131:585-600. [PMID: 36656962 PMCID: PMC10147327 DOI: 10.1093/aob/mcad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/10/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Southwestern Asia is a significant centre of biodiversity and a cradle of diversification for many plant groups, especially xerophytic elements. In contrast, little is known about the evolution and diversification of its hygrophytic flora. To fill this gap, we focus on Cardamine (Brassicaceae) species that grow in wetlands over a wide altitudinal range. We aimed to elucidate their evolution, assess the extent of presumed historical gene flow between species, and draw inferences about intraspecific structure. METHODS We applied the phylogenomic Hyb-Seq approach, ecological niche analyses and multivariate morphometrics to a total of 85 Cardamine populations from the target region of Anatolia-Caucasus, usually treated as four to six species, and supplemented them with close relatives from Europe. KEY RESULTS Five diploids are recognized in the focus area, three of which occur in regions adjacent to the Black and/or Caspian Sea (C. penzesii, C. tenera, C. lazica), one species widely distributed from the Caucasus to Lebanon and Iran (C. uliginosa), and one western Anatolian entity (provisionally C. cf. uliginosa). Phylogenomic data suggest recent speciation during the Pleistocene, likely driven by both geographic separation (allopatry) and ecological divergence. With the exception of a single hybrid (allotetraploid) speciation event proven for C. wiedemanniana, an endemic of southern Turkey, no significant traces of past or present interspecific gene flow were observed. Genetic variation within the studied species is spatially structured, suggesting reduced gene flow due to geographic and ecological barriers, but also glacial survival in different refugia. CONCLUSIONS This study highlights the importance of the refugial regions of the Black and Caspian Seas for both harbouring and generating hygrophytic species diversity in Southwestern Asia. It also supports the significance of evolutionary links between Anatolia and the Balkan Peninsula. Reticulation and polyploidization played a minor evolutionary role here in contrast to the European relatives.
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Affiliation(s)
- Adam Kantor
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, 128 01Prague, Czechia
| | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
| | - Marek Šlenker
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
| | - Joêlle Breidy
- National Genebank, Lebanese Agricultural Research Institute, Zahle 1801, Lebanon
| | - Ali A Dönmez
- Botany Section, Department of Biology, Faculty of Science, Hacettepe University, 06800 Beytepe-Ankara, Turkey
| | - Karol Marhold
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, 128 01Prague, Czechia
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, 128 01Prague, Czechia
| | - Marek Svitok
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, 960 01Zvolen, Slovakia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Judita Zozomová-Lihová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, 845 23 Bratislava, Slovakia
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Demeulenaere E, Schils T, Burleigh JG, Ringelberg JJ, Koenen EJM, Ickert-Bond SM. Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider ingoid clade (Leguminosae, Caesalpinioideae). PHYTOKEYS 2022; 205:335-361. [PMID: 36762011 PMCID: PMC9849021 DOI: 10.3897/phytokeys.205.79144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/02/2022] [Indexed: 05/03/2023]
Abstract
The Indo-Pacific legume genus Serianthes was recently placed in the Archidendron clade (sensu Koenen et al. 2020), a subclade of the mimosoid clade in subfamily Caesalpinioideae, which also includes Acacia, Archidendron, Archidendropsis, Falcataria, Pararchidendron, Paraserianthes and Wallaceodendron. Serianthes comprises ca. 18 species, five subspecies and two varieties that are characterised by bipinnately compound leaves with alternate sessile leaflets, branched axillary corymbiform panicles and woody indehiscent pods. Generic relationships, as well as species relationships within genera in the Archidendron clade, remain uncertain. While the sister relationship between Serianthes and the genus Falcataria is strongly supported by molecular data, the distinction between Serianthes and the monotypic genus Wallaceodendron has been questioned, based on their similar flower and fruit morphologies. We combined three gene-enriched hybrid capture DNA sequence datasets (generated from the 964 mimobaits v1 probe set, the expanded 997 mimobaits v2 probe set and the GoFlag angiosperm 408 probe set) and used their overlapping markers (77 loci of the target exonic and flanking regions) to test the monophyly of Serianthes and to investigate generic relationships within the Archidendron clade using 55 ingoid plus two outgroup taxa. We show that Serianthes is monophyletic, confirm the Serianthes + Falcataria sister relationship to Wallaceodendron and recognise this combined clade as the Serianthes clade within the Archidendron clade. We also evaluated the use of overlapping loci across datasets in combination with concordance analyses to test generic relationships and further investigate previously unresolved relationships across the wider ingoid clade. Concordance analysis revealed limited gene tree conflicts near the tips of the Archidendron clade, but increased discordance at the base of the clade, which could be attributed to rapid lineage divergence (radiation) and/or incomplete lineage sorting.
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Affiliation(s)
- Else Demeulenaere
- Center for Island Sustainability, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - Tom Schils
- Center for Island Sustainability, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - J. Gordon Burleigh
- Marine Laboratory, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - Jens J. Ringelberg
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Stefanie M. Ickert-Bond
- Evolutionary Biology & Ecology, Free University of Brussels, Av. F.D. Roosevelt, 50, CP 160/12 - B-1050 Brussels, Belgium
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Woudstra Y, Viruel J, Fritzsche M, Bleazard T, Mate R, Howard C, Rønsted N, Grace OM. A customised target capture sequencing tool for molecular identification of Aloe vera and relatives. Sci Rep 2021; 11:24347. [PMID: 34934068 PMCID: PMC8692607 DOI: 10.1038/s41598-021-03300-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022] Open
Abstract
Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.
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Affiliation(s)
- Yannick Woudstra
- Royal Botanic Gardens, Kew, Surrey, TW9 3AE, UK.
- Natural History Museum Denmark, University of Copenhagen, Gothersgade 130, 1153, Copenhagen, Denmark.
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Surrey, TW9 3AE, UK
| | - Martin Fritzsche
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Thomas Bleazard
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Ryan Mate
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Caroline Howard
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Nina Rønsted
- Natural History Museum Denmark, University of Copenhagen, Gothersgade 130, 1153, Copenhagen, Denmark
- National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, HI, 96741, USA
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Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O, Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol Ecol Resour 2021; 22:927-945. [PMID: 34606683 PMCID: PMC9292372 DOI: 10.1111/1755-0998.13523] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
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Affiliation(s)
- Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Margot Paris
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany
| | - Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Norma Rivera
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Valeria Guzmán-Jacob
- Biodiversity, Macroecology and Biogeography, University of Goettingen, Göttingen, Germany
| | - Thorsten Krömer
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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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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