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Imwattana K, Aguero B, Duffy A, Shaw AJ. Demographic history and gene flow in the peatmosses
Sphagnum recurvum
and
Sphagnum flexuosum
(Bryophyta: Sphagnaceae). Ecol Evol 2022; 12:e9489. [PMCID: PMC9667404 DOI: 10.1002/ece3.9489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/28/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Karn Imwattana
- Department of Biology & L. E. Anderson Bryophyte Herbarium Duke University Durham North Carolina USA
| | - Blanka Aguero
- Department of Biology & L. E. Anderson Bryophyte Herbarium Duke University Durham North Carolina USA
| | - Aaron Duffy
- Department of Biology & L. E. Anderson Bryophyte Herbarium Duke University Durham North Carolina USA
| | - A. Jonathan Shaw
- Department of Biology & L. E. Anderson Bryophyte Herbarium Duke University Durham North Carolina USA
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Flatberg KI, Hassel K, Prestø T, Kyrkjeeide MO, Shaw AJ, Ahti T. Sphagnum magniporosum (Sphagnaceae, subgenus Subsecunda) a new peatmoss species from Venezuela. LINDBERGIA 2022. [DOI: 10.25227/linbg.01161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Kjell Ivar Flatberg
- K. I. Flatberg, K. Hassel (https://orcid.org/0000-0002-1906-8166) ✉ and T. Prestø, Dept of Natural History, NTNU Univ. Museum, Norwegian Univ. of Science and Technology, Trondheim, Norway
| | - Kristian Hassel
- K. I. Flatberg, K. Hassel (https://orcid.org/0000-0002-1906-8166) ✉ and T. Prestø, Dept of Natural History, NTNU Univ. Museum, Norwegian Univ. of Science and Technology, Trondheim, Norway
| | - Tommy Prestø
- K. I. Flatberg, K. Hassel (https://orcid.org/0000-0002-1906-8166) ✉ and T. Prestø, Dept of Natural History, NTNU Univ. Museum, Norwegian Univ. of Science and Technology, Trondheim, Norway
| | | | - A. Jonathan Shaw
- A. J. Shaw, Dept of Biology, L.E. Anderson Bryophyte Herbarium, Duke Univ., Durham, NC, USA
| | - Teuvo Ahti
- T. Ahti, Botany Dept, Finnish Museum of Natural History, Univ. of Helsinki, Helsinki, Finland
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Duffy AM, Aguero B, Stenøien HK, Flatberg KI, Ignatov MS, Hassel K, Shaw AJ. Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta) in relation to taxonomy and geography. AMERICAN JOURNAL OF BOTANY 2020; 107:1283-1295. [PMID: 32930404 DOI: 10.1002/ajb2.1525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2002] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
PREMISE The Sphagnum recurvum complex comprises a group of closely related peat mosses that are dominant components of many northern wetland ecosystems. Taxonomic hypotheses for the group range from interpreting the whole complex as one polymorphic species to distinguishing 6-10 species. The complex occurs throughout the Northern Hemisphere, and some of the putative species have intercontinental ranges. Our goals were to delimit the complex and assess its phylogenetic structure in relation to morphologically defined species and intercontinental geography. METHODS RADseq analyses were applied to a sample of 384 collections from Europe, North America, and Asia. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software STRUCTURE and multivariate ordination approaches. RESULTS The S. recurvum complex includes S. angustifolium, S. fallax, S. flexuosum, S. pacificum, and S. recurvum as clades with little evidence of admixture. We also resolved an unnamed clade that is referred to here as S. "pseudopacificum." We confirm that S. balticum and S. obtusum are nested within the complex. Species with bluntly acute to obtuse stem leaf apices are sister to those with acute to apiculate leaves. Most of the species exhibit some differentiation between intraspecific population systems disjunct on different continents. CONCLUSIONS We recognize seven species in the amended S. recurvum complex, including S. balticum and S. obtusum, in addition to the informal clade S. "pseudopacificum." Although we detected some geographically correlated phylogenetic structure within widespread morphospecies, our RADseq data support the interpretation that these species have intercontinental geographic ranges.
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Affiliation(s)
- Aaron M Duffy
- Lewis E. Anderson Bryophyte Herbarium, Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Blanka Aguero
- Lewis E. Anderson Bryophyte Herbarium, Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Hans K Stenøien
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kjell Ivar Flatberg
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Michael S Ignatov
- Tsitsin Main Botanical Garden of Russian Academy of Sciences, Moscow, Russia
| | - Kristian Hassel
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - A Jonathan Shaw
- Lewis E. Anderson Bryophyte Herbarium, Department of Biology, Duke University, Durham, North Carolina, 27708, USA
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4
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Lee GE, Condamine FL, Bechteler J, Pérez-Escobar OA, Scheben A, Schäfer-Verwimp A, Pócs T, Heinrichs J. An ancient tropical origin, dispersals via land bridges and Miocene diversification explain the subcosmopolitan disjunctions of the liverwort genus Lejeunea. Sci Rep 2020; 10:14123. [PMID: 32839508 PMCID: PMC7445168 DOI: 10.1038/s41598-020-71039-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the biogeographical and diversification processes explaining current diversity patterns of subcosmopolitan-distributed groups is challenging. We aimed at disentangling the historical biogeography of the subcosmopolitan liverwort genus Lejeunea with estimation of ancestral areas of origin and testing if sexual system and palaeotemperature variations can be factors of diversification. We assembled a dense taxon sampling for 120 species sampled throughout the geographical distribution of the genus. Lejeunea diverged from its sister group after the Paleocene-Eocene boundary (52.2 Ma, 95% credibility intervals 50.1-54.2 Ma), and the initial diversification of the crown group occurred in the early to middle Eocene (44.5 Ma, 95% credibility intervals 38.5-50.8 Ma). The DEC model indicated that (1) Lejeunea likely originated in an area composed of the Neotropics and the Nearctic, (2) dispersals through terrestrial land bridges in the late Oligocene and Miocene allowed Lejeunea to colonize the Old World, (3) the Boreotropical forest covering the northern regions until the late Eocene did not facilitate Lejeunea dispersals, and (4) a single long-distance dispersal event was inferred between the Neotropics and Africa. Biogeographical and diversification analyses show the Miocene was an important period when Lejeunea diversified globally. We found slight support for higher diversification rates of species with both male and female reproductive organs on the same individual (monoicy), and a moderate positive influence of palaeotemperatures on diversification. Our study shows that an ancient origin associated with a dispersal history facilitated by terrestrial land bridges and not long-distance dispersals are likely to explain the subcosmopolitan distribution of Lejeunea. By enhancing the diversification rates, monoicy likely favoured the colonisations of new areas, especially in the Miocene that was a key epoch shaping the worldwide distribution.
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Affiliation(s)
- Gaik Ee Lee
- Faculty of Science and Marine Environment, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Julia Bechteler
- Nees Institute for Biodiversity of Plants, University of Bonn, 53115, Bonn, Germany
| | | | - Armin Scheben
- School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Tamás Pócs
- Botany Department, Institute of Biology, Eszterházy University, Pf. 43, Eger, 3301, Hungary
| | - Jochen Heinrichs
- Department of Biology I, Systematic Botany and Mycology, Geobio-Center, University of Munich (LMU), Menzinger Str. 67, 80638, Munich, Germany
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5
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Singer D, Mitchell EAD, Payne RJ, Blandenier Q, Duckert C, Fernández LD, Fournier B, Hernández CE, Granath G, Rydin H, Bragazza L, Koronatova NG, Goia I, Harris LI, Kajukało K, Kosakyan A, Lamentowicz M, Kosykh NP, Vellak K, Lara E. Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists. Mol Ecol 2019; 28:3089-3100. [DOI: 10.1111/mec.15117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/26/2022]
Affiliation(s)
- David Singer
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Department of Zoology, Institute of Biosciences University of São Paulo São Paulo Brazil
| | - Edward A. D. Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Jardin Botanique de Neuchâtel Neuchâtel Switzerland
| | | | - Quentin Blandenier
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Real Jardín Botánico CSIC Madrid Spain
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
| | - Leonardo D. Fernández
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS) Universidad Bernardo O'Higgins Santiago Chile
| | - Bertrand Fournier
- Community and Quantitative Ecology Laboratory, Department of Biology Concordia University Montreal QC Canada
| | - Cristián E. Hernández
- Facultad de Ciencias Naturales y Oceanográficas, Departamento de Zoología Universidad de Concepción Barrio Universitario de Concepción Chile
| | - Gustaf Granath
- Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Håkan Rydin
- Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Luca Bragazza
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research Lausanne Switzerland
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Féderale de Lausanne (EPFL) School of Architecture, Civil and Environmental Engineering (ENAC) Lausanne Switzerland
- Department of Life Science and Biotechnologies University of Ferrara Ferrara Italy
| | - Natalia G. Koronatova
- Laboratory of Biogeocenology, Institute of Soil Science and Agrochemistry Siberian Branch of Russian Academy of Sciences Novosibirsk Russia
| | - Irina Goia
- Department of Taxonomy and Ecology, Faculty of Biology and Geology Babeș‐Bolyai University Cluj‐Napoca Romania
| | - Lorna I. Harris
- School of Geography and Earth Sciences McMaster University Hamilton ON Canada
| | - Katarzyna Kajukało
- Laboratory of Wetland Ecology and Monitoring, Faculty of Geographical and Geological Sciences and Department of Biogeography and Paleoecology Adam Mickiewicz University Poznań Poland
| | - Anush Kosakyan
- Institute of Parasitology, Biology Center Czech Academy of Sciences České Budĕjovice Czech Republic
| | - Mariusz Lamentowicz
- Laboratory of Wetland Ecology and Monitoring, Faculty of Geographical and Geological Sciences and Department of Biogeography and Paleoecology Adam Mickiewicz University Poznań Poland
| | - Natalia P. Kosykh
- Laboratory of Biogeocenology, Institute of Soil Science and Agrochemistry Siberian Branch of Russian Academy of Sciences Novosibirsk Russia
| | - Kai Vellak
- Institute of Ecology and Earth Sciences, Natural History Museum University of Tartu Tartu Estonia
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Real Jardín Botánico CSIC Madrid Spain
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Shaw AJ, Carter BE, Aguero B, da Costa DP, Crowl AA. Range change evolution of peat mosses (Sphagnum) within and between climate zones. GLOBAL CHANGE BIOLOGY 2019; 25:108-120. [PMID: 30346105 DOI: 10.1111/gcb.14485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Peat mosses (Sphagnum) hold exceptional importance in the control of global carbon fluxes and climate because of the vast stores of carbon bound up in partially decomposed biomass (peat). This study tests the hypothesis that the early diversification of Sphagnum was in the Northern Hemisphere, with subsequent range expansions to tropical latitudes and the Southern Hemisphere. A phylogenetic analysis of 192 accessions representing the moss class Sphagnopsida based on four plastid loci was conducted in conjunction with biogeographic analyses using BioGeoBEARS to investigate the tempo and mode of geographic range evolution. Analyses support the hypothesis that the major intrageneric clades of peat-forming species accounting for >90% of peat moss diversity originated and diversified at northern latitudes. The genus underwent multiple range expansions into tropical and Southern Hemisphere regions. Range evolution in peat mosses was most common within latitudinal zones, attesting to the relative difficulty of successfully invading new climate zones. Allopolyploidy in Sphagnum (inferred from microsatellite heterozygosity) does not appear to be biased with regard to geographic region nor intrageneric clade. The inference that Sphagnum diversified in cool-or cold-climate regions and repeatedly expanded its range into tropical regions makes the genus an excellent model for studying morphological, physiological, and genomic traits associated with adaptation to warming climates.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina
| | - Benjamin E Carter
- Department of Biological Sciences, San Jose State University, San Jose, California
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Andrew A Crowl
- Department of Biology, Duke University, Durham, North Carolina
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Meleshko O, Stenøien HK, Speed JDM, Flatberg KI, Kyrkjeeide MO, Hassel K. Is interspecific gene flow and speciation in peatmosses ( Sphagnum) constrained by phylogenetic relationship and life-history traits? LINDBERGIA 2018. [DOI: 10.25227/linbg.01107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Olena Meleshko
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Hans K. Stenøien
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - James D. M. Speed
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Kjell I. Flatberg
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | | | - Kristian Hassel
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
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8
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Ikeda H, Setoguchi H. Importance of Beringia for the divergence of two northern Pacific alpine plants, Phyllodoce aleutica and Phyllodoce glanduliflora (Ericaceae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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9
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Baughman JT, Payton AC, Paasch AE, Fisher KM, McDaniel SF. Multiple factors influence population sex ratios in the Mojave Desert moss Syntrichia caninervis. AMERICAN JOURNAL OF BOTANY 2017; 104:733-742. [PMID: 28490519 DOI: 10.3732/ajb.1700045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF RESEARCH Natural populations of many mosses appear highly female-biased based on the presence of reproductive structures. This bias could be caused by increased male mortality, lower male growth rate, or a higher threshold for achieving sexual maturity in males. Here we test these hypotheses using samples from two populations of the Mojave Desert moss Syntrichia caninervis. METHODS We used double-digest restriction-site associated DNA (RAD) sequencing to identify candidate sex-associated loci in a panel of sex-expressing plants. Next, we used putative sex-associated markers to identify the sex of individuals without sex structures. KEY RESULTS We found a 17:1 patch-level phenotypic female to male sex ratio in the higher elevation site (Wrightwood) and no sex expression at the low elevation site (Phelan). In contrast, on the basis of genetic data, we found a 2:1 female bias at the Wrightwood site and only females at the Phelan site. The relative area occupied by male and female genets was indistinguishable, but males were less genetically diverse. CONCLUSIONS Our data suggest that both male-biased mortality and sexual dimorphism in thresholds for sex expression could explain genetic and phenotypic sex ratio biases and that phenotypic sex expression alone over-estimates the extent of actual sex ratio bias present in these two populations of S. caninervis.
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Affiliation(s)
- Jenna T Baughman
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Adam C Payton
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida 32611 USA
| | - Amber E Paasch
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida 32611 USA
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10
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Bechteler J, Schäfer-Verwimp A, Lee GE, Feldberg K, Pérez-Escobar OA, Pócs T, Peralta DF, Renner MAM, Heinrichs J. Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts. Ecol Evol 2016; 7:638-653. [PMID: 28116059 PMCID: PMC5243195 DOI: 10.1002/ece3.2656] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/21/2016] [Accepted: 11/05/2016] [Indexed: 01/13/2023] Open
Abstract
The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL-F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum-likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9-93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2-52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio-Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long-distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large-scale distribution of humid tropical angiosperm forests in the Eocene.
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Affiliation(s)
- Julia Bechteler
- Department of Biology I, Systematic Botany and Mycology GeoBio-Center University of Munich (LMU) Munich Germany
| | | | - Gaik Ee Lee
- Department of Biology I, Systematic Botany and Mycology GeoBio-Center University of Munich (LMU) Munich Germany; School of Marine and Environmental Sciences University of Malaysia Terengganu Kuala Terengganu Terengganu Malaysia
| | - Kathrin Feldberg
- Department of Biology I, Systematic Botany and Mycology GeoBio-Center University of Munich (LMU) Munich Germany
| | | | - Tamás Pócs
- Botany Department Eszterházy University Eger Hungary
| | | | | | - Jochen Heinrichs
- Department of Biology I, Systematic Botany and Mycology GeoBio-Center University of Munich (LMU) Munich Germany
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11
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Carter BE, Larraín J, Manukjanová A, Shaw B, Shaw AJ, Heinrichs J, de Lange P, Suleiman M, Thouvenot L, von Konrat M. Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta). Mol Phylogenet Evol 2016; 107:16-26. [PMID: 27744015 DOI: 10.1016/j.ympev.2016.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/27/2016] [Accepted: 10/05/2016] [Indexed: 11/30/2022]
Abstract
Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.
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Affiliation(s)
- Benjamin E Carter
- Department of Biology, Duke University, 139 Biological Sciences Building, Box 90338, Durham, NC 27708, USA.
| | - Juan Larraín
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - Alžběta Manukjanová
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370 05 České Budějovice, Czech Republic
| | - Blanka Shaw
- Department of Biology, Duke University, 139 Biological Sciences Building, Box 90338, Durham, NC 27708, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, 139 Biological Sciences Building, Box 90338, Durham, NC 27708, USA
| | - Jochen Heinrichs
- Department of Biology I and Geobio-Center, Ludwig Maximilian University, Menzinger Str. 67, 80638 Munich, Germany
| | - Peter de Lange
- Science & Policy Group, Department of Conservation, Private Bag 68908, Newton, Auckland 1145, New Zealand
| | - Monica Suleiman
- Institute for Tropical Biology and Conservation, University Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Malaysia
| | | | - Matt von Konrat
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
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Norhazrina N, Vanderpoorten A, Hedenäs L, Patiño J. What are the evolutionary mechanisms explaining the similar species richness patterns in tropical mosses? Insights from the phylogeny of the pantropical genus Pelekium. Mol Phylogenet Evol 2016; 105:139-145. [PMID: 27530707 DOI: 10.1016/j.ympev.2016.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/02/2016] [Accepted: 08/12/2016] [Indexed: 11/25/2022]
Abstract
As opposed to angiosperms, moss species richness is similar among tropical regions of the world, in line with the hypothesis that tropical bryophytes are extremely good dispersers. Here, we reconstructed the phylogeny of the pantropical moss genus Pelekium to test the hypothesis that high migration rates erase any difference in species richness among tropical regions. In contrast with this hypothesis, several species considered to have a pantropical range were resolved as a complex of species with a strong geographic structure. Consequently, a significant phylogeographical signal was found in the data, evidencing that cladogenetic diversification within regions takes place at a faster rate than intercontinental migration. The shape of the Pelekium phylogeny, along with the selection of a constant-rate model of diversification among species in the genus, suggests, however, that the cladogenetic speciation patterns observed in Pelekium are not comparable to some of the spectacular examples of tropical radiations reported in angiosperms. Rather, the results presented here point to the constant accumulation of diversity through time in Pelekium. This, combined with evidence for long-distance dispersal limitations in the genus, suggests that the similar patterns of species richness among tropical areas are better explained in terms of comparable rates of diversification across tropical regions than by the homogenization of species richness by recurrent migrations.
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Affiliation(s)
- Nik Norhazrina
- University of Liege, Institute of Botany, B22 Sart Tilman, Liege, Belgium; School of Environmental and Natural Resource Sciences, Faculty of Sciences, National University of Malaysia, 43600 Bangi, Selangor, Malaysia
| | | | - Lars Hedenäs
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Laguna, Tenerife, Canary Islands, 38206, Spain
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13
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Jonathan Shaw A, Devos N, Liu Y, Cox CJ, Goffinet B, Flatberg KI, Shaw B. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). ANNALS OF BOTANY 2016; 118:185-96. [PMID: 27268484 PMCID: PMC4970357 DOI: 10.1093/aob/mcw086] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/11/2016] [Accepted: 03/28/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided. METHODS We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium KEY RESULTS Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium CONCLUSIONS Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Nicolas Devos
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Yang Liu
- Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, Storrs, CT 06269, USA
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Edif. 7, 8005-139 Faro, Portugal
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, Storrs, CT 06269, USA
| | - Kjell Ivar Flatberg
- NTNU University Museum, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Blanka Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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14
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Yuan H, Jiang J, Jiménez FA, Hoberg EP, Cook JA, Galbreath KE, Li C. Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms. Mol Ecol Resour 2016; 16:1095-106. [PMID: 27037792 DOI: 10.1111/1755-0998.12532] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/02/2016] [Accepted: 03/17/2016] [Indexed: 01/02/2023]
Abstract
The Cyclophyllidea is the most diverse order of tapeworms, encompassing species that infect all classes of terrestrial tetrapods including humans and domesticated animals. Available phylogenetic reconstructions based either on morphology or molecular data lack the resolution to allow scientists to either propose a solid taxonomy or infer evolutionary associations. Molecular markers available for the Cyclophyllidea mostly include ribosomal DNA and mitochondrial loci. In this study, we identified 3641 single-copy nuclear coding loci by comparing the genomes of Hymenolepis microstoma, Echinococcus granulosus and Taenia solium. We designed RNA baits based on the sequence of H. microstoma, and applied target enrichment and Illumina sequencing to test the utility of those baits to recover loci useful for phylogenetic analyses. We captured DNA from five species of tapeworms representing two families of cyclophyllideans. We obtained an average of 3284 (90%) of the targets from the test samples and then used captured sequences (2 181 361 bp in total; fragment size ranging from 301 to 6969 bp) to reconstruct a phylogeny for the five test species plus the three species for which genomic data are available. The results were consistent with the current consensus regarding cyclophyllidean relationships. To assess the potential for our method to yield informative genetic variation at intraspecific scales, we extracted 14 074 single nucleotide polymorphisms (SNPs) from alignments of four Arostrilepis macrocirrosa and two A. cooki and successfully inferred their relationships. The results showed that our target gene tools yield data sets that provide robust inferences at a range of taxonomic scales in the Cyclophyllidea.
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Affiliation(s)
- Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiamei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | | | - Eric P Hoberg
- US National Parasite Collection and Animal Parasitic Disease Laboratory, USDA Agricultural Research Service, BARC East No. 1180, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA
| | - Joseph A Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, 49855, USA
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
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15
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Carter BE, Shaw B, Shaw AJ. Endemism in the moss flora of North America. AMERICAN JOURNAL OF BOTANY 2016; 103:769-779. [PMID: 27056933 DOI: 10.3732/ajb.1500484] [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: 11/15/2015] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Identifying regions of high endemism is a critical step toward understanding the mechanisms underlying diversification and establishing conservation priorities. Here, we identified regions of high moss endemism across North America. We also identified lineages that contribute disproportionately to endemism and document the progress of efforts to inventory the endemic flora. METHODS To understand the documentation of endemic moss diversity in North America, we tabulated species publication dates to document the progress of species discovery across the continent. We analyzed herbarium specimen data and distribution data from the Flora of North America project to delineate major regions of moss endemism. Finally, we surveyed the literature to assess the importance of intercontinental vs. within-continent diversification for generating endemic species. KEY RESULTS Three primary regions of endemism were identified and two of these were further divided into a total of nine subregions. Overall endemic richness has two peaks, one in northern California and the Pacific Northwest, and the other in the southern Appalachians. Description of new endemic species has risen steeply over the last few decades, especially in western North America. Among the few studies documenting sister species relationships of endemics, recent diversification appears to have played a larger role in western North America, than in the east. CONCLUSIONS Our understanding of bryophyte endemism continues to grow rapidly. Large continent-wide data sets confirm early views on hotspots of endemic bryophyte richness and indicate a high rate of ongoing species discovery in North America.
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Affiliation(s)
- Benjamin E Carter
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Blanka Shaw
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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16
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Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid. PLoS One 2016; 11:e0148447. [PMID: 26859563 PMCID: PMC4747574 DOI: 10.1371/journal.pone.0148447] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/18/2016] [Indexed: 11/25/2022] Open
Abstract
Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.
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Patiño J, Goffinet B, Sim-Sim M, Vanderpoorten A. Is the sword moss (Bryoxiphium) a preglacial Tertiary relict? Mol Phylogenet Evol 2015; 96:200-206. [PMID: 26708122 DOI: 10.1016/j.ympev.2015.12.004] [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: 10/02/2015] [Revised: 12/01/2015] [Accepted: 12/11/2015] [Indexed: 12/15/2022]
Abstract
The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.
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Affiliation(s)
- Jairo Patiño
- University of Liege, Institute of Botany, B22 Sart Tilman, Liege, Belgium; cE3c - Centre for Ecology, Evolution and Environmental Changes and Platform for Enhancing Ecological Research & Sustainability, Universidade dos Açores, Angra do Heroísmo, Terceira, Açores, Portugal; Department of Plant Biology, University of La Laguna, Tenerife, Spain.
| | - Bernard Goffinet
- University of Connecticut, Department of Ecology and Evolutionary Biology, Storrs, CT, USA
| | - Manuela Sim-Sim
- cE3c, Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Faculdade de Ciências de Lisboa, Departamento de Biologia Vegetal and Museu Nacional de História Natural e da Ciência, Jardim Botânico, Lisboa, Portugal
| | - Alain Vanderpoorten
- University of Liege, Institute of Botany, B22 Sart Tilman, Liege, Belgium; cE3c - Centre for Ecology, Evolution and Environmental Changes and Platform for Enhancing Ecological Research & Sustainability, Universidade dos Açores, Angra do Heroísmo, Terceira, Açores, Portugal
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18
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Weston DJ, Timm CM, Walker AP, Gu L, Muchero W, Schmutz J, Shaw AJ, Tuskan GA, Warren JM, Wullschleger SD. Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function. PLANT, CELL & ENVIRONMENT 2015; 38:1737-1751. [PMID: 25266403 DOI: 10.1111/pce.12458] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 06/03/2023]
Abstract
Peatlands harbour more than one-third of terrestrial carbon leading to the argument that the bryophytes, as major components of peatland ecosystems, store more organic carbon in soils than any other collective plant taxa. Plants of the genus Sphagnum are important components of peatland ecosystems and are potentially vulnerable to changing climatic conditions. However, the response of Sphagnum to rising temperatures, elevated CO2 and shifts in local hydrology have yet to be fully characterized. In this review, we examine Sphagnum biology and ecology and explore the role of this group of keystone species and its associated microbiome in carbon and nitrogen cycling using literature review and model simulations. Several issues are highlighted including the consequences of a variable environment on plant-microbiome interactions, uncertainty associated with CO2 diffusion resistances and the relationship between fixed N and that partitioned to the photosynthetic apparatus. We note that the Sphagnum fallax genome is currently being sequenced and outline potential applications of population-level genomics and corresponding plant photosynthesis and microbial metabolic modelling techniques. We highlight Sphagnum as a model organism to explore ecosystem response to a changing climate and to define the role that Sphagnum can play at the intersection of physiology, genetics and functional genomics.
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Affiliation(s)
- David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anthony P Walker
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Lianhong Gu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeffrey M Warren
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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19
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Shaw AJ, Shaw B, Johnson MG, Devos N, Stenøien HK, Flatberg KI, Carter BE. Phylogenetic structure and biogeography of the Pacific Rim clade ofSphagnumsubgen.Subsecunda: haploid and allodiploid taxa. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12586] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Blanka Shaw
- Department of Biology; Duke University; Durham NC 27708 USA
| | | | - Nicolas Devos
- Department of Biology; Duke University; Durham NC 27708 USA
| | - Hans K. Stenøien
- NTNU University Museum; Norwegian University of Science and Technology; N-7491 Trondheim Norway
| | - Kjell I. Flatberg
- NTNU University Museum; Norwegian University of Science and Technology; N-7491 Trondheim Norway
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