1
|
Suetsugu K, Hirota SK, Hayakawa H, Fujimori S, Ishibashi M, Hsu TC, Suyama Y. Spiranthes hachijoensis (Orchidaceae), a new species within the S. sinensis species complex in Japan, based on morphological, phylogenetic, and ecological evidence. JOURNAL OF PLANT RESEARCH 2023; 136:333-348. [PMID: 36930386 PMCID: PMC10126103 DOI: 10.1007/s10265-023-01448-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/23/2023] [Indexed: 05/25/2023]
Abstract
The systematics of the Old World Spiranthes sinensis (Pers.) Ames species complex (Orchidaceae) has been complicated by its wide distribution and morphological variations. Within the species complex, S. australis Lindl. has been generally accepted as the only Spiranthes Rich. species distributed on the Japanese mainland. The present study provides morphological, phylogenetic, and ecological evidence for the recognition of S. hachijoensis Suetsugu as a new species of the S. sinensis species complex on the Japanese mainland. Spiranthes hachijoensis is morphologically similar to S. hongkongensis S.Y. Hu & Barretto and S. nivea T.P. Lin & W.M. Lin, sharing a degenerated rostellum, pollinia without a viscidium, and distinctly trilobed stigma. However, the taxon can be morphologically distinguished from S. hongkongensis by its glabrous rachis, ovaries, and sepals, and from S. nivea by its papillate labellum disc, larger papillate basal labellum callosities, and glabrous rachis, ovaries, and sepals. The autogamy and flowering phenology (i.e., earlier flowering) of S. hachijoensis are most likely responsible for premating isolation from the sympatric S. australis. A MIG-seq-based high-throughput molecular analysis indicated that the genetic difference between S. hachijoensis and its putative sister species S. sinensis is comparable to, or even greater than, the genetic difference between pairs of other species within the S. sinensis species complex. Our multifaceted approach strongly supports the recognition of S. hachijoensis as a morphologically, phenologically, phylogenetically, and ecologically distinct species.
Collapse
Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan.
- Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-Ku, Kobe, Hyogo, 657-8501, Japan.
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
- Botanical Gardens, Osaka Metropolitan University, 2000 Kisaichi, Katano City, Osaka, 576-0004, Japan
| | - Hiroshi Hayakawa
- Museum of Natural and Environmental History, Shizuoka, 5762 Oya, Suruga, Shizuoka, Shizuoka, Japan
| | - Shohei Fujimori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | | | - Tian-Chuan Hsu
- Botanical Garden Division, Taiwan Forestry Research Institute, No. 53, Nanhai Rd, Taipei, 100, Taiwan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| |
Collapse
|
2
|
Suetsugu K, Hirota SK, Hsu TC, Kurogi S, Imamura A, Suyama Y. Monotropastrum kirishimense (Ericaceae), a new mycoheterotrophic plant from Japan based on multifaceted evidence. JOURNAL OF PLANT RESEARCH 2023; 136:3-18. [PMID: 36445504 PMCID: PMC9832082 DOI: 10.1007/s10265-022-01422-8] [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: 08/15/2022] [Accepted: 10/26/2022] [Indexed: 05/10/2023]
Abstract
Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity.
Collapse
Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan.
- The Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Tian-Chuan Hsu
- Botanical Garden Division, Taiwan Forestry Research Institute, No. 53, Nanhai Rd., Taipei, 100, Taiwan
| | - Shuichi Kurogi
- Miyazaki Prefectural Museum of Nature and History, 2-4-4, Jingû, Miyazaki, 880-0053, Japan
| | - Akio Imamura
- Hokkaido University of Education, Sapporo, 002-8501, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| |
Collapse
|
3
|
Joffard N, Buatois B, Arnal V, Véla E, Montgelard C, Schatz B. Delimiting species in the taxonomically challenging orchid section Pseudophrys: Bayesian analyses of genetic and phenotypic data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1058550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accurate species delimitation is critical for biodiversity conservation. Integrative taxonomy has been advocated for a long time, yet tools allowing true integration of genetic and phenotypic data have been developed quite recently and applied to few models, especially in plants. In this study, we investigated species boundaries within a group of twelve Pseudophrys taxa from France by analyzing genetic, morphometric and chemical (i.e., floral scents) data in a Bayesian framework using the program integrated Bayesian Phylogenetics and Phylogeography (iBPP). We found that these twelve taxa were merged into four species when only genetic data were used, while most formally described species were recognized as such when only phenotypic (either morphometric or chemical) data were used. The result of the iBPP analysis performed on both genetic and phenotypic data supports the proposal to merge Ophrys bilunulata and O. marmorata on the one hand, and O. funerea and O. zonata on the other hand. Our results show that phenotypic data are particularly informative in the section Pseudophrys and that their integration in a model-based method significantly improves the accuracy of species delimitation. We are convinced that the integrative taxonomic approach proposed in this study holds great promise to conduct taxonomic revisions in other orchid groups.
Collapse
|
4
|
Suetsugu K, Hirota SK, Nakato N, Suyama Y, Serizawa S. Morphological, ecological, and molecular phylogenetic approaches reveal species boundaries and evolutionary history of Goodyeracrassifolia (Orchidaceae, Orchidoideae) and its closely related taxa. PHYTOKEYS 2022; 212:111-134. [PMID: 36761312 PMCID: PMC9836457 DOI: 10.3897/phytokeys.212.91536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/23/2022] [Indexed: 06/18/2023]
Abstract
Species delimitation within the genus Goodyera is challenging among closely related species, because of phenotypic plasticity, ecological variation, and hybridization that confound identification methods based solely on morphology. In this study, we investigated the identity of Goodyeracrassifolia H.-J.Suh, S.-W.Seo, S.-H.Oh & T.Yukawa, morphologically similar to Goodyeraschlechtendaliana Rchb.f. This recently described taxon has long been known in Japan as "Oh-miyama-uzura" or "Gakunan" and considered a natural hybrid of G.schlechtendaliana and G.similis Blume (= G.velutina Maxim. ex Regel). Because the natural hybrid between G.schlechtendaliana and G.similis was described as G.×tamnaensis N.S.Lee, K.S.Lee, S.H.Yeau & C.S.Lee before the description of G.crassifolia, the latter might be a synonym of G.×tamnaensis. Consequently, we investigated species boundaries and evolutionary history of G.crassifolia and its closely related taxa based on multifaceted evidence. Consequently, morphological examination enabled us to distinguish G.crassifolia from other closely related species owing to the following characteristics: coriaceous leaf texture, laxly flowered inflorescence, long pedicellate ovary, large and weakly opened flowers, and column with lateral appendages. Ecological investigation indicates that G.crassifolia (2n = 60) is agamospermous, requiring neither pollinators nor autonomous self-pollination for fruit set, whereas G.schlechtendaliana (2n = 30) is neither autogamous nor agamospermous but is obligately pollinator-dependent. MIG-seq-based phylogenetic analysis provided no evidence of recent hybridization between G.crassifolia and its close congeners. Thus, molecular phylogeny reconstructed from MIG-seq data together with morphological, cytological, and ecological analyses support the separation of G.crassifolia as an independent species.
Collapse
Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Sakyo, JapanKobe UniversitySakyoJapan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, JapanTohoku UniversityOsakiJapan
| | - Narumi Nakato
- Narahashi 1–363, Higashiyamato, Tokyo 207-0031, JapanUnaffiliatedHigashiyamatoJapan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, JapanTohoku UniversityOsakiJapan
| | - Shunsuke Serizawa
- Aichi Green Association, Urahata 198-1, Nagamaki, Oharu-sho, Aichi 490-1131, JapanAichi Green AssociationAichiJapan
| |
Collapse
|
5
|
Has taxonomic vandalism gone too far? A case study, the rise of the pay-to-publish model and the pitfalls of Morchella systematics. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01755-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
6
|
Sinn BT, Simon SJ, Santee MV, DiFazio SP, Fama NM, Barrett CF. ISSRseq: An extensible method for reduced representation sequencing. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brandon T. Sinn
- Department of Biology and Earth Science Otterbein University Westerville OH USA
- Department of Biology West Virginia University Morgantown WV USA
| | - Sandra J. Simon
- Department of Biology West Virginia University Morgantown WV USA
- Institute for Sustainability, Energy, and Environment (ISEE) University of Illinois at Urbana‐Champaign Urbana IL USA
- Department of Biology West Virginia University Institute of Technology Beckley WV USA
| | | | | | - Nicole M. Fama
- Department of Biology West Virginia University Morgantown WV USA
- Genetic Immunotherapy Section National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MD USA
| | - Craig F. Barrett
- Department of Biology West Virginia University Morgantown WV USA
| |
Collapse
|
7
|
Chiapella JO, Xue ZQ, Greimler J. The genus Deschampsia and the epithet " alpina". PHYTOKEYS 2021; 181:95-103. [PMID: 34566450 PMCID: PMC8433124 DOI: 10.3897/phytokeys.181.69546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The epithet "alpina" has been recurrently used in the genus Deschampsia to name plants located in northern regions of Europe, Asia and North America, as a species (Deschampsiaalpina (L.) Roem. & Schult.), but also in infraspecific categories (Deschampsiacespitosasubsp.alpina Tzvel. and Deschampsiacespitosavar.alpina Schur.). The morphological and molecular available evidence suggests the existence of a single species, Deschampsiacespitosa (L.) P. Beauv., in which individuals belonging to the same morphological gradient have received different names in different taxonomic categories throughout its wide distribution range. An evaluation of the available names indicates that all uses of the epithet "alpina" are illegitimate. A new combination is proposed at the infraspecific level as Deschampsiacespitosasubsp.neoalpina Chiapella, Xue & Greimler.
Collapse
Affiliation(s)
- Jorge O. Chiapella
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA-CONICET-Universidad Nacional del Comahue), Quintral 1250, R8400FRF Bariloche, Río Negro, ArgentinaUniversidad Nacional del ComahueBarilocheArgentina
| | - Zhi-Qing Xue
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, AustriaUniversity of ViennaViennaAustria
| | - Josef Greimler
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, AustriaUniversity of ViennaViennaAustria
| |
Collapse
|
8
|
Alves MF, Pinheiro F, Nunes CEP, Prosdocimi F, Sarzi DS, Furtado C, Mayer JLS. Reproductive development and genetic structure of the mycoheterotrophic orchid Pogoniopsis schenckii Cogn. BMC PLANT BIOLOGY 2021; 21:332. [PMID: 34253186 PMCID: PMC8276481 DOI: 10.1186/s12870-021-03118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Pogoniopsis schenckii Cogn. is a mycoheterotrophic orchid that can be used as a model to understand the influence of mycoheterotrophy at different stages of the reproductive cycle. We aimed to verify the presence of endophytic and epiphytic fungi at each stage of the reproductive process and investigated how the breeding system may relate to genetic structure and diversity of populations. In this study we performed anatomical and ultrastructural analyses of the reproductive organs, field tests to confirm the breeding system, and molecular analysis to assess genetic diversity and structure of populations. RESULTS During the development of the pollen grain, embryo sac and embryogenesis, no fungal infestation was observed. The presence of endophytic fungal hyphae was observed just within floral stems and indehiscent fruit. Beyond assuring the presence of fungus that promote seed germination, specific fungi hyphae in the fruit may affect other process, such as fruit ripening. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. CONCLUSIONS We discuss an interesting interaction: fungal hyphae in the indehiscent fruit. These fungal hyphae seem to play different roles inside fruit tissues, such as acting in the fruit maturation process and increasing the proximity between fungi and plant seeds even before dispersion occurs. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. Altogether, our findings provide important novel information about the mechanisms shaping ecology and evolution of fragmented populations of mycoheterotrophic plant.
Collapse
Affiliation(s)
- Mariana Ferreira Alves
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil.
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | | | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Departamento de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | |
Collapse
|
9
|
Binks RM, Steane DA, Byrne M. Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris. Ecol Evol 2021; 11:5096-5110. [PMID: 34025994 PMCID: PMC8131811 DOI: 10.1002/ece3.7403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non-contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.
Collapse
Affiliation(s)
- Rachel M. Binks
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
| | - Dorothy A. Steane
- School of Natural Sciences and ARC Training Centre for Forest ValueUniversity of TasmaniaHobartTasmaniaAustralia
- CSIRO Land and WaterSandy BayTasmaniaAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
| |
Collapse
|
10
|
Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth-sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
Collapse
Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France.
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
| |
Collapse
|
11
|
Pozzi L, Penna A, Bearder SK, Karlsson J, Perkin A, Disotell TR. Cryptic diversity and species boundaries within the Paragalago zanzibaricus species complex. Mol Phylogenet Evol 2020; 150:106887. [PMID: 32534184 DOI: 10.1016/j.ympev.2020.106887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/04/2020] [Accepted: 06/03/2020] [Indexed: 11/17/2022]
Abstract
The recently described genus Paragalago is a complex of several nocturnal and morphologically cryptic species distributed in the forests of eastern Africa. Species diversity within this genus has been mainly described using species-specific differences in their loud calls. However, molecular data are still lacking for this group and species boundaries remain unclear. In this study, we explore species diversity within the zanzibaricus-complex using a combination of mitochondrial and nuclear data and comparing multiple species delimitation methods. Our results consistently support the existence of three independent lineages, P. cocos, P. zanzibaricus, and P. granti, confirming previous hypotheses based on vocal data. We conclude that these three lineages represent valid cryptic species and we hypothesize that speciation within this complex was characterized by cycles of forest expansion and contraction in the Plio-Pleistocene.
Collapse
Affiliation(s)
- Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Anna Penna
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Todd R Disotell
- Department of Anthropology, New York University, New York, NY, USA; Department of Anthropology, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|
12
|
Lagourgue L, Puillandre N, Payri CE. Exploring the Udoteaceae diversity (Bryopsidales, Chlorophyta) in the Caribbean region based on molecular and morphological data. Mol Phylogenet Evol 2018; 127:758-769. [DOI: 10.1016/j.ympev.2018.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 06/03/2018] [Accepted: 06/11/2018] [Indexed: 11/26/2022]
|
13
|
Barrett CF, Wicke S, Sass C. Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex. THE NEW PHYTOLOGIST 2018; 218:1192-1204. [PMID: 29502351 PMCID: PMC5902423 DOI: 10.1111/nph.15072] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/23/2018] [Indexed: 05/08/2023]
Abstract
Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here, we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of genomic change among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help to fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Collapse
Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 5218 Life Sciences Building, 53 Campus Drive, Morgantown, WV 26501, USA
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, 48149 Muenster, Germany
| | - Chodon Sass
- Department of Plant and Microbial Biology, University of California, Berkeley, 431 Koshland Hall, Berkeley, California 94720, USA
| |
Collapse
|
14
|
Camelier P, Menezes NA, Costa-Silva GJ, Oliveira C. Molecular and morphological data of the freshwater fish Glandulocauda melanopleura (Characiformes: Characidae) provide evidences of river captures and local differentiation in the Brazilian Atlantic Forest. PLoS One 2018; 13:e0194247. [PMID: 29579069 PMCID: PMC5868800 DOI: 10.1371/journal.pone.0194247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/27/2018] [Indexed: 01/16/2023] Open
Abstract
The current distribution of freshwater fishes across multiple basins along Eastern Brazil can be associated to two main events: river captures or temporary paleoconnections. Apparently, river captures had a more significant role on distribution and structuring of species from upland areas, such as Glandulocauda melanopleura. Populations of this species are found in contiguous drainages in presently isolated upper parts of Rio Tietê and the coastal basins of Guaratuba, Itatinga, Itanháem, and Ribeira de Iguape, in the Atlantic Forest domain. The allopatric and disjoint distribution of G. melanopleura associated with variation of morphological characters detected among geographically isolated populations stimulated this study. Thus, an integrative approach was undertaken, including morphological and molecular data, to better understand the evolutionary history of the species and the area where it occurs. Molecular analyses based on two mitochondrial markers revealed a strong genetic structure within G. melanopleura, that allowed recognition of two lineages, one distributed in both the upper Tietê and Itanhaém and the other in the Guaratuba. Overall, morphological data revealed some intraspecific overlapping variation, indicating that all samples are conspecific. Phylogenetic and phylogeographic analyses allied to divergence times and geomorphological information indicate that the current distribution of G. melanopleura is a result of relatively recent river captures involving the Tietê and some other coastal drainages. Although of recent origin, they occurred long enough to completely isolate these populations, since there are no haplotypes sharing between them. The conservation status of this species is also discussed, and our results corroborate the need to understand population structure for conservation planning.
Collapse
Affiliation(s)
- Priscila Camelier
- Museu de Zoologia da Universidade de São Paulo, CEP, São Paulo, SP, Brazil
| | | | - Guilherme José Costa-Silva
- Universidade Santo Amaro, Rua Prof. Enéas de Siqueira Neto, Jardim das Imbuias, CEP, São Paulo, SP, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito Rubião Jr., CEP, Botucatu, SP, Brazil
| |
Collapse
|
15
|
Freudenstein JV, Broe MB, Folk RA, Sinn BT. Biodiversity and the Species Concept-Lineages are not Enough. Syst Biol 2018; 66:644-656. [PMID: 27798406 DOI: 10.1093/sysbio/syw098] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/14/2016] [Indexed: 11/13/2022] Open
Abstract
The nature and definition of species continue to be matters of debate. Current views of species often focus on their nature as lineages-maximal reproductive communities through time. Whereas many authors point to the Evolutionary Species Concept as optimal, in its original form it stressed the ecological role of species as well as their history as lineages, but most recent authors have ignored the role aspect of the concept, making it difficult to apply unambiguously in a time-extended way. This trend has been exacerbated by the application of methods and concepts emphasizing the notion of monophyly, originally applied only at higher levels, to the level of individuals, as well as by the current emphasis on molecular data. Hence, some current authors recognize units that are no more than probable exclusive lineages as species. We argue that biodiversity is inherently a phenotypic concept and that role, as manifested in the organismal extended phenotype, is a necessary component of the species concept. Viewing species as historically connected populations with unique role brings together the temporal and phenotypic natures of species, providing a clear way to view species both in a time-limited and time-extended way. Doing so alleviates perceived issues with "paraphyletic species" and returns the focus of species to units that are most relevant for biodiversity.
Collapse
Affiliation(s)
- John V Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA
| | - Michael B Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA
| | - Ryan A Folk
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA.,Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Brandon T Sinn
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA.,New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10458, USA
| |
Collapse
|
16
|
Merényi Z, Varga T, Hubai AG, Pitlik P, Erős Á, Trappe JM, Bratek Z. Challenges in the delimitation of morphologically similar species: a case study of Tuber brumale agg. (Ascomycota, Pezizales). Mycol Prog 2017. [DOI: 10.1007/s11557-017-1296-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
17
|
Díaz-Cárdenas B, Ruiz-Sanchez E, Castro-Felix P, Castañeda-Gaytán G, Ruiz-Santana S, Gadsden H. Species delimitation of the blue-spotted spiny lizard within a multilocus, multispecies coalescent framework, results in the recognition of a new Sceloporus species. Mol Phylogenet Evol 2017; 111:185-195. [PMID: 28392486 DOI: 10.1016/j.ympev.2017.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/03/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
Species delimitation is a major topic in systematics. Species delimitation methods based on molecular data have become more common since this approach provides insights about species identification via levels of gene flow, the degree of hybridization and phylogenetic relationships. Also, combining multilocus mitochondrial and nuclear DNA leads to more reliable conclusions about species limits. Coalescent-based species delimitation methods explicitly reveal separately evolving lineages using probabilistic approaches and testing the delimitation hypotheses for several species. Within a multispecies, multilocus, coalescent framework, we were able to clarify taxonomic uncertainties within S. cyanostictus, an endangered lizard that inhabits a narrow strip of the Chihuahuan Desert in Mexico. We included, for the first time in a phylogenetic analysis, lizards from the three populations of S. cyanostictus recognized so far (East Coahuila, West Coahuila and Nuevo León). Phylogenetic analysis corroborates the hypothesis of two separately evolving lineages, i.e. the East and West Coahuila populations, as proposed in a previous study. We also found a distant phylogenetic relationship between the lizards from Nuevo León and those of East and West Coahuila. Finally, based on the species delimitation results, we propose and describe a new species of Sceloporus: S. gadsdeni sp. nov.
Collapse
Affiliation(s)
- Brenda Díaz-Cárdenas
- Instituto de Ecología, A. C., Carretera antigua a Coatepec 351, El Haya, C.P. 91070 Xalapa Enríquez, Veracruz, Mexico
| | - Eduardo Ruiz-Sanchez
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Nextipac, Zapopán, Jalisco 45510, Mexico.
| | - Patricia Castro-Felix
- Departamento de Biología Celular y Molecular, Universidad de Guadalajara, Centro Universitario de Ciencias Biológicas y Agropecuarias, Camino Ing. Ramón Padilla Sánchez 2100, Nextipac, C.P. 45510 Zapopan, Jalisco, Mexico
| | - Gamaliel Castañeda-Gaytán
- Universidad Juárez del Estado de Durango, Facultad de Ciencias Biológicas, Av. Universidad S/N col. Filadelfia, C.P. 35010 Gómez Palacio, Durango, Mexico
| | - Sergio Ruiz-Santana
- Instituto de Ecología, A. C., Carretera antigua a Coatepec 351, El Haya, C.P. 91070 Xalapa Enríquez, Veracruz, Mexico
| | - Héctor Gadsden
- Instituto de Ecología, A. C., Centro Regional de Bajío, Av. Lázaro Cárdenas 253, 61600 Pátzcuaro, Michoacán, Mexico
| |
Collapse
|
18
|
Welton LJ, Siler CD, Grismer LL, Diesmos AC, Sites JW, Brown RM. Archipelago-wide survey of Philippine forest dragons (Agamidae:Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luke J. Welton
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology; 2401 Chautauqua Ave., University of Oklahoma; Norman OK 73072-7029 USA
| | - L. L. Grismer
- Department of Biology; 4500 Riverwalk Parkway, La Sierra University; Riverside CA 92515-8247 USA
| | - Arvin C. Diesmos
- Herpetology Section; Zoology Division; National Museum of the Philippines; Rizal Park Padre Burgos Avenue Manila Philippines
| | - Jack W. Sites
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
| |
Collapse
|
19
|
Wang N, Liang B, Wang J, Yeh CF, Liu Y, Liu Y, Liang W, Yao CT, Li SH. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves). Mol Phylogenet Evol 2016; 102:62-73. [PMID: 27233437 DOI: 10.1016/j.ympev.2016.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/26/2016] [Accepted: 05/20/2016] [Indexed: 01/11/2023]
Abstract
Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process.
Collapse
Affiliation(s)
- Ning Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bin Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yang Liu
- State Key Laboratory of BioControl, College of Ecology and Evolution/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanlin Liu
- Institute of Forestry Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Cheng-Te Yao
- High-Altitude Experimental Station, Taiwan Endemic Species Research Institute, Chi-chi 55244, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
| |
Collapse
|
20
|
Liu J, Zhou W, Gong X. Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China. FRONTIERS IN PLANT SCIENCE 2015; 6:696. [PMID: 26442013 PMCID: PMC4562272 DOI: 10.3389/fpls.2015.00696] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/21/2015] [Indexed: 06/02/2023]
Abstract
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.
Collapse
Affiliation(s)
- Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Wei Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- Yunnan Key Laboratory for Wild Plant ResourcesKunming, China
| |
Collapse
|
21
|
Kekkonen M, Mutanen M, Kaila L, Nieminen M, Hebert PDN. Delineating species with DNA barcodes: a case of taxon dependent method performance in moths. PLoS One 2015; 10:e0122481. [PMID: 25849083 PMCID: PMC4406103 DOI: 10.1371/journal.pone.0122481] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/22/2015] [Indexed: 11/26/2022] Open
Abstract
The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.
Collapse
Affiliation(s)
- Mari Kekkonen
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Oulu, Finland
| | - Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
| | - Marko Nieminen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
22
|
McKay BD, Mays HL, Wu Y, Li H, Yao CT, Nishiumi I, Zou F. An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex. Mol Ecol 2014; 22:4943-57. [PMID: 24073650 DOI: 10.1111/mec.12446] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 11/30/2022]
Abstract
The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography (BPP), a coalescent-based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation-with-distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data.
Collapse
Affiliation(s)
- Bailey D McKay
- Bell Museum of Natural History, Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science that provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth to sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification, the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity enters its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
Collapse
|
24
|
Linde CC, Phillips RD, Crisp MD, Peakall R. Congruent species delineation of Tulasnella using multiple loci and methods. THE NEW PHYTOLOGIST 2014; 201:6-12. [PMID: 24028679 DOI: 10.1111/nph.12492] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Celeste C Linde
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Ryan D Phillips
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
- The Botanic Garden and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, 6005, Australia
- School of Plant Biology, The University of Western Australia, Nedlands, WA, 6009, Australia
| | - Michael D Crisp
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Rod Peakall
- Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| |
Collapse
|
25
|
Barley AJ, White J, Diesmos AC, Brown RM. THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS. Evolution 2013; 67:3556-72. [DOI: 10.1111/evo.12219] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/08/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | - Jordan White
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | | | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| |
Collapse
|
26
|
Krug PJ, Vendetti JE, Rodriguez AK, Retana JN, Hirano YM, Trowbridge CD. Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control. Mol Phylogenet Evol 2013; 69:1101-19. [PMID: 23876292 DOI: 10.1016/j.ympev.2013.07.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 11/30/2022]
Abstract
DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed "species" each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The "circumtropical" Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The "monotypic" and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated.
Collapse
Affiliation(s)
- Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA.
| | | | | | | | | | | |
Collapse
|
27
|
Carstens BC, Pelletier TA, Reid NM, Satler JD. How to fail at species delimitation. Mol Ecol 2013; 22:4369-83. [PMID: 23855767 DOI: 10.1111/mec.12413] [Citation(s) in RCA: 642] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 11/29/2022]
Abstract
Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.
Collapse
Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210-1293, USA.
| | | | | | | |
Collapse
|
28
|
Satler JD, Carstens BC, Hedin M. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus). Syst Biol 2013; 62:805-23. [PMID: 23771888 DOI: 10.1093/sysbio/syt041] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
Collapse
Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio University, Columbus, OH 43210, USA and Department of Biology, San Diego University, San Diego, CA 92182, USA
| | | | | |
Collapse
|
29
|
Arthofer W, Rauch H, Thaler-Knoflach B, Moder K, Muster C, Schlick-Steiner BC, Steiner FM. How diverse isMitopus morio? Integrative taxonomy detects cryptic species in a small-scale sample of a widespread harvestman. Mol Ecol 2013; 22:3850-63. [DOI: 10.1111/mec.12340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Wolfgang Arthofer
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Hannes Rauch
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Barbara Thaler-Knoflach
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Karl Moder
- Institute of Mathematics and Applied Statistics; Department of Spatial, Landscape, and Infrastructure Sciences; University of Natural Resources and Life Sciences; Peter Jordan-Strasse 82, 1180 Vienna Austria
| | - Christoph Muster
- General Zoology and Zoological Systematics; Zoological Institute and Museum; University of Greifswald; Johann Sebastian Bach-Str 11/12, 17487 Greifswald Germany
| | - Birgit C. Schlick-Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| | - Florian M. Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstrasse 25, 6020 Innsbruck Austria
| |
Collapse
|
30
|
Welton LJ, Siler CD, Oaks JR, Diesmos AC, Brown RM. Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards. Mol Ecol 2013; 22:3495-510. [DOI: 10.1111/mec.12324] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 03/17/2013] [Accepted: 03/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- L. J. Welton
- Department of Biology; Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - C. D. Siler
- Department of Biology; University of South Dakota; Vermillion SD 57069 USA
| | - J. R. Oaks
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| | - A. C. Diesmos
- Herpetology Section; Zoology Division; Philippine National Museum; Rizal Park, Burgos Street Manila Philippines
| | - R. M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045-7561 USA
| |
Collapse
|
31
|
Carstens BC, Satler JD. The carnivorous plant described asSarracenia alatacontains two cryptic species. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12093] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; Ohio State University; Columbus; OH; 43210; USA
| | - Jordan D. Satler
- Department of Evolution, Ecology and Organismal Biology; Ohio State University; Columbus; OH; 43210; USA
| |
Collapse
|
32
|
Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
| |
Collapse
|
33
|
Barrett CF, Davis JI. The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. AMERICAN JOURNAL OF BOTANY 2012; 99:1513-23. [PMID: 22935364 DOI: 10.3732/ajb.1200256] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Plastid genomes of nonphotosynthetic, mycoheterotrophic plants represent apt systems in which to study effects of relaxed evolutionary constraints. The few mycoheterotrophic angiosperm plastomes sequenced to date display drastic patterns of degradation/reduction relative to those of photosynthetic relatives. The goal of this study was to focus on a mycoheterotrophic orchid hypothesized to be in the "early" stages of plastome degradation, to provide perspective on this process. METHODS Short-read sequencing was used to generate a complete plastome sequence for Corallorhiza striata var. vreelandii, a mycoheterotrophic orchid, to investigate the extent of plastome degradation. Patterns of nonsynonymous/synonymous mutations were also assessed, and comparisons were made between Corallorhiza and other heterotrophic plant lineages. KEY RESULTS Corallorhiza yielded a plastome of 137505 bp, with several photosynthesis-related genes either lost or pseudogenized. Members of all major photosynthesis complexes, except ATP-synthase genes, were affected. "Housekeeping" genes were intact, despite the loss of a single tRNA. Intact photosynthesis genes (excluding atp genes) together displayed elevated nonsynonymous changes, while housekeeping genes did not. CONCLUSIONS The Corallorhiza plastome is not drastically reduced in overall size (∼6% reduction relative to that of photosynthetic Oncidium), but displays a pattern congruent with a loss of photosynthetic function. Comparing Corallorhiza with other heterotrophs allows some emergent evolutionary patterns to be inferred, but these remain as hypotheses to be tested, especially at lower taxonomic levels, and in lineages illustrating transitions from autotrophy to heterotrophy. The independent, unique processes of plastome modification among mycoheterotrophic lineages illustrate the urgency of their conservation.
Collapse
Affiliation(s)
- Craig F Barrett
- Department of Plant Biology and L.H. Bailey Hortorium, 412 Mann Library, Cornell University, Ithaca, New York 14853, USA.
| | | |
Collapse
|
34
|
Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol Evol 2012; 27:480-8. [PMID: 22633974 DOI: 10.1016/j.tree.2012.04.012] [Citation(s) in RCA: 500] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 04/09/2012] [Accepted: 04/24/2012] [Indexed: 11/21/2022]
|
35
|
|
36
|
LEGA MARGHERITA, FIOR SIMONE, PROSSER FILIPPO, BERTOLLI ALESSIO, LI MINGAI, VAROTTO CLAUDIO. Application of the unified species concept reveals distinct lineages for disjunct endemics of the Brassica repanda (Brassicaceae) complex. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01887.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
37
|
Bacon CD, McKenna MJ, Simmons MP, Wagner WL. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). BMC Evol Biol 2012; 12:23. [PMID: 22353848 PMCID: PMC3356231 DOI: 10.1186/1471-2148-12-23] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages. RESULTS Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups. CONCLUSIONS Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.
Collapse
Affiliation(s)
- Christine D Bacon
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
- Smithsonian Tropical Research, Box 0843-03092, Balboa, Ancón, Republic of Panamá
| | - Miles J McKenna
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Warren L Wagner
- Department of Botany, Smithsonian Institution, MRC-166, P.O. Box 37012, Washington, D.C. 20013-7012, USA
| |
Collapse
|
38
|
Gebiola M, Gómez-Zurita J, Monti MM, Navone P, Bernardo U. Integration of molecular, ecological, morphological and endosymbiont data for species delimitation within the Pnigalio soemius complex (Hymenoptera: Eulophidae). Mol Ecol 2012; 21:1190-208. [PMID: 22268975 DOI: 10.1111/j.1365-294x.2011.05428.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integrative taxonomy is a recently developed approach that uses multiple lines of evidence such as molecular, morphological, ecological and geographical data to test species limits, and it stands as one of the most promising approaches to species delimitation in taxonomically difficult groups. The Pnigalio soemius complex (Hymenoptera: Eulophidae) represents an interesting taxonomical and ecological study case, as it is characterized by a lack of informative morphological characters, deep mitochondrial divergence, and is susceptible to infection by parthenogenesis-inducing Rickettsia. We tested the effectiveness of an integrative taxonomy approach in delimiting species within the P. soemius complex. We analysed two molecular markers (COI and ITS2) using different methods, performed multivariate analysis on morphometric data and exploited ecological data such as host-plant system associations, geographical separation, and the prevalence, type and effects of endosymbiont infection. The challenge of resolving different levels of resolution in the data was met by setting up a formal procedure of data integration within and between conflicting independent lines of evidence. An iterative corroboration process of multiple sources of data eventually indicated the existence of several cryptic species that can be treated as stable taxonomic hypotheses. Furthermore, the integrative approach confirmed a trend towards host specificity within the presumed polyphagous P. soemius and suggested that Rickettsia could have played a major role in the reproductive isolation and genetic diversification of at least two species.
Collapse
Affiliation(s)
- M Gebiola
- CNR-Istituto per la Protezione delle Piante, UOS di Portici, Via Università 133, Portici (NA), Italy.
| | | | | | | | | |
Collapse
|
39
|
|