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Garner AG, Goulet-Scott BE, Hopkins R. Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers. THE NEW PHYTOLOGIST 2024; 243:451-465. [PMID: 38764373 DOI: 10.1111/nph.19802] [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: 10/06/2023] [Accepted: 03/22/2024] [Indexed: 05/21/2024]
Abstract
The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non-model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.
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Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
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2
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Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
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Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
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3
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Zhang B, Yu Z, Xu Z, Zheng B. A Phylogenetic and Morphological Evolution Study of Ribes L. in China Using RAD-Seq. PLANTS (BASEL, SWITZERLAND) 2023; 12:829. [PMID: 36840182 PMCID: PMC9960833 DOI: 10.3390/plants12040829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Ribes L. belongs to the Grossulariaceae family and has important edible, medicinal, ornamental, and landscaping values. Taxonomic classification within this genus is difficult due to its large variety of species, wide distribution, large morphological variations, and presence of two complex taxonomic groups with bisexual or unisexual flowers. Our study aims to clarify the phylogenetic relationships of Ribes L. taxa in China, and further, to provide a reference for a revised global classification of it. The phylogenetic analysis of 52 Ribes L. samples from 30 species was constructed based on restriction site-associated DNA sequencing and single nucleotide polymorphisms. Afterward, two important taxonomic characters were selected for ancestral state reconstruction over the molecular phylogeny. The results showed that the 52 samples could be divided into six branches, i.e., six subgenera, which caused some controversy regarding the morphological classification of Ribes L. in China. The molecular phylogeny supported the separation of subg. Coreosma from subg. Ribesia and subg. Hemibotrya from subg. Berisia and validated the rationale for recognizing subg. Grossularia as an independent subgenus, the rationality of which was further verified by the reconstruction of ancestor traits. Gene flow among Ribes L. was identified and further confirmed our results.
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Affiliation(s)
- Baoshan Zhang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Sustainable Forest Management and Environmental Microorganism Engineering of Heilongjiang Province, Northeast Forestry University, Harbin 150040, China
| | - Ziyang Yu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Baojiang Zheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Northeast Asia Biodiversity Research Center, Harbin 150040, China
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4
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Addressing inconsistencies in Cyperaceae and Juncaceae taxonomy: Comment on Brožová et al. (2022). Mol Phylogenet Evol 2023; 179:107665. [PMID: 36375790 DOI: 10.1016/j.ympev.2022.107665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
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5
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Brožová V, Proćków J, Záveská Drábková L. Toward finally unraveling the phylogenetic relationships of Juncaceae with respect to another cyperid family, Cyperaceae. Mol Phylogenet Evol 2022; 177:107588. [PMID: 35907594 DOI: 10.1016/j.ympev.2022.107588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/06/2021] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
Juncaceae is a cosmopolitan family belonging to the cyperid clade of Poales together with Cyperaceae and Thurniaceae. These families have global economic and ethnobotanical significance and are often keystone species in wetlands around the world, with a widespread cosmopolitan distribution in temperate and arctic regions in both hemispheres. Currently, Juncaceae comprises more than 474 species in eight genera: Distichia, Juncus, Luzula, Marsippospermum, Oreojuncus, Oxychloë, Patosia and Rostkovia. The phylogeny of cyperids has not been studied before in a complex view based on most sequenced species from all three families. In this study, most sequenced regions from chloroplast (rbcL, trnL, trnL-trnF) and nuclear (ITS1-5.8S-ITS2) genomes were employed from more than a thousand species of cyperids covering all infrageneric groups from their entire distributional range. We analyzed them by maximum parsimony, maximum likelihood, and Bayesian inference to revise the phylogenetic relationships in Juncaceae and Cyperaceae. Our major results include the delimitation of the most problematic paraphyletic genus Juncus, in which six new genera are recognized and proposed to recover monophyly in this group: Juncus, Verojuncus, gen. nov., Juncinella, gen. et stat. nov., Alpinojuncus, gen. nov., Australojuncus, gen. nov., Boreojuncus, gen. nov. and Agathryon, gen. et stat. nov. For these genera, a new category, Juncus supragen. et stat. nov., was established. This new classification places most groups recognized within the formal Juncus clade into natural genera that are supported by morphological characters.
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Affiliation(s)
- Viktorie Brožová
- Department of Botany, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, ul. Kożuchowska 7a, 51-631 Wrocław, Poland
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 165 02 Praha 6, Czech Republic.
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6
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Cui H, Ford B, Starr J, Reznicek A, Zhang L, Macklin JA. Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications. Database (Oxford) 2022; 2022:6519872. [PMID: 35106535 PMCID: PMC9278328 DOI: 10.1093/database/baac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/24/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022]
Abstract
Critical to answering large-scale questions in biology is the integration of knowledge from different disciplines into a coherent, computable whole. Controlled vocabularies such as ontologies represent a clear path toward this goal. Using survey questionnaires, we examined the attitudes of biologists toward adopting controlled vocabularies in phenotype publications. Our questions cover current experience and overall attitude with controlled vocabularies, the awareness of the issues around ambiguity and inconsistency in phenotype descriptions and post-publication professional data curation, the preferred solutions and the effort and desired rewards for adopting a new authoring workflow. Results suggest that although the existence of controlled vocabularies is widespread, their use is not common. A majority of respondents (74%) are frustrated with ambiguity in phenotypic descriptions, and there is a strong agreement (mean agreement score 4.21 out of 5) that author curation would better reflect the original meaning of phenotype data. Moreover, the vast majority (85%) of researchers would try a new authoring workflow if resultant data were more consistent and less ambiguous. Even more respondents (93%) suggested that they would try and possibly adopt a new authoring workflow if it required 5% additional effort as compared to normal, but higher rates resulted in a steep decline in likely adoption rates. Among the four different types of rewards, two types of citations were the most desired incentives for authors to produce computable data. Overall, our results suggest the adoption of a new authoring workflow would be accelerated by a user-friendly and efficient software-authoring tool, an increased awareness of the challenges text ambiguity creates for external curators and an elevated appreciation of the benefits of controlled vocabularies.
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Affiliation(s)
- Hong Cui
- School of Information, University of Arizona , 1103 E. Second Street, Tucson, AZ 85705, USA
| | - Bruce Ford
- Department of Biological Sciences, University of Manitoba , 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Julian Starr
- Department of Biology, University of Ottawa , 30 Marie Curie Road, Ottawa, ON K1N 6N5, Canada
| | - Anton Reznicek
- SLA Herbarium, University of Michigan , 3600 Varsity Drive #1046, Ann Arbor, MI 48019, USA
| | - Limin Zhang
- School of Information, University of Arizona , 1103 E. Second Street, Tucson, AZ 85705, USA
| | - James A Macklin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
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7
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Forthman M, Braun EL, Kimball RT. Gene tree quality affects empirical coalescent branch length estimation. ZOOL SCR 2021. [DOI: 10.1111/zsc.12512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Michael Forthman
- Department of Entomology & Nematology University of Florida Gainesville FL USA
- California State Collection of Arthropods Plant Pest Diagnostics Branch California Department of Food & Agriculture Sacramento CA USA
| | - Edward L. Braun
- Department of Biology University of Florida Gainesville FL USA
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8
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Uckele KA, Jahner JP, Tepe EJ, Richards LA, Dyer LA, Ochsenrider KM, Philbin CS, Kato MJ, Yamaguchi LF, Forister ML, Smilanich AM, Dodson CD, Jeffrey CS, Parchman TL. Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs. Sci Rep 2021; 11:17247. [PMID: 34446754 PMCID: PMC8390663 DOI: 10.1038/s41598-021-96431-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.
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Affiliation(s)
- Kathryn A Uckele
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Joshua P Jahner
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.
- Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Eric J Tepe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Lora A Richards
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Lee A Dyer
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
- Sección Invertebrados, Museo Ecuatoriano de Ciencias Naturales, Quito, Ecuador
| | | | - Casey S Philbin
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Massuo J Kato
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Lydia F Yamaguchi
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Matthew L Forister
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Angela M Smilanich
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
| | - Craig D Dodson
- Department of Chemistry, University of Nevada, Reno, NV, 89557, USA
| | - Christopher S Jeffrey
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
- Department of Chemistry, University of Nevada, Reno, NV, 89557, USA
| | - Thomas L Parchman
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
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9
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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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10
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The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae. Mol Phylogenet Evol 2020; 151:106896. [PMID: 32562821 DOI: 10.1016/j.ympev.2020.106896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/22/2020] [Accepted: 06/10/2020] [Indexed: 11/23/2022]
Abstract
The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci.
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