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Yan Y, da Fonseca RR, Rahbek C, Borregaard MK, Davis CC. A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia. Mol Phylogenet Evol 2024; 196:108089. [PMID: 38679302 DOI: 10.1016/j.ympev.2024.108089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 03/08/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
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Affiliation(s)
- Yujing Yan
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA.
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Life Sciences, Imperial College London, Silkwood Park campus, Ascot SL5 7PY, UK; Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael K Borregaard
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA
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2
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Simpson L, Clements MA, Orel HK, Crayn DM, Nargar K. Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum. FRONTIERS IN PLANT SCIENCE 2024; 14:1219354. [PMID: 38854888 PMCID: PMC11157511 DOI: 10.3389/fpls.2023.1219354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 06/11/2024]
Abstract
The hyperdiverse orchid genus Bulbophyllum is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only Bulbophyllum section with a center of diversity in Australasia is sect. Adelopetalum. However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within Bulbophyllum, and interspecific relationships within sect. Adelopetalum, a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (matK and ycf1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in Bulbophyllum, including phylogenetic evidence for the non-monophyly of sections Beccariana, Brachyantha, Brachypus, Cirrhopetaloides, Cirrhopetalum, Desmosanthes, Minutissima, Oxysepala, Polymeres, and Sestochilos. Section Adelopetalum and sect. Minutissima s.s. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of Bulbophyllum in the Early Oligocene (ca. 33.2 Ma) and sect. Adelopetalum in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. Adelopetalum. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. Adelopetalum facilitating allopatric speciation.
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Affiliation(s)
- Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Mark A. Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and Commonwealth Industrial and Scientific Research Organisation (CSIRO)), Canberra, ACT, Australia
| | - Harvey K. Orel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Darren M. Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia
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3
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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4
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Jin ZT, Hodel RGJ, Ma DK, Wang H, Liu GN, Ren C, Ge BJ, Fan Q, Jin SH, Xu C, Wu J, Liu BB. Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era. Mol Phylogenet Evol 2023; 189:107914. [PMID: 37666378 DOI: 10.1016/j.ympev.2023.107914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.
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Affiliation(s)
- Ze-Tao Jin
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Dai-Kun Ma
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wang
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | | | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Bin-Jie Ge
- Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Shui-Hu Jin
- College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Chao Xu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Bin-Bin Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China.
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5
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Ball LD, Bedoya AM, Taylor CM, Lagomarsino LP. A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11554. [PMID: 38106541 PMCID: PMC10719880 DOI: 10.1002/aps3.11554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 12/19/2023]
Abstract
Premise Rubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking. Methods Here, we use publicly accessible genomic resources to identify putatively single-copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent-aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae. Results We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance. Discussion Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.
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Affiliation(s)
- Laymon D Ball
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
| | - Ana M Bedoya
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
| | - Charlotte M Taylor
- Missouri Botanical Garden 4344 Shaw Blvd. Saint Louis Missouri 63110 USA
| | - Laura P Lagomarsino
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
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6
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Moreyra LD, Garcia-Jacas N, Roquet C, Ackerfield JR, Arabacı T, Blanco-Gavaldà C, Brochmann C, Calleja JA, Dirmenci T, Fujikawa K, Galbany-Casals M, Gao T, Gizaw A, López-Alvarado J, Mehregan I, Vilatersana R, Yıldız B, Leliaert F, Seregin AP, Susanna A. African Mountain Thistles: Three New Genera in the Carduus-Cirsium Group. PLANTS (BASEL, SWITZERLAND) 2023; 12:3083. [PMID: 37687332 PMCID: PMC10489743 DOI: 10.3390/plants12173083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization.
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Affiliation(s)
- Lucía D. Moreyra
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | | | - Turan Arabacı
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Inönü University, 44280 Malatya, Türkiye;
| | - Carme Blanco-Gavaldà
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | - Christian Brochmann
- Natural History Museum, University of Oslo, Blindern, 0318 Oslo, Norway; (C.B.); (A.G.)
| | - Juan Antonio Calleja
- Department of Biology, Autonomous University of Madrid, 28049 Madrid, Spain;
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Tuncay Dirmenci
- Department of Biology, Faculty of Necatibey Education, Balıkesir University, 10145 Balıkesir, Türkiye;
| | - Kazumi Fujikawa
- Kochi Prefectural Makino Botanical Garden, 4200-6, Godaisan, Kochi 781-8125, Japan;
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | - Tiangang Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Abel Gizaw
- Natural History Museum, University of Oslo, Blindern, 0318 Oslo, Norway; (C.B.); (A.G.)
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa P.O. Box 3434, Ethiopia
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants (UAB)—Associated Unit to CSIC by IBB, Autonomous University of Barcelona, 08193 Cerdanyola del Vallès, Spain; (C.R.); (C.B.-G.); (M.G.-C.)
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran;
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
| | - Bayram Yıldız
- Ismail Cem Street, No. 35, Yenikale District, 35320 Narlidere Türkiye;
| | | | - Alexey P. Seregin
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia, s.n., 08038 Barcelona, Spain; (L.D.M.); (N.G.-J.); (R.V.)
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7
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Blanco-Gavaldà C, Galbany-Casals M, Susanna A, Andrés-Sánchez S, Bayer RJ, Brochmann C, Cron GV, Bergh NG, Garcia-Jacas N, Gizaw A, Kandziora M, Kolář F, López-Alvarado J, Leliaert F, Letsara R, Moreyra LD, Razafimandimbison SG, Schmickl R, Roquet C. Repeatedly Northwards and Upwards: Southern African Grasslands Fuel the Colonization of the African Sky Islands in Helichrysum (Compositae). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112213. [PMID: 37299192 DOI: 10.3390/plants12112213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene-Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.
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Affiliation(s)
- Carme Blanco-Gavaldà
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia s/n, ES-08038 Barcelona, Spain
| | - Santiago Andrés-Sánchez
- Department of Botany and Plant Physiology and Plant DNA Biobank, DNA National Bank, University of Salamanca, Edificio I+D+i, Espejo St., ES-37007 Salamanca, Spain
| | - Randall J Bayer
- Department of Biological Sciences, Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Christian Brochmann
- Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
| | - Glynis V Cron
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Private Bag 3, Johannesburg 2050, South Africa
| | - Nicola G Bergh
- Foundational Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute, Private Bag X7, Newlands, Cape Town 7735, South Africa
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia s/n, ES-08038 Barcelona, Spain
| | - Abel Gizaw
- Natural History Museum, University of Oslo, P.O. Box 1172, NO-0318 Oslo, Norway
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa P.O. Box 3434, Ethiopia
| | - Martha Kandziora
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, CZ-25243 Průhonice, Czech Republic
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
| | | | - Rokiman Letsara
- Herbarium of the Parc Botanique et Zoologique of Tsimbazaza (PBZT), Antananarivo 3G9G+V6C, Madagascar
| | - Lucía D Moreyra
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Pg. Migdia s/n, ES-08038 Barcelona, Spain
| | | | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-12801 Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, CZ-25243 Průhonice, Czech Republic
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants-Associated Unit to CSIC by IBB, Department of Animal Biology, Plant Biology and Ecology, Faculty of Biosciences, Autonomous University of Barcelona, ES-08193 Bellaterra, Spain
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8
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Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
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Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
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Fonseca LHM, Carlsen MM, Fine PVA, Lohmann LG. A nuclear target sequence capture probe set for phylogeny reconstruction of the charismatic plant family Bignoniaceae. Front Genet 2023; 13:1085692. [PMID: 36699458 PMCID: PMC9869424 DOI: 10.3389/fgene.2022.1085692] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The plant family Bignoniaceae is a conspicuous and charismatic element of the tropical flora. The family has a complex taxonomic history, with substantial changes in the classification of the group during the past two centuries. Recent re-classifications at the tribal and generic levels have been largely possible by the availability of molecular phylogenies reconstructed using Sanger sequencing data. However, our complete understanding of the systematics, evolution, and biogeography of the family remains incomplete, especially due to the low resolution and support of different portions of the Bignoniaceae phylogeny. To overcome these limitations and increase the amount of molecular data available for phylogeny reconstruction within this plant family, we developed a bait kit targeting 762 nuclear genes, including 329 genes selected specifically for the Bignoniaceae; 348 genes obtained from the Angiosperms353 with baits designed specifically for the family; and, 85 low-copy genes of known function. On average, 77.4% of the reads mapped to the targets, and 755 genes were obtained per species. After removing genes with putative paralogs, 677 loci were used for phylogenetic analyses. On-target genes were compared and combined in the Exon-Only dataset, and on-target + off-target regions were combined in the Supercontig dataset. We tested the performance of the bait kit at different taxonomic levels, from family to species-level, using 38 specimens of 36 different species of Bignoniaceae, representing: 1) six (out of eight) tribal level-clades (e.g., Bignonieae, Oroxyleae, Tabebuia Alliance, Paleotropical Clade, Tecomeae, and Jacarandeae), only Tourrettieae and Catalpeae were not sampled; 2) all 20 genera of Bignonieae; 3) seven (out of nine) species of Dolichandra (e.g., D. chodatii, D. cynanchoides, D. dentata, D. hispida, D. quadrivalvis, D. uncata, and D. uniguis-cati), only D. steyermarkii and D. unguiculata were not sampled; and 4) three individuals of Dolichandra unguis-cati. Our data reconstructed a well-supported phylogeny of the Bignoniaceae at different taxonomic scales, opening new perspectives for a comprehensive phylogenetic framework for the family as a whole.
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Affiliation(s)
- Luiz Henrique M. Fonseca
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil,Systematic and Evolutionary Botany Laboratory, Department of Biology, Ghent University, Ghent, Belgium,*Correspondence: Luiz Henrique M. Fonseca, ; Lúcia G. Lohmann,
| | | | - Paul V. A. Fine
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Lúcia G. Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil,University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States,*Correspondence: Luiz Henrique M. Fonseca, ; Lúcia G. Lohmann,
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Thureborn O, Razafimandimbison SG, Wikström N, Rydin C. Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:967456. [PMID: 36160958 PMCID: PMC9493367 DOI: 10.3389/fpls.2022.967456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | | | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bergius Foundation, Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bergius Foundation, Royal Swedish Academy of Sciences, Stockholm, Sweden
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11
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Hatami E, Jones KE, Kilian N. New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq). FRONTIERS IN PLANT SCIENCE 2022; 13:851716. [PMID: 35873957 PMCID: PMC9298463 DOI: 10.3389/fpls.2022.851716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1-3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.
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Affiliation(s)
- Elham Hatami
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Katy E. Jones
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Norbert Kilian
- Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
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12
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Murillo-A J, Valencia-D J, Orozco CI, Parra-O C, Neubig KM. Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification. AMERICAN JOURNAL OF BOTANY 2022; 109:1139-1156. [PMID: 35709353 DOI: 10.1002/ajb2.16025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
PREMISE To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. METHODS We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia. RESULTS Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. CONCLUSIONS Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character-state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.
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Affiliation(s)
- José Murillo-A
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia
| | - Janice Valencia-D
- School of Biological Sciences, Southern Illinois University Carbondale, 1125 Lincoln Dr., Carbondale, Illinois, 62901-6509, USA
| | - Clara I Orozco
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia
| | - Carlos Parra-O
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia
| | - Kurt M Neubig
- School of Biological Sciences, Southern Illinois University Carbondale, 1125 Lincoln Dr., Carbondale, Illinois, 62901-6509, USA
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Lagomarsino LP, Frankel L, Uribe-Convers S, Antonelli A, Muchhala N. Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation. ANNALS OF BOTANY 2022; 129:723-736. [PMID: 35363863 PMCID: PMC9113290 DOI: 10.1093/aob/mcac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/24/2022] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centred rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. METHODS Targeted sequence capture using a probe-set recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. KEY RESULTS While silica-dried leaf tissue resulted in longer assembled sequence data, the inclusion of herbarium samples improved taxonomic representation. Relationships among baccate lineages are similar to those inferred in previous studies, although they differ for lineages within and among capsular clades. We improve the phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. CONCLUSIONS This first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict and well-supported differences between analyses based on different nuclear loci. Together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is probably present in many other species-rich Andean plant radiations.
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Affiliation(s)
- Laura P Lagomarsino
- Shirley C. Tucker Herbarium, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Lauren Frankel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Simon Uribe-Convers
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
- Invitae Corporation, San Francisco, CA, USA
| | - 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 Science, University of Oxford, Oxford, UK
| | - Nathan Muchhala
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA
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A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae. Genes (Basel) 2022; 13:genes13040707. [PMID: 35456513 PMCID: PMC9032687 DOI: 10.3390/genes13040707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.
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15
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Effectiveness of Two Universal Angiosperm Probe Sets Tested In Silico for Caryophyllids Taxa with Emphasis on Cacti Species. Genes (Basel) 2022; 13:genes13040570. [PMID: 35456376 PMCID: PMC9032312 DOI: 10.3390/genes13040570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships.
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Acha S, Majure LC. A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. Genes (Basel) 2022; 13:genes13020350. [PMID: 35205394 PMCID: PMC8871817 DOI: 10.3390/genes13020350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.
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17
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Morales-Briones DF, Gehrke B, Huang CH, Liston A, Ma H, Marx HE, Tank DC, Yang Y. Analysis of Paralogs in Target Enrichment Data Pinpoints Multiple Ancient Polyploidy Events in Alchemilla s.l. (Rosaceae). Syst Biol 2021; 71:190-207. [PMID: 33978764 PMCID: PMC8677558 DOI: 10.1093/sysbio/syab032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022] Open
Abstract
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment data sets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here, we used an automated approach for orthology inference in a target enrichment data set of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration and inferring orthologs from target enrichment data, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach, we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here, we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic data sets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment data sets.[Alchemilla; allopolyploidy; autopolyploidy; gene tree discordance; orthology inference; paralogs; Rosaceae; target enrichment; whole genome duplication.].
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Affiliation(s)
- Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844, USA
| | - Berit Gehrke
- University Gardens, University Museum, University of Bergen, Mildeveien 240, 5259 Hjellestad, Norway
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA
| | - Hong Ma
- Department of Biology, the Huck Institute of the Life Sciences, the Pennsylvania State University, 510D Mueller Laboratory, University Park, PA 16802 USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - David C Tank
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St. Paul, MN 55108, USA
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Calderón-Acevedo CA, Bagley JC, Muchhala N. Genome-wide ultraconserved elements resolve phylogenetic relationships and biogeographic history among Neotropical leaf-nosed bats in the genus Anoura (Phyllostomidae). Mol Phylogenet Evol 2021; 167:107356. [PMID: 34774763 DOI: 10.1016/j.ympev.2021.107356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/26/2021] [Accepted: 11/08/2021] [Indexed: 10/19/2022]
Abstract
AnouraGray, 1838 are Neotropical nectarivorous bats and the most speciose genus within the phyllostomid subfamily Glossophaginae. However, Anoura species limits remain debated, and phylogenetic relationships remain poorly known, because previous studies used limited Anoura taxon sampling or focused primarily on higher-level relationships. Here, we conduct the first phylogenomic study of Anoura by analyzing 2039 genome-wide ultraconserved elements (UCEs) sequenced for 42 individuals from 8 Anoura species/lineages plus two outgroups. Overall, our results based on UCEs resolved relationships in the genus and supported (1) the monophyly of small-bodied Anoura species (previously genus Lonchoglossa); (2) monotypic status of A. caudifer; and (3) nested positions of "A. carishina", A. caudifer aequatoris, and A. geoffroyi peruana specimens within A. latidens, A. caudifer and A. geoffroyi, respectively (suggesting that these taxa are not distinct species). Additionally, (4) phylogenetic networks allowing reticulate edges did not explain gene tree discordance better than the species tree (without introgression), indicating that a coalescent model accounting for discordance solely through incomplete lineage sorting fit our data well. Sensitivity analyses indicated that our species tree results were not adversely affected by varying taxon sampling across loci. Tree calibration and Bayesian coalescent analyses dated the onset of diversification within Anoura to around ∼ 6-9 million years ago in the Miocene, with extant species diverging mainly within the past ∼ 4 million years. We inferred a historical biogeographical scenario for Anoura of parapatric speciation fragmenting the range of a wide-ranging ancestral lineage centered in the Central to Northern Andes, along with Pliocene-Pleistocene dispersal or founder event speciation in Amazonia and the Brazilian Atlantic forest during the last ∼ 2.5 million years.
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Affiliation(s)
- Camilo A Calderón-Acevedo
- Department of Biology, University of Missouri-St. Louis, One University Blvd., 223 Research Bldg., St. Louis, MO 63121, USA; Department of Earth and Environmental Science, Rutgers University, 195 University Ave., Boyden Hall 433, Newark, NJ, 07102 USA.
| | - Justin C Bagley
- Department of Biology, University of Missouri-St. Louis, One University Blvd., 223 Research Bldg., St. Louis, MO 63121, USA; Department of Biology, Jacksonville State University, 242 Martin Hall, 700 Pelham Rd North, Jacksonville, AL 36265, USA; Department of Biology, Virginia Commonwealth University, 1000 W Cary St., Suite 126, Richmond, VA 23284, USA.
| | - Nathan Muchhala
- Department of Biology, University of Missouri-St. Louis, One University Blvd., 223 Research Bldg., St. Louis, MO 63121, USA.
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19
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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: 16] [Impact Index Per Article: 5.3] [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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20
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Thomas AE, Igea J, Meudt HM, Albach DC, Lee WG, Tanentzap AJ. Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica. AMERICAN JOURNAL OF BOTANY 2021; 108:1289-1306. [PMID: 34173225 DOI: 10.1002/ajb2.1678] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
PREMISE Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations. METHODS Here we applied target sequence capture with 353 protein-coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5-10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species. RESULTS We obtained approximately 150 kbp of 353 protein-coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene-tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation. CONCLUSIONS Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.
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Affiliation(s)
- Anne E Thomas
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Javier Igea
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Heidi M Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Dirk C Albach
- Carl von Ossietzky-University, Oldenburg, D-26111, Germany
| | - William G Lee
- Manaaki Whenua - Landcare Research Otago, Dunedin, New Zealand
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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21
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Arcila D, Hughes LC, Meléndez-Vazquez F, Baldwin CC, White W, Carpenter K, Williams JT, Santos MD, Pogonoski J, Miya M, Ortí G, Betancur-R R. Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria). Syst Biol 2021; 70:1123-1144. [PMID: 33783539 DOI: 10.1093/sysbio/syab018] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/13/2021] [Indexed: 12/19/2022] Open
Abstract
The use of high-throughput sequencing technologies to produce genome-scale datasets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these datasets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch support metrics to an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published UCE data and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was lower for interfamilial relationships (except the SH-like aLRT and aBayes methods) regardless of the type of marker used. Several nodes that were highly supported with bootstrap had very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths in the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic datasets.
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Affiliation(s)
- Dahiana Arcila
- Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, Oklahoma, U.S.A.,Department of Biology, University of Oklahoma, Norman, Oklahoma, U.S.A
| | - Lily C Hughes
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, U.S.A.,Department of Organismal Biology and Anatomy, The University of Chicago, Illinois, Chicago, U.S.A.,Department of Vertebrate Zoology, Smithsonian Institution National Museum of Natural History, Washington, District of Columbia, U.S.A
| | - Fernando Meléndez-Vazquez
- Department of Ichthyology, Sam Noble Oklahoma Museum of Natural History, Norman, Oklahoma, U.S.A.,Department of Biology, University of Oklahoma, Norman, Oklahoma, U.S.A
| | - Carole C Baldwin
- Department of Vertebrate Zoology, Smithsonian Institution National Museum of Natural History, Washington, District of Columbia, U.S.A
| | - William White
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Hobart, Tasmania, Australia
| | - Kent Carpenter
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, U.S.A
| | - Jeffrey T Williams
- Department of Vertebrate Zoology, Smithsonian Institution National Museum of Natural History, Washington, District of Columbia, U.S.A
| | | | - John Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Hobart, Tasmania, Australia
| | - Masaki Miya
- Natural History Museum and Institute, Chiba, Aoba-cho, Chuo-ku, Chiba, Japan
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, U.S.A.,Department of Vertebrate Zoology, Smithsonian Institution National Museum of Natural History, Washington, District of Columbia, U.S.A
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22
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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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23
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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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24
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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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