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Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [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: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
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Wu Y, Linan AG, Hoban S, Hipp AL, Ricklefs RE. Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak). J Hered 2024; 115:575-587. [PMID: 38881254 DOI: 10.1093/jhered/esae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.
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Affiliation(s)
- Yingtong Wu
- Biology Department, University of Missouri-St. Louis, St. Louis, MO, United States
- Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO, United States
| | - Alexander G Linan
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, United States
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL, United States
| | - Andrew L Hipp
- Center for Tree Science, The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Integrative Research Center, Chicago, IL, United States
| | - Robert E Ricklefs
- Biology Department, University of Missouri-St. Louis, St. Louis, MO, United States
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3
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Sevillya G. Relation between two evolutionary clocks reveal new insights in bacterial evolution. Access Microbiol 2022; 4:000265. [PMID: 35355876 PMCID: PMC8941958 DOI: 10.1099/acmi.0.000265] [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: 02/11/2021] [Accepted: 07/26/2021] [Indexed: 12/02/2022] Open
Abstract
New insights in evolution are available thanks to next-generation sequencing technologies in recent years. However, due to the network of complex relations between species, caused by the intensive horizontal gene transfer (HGT) between different bacterial species, it is difficult to discover bacterial evolution. This difficulty leads to new research in the field of phylogeny, including the gene-based phylogeny, in contrast to sequence-based phylogeny. In previous articles, we presented evolutionary insights of Synteny Index (SI) study on a large biological dataset. We showed that the SI approach naturally clusters 1133 species into 39 cliques of closely related species. In addition, we presented a model that enables calculation of the number of translocation events between genomes based on their SI distance. Here, these two studies are combined together and lead to new insights. A principal result is the relation between two evolutionary clocks: the well-known sequence-based clock influenced by point mutations, and SI distance clock influenced by translocation events. A surprising linear relation between these two evolutionary clocks rising for closely related species across all genus. In other words, these two different clocks are ticking at the same rate inside the genus level. Conversely, a phase-transition manner discovered between these two clocks across non-closely related species. This may suggest a new genus definition based on an analytic approach, since the phase-transition occurs where each gene, on average, undergoes one translocation event. In addition, rare cases of HGT among highly conserved genes can be detected as outliers from the phase-transition pattern.
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Affiliation(s)
- Gur Sevillya
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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Stasinski L, White DM, Nelson PR, Ree RH, Meireles JE. Reading light: leaf spectra capture fine-scale diversity of closely related, hybridizing arctic shrubs. THE NEW PHYTOLOGIST 2021; 232:2283-2294. [PMID: 34510452 PMCID: PMC9297881 DOI: 10.1111/nph.17731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/06/2021] [Indexed: 05/26/2023]
Abstract
Leaf reflectance spectroscopy is emerging as an effective tool for assessing plant diversity and function. However, the ability of leaf spectra to detect fine-scale plant evolutionary diversity in complicated biological scenarios is not well understood. We test if reflectance spectra (400-2400 nm) can distinguish species and detect fine-scale population structure and phylogenetic divergence - estimated from genomic data - in two co-occurring, hybridizing, ecotypically differentiated species of Dryas. We also analyze the correlation among taxonomically diagnostic leaf traits to understand the challenges hybrids pose to classification models based on leaf spectra. Classification models based on leaf spectra identified two species of Dryas with 99.7% overall accuracy and genetic populations with 98.9% overall accuracy. All regions of the spectrum carried significant phylogenetic signal. Hybrids were classified with an average overall accuracy of 80%, and our morphological analysis revealed weak trait correlations within hybrids compared to parent species. Reflectance spectra captured genetic variation and accurately distinguished fine-scale population structure and hybrids of morphologically similar, closely related species growing in their home environment. Our findings suggest that fine-scale evolutionary diversity is captured by reflectance spectra and should be considered as spectrally-based biodiversity assessments become more prevalent.
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Affiliation(s)
- Lance Stasinski
- School of Biology and EcologyUniversity of MaineOronoME04469USA
| | - Dawson M. White
- Department of Science and EducationField MuseumChicagoIL60605USA
| | - Peter R. Nelson
- Schoodic InstituteWinter HarborME04693USA
- School of Forest ResourcesUniversity of MaineOronoME04469USA
| | - Richard H. Ree
- Department of Science and EducationField MuseumChicagoIL60605USA
| | - José Eduardo Meireles
- School of Biology and EcologyUniversity of MaineOronoME04469USA
- Maine Center for Genetics in the EnvironmentUniversity of MaineOronoME04469USA
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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation. IMA Fungus 2021; 12:16. [PMID: 34193315 PMCID: PMC8246709 DOI: 10.1186/s43008-021-00068-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/23/2021] [Indexed: 02/06/2023] Open
Abstract
The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
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White DM, Huang JP, Jara-Muñoz OA, MadriñáN S, Ree RH, Mason-Gamer RJ. The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes. Syst Biol 2020; 70:1-13. [PMID: 32979264 PMCID: PMC7744036 DOI: 10.1093/sysbio/syaa074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022] Open
Abstract
Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]
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Affiliation(s)
- Dawson M White
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Grainger Bioinformatics Center, The Field Museum, Chicago, IL 60605, USA
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Santiago MadriñáN
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.,Jardín Botánico de Cartagena "Guillermo Piñeres", Turbaco, Bolívar, Colombia
| | - Richard H Ree
- Grainger Bioinformatics Center, The Field Museum, Chicago, IL 60605, USA
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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Bangs MR, Douglas MR, Chafin TK, Douglas ME. Gene flow and species delimitation in fishes of Western North America: Flannelmouth ( Catostomus latipinnis) and Bluehead sucker ( C. Pantosteus discobolus). Ecol Evol 2020; 10:6477-6493. [PMID: 32724527 PMCID: PMC7381754 DOI: 10.1002/ece3.6384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction site-associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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Reydon TAC, Kunz W. Species as natural entities, instrumental units and ranked taxa: new perspectives on the grouping and ranking problems. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Thomas A C Reydon
- Institute of Philosophy, Leibniz University Hannover, Hannover, Germany
- Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, Hannover, Germany
| | - Werner Kunz
- Institute for Genetics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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Conix S. Radical pluralism, classificatory norms and the legitimacy of species classifications. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2019; 73:27-34. [PMID: 30429047 DOI: 10.1016/j.shpsc.2018.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 06/09/2023]
Abstract
Moderate pluralism is a popular position in contemporary philosophy of biology. Despite its popularity, various authors have argued that it tends to slide off into a radical form of pluralism that is both normatively and descriptively unacceptable. This paper looks at the case of biological species classification, and evaluates a popular way of avoiding radical pluralism by relying on the shared aims and norms of a discipline. The main contention is that while these aims and norms may play an important role in the legitimacy of species classifications, they fail to fend off radical pluralism. It follows from this that the legitimacy of species classifications is also determined by local decisions about the aims of research and how to operationalize and balance these. This is important, I argue, because it means that any acceptable view on the legitimacy of classification should be able to account for these local decisions.
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Affiliation(s)
- Stijn Conix
- Centre for Logic and Philosophy of Science, KU Leuven, Andreas Vesaliusstraat 2, 3000, Leuven, Belgium.
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10
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White DM, Islam MB, Mason-Gamer RJ. Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species). AMERICAN JOURNAL OF BOTANY 2019; 106:154-165. [PMID: 30629286 DOI: 10.1002/ajb2.1224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/19/2018] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. METHODS We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. KEY RESULTS We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal. CONCLUSIONS Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.
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Affiliation(s)
- Dawson M White
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street Room 3256 (M/C 066), Chicago, IL, 60612, USA
- Department of Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Melissa B Islam
- Department of Ecology and Evolutionary Biology, University of Colorado, Ramaley N122, Campus Box 334, Boulder, CO, 80309, USA
| | - Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street Room 3256 (M/C 066), Chicago, IL, 60612, USA
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11
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The Species Problem from the Modeler's Point of View. Bull Math Biol 2018; 81:878-898. [PMID: 30535845 DOI: 10.1007/s11538-018-00536-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 11/27/2018] [Indexed: 01/12/2023]
Abstract
How to define a partition of individuals into species is a long-standing question called the species problem in systematics. Here, we focus on this problem in the thought experiment where individuals reproduce clonally and both the differentiation process and the population genealogies are explicitly known. We specify three desirable properties of species partitions: (A) Heterotypy between species, (B) Homotypy within species and (M) Genealogical monophyly of each species. We then ask: How and when is it possible to delineate species in a way satisfying these properties? We point out that the three desirable properties cannot in general be satisfied simultaneously, but that any two of them can. We mathematically prove the existence of the finest partition satisfying (A) and (M) and the coarsest partition satisfying (B) and (M). For each of them, we propose a simple algorithm to build the associated phylogeny out of the genealogy. The ways we propose to phrase the species problem shed new light on the interaction between the genealogical and phylogenetic scales in modeling work. The two definitions centered on the monophyly property can readily be used at a higher taxonomic level as well, e.g., to cluster species into monophyletic genera.
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Wright ES, Baum DA. Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow. BMC Genomics 2018; 19:724. [PMID: 30285620 PMCID: PMC6171291 DOI: 10.1186/s12864-018-5099-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/21/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization. RESULTS Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa, although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species. CONCLUSIONS The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.
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Affiliation(s)
- Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA.
- Pittsburgh Center for Evolutionary Biology and Medicine, Pittsburgh, USA.
| | - David A Baum
- Department of Botany, University of Wisconsin-Madison, Madison, USA
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Hoppe A, Türpitz S, Steel M. Species notions that combine phylogenetic trees and phenotypic partitions. J Math Biol 2018. [PMID: 30043242 DOI: 10.1101/075580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A recent paper (Manceau and Lambert in bioRxiv, 2017. https://doi.org/10.1101/075580 ) developed a novel approach for describing two well-defined notions of 'species' based on a phylogenetic tree and a phenotypic partition. In this paper, we explore some further combinatorial properties of this approach and describe an extension that allows an arbitrary number of phenotypic partitions to be combined with a phylogenetic tree for these two species notions.
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Affiliation(s)
- Anica Hoppe
- Institute of Mathematics and Computer Science, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Sonja Türpitz
- Institute of Mathematics and Computer Science, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.
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Stoughton TR, Kriebel R, Jolles DD, O'Quinn RL. Next-generation lineage discovery: A case study of tuberous Claytonia L. AMERICAN JOURNAL OF BOTANY 2018; 105:536-548. [PMID: 29672830 DOI: 10.1002/ajb2.1061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/18/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Species formation is an intuitive endpoint of reproductive isolation, but circumscribing taxa that arise during speciation can be difficult because of gene flow, morphological continuity, hybridization or polyploidization, and low sequence variation among newly diverged lineages. Nonetheless, species complexes are ubiquitous, and their classification is essential for understanding how diversity influences ecosystem function. METHODS We used modern sequencing technology to identify lineages of perennial Claytonia L. and assessed correspondence between genetic lineages and morphological/ecological variation. Subsets of 18 taxa from 63 populations were used for (a) lineage discovery using network and coalescent analyses, (b) leaf shape analyses using elliptical Fourier analysis and ordination, and (c) ecological analyses (soil chemistry, climate) using ANOVA and ordination. KEY RESULTS Samples mainly aggregated into groups representing each of the previously recognized species in each of the genetic data sets. Compared to the double-digest restriction-site-associated DNA sequencing data set, genome skimming data provided more resolution and further opportunity to probe into patterns of nuclear and chloroplast genome diversity. Morphological and ecological associations are significantly different (albeit intergrading) among the taxa investigated. A new species, Claytonia crawfordii, is described based on morphological data presented here. CONCLUSIONS Genetic data presented in this study provide some of the first insights into phylogenetic relationships among recently diverged perennial Claytonia and are suggestive of past hybridization among caudicose and tuberous species. Given prior difficulties in understanding species boundaries among newly diverged plant lineages, this case study demonstrates the revolutionary breakthrough for systematics research that high throughput sequencing represents.
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Affiliation(s)
- Thomas R Stoughton
- Center for the Environment and Department of Biological Sciences, Plymouth State University, 17 High Street, Plymouth, NH, 03264-1594, USA
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Diana D Jolles
- Center for the Environment and Department of Biological Sciences, Plymouth State University, 17 High Street, Plymouth, NH, 03264-1594, USA
| | - Robin L O'Quinn
- Department of Biology, Eastern Washington University, 258 Science Building, 526 5th Street, Cheney, WA, 99004-2440, USA
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Ryberg M, Nilsson RH. New light on names and naming of dark taxa. MycoKeys 2018:31-39. [PMID: 29681731 PMCID: PMC5904500 DOI: 10.3897/mycokeys.30.24376] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
Abstract
A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as “dark taxa” or “dark matter fungi”. As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.
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Affiliation(s)
- Martin Ryberg
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
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16
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Wallis GP, Cameron-Christie SR, Kennedy HL, Palmer G, Sanders TR, Winter DJ. Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Mol Ecol 2017; 26:3116-3127. [DOI: 10.1111/mec.14096] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Graham P. Wallis
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Sophia R. Cameron-Christie
- Women's and Children's Health; Paediatrics & Child Health; Dunedin School of Medicine; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Hannah L. Kennedy
- Molecular Pathology Laboratory; Canterbury Health Laboratories; PO Box 151 Christchurch 8140 New Zealand
- Department of Pathology; University of Otago; Riccarton Avenue PO Box 4345 Christchurch 8140 New Zealand
| | - Gemma Palmer
- Melbourne IVF; Suite 10 320 Victoria Parade East Melbourne Vic. 3002 Australia
| | - Tessa R. Sanders
- National Institutes of Health; 9000 Rockville Pike Bethesda MD 20892 USA
| | - David J. Winter
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
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Affiliation(s)
- David Hibbett
- Biology Department, Clark University, Worcester, MA 01610, USA.
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18
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Rittmeyer EN, Austin CC. Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus). Mol Ecol 2015; 24:466-83. [PMID: 25470077 DOI: 10.1111/mec.13030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 11/17/2014] [Accepted: 11/28/2014] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next-generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the islands of Buka and Bougainville in the Solomon Archipelago. We used the Ion Torrent PGM to collect over 648 Mbp of sequence data for 12 samples, representing 1526 loci recovered from all samples, and 3342 were recovered from at least six samples. Genetic structure analyses strongly support the distinctiveness of these two populations, and Bayes factor delimitations decisively select speciation between Buka and Bougainville. Principal components and discriminant function analyses reveal concordant morphological divergence. Finally, demographic analyses via diffusion approximation and approximate Bayesian computation prefer a complex model of mid-Pleistocene divergence with migration, and a later decrease or cessation of migration and population size shift, suggesting a scenario in which migration was enabled by Pleistocene merging of these two islands, and limited when isolated by higher sea levels. Further analysis of four Sanger sequenced loci in IMa2 had limited power to distinguish among models including and excluding migration, but resulted in similar population size and divergence time estimates, although with much broader confidence intervals. This study represents a framework for how next-generation sequencing and morphological data can be combined and leveraged towards validating putative species and testing demographic scenarios for speciation.
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Affiliation(s)
- Eric N Rittmeyer
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA
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19
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Steel M, Velasco JD. Axiomatic Opportunities and Obstacles for Inferring a Species Tree from Gene Trees. Syst Biol 2014; 63:772-8. [DOI: 10.1093/sysbio/syu043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mike Steel
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Canterbury, Christchurch, New Zealand; and 2Department of Philosophy, Texas Tech University, Box 43092, Lubbock, TX 79409, USA
| | - Joel D. Velasco
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Canterbury, Christchurch, New Zealand; and 2Department of Philosophy, Texas Tech University, Box 43092, Lubbock, TX 79409, USA
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21
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Cotterill FPD, Taylor PJ, Gippoliti S, Bishop JM, Groves CP. Why One Century of Phenetics is Enough: Response to “Are There Really Twice As Many Bovid Species As We Thought?”. Syst Biol 2014; 63:819-32. [DOI: 10.1093/sysbio/syu003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Since Darwin's time, the question "what a species" has provoked fierce disputes and a tremendous number of publications, from short opinion papers to thick volumes. The debates covered fundamental philosophical questions, such as: Do species exist at all independently of a human observer or are they just a construct of the human mind to categorize nature's organismic diversity and serve as a semantic tool in human communication about biodiversity? or: Are species natural kinds (classes) or individuals that are "born" by speciation, change in course of time, and finally "die" when they go extinct or diverge into new species? Also included was the problem of species as taxa (taxonomic) versus species as products of the speciation process (evolutionary). More pragmatic issues arose, such as: How can we reliably delineate and delimitate species? The great interest in what a species is reflects the importance of "species" as fundamental units in most fields of biology, especially evolutionary biology, ecology, and conservation.
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23
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Sullivan BK, Walker JM, Taylor HL, Cordes JE, Kwiatkowski MA, Sullivan KO, Sullivan JR, Douglas MR, Douglas ME. Morphological Diagnosability ofAspidoscelis arizonae(Squamata: Teiidae) as an Indication of Evolutionary Divergence in theAspidoscelis inornataComplex. COPEIA 2013. [DOI: 10.1643/ch-12-097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Infinite graphs in systematic biology, with an application to the species problem. Acta Biotheor 2013; 61:181-201. [PMID: 23297024 DOI: 10.1007/s10441-012-9168-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 12/12/2012] [Indexed: 10/27/2022]
Abstract
We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T. A. Knight and C. Darwin, and sketch a decomposition result involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels' question, "Can biology lead to new theorems?"
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Prévot V, Jordaens K, Sonet G, Backeljau T. Exploring species level taxonomy and species delimitation methods in the facultatively self-fertilizing land snail genus Rumina (gastropoda: pulmonata). PLoS One 2013; 8:e60736. [PMID: 23577154 PMCID: PMC3618274 DOI: 10.1371/journal.pone.0060736] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/01/2013] [Indexed: 11/19/2022] Open
Abstract
Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected.
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Affiliation(s)
- Vanya Prévot
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Laboratoire d’Evolution Biologique et Ecologie, Université Libre de Bruxelles, Brussels, Belgium
| | - Kurt Jordaens
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Tervuren, Belgium and Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Gontran Sonet
- Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Tervuren, Belgium and Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Tervuren, Belgium and Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Abstract
Species as evolutionary lineages are expected to show greater evolutionary independence from one another than are populations within species. Two measures of evolutionary independence that stem from the study of isolation-with-migration models, one reflecting the amount of gene exchange and one reflecting the time of separation, were drawn from the literature for a large number of pairs of closely related species and pairs of populations within species. Both measures, for gene flow and time, showed broadly overlapping distributions for pairs of species and for pairs of populations within species. Species on average show more time and less gene flow than populations, but the similarity of the distributions argues against there being a qualitative difference associated with species status, as compared to populations. The two measures of evolutionary independence were similarly correlated with F(ST) estimates, which in turn also showed similar distributions for species comparisons relative to population comparisons. The measures of gene flow and separation time were examined for the capacity to discriminate intraspecific differences from interspecific differences. If used together, the two measures could be used to develop an objective (in the sense of being repeatable) measure for species diagnosis.
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Affiliation(s)
- Jody Hey
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA.
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27
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28
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Affiliation(s)
- Nico Cellinese
- Florida Museum of Natural History, University of Florida, 354 Dickinson Hall, Gainesville, FL 32611-7800; 2Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; and 3University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - David A. Baum
- Florida Museum of Natural History, University of Florida, 354 Dickinson Hall, Gainesville, FL 32611-7800; 2Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; and 3University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Brent D. Mishler
- Florida Museum of Natural History, University of Florida, 354 Dickinson Hall, Gainesville, FL 32611-7800; 2Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; and 3University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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GWIAZDOWSKI RODGERA, VEA ISABELLEM, ANDERSEN JEREMYC, NORMARK BENJAMINB. Discovery of cryptic species among North American pine-feedingChionaspisscale insects (Hemiptera: Diaspididae). Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01716.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Dress A, Moulton V, Steel M, Wu T. Species, clusters and the ‘Tree of life’: A graph-theoretic perspective. J Theor Biol 2010; 265:535-42. [DOI: 10.1016/j.jtbi.2010.05.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 05/25/2010] [Accepted: 05/26/2010] [Indexed: 10/19/2022]
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32
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Wilkins JS. What is a species? Essences and generation. Theory Biosci 2010; 129:141-8. [DOI: 10.1007/s12064-010-0090-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 11/10/2009] [Indexed: 11/30/2022]
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