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Loría-Cervera EN, Sosa-Bibiano EI, López-Ávila KB, de Oca-Aguilar ACM, Moreno-Nava MS, Torres-Castro JR. Viable Leishmania parasites in the absence of an in vitro IFN-γ response in asymptomatic carriers. Rev Inst Med Trop Sao Paulo 2024; 66:e13. [PMID: 38381898 PMCID: PMC10881064 DOI: 10.1590/s1678-9946202466013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/08/2023] [Indexed: 02/23/2024] Open
Abstract
Asymptomatic infection (the absence or inapparent signs and symptoms) has been observed in many endemic areas of leishmaniasis, however, little is known about the parasitological and immunological factors associated with this type of infection. This study aimed to identify the in vitro expression of IFN-γ in asymptomatic carriers of viable Leishmania parasites. Asymptomatic infection was identified using the Montenegro skin test in an at-risk population from Yucatan, Mexico. Parasite viability was evinced in the blood by 7SL RNA transcripts amplification. The expression of mRNA IFN-γ was analyzed in peripheral blood mononuclear cells stimulated with soluble Leishmania antigen, using RT-qPCR. Parasite viability was observed in 33.3 % (5/15) of asymptomatic subjects. No differences were found in the expression of IFN-γ between asymptomatic and healthy subjects, and no correlation was found between the presence of viable parasites and the expression of IFN-γ. This study demonstrates the persistence of Leishmania parasites in the absence of an in vitro IFN-γ response in asymptomatic carriers from Mexico.
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Affiliation(s)
- Elsy Nalleli Loría-Cervera
- Universidad Autónoma de Yucatán, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Laboratorio de Inmunología, Mérida, Yucatán, Mexico
| | - Erika Ivett Sosa-Bibiano
- Universidad Autónoma de Yucatán, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Laboratorio de Inmunología, Mérida, Yucatán, Mexico
| | - Karina Beatriz López-Ávila
- Universidad Autónoma de Yucatán, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Laboratorio de Inmunología, Mérida, Yucatán, Mexico
| | - Ana Celia Montes de Oca-Aguilar
- Universidad Autónoma de Yucatán, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Laboratorio de Inmunología, Mérida, Yucatán, Mexico
| | - Marisol Sarahí Moreno-Nava
- Universidad Autónoma de Yucatán, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Laboratorio de Inmunología, Mérida, Yucatán, Mexico
| | - Jimmy Raymundo Torres-Castro
- Servicios de Salud del Estado de Yucatán, Dirección de Prevención y Protección de la Salud, Mérida, Yucatán, Mexico
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Razafimandimbison SG, Wikström N, Khodabandeh A, Rydin C. Phylogeny of the Madagascar-centred tribe Danaideae (Rubiaceae) as a precursor to taxonomic revision: insights into its generic and species limits, affinities and distribution. ANNALS OF BOTANY 2022; 130:849-867. [PMID: 36149802 PMCID: PMC9758302 DOI: 10.1093/aob/mcac121] [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: 07/14/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS The tribe Danaideae (Rubiaceae) is almost exclusively endemic to the Western Indian Ocean Region (WIOR), and encompasses the genera Danais, Payera and Schismatoclada that occur in humid, sub-humid and mountain and mountain bio climate zones. Much of the species diversity is endemic to restricted, remote and/or mountainous areas of Madagascar and recent field work on the island indicates substantial unknown diversity of the Danaideae. Furthermore, the monophyly of the Malagasy genera Payera and Schismatoclada has been questioned in previous work, species delimitations and phylogenetic relationships within the genera are poorly understood, and the distribution and evolution of gross morphological features have not been assessed. METHODS We conducted morphological investigations, and produced robust phylogenies of Danaideae based on nuclear and plastid sequence data from 193 terminals. Ample plant material has been newly collected in the WIOR for the purpose of the present study, including potentially new species unknown to science. We performed Bayesian non-clock and relaxed-clock analyses employing three alternative clock models of a dataset with a dense sample of taxa from the entire geographical ranges of Danaideae. Based on the results, we discuss species diversity and distribution, relationships, and morphology in Danaideae. KEY RESULTS Our results demonstrate the monophyly of Danaideae, its three genera and 42 species. Nine species are resolved as non-monophyletic. Many geographically distinct but morphologically heterogeneous lineages were identified, and morphological features traditionally considered diagnostic of subgroups of the genera, used for example in species identification keys, are not clade-specific. CONCLUSIONS Our results demonstrate that Madagascar contains ample previously undocumented morphological and species diversity of Danaideae. Our novel approach to molecular phylogenetic analyses as a precursor to taxonomic revisions provides numerous benefits for the latter. There are tentative indications of parallel northward diversification in Payera and Schismatoclada on Madagascar, and of geographical phylogenetic clustering despite the anemochorous condition of Danaideae.
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Affiliation(s)
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
- The Bergius Foundation, The Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Anbar Khodabandeh
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
- The Bergius Foundation, The Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
- The Bergius Foundation, The Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
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3
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Simmons MP, Maurin O, Bailey P, Brewer GE, Roy S, Lombardi JA, Forest F, Baker WJ. Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales. Cladistics 2022; 38:595-611. [PMID: 35569142 DOI: 10.1111/cla.12507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2022] [Indexed: 01/31/2023] Open
Abstract
We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523-1878, USA
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Julio A Lombardi
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista - UNESP, Av. 24-A 1515 - Bela Vista, Caixa Postal 199, São Paulo, Brazil
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Chen YP, Turdimatovich TO, Nuraliev MS, Lazarević P, Drew BT, Xiang CL. Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae). Cladistics 2022; 38:429-451. [PMID: 35358338 DOI: 10.1111/cla.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/28/2022] Open
Abstract
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Maxim S Nuraliev
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Predrag Lazarević
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, 68849, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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5
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Nge FJ, Biffin E, Waycott M, Thiele KR. Phylogenomics and continental biogeographic disjunctions: insight from the Australian starflowers (Calytrix). AMERICAN JOURNAL OF BOTANY 2022; 109:291-308. [PMID: 34671970 DOI: 10.1002/ajb2.1790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Continental-scale disjunctions and associated drivers are core research interests in biogeographic studies. Here, we selected a species-rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns. Species of this endemic Australian starflower genus have a disjunct distribution across the mesic fringes of the continent and are largely absent from the arid center. METHODS We used high-throughput sequencing to generate unprecedented resolution and near complete species-level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal. RESULTS Present-day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental center to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the center as well as (2) origination of ancestral lineages in southwestern Australia (SWA) for species-rich clades. The SWA biodiversity hotspot is a major diversification center and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region. CONCLUSIONS Our results suggest that major extinction, as a result of cooling and drying of the Australian continent in the Eocene-Miocene, shaped the present-day biogeography of Calytrix. We hypothesize that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis.
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Affiliation(s)
- Francis J Nge
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, G.P.O. Box 1047, Adelaide, South Australia, 5001, Australia
| | - Ed Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, G.P.O. Box 1047, Adelaide, South Australia, 5001, Australia
| | - Michelle Waycott
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, G.P.O. Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kevin R Thiele
- School of Biological Sciences, University of Western Australia, 35 Stirling Hwy, Crawley (Perth), WA, 6009, Australia
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Bacon CD, Gutiérrez‐Pinto N, Flantua S, Castellanos Suárez D, Jaramillo C, Pennington RT, Antonelli A. The seasonally dry tropical forest species
Cavanillesia chicamochae
has a middle Quaternary origin. Biotropica 2021. [DOI: 10.1111/btp.13031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christine D. Bacon
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Laboratório de Biología Molecular (CINBIN) Department of Biology Universidad Industrial de Santander Bucaramanga Colombia
| | - Natalia Gutiérrez‐Pinto
- Laboratório de Biología Molecular (CINBIN) Department of Biology Universidad Industrial de Santander Bucaramanga Colombia
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln Nebraska USA
| | - Suzette Flantua
- Department of Biological Sciences University of Bergen Bergen Norway
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam the Netherlands
| | - Diego Castellanos Suárez
- Laboratório de Biología Molecular (CINBIN) Department of Biology Universidad Industrial de Santander Bucaramanga Colombia
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute Balboa, Ancon Republic of Panama
- Institut des Sciences de l’Evolution Montpellier University of MontpellierCNRSEPHE Montpellier IRD France
- Department of Geology University of Salamanca Salamanca Spain
| | - R. Toby Pennington
- Royal Botanic Garden Edinburgh Edinburgh UK
- Geography University of Exeter Exeter UK
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Royal Botanic Gardens Kew Richmond Surrey UK
- Department of Plant Sciences University of Oxford Oxford UK
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7
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Lehtonen S. Phenotypic characters of static homology increase phylogenetic stability under direct optimization of otherwise dynamic homology characters. Cladistics 2021; 36:617-626. [PMID: 34618977 DOI: 10.1111/cla.12438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/29/2022] Open
Abstract
Direct optimization of unaligned sequence characters provides a natural framework to explore the sensitivity of phylogenetic hypotheses to variation in analytical parameters. Phenotypic data, when combined into such analyses, are typically analyzed with static homology correspondences unlike the dynamic homology sequence data. Static homology characters may be expected to constrain the direct optimization and thus, potentially increase the similarity of phylogenetic hypotheses under different cost sets. However, whether a total-evidence approach increases the phylogenetic stability or not remains empirically largely unexplored. Here, I studied the impact of static homology data on sensitivity using six empirical data sets composed of several molecular markers and phenotypic data. The inclusion of static homology phenotypic data increased the average stability of phylogenetic hypothesis in five out of the six data sets. To investigate if any static homology characters would have similar effect, the analyses were repeated with randomized phenotypic data, and with one of the molecular markers fixed as static homology characters. These analyses had, on average, almost no effect on the phylogenetic stability, although the randomized phenotypic data sometimes resulted in even higher stability than empirical phenotypic data. The impact was related to the strength of the phylogenetic signal in the phenotypic data: higher average jackknife support of the phenotypic tree correlated with stronger stabilizing effect in the total-evidence analysis. Phenotypic data with a strong signal made the total-evidence trees topologically more similar to the phenotypic trees, thus, they constrained the dynamic homology correspondences of the sequence data. Characters that increase phylogenetic stability are particularly valuable for phylogenetic inference. These results indicate an important role and additive value of phenotypic data in increasing the stability of phylogenetic hypotheses in total-evidence analyses.
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Affiliation(s)
- Samuli Lehtonen
- Biodiversity Unit, University of Turku, Turku, FI-20014, Finland
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8
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Baldwin BG, Wood KR, Freyman WA. Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae). AMERICAN JOURNAL OF BOTANY 2021; 108:2015-2037. [PMID: 34694624 DOI: 10.1002/ajb2.1757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Expanded phylogenetic analyses of the Hawaiian silversword alliance (Argyroxiphium, Dubautia, Wilkesia; Compositae) were undertaken to assess evolutionary and biogeographic informativeness of cytonuclear discordance and any biases in evolutionary directionality of ecological transitions within this prominent example of adaptive radiation. METHODS Samples spanning the geographic and ecological distributions of all recognized taxa were included in phylogenetic and biogeographic analyses of nuclear ribosomal DNA (nrDNA) and cpDNA sequences. Bayesian model testing approaches were used to model ecological evolution and the evolution of nuclear chromosomal arrangements while accounting for phylogenetic uncertainty. RESULTS Cytonuclear discordance detected previously appears to reflect chloroplast capture, at least in part, with nrDNA trees being largely congruent with nuclear chromosomal structural data and fine-scale taxonomy. Comparison of biogeographic histories estimated from the posterior distributions of nrDNA and cpDNA trees, including inferred chloroplast-capture events, provides additional resolution of dispersal history, including a back-dispersal to Maui Nui from Hawai'i. A newly resolved major nrDNA clade of endemic Kaua'i taxa that mostly were described as new-to-science since the 1980s strengthens the earlier hypothesis that diversification on Kaua'i has not waned since the island began to decline in area through subsidence and erosion. Bias in habitat shifts was estimated, with transitions from dry-to-mesic or -wet and from wet-to-mesic or -bog habitats dominating diversification of the silversword alliance from a dry-adapted tarweed ancestor. CONCLUSIONS The habitat-transition biases estimated here may indicate more limited pathways of ecological evolution than proposed previously for an adaptive radiation involving such major ecological shifts.
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Affiliation(s)
- Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California, 94720-2465, USA
| | - Kenneth R Wood
- National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, Hawaii, 96741, USA
| | - William A Freyman
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California, 94720-2465, USA
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9
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King B, Rücklin M. A Bayesian approach to dynamic homology of morphological characters and the ancestral phenotype of jawed vertebrates. eLife 2020; 9:e62374. [PMID: 33274719 PMCID: PMC7793628 DOI: 10.7554/elife.62374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022] Open
Abstract
Phylogenetic analysis of morphological data proceeds from a fixed set of primary homology statements, the character-by-taxon matrix. However, there are cases where multiple conflicting homology statements can be justified from comparative anatomy. The upper jaw bones of placoderms have traditionally been considered homologous to the palatal vomer-dermopalatine series of osteichthyans. The discovery of 'maxillate' placoderms led to the alternative hypothesis that 'core' placoderm jaw bones are premaxillae and maxillae lacking external (facial) laminae. We introduce a BEAST2 package for simultaneous inference of homology and phylogeny, and find strong evidence for the latter hypothesis. Phenetic analysis of reconstructed ancestors suggests that maxillate placoderms are the most plesiomorphic known gnathostomes, and the shared cranial architecture of arthrodire placoderms, maxillate placoderms and osteichthyans is inherited. We suggest that the gnathostome ancestor possessed maxillae and premaxillae with facial and palatal laminae, and that these bones underwent divergent evolutionary trajectories in placoderms and osteichthyans.
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Köhler M, Reginato M, Souza-Chies TT, Majure LC. Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies. FRONTIERS IN PLANT SCIENCE 2020; 11:729. [PMID: 32636853 PMCID: PMC7317007 DOI: 10.3389/fpls.2020.00729] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 05/22/2023]
Abstract
Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.
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Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Florida Museum of Natural History, University of Florida Herbarium (FLAS), Gainesville, FL, United States
| | - Marcelo Reginato
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Lucas C Majure
- Florida Museum of Natural History, University of Florida Herbarium (FLAS), Gainesville, FL, United States
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, United States
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11
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Silva OLM, Riina R, Cordeiro I. Phylogeny and biogeography of Astraea with new insights into the evolutionary history of Crotoneae (Euphorbiaceae). Mol Phylogenet Evol 2020; 145:106738. [PMID: 32001365 DOI: 10.1016/j.ympev.2020.106738] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/03/2020] [Accepted: 01/23/2020] [Indexed: 11/30/2022]
Abstract
We investigated species relationships in Astraea, a primarily Neotropical genus of tribe Crotoneae centered in Brazil, using data from the nuclear ribosomal ITS, and the plastid trnL-trnF and psbA-trnH spacers. With all species of Astraea sampled, along with representatives from across Crotoneae, the evolutionary history of Astraea was interpreted in a broader framework, as well as divergence time estimates and reconstructions of ancestral areas and morphological character states for Crotoneae. Our results show that Astraea is monophyletic, consisting of three main clades, and that most of its diversification took place from the Oligocene to the Pliocene, coincident with the formation of the South American "dry diagonal". As for Crotoneae, our data show incongruent phylogenetic positions between the nuclear and chloroplast data for most of its genera, and that the ancestor of the tribe was probably arborescent and might have occupied the Amazon Basin, most likely in moist forest, from which it spread throughout South America in the early Eocene. Ancestral state reconstruction recovered deeply lobed leaves and staminate petals bearing moniliform trichomes as putative synapomorphies for Astraea, whereas the absence or strong reduction of pistillate petals is widespread in Crotoneae and may be a synapomorphy for the tribe.
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Affiliation(s)
- Otávio Luis Marques Silva
- Núcleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo 04301-902, SP, Brazil.
| | - Ricarda Riina
- Real Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, Madrid 28014, Spain
| | - Inês Cordeiro
- Núcleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo 04301-902, SP, Brazil
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Ouyang F, Hu J, Wang J, Ling J, Wang Z, Wang N, Ma J, Zhang H, Mao JF, Wang J. Complete plastome sequences of Picea asperata and P. crassifolia and comparative analyses with P. abies and P. morrisonicola. Genome 2019; 62:317-328. [PMID: 30998854 DOI: 10.1139/gen-2018-0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.
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Affiliation(s)
- Fangqun Ouyang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Jiwen Hu
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Junchen Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China.,b Northwest Agriculture & Forestry University, Xi'an, P.R. China
| | - Juanjuan Ling
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Zhi Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Nan Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
| | - Jianwei Ma
- c Research Institute of Forestry of Xiaolong Mountain, Gansu Provincial Key Laboratory of Secondary Forest Cultivation, Gansu, P.R. China
| | - Hanguo Zhang
- d State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, P.R. China
| | - Jian-Feng Mao
- e National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plant of Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Junhui Wang
- a State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, P.R. China
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13
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Palci A, Lee MSY. Geometric morphometrics, homology and cladistics: review and recommendations. Cladistics 2019; 35:230-242. [PMID: 34622971 DOI: 10.1111/cla.12340] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 11/29/2022] Open
Abstract
Geometric morphometric (GM) data has a long and contentious history in phylogenetic analyses. Often associated with phenetics, GM has been considered by many to be unable to provide meaningful information on phylogenetic relationships. However, the concepts of primary and secondary homology as developed for discrete characters can be readily extended to GM data: raw similarity in aligned landmark positions represents primary homology, and similarity ascribable to common ancestry represents secondary homology. We review fundamental concepts from the literature and provide a series of practical guidelines for the use of GM data in phylogenetics: (i) alignments that minimize linear distances between landmarks (or their approximation) perform better in highlighting apomorphic traits; (ii) Type I, Type II and linear semi-landmarks are preferable to Type III and surface semi-landmarks; (iii) excluding bilateral landmarks after, rather than before, alignment will prevent artefactual mediolateral displacement of midsagittal landmarks; (iv) phylogenetic analyses should employ linear rather than squared-change parsimony analysis of landmark displacements; (v) optimization of shape changes across a tree can be improved with methods that re-align the landmark configurations based on the results of the phylogenetic analysis; and (vi) GM data are no substitute for traditional morphological characters, but rather a complementary descriptor of shape diversity.
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Affiliation(s)
- Alessandro Palci
- Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia.,College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Michael S Y Lee
- Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, SA, 5000, Australia.,College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
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14
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Freitas CG, Bacon CD, Souza-Neto AC, Collevatti RG. Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms. FRONTIERS IN PLANT SCIENCE 2019; 10:55. [PMID: 30804955 PMCID: PMC6370682 DOI: 10.3389/fpls.2019.00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Environmental and geographical variables are known drivers of community assembly, however their influence on phylogenetic structure and phylogenetic beta diversity of lineages within different bioregions is not well-understood. Using Neotropical palms as a model, we investigate how environmental and geographical variables affect the assembly of lineages into bioregions across an evolutionary time scale. We also determine lineage shifts between tropical (TRF) and non-tropical (non-TRF) forests. Our results identify that distance and area explain phylogenetic dissimilarity among bioregions. Lineages in smaller bioregions are a subset of larger bioregions and contribute significantly to the nestedness component of phylogenetic dissimilarity, here interpreted as evidence for a bioregional shift. We found a significant tendency of habitat shifts occurring preferentially between TRF and non-TRF bioregions (31 shifts) than from non-TRF to TRF (24) or from TRF to TRF (11) and non-TRF to non-TRF (9). Our results also present cases where low dissimilarity is found between TRF and non-TRF bioregions. Most bioregions showed phylogenetic clustering and larger bioregions tended to be more clustered than smaller ones, with a higher species turnover component of phylogenetic dissimilarity. However, phylogenetic structure did not differ between TRF and non-TRF bioregions and diversification rates were higher in only two lineages, Attaleinae and Bactridinae, which are widespread and overabundant in both TRF and non-TRF bioregions. Area and distance significantly affected Neotropical palm community assembly and contributed more than environmental variables. Despite palms being emblematic humid forest elements, we found multiple shifts from humid to dry bioregions, showing that palms are also important components of these environments.
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Affiliation(s)
- Cintia G. Freitas
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Christine D. Bacon
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Advaldo C. Souza-Neto
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Rosane G. Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
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15
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Cardinal-McTeague WM, Wurdack KJ, Sigel EM, Gillespie LJ. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evol Biol 2019; 19:29. [PMID: 30670006 PMCID: PMC6341577 DOI: 10.1186/s12862-018-1308-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/23/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model. RESULTS Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas. CONCLUSIONS The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.
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Affiliation(s)
- Warren M. Cardinal-McTeague
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Kenneth J. Wurdack
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012 USA
| | - Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Billeaud Hall, Room 108, 410 E. St. Mary Blvd, Lafayette, LA 70503 USA
| | - Lynn J. Gillespie
- Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario K1N 6N5 Canada
- Research and Collections, Canadian Museum of Nature, PO Box 3443, Station D, Ottawa, Ontario K1P 6P4 Canada
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16
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Hurbath F, Leal BÁSS, Da Silva OLM, Palma-Silva C, Cordeiro IN. A new species and molecular phylogeny of Brazilian succulent Euphorbia sect. Brasilienses. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1473897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Fernanda Hurbath
- Nucleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo, 04045-972, SP, Brazil
| | - BÁrbara SimÕes Santos Leal
- Laboratório de Ecologia Molecular, Departamento de Ecologia, Universidade Estadual Paulista – Rio Claro, Avenida 24A 1515, Rio Claro, 13506-900, SP, Brazil
| | - Otávio Luis Marques Da Silva
- Nucleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo, 04045-972, SP, Brazil
| | - Clarisse Palma-Silva
- Laboratório de Ecologia Molecular, Departamento de Ecologia, Universidade Estadual Paulista – Rio Claro, Avenida 24A 1515, Rio Claro, 13506-900, SP, Brazil
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz – Barão Geraldo, Campinas, 13083-863, SP, Brazil
| | - INês Cordeiro
- Nucleo de Pesquisa Curadoria do Herbário SP, Instituto de Botânica, Avenida Miguel Stéfano 3687, São Paulo, 04045-972, SP, Brazil
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17
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Ohdachi SD, Yoshizawa K, Takada Y, Motokawa M, Iwasa MA, Arai S, Moribe J, Uematsu Y, Sakai E, Tateishi T, Oh HS, Kinoshita G. Phylogeography of the Japanese White-Toothed Shrew (Eulipotyphla: Soricidae): A Clear Division of Haplogroups between Eastern and Western Japan and their Recent Introduction to Some Regions. MAMMAL STUDY 2018. [DOI: 10.3106/ms2017-0059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Satoshi D. Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Kita 19 Nishi 8, Kita-ku, Sapporo 060-081
| | - Kazunori Yoshizawa
- Systematic Entomology, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-858
| | | | - Masaharu Motokawa
- The Kyoto University Museum, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro A. Iwasa
- College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Toyama 1-23-1, Sh
| | - Junji Moribe
- Research Center for Wildlife Management, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Yasushi Uematsu
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoy
| | - Eiichi Sakai
- Department of Dental Hygiene, Aichi-Gakuin Junior College, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650
| | | | - Hong-Shik Oh
- Faculty of Science Education, Jeju National University, Ara-dong 1, Jeju, Jeju-do 690-756, Republic
| | - Gohta Kinoshita
- Laboratory of Forest Biology, Division of Forest & Biomaterials Science, Graduate School of Agricult
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18
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Wynns JT, Munk KR, Lange CBA. Molecular phylogeny of Plagiothecium and similar hypnalean mosses, with a revised sectional classification of Plagiothecium. Cladistics 2018; 34:469-501. [PMID: 34649367 DOI: 10.1111/cla.12210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2017] [Indexed: 11/27/2022] Open
Abstract
We investigated the systematic relationships within the pleurocarpous moss genus Plagiothecium, based on cladistic analyses of sequence data from one nuclear (ITS) and two plastid (trnK-psbA (matK) and rpl16 intron) DNA regions for 110 specimens of Plagiothecium and similar hypnalean mosses. Plastid and nuclear trees were mostly similar, but differed in the placement of several species of Plagiothecium, and in the relationships among other genera. The phylogenetic hypotheses based on plastid markers were well resolved; in contrast, nuclear data were insufficient to resolve some of the lowest-level relationships within the genus. In the main Plagiothecium is natural, includes more taxa than are often recognized, and is most closely related to Isopterygiopsis and Herzogiella. Nine sections are recognized within Plagiothecium, four new: Section Pseudo-Neckera to accommodate P. neckeroideum and its allies, Section Ortholimnobium for P. handelii and P. paleaceum, Section Struckia for P. argentatum and P. enerve, and Section Rectithecium for P. piliferum. The geographical distribution of the sections suggests that Plagiothecium originated in Asia. The derived, mainly autoicous sections Plagiothecium and Leptophyllum may have spread to the Southern Hemisphere through long distance dispersal. Three new species in section Leptophyllum (P. funale, P. pacificum and P. rhizolucidum) and two new taxa in section Pseudo-Neckera (P. decoratum and P. neckeroideum fo. exile) are described. A limited phylogenetic hypothesis for the superficially similar hypnalean genus Taxiphyllum, which was used as outgroup, is included. A related genus (Longiella) is described, with a single species (L. plagiothecioides). The aquarium species T. barbieri is transferred to Ectropothecium.
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Affiliation(s)
- Justin T Wynns
- Natural History Museum of Denmark, Øster Farimagsgade 2D, opg. E, 3, DK-1353, Copenhagen, Denmark
| | - Karen Rysbjerg Munk
- Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Denmark
| | - Conny B Asmussen Lange
- Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg, Denmark
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19
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Villaverde T, Pokorny L, Olsson S, Rincón-Barrado M, Johnson MG, Gardner EM, Wickett NJ, Molero J, Riina R, Sanmartín I. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. THE NEW PHYTOLOGIST 2018; 220:636-650. [PMID: 30016546 DOI: 10.1111/nph.15312] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 05/20/2023]
Abstract
Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.
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Affiliation(s)
- Tamara Villaverde
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Lisa Pokorny
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre (INIA-CIFOR), Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, 79409-43131, USA
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | | | - Norman J Wickett
- Department of Plant Science and Conservation, Chicago Botanical Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Program in Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Julià Molero
- Laboratori de Botànica, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Ricarda Riina
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Isabel Sanmartín
- Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
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20
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The Complete Chloroplast Genome of Catha edulis: A Comparative Analysis of Genome Features with Related Species. Int J Mol Sci 2018; 19:ijms19020525. [PMID: 29425128 PMCID: PMC5855747 DOI: 10.3390/ijms19020525] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
Qat (Catha edulis, Celastraceae) is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for C. edulis are limited, hindering studies regarding interspecific and intraspecific relationships. Herein, the complete chloroplast (cp) genome of Catha edulis is reported. This genome is 157,960 bp in length with 37% GC content and is structurally arranged into two 26,577 bp inverted repeats and two single-copy areas. The size of the small single-copy and the large single-copy regions were 18,491 bp and 86,315 bp, respectively. The C. edulis cp genome consists of 129 coding genes including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 84 protein coding genes. For those genes, 112 are single copy genes and 17 genes are duplicated in two inverted regions with seven tRNAs, four rRNAs, and six protein coding genes. The phylogenetic relationships resolved from the cp genome of qat and 32 other species confirms the monophyly of Celastraceae. The cp genomes of C. edulis, Euonymus japonicus and seven Celastraceae species lack the rps16 intron, which indicates an intron loss took place among an ancestor of this family. The cp genome of C. edulis provides a highly valuable genetic resource for further phylogenomic research, barcoding and cp transformation in Celastraceae.
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21
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Abstract
Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.
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Affiliation(s)
- Simon Creer
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, United Kingdom
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22
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Archibald JK, Cook J, Anderson B, Johnson SD, Mort ME. A reassessment of the phylogeny and circumscription of Zaluzianskya (Scrophulariaceae). Mol Phylogenet Evol 2017; 112:194-208. [PMID: 28411161 DOI: 10.1016/j.ympev.2017.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/26/2017] [Accepted: 04/10/2017] [Indexed: 10/19/2022]
Abstract
The genus Zaluzianskya (Scrophulariaceae s.s.) encompasses a diversity of floral and ecological traits. However, this diversity, as described by the current taxonomic circumscription of Zaluzianskya, is an underestimate. We present molecular data suggesting that this genus requires expansion via incorporation of species from other genera and recognition of unnamed cryptic species. This study advances prior molecular phylogenies of the southern African genus through the addition of DNA regions and 51 populations that had not previously been sampled in a published phylogeny. A total of 82 species of Zaluzianskya and related genera are included, adding 48 to those previously sampled. Results are presented from analyses of five DNA regions, including nuclear ITS and four rapidly evolving chloroplast regions (trnL-trnF, rpl16, rps16, and trnS-trnfM). Our primary finding is that the genus Phyllopodium is polyphyletic as currently circumscribed, with some species placed within Zaluzianskya and others grouping with Polycarena, indicating the need for further phylogenetic work on these genera. Preliminary support for the incorporation of Reyemia into Zaluzianskya is reinforced here by the first molecular analysis to include both species of Reyemia and a strong sampling of species across Zaluzianskya and major clades of tribe Limoselleae. The two disjunct, tropical African species of Zaluzianskya are also confirmed as members of this genus. Finally, a broad sampling of 21 populations of Z. microsiphon establishes their phylogenetic division into two to five separate lineages. Hybridization, coevolution, and cryptic speciation may each play a role in the evolution of Z. microsiphon. Further resolution within a clade comprising sections Nycterinia and Macrocalyx is needed to better understand their relationships.
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Affiliation(s)
- Jenny K Archibald
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | | | - Bruce Anderson
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Steven D Johnson
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Mark E Mort
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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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.
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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
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Bacon CD, Moraes R M, Jaramillo C, Antonelli A. Endemic palm species shed light on habitat shifts and the assembly of the Cerrado and Restinga floras. Mol Phylogenet Evol 2017; 110:127-133. [PMID: 28288942 DOI: 10.1016/j.ympev.2017.03.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/19/2022]
Abstract
Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters. To detect habit shifts in absolute time, we used one plastid and nine nuclear genes to reconstruct the phylogenetic and biogeographic history of Allagoptera. We used light microscopy and stable isotope analysis to explore whether morphological adaptations occurred concomitantly with habitat shifts. Phylogenetic relationships were well supported and we found ancestral lineages of Allagoptera to be widely distributed throughout habitats that are currently occupied by extant species. Over the last ca. 7Ma Allagoptera has shifted its preference to increasingly dry habitats. Coincident with the colonization of the Cerrado and Restinga, morphological adaptations also evolved, including subterranean stems that are fire-resistant and long underground stem and root systems that facilitate water access. We did not find differences in metabolic pathway or modifications to pollen morphology when compared to other palm lineages. Assuming that the evolutionary history of Allagoptera is indicative of the habitat in which it occurs, our results infer a recent origin for Cerrado species. Although little is known about the formation of the Restinga habitat, our results also suggest a longer history than currently proposed; with an origin of Restinga habitats dating back to the Late Pliocene.
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Affiliation(s)
- Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.
| | - Monica Moraes R
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden; Gothenburg Botanical Garden, Göteborg, Sweden
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Mu XY, Zhao LC, Zhang ZX. Molecular Analysis of Chinese Celastrus and Tripterygium and Implications in Medicinal and Pharmacological Studies. PLoS One 2017; 12:e0169973. [PMID: 28081198 PMCID: PMC5231332 DOI: 10.1371/journal.pone.0169973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/24/2016] [Indexed: 11/18/2022] Open
Abstract
Celastrus and Tripterygium species, which are used in traditional Chinese medicine, have attracted much attention due to their anti-tumor promoting and neuroprotective activities, in addition to their applications in autoimmune disorders. However, systematic relationships between them and among species are unclear, and it may disturb their further medicinal utilization. In the present study, the molecular analysis of combined chloroplast and nuclear markers of all Chinese Celastrus and Tripterygium was performed, and clear inter- and intra-genus relationships were presented. The result suggests that Tripterygium constitute a natural monophyletic clade within Celastrus with strong support value. Fruit and seed type are better than inflorescence in subgeneric classification. Chinese Celastrus are classified for three sections: Sect. Sempervirentes (Maxim.) CY Cheng & TC Kao, Sect. Lunatus XY Mu & ZX Zhang, sect. nov., and Sect. Ellipticus XY Mu & ZX Zhang, sect. nov. The phylogenetic data was consistent with their chemical components reported previously. Owing to the close relationship, several evergreen Celastrus species are recommended for chemical and pharmacological studies. Our results also provide reference for molecular identification of Chinese Celastrus and Tripterygium.
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Affiliation(s)
- Xian-Yun Mu
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, PR China
- * E-mail: (XYM); (ZXZ)
| | - Liang-Cheng Zhao
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, PR China
| | - Zhi-Xiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing, PR China
- * E-mail: (XYM); (ZXZ)
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26
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Calió MF, Lepis KB, Pirani JR, Struwe L. Phylogeny of Helieae (Gentianaceae): Resolving taxonomic chaos in a Neotropical clade. Mol Phylogenet Evol 2017; 106:192-208. [DOI: 10.1016/j.ympev.2016.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/19/2016] [Accepted: 09/14/2016] [Indexed: 11/24/2022]
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27
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Cardoso D, Harris DJ, Wieringa JJ, São-Mateus WMB, Batalha-Filho H, Torke BM, Prenner G, Queiroz LPD. A molecular-dated phylogeny and biogeography of the monotypic legume genus Haplormosia, a missing African branch of the otherwise American-Australian Brongniartieae clade. Mol Phylogenet Evol 2016; 107:431-442. [PMID: 27965083 DOI: 10.1016/j.ympev.2016.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 11/17/2022]
Abstract
A comprehensively sampled reassessment of the molecular phylogeny of the genistoid legumes questions the traditional placement of Haplormosia, an African monotypic genus traditionally classified within tribe Sophoreae close to the Asian-American geographically disjunct genus Ormosia. Plastid matK sequences placed Haplormosia as sister to the American-Australian tribe Brongniartieae. Despite a superficial resemblance between Haplormosia and Ormosia, a re-examination of the morphology of Haplormosia corroborates the new phylogenetic result. The reciprocally monophyletic deep divergence of the Haplormosia stem lineage from the remaining Brongniartieae is dated to ca. 52Mya, thus supporting a signature of an old single long-distance dispersal during the early Eocene. Conversely, we estimated a relatively recent long-distance dispersal rooted in the Early Miocene for the Australian Brongniartieae clade emerging from within a grade of American Brongniartieae. The Bayesian ancestral area reconstruction revealed the coming and going of neotropical ancestors during the diversification history of the Brongniartieae legumes in Africa and all over the Americas and Australia.
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Affiliation(s)
- Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil.
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Wallace M B São-Mateus
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Benjamin M Torke
- Institute of Systematic Botany, The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458-5126, USA
| | - Gerhard Prenner
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
| | - Luciano Paganucci de Queiroz
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
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Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella
is supported as sister and Observed Variability is biased. Cladistics 2016; 33:488-512. [DOI: 10.1111/cla.12177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2016] [Indexed: 01/16/2023] Open
Affiliation(s)
- Mark P. Simmons
- Department of Biology; Colorado State University; Fort Collins CO 80523-1878 USA
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Cheek M, Challen G, Lebbie A, Banks H, Barberá P, Riina R. Discovering Karima (Euphorbiaceae), a New Crotonoid Genus from West Tropical Africa Long Hidden within Croton. PLoS One 2016; 11:e0152110. [PMID: 27049519 PMCID: PMC4822767 DOI: 10.1371/journal.pone.0152110] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/03/2016] [Indexed: 11/18/2022] Open
Abstract
Croton scarciesii (Euphorbiaceae-Crotonoideae), a rheophytic shrub from West Africa, is shown to have been misplaced in Croton for 120 years, having none of the diagnostic characters of that genus, but rather a set of characters present in no known genus of the family. Pollen analysis shows that the new genus Karima belongs to the inaperturate crotonoid group. Analysis of a concatenated molecular dataset combining trnL-F and rbcL sequences positioned Karima as sister to Neoholstia from south eastern tropical Africa in a well-supported clade comprised of genera of subtribes Grosserineae and Neoboutonieae of the inaperturate crotonoid genera. Several morphological characters support the relationship of Karima with Neoholstia, yet separation is merited by numerous characters usually associated with generic rank in Euphorbiaceae. Quantitative ecological data and a conservation assessment supplement illustrations and descriptions of the taxon.
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Affiliation(s)
- Martin Cheek
- Science Department, Royal Botanic Gardens, Kew, Surrey, United Kingdom
- * E-mail: (MC); (RR)
| | - Gill Challen
- Science Department, Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Aiah Lebbie
- National Herbarium of Sierra Leone, Dept. of Biological Sciences, Njala University, PMB, Freetown, Sierra Leone
| | - Hannah Banks
- Science Department, Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Patricia Barberá
- Department of Biodiversity and Conservation, Real Jardín Botánico, RJB-CSIC, Plaza de Murillo, Madrid, Spain
| | - Ricarda Riina
- Department of Biodiversity and Conservation, Real Jardín Botánico, RJB-CSIC, Plaza de Murillo, Madrid, Spain
- * E-mail: (MC); (RR)
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Wan D, Feng J, Jiang D, Mao K, Duan Y, Miehe G, Opgenoorth L. The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai-Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae). Ecol Evol 2016; 6:1977-95. [PMID: 27099706 PMCID: PMC4831433 DOI: 10.1002/ece3.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 01/15/2023] Open
Abstract
Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai-Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well-differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.
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Affiliation(s)
- Dong‐Shi Wan
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhou730000GansuChina
| | - Jian‐Ju Feng
- College of Plant SciencesXinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim BasinTarimu UniversityAlarXinjiangChina
| | - De‐Chun Jiang
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhou730000GansuChina
| | - Kang‐Shan Mao
- State Key Laboratory of Grassland Agro‐EcosystemSchool of Life SciencesLanzhou UniversityLanzhou730000GansuChina
- Key Laboratory for Bio‐resources and Eco‐environment of Ministry of EducationCollege of Life ScienceSichuan UniversityChengdu610064China
| | - Yuan‐Wen Duan
- Key Laboratory of Biodiversity and BiogeographyKunming Institute of BotanyChinese Academy of SciencesLanhei Road 132, HeilongtanKunming650204YunnanChina
| | - Georg Miehe
- Faculty of Biology and GeologyUniversity of Marburg35032MarburgGermany
| | - Lars Opgenoorth
- Faculty of Biology and GeologyUniversity of Marburg35032MarburgGermany
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31
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Gu C, Tembrock LR, Johnson NG, Simmons MP, Wu Z. The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae). PLoS One 2016; 11:e0150752. [PMID: 26950701 PMCID: PMC4780714 DOI: 10.1371/journal.pone.0150752] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/17/2016] [Indexed: 11/19/2022] Open
Abstract
Lagerstroemia (crape myrtle) is an important plant genus used in ornamental horticulture in temperate regions worldwide. As such, numerous hybrids have been developed. However, DNA sequence resources and genome information for Lagerstroemia are limited, hindering evolutionary inferences regarding interspecific relationships. We report the complete plastid genome of Lagerstroemia fauriei. To our knowledge, this is the first reported whole plastid genome within Lythraceae. This genome is 152,440 bp in length with 38% GC content and consists of two single-copy regions separated by a pair of 25,793 bp inverted repeats. The large single copy and the small single copy regions span 83,921 bp and 16,933 bp, respectively. The genome contains 129 genes, including 17 located in each inverted repeat. Phylogenetic analysis of genera sampled from Geraniaceae, Myrtaceae, and Onagraceae corroborated the sister relationship between Lythraceae and Onagraceae. The plastid genomes of L. fauriei and several other Lythraceae species lack the rpl2 intron, which indicating an early loss of this intron within the Lythraceae lineage. The plastid genome of L. fauriei provides a much needed genetic resource for further phylogenetic research in Lagerstroemia and Lythraceae. Highly variable markers were identified for application in phylogenetic, barcoding and conservation genetic applications.
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Affiliation(s)
- Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, P.R. China
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Nels G. Johnson
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, 37996, Tennessee, United States of America
| | - Mark P. Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
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Nie ZL, Funk VA, Meng Y, Deng T, Sun H, Wen J. Recent assembly of the global herbaceous flora: evidence from the paper daisies (Asteraceae: Gnaphalieae). THE NEW PHYTOLOGIST 2016; 209:1795-806. [PMID: 26528674 DOI: 10.1111/nph.13740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 10/01/2015] [Indexed: 05/10/2023]
Abstract
The global flora is thought to contain a large proportion of herbs, and understanding the general spatiotemporal processes that shaped the global distribution of these communities is one of the most difficult issues in biogeography. We explored patterns of world-wide biogeography in a species-rich herbaceous group, the paper daisy tribe Gnaphalieae (Asteraceae), based on the hitherto largest taxon sampling, a total of 835 terminal accessions representing 80% of the genera, and encompassing the global geographic range of the tribe, with nuclear internal transcribed spacer (ITS) and external transcribed spacer (ETS) sequences. Biogeographic analyses indicate that Gnaphalieae originated in southern Africa during the Oligocene, followed by repeated migrations into the rest of Africa and the Mediterranean region, with subsequent entries into other continents during various periods starting in the Miocene. Expansions in the late Miocene to Pliocene appear to have been the driving force that shaped the global distribution of the tribe as forests were progressively broken up by the mid-continent aridification and savannas and grasslands expanded into the interior of the major continents. This pattern of recent colonizations may explain the world-wide distribution of many other organisms in open ecosystems and it is highlighted here as an emerging pattern in the evolution of the global flora.
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Affiliation(s)
- Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ying Meng
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, 416000, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
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Tsou CH, Li L, Vijayan K. The Intra-familial Relationships of Pentaphylacaceae s.l. as Revealed by DNA Sequence Analysis. Biochem Genet 2016; 54:270-282. [DOI: 10.1007/s10528-016-9717-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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Crowl AA, Miles NW, Visger CJ, Hansen K, Ayers T, Haberle R, Cellinese N. A global perspective on Campanulaceae: Biogeographic, genomic, and floral evolution. AMERICAN JOURNAL OF BOTANY 2016; 103:233-45. [PMID: 26865121 DOI: 10.3732/ajb.1500450] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/04/2016] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY The Campanulaceae are a diverse clade of flowering plants encompassing more than 2300 species in myriad habitats from tropical rainforests to arctic tundra. A robust, multigene phylogeny, including all major lineages, is presented to provide a broad, evolutionary perspective of this cosmopolitan clade. METHODS We used a phylogenetic framework, in combination with divergence dating, ancestral range estimation, chromosome modeling, and morphological character reconstruction analyses to infer phylogenetic placement and timing of major biogeographic, genomic, and morphological changes in the history of the group and provide insights into the diversification of this clade across six continents. KEY RESULTS Ancestral range estimation supports an out-of-Africa diversification following the Cretaceous-Tertiary extinction event. Chromosomal modeling, with corroboration from the distribution of synonymous substitutions among gene duplicates, provides evidence for as many as 20 genome-wide duplication events before large radiations. Morphological reconstructions support the hypothesis that switches in floral symmetry and anther dehiscence were important in the evolution of secondary pollen presentation mechanisms. CONCLUSIONS This study provides a broad, phylogenetic perspective on the evolution of the Campanulaceae clade. The remarkable habitat diversity and cosmopolitan distribution of this lineage appears to be the result of a complex history of genome duplications and numerous long-distance dispersal events. We failed to find evidence for an ancestral polyploidy event for this clade, and our analyses indicate an ancestral base number of nine for the group. This study will serve as a framework for future studies in diverse areas of research in Campanulaceae.
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Affiliation(s)
- Andrew A Crowl
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Nicholas W Miles
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Clayton J Visger
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | - Kimberly Hansen
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 USA
| | - Tina Ayers
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011 USA
| | - Rosemarie Haberle
- Biology Department, Pacific Lutheran University, Tacoma, Washington 98447 USA
| | - Nico Cellinese
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
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Burgess MB, Cushman KR, Doucette ET, Frye CT, Campbell CS. Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier. AMERICAN JOURNAL OF BOTANY 2015; 102:2041-2057. [PMID: 26643889 DOI: 10.3732/ajb.1500330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity. METHODS We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM. KEY RESULTS Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B. CONCLUSIONS Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.
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Affiliation(s)
- Michael B Burgess
- Department of Biological Sciences, State University of New York Plattsburgh, Plattsburgh, New York 12901, USA
| | - Kevin R Cushman
- School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA
| | - Eric T Doucette
- School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA
| | - Christopher T Frye
- Maryland Department of Natural Resources, Natural Heritage Program, 909 Wye Mills Road, Wye Mills, Maryland 21679, USA
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Tsai JF, Kudo SI, Yoshizawa K. Maternal care in Acanthosomatinae (Insecta: Heteroptera: Acanthosomatidae)--correlated evolution with morphological change. BMC Evol Biol 2015; 15:258. [PMID: 26586480 PMCID: PMC4653913 DOI: 10.1186/s12862-015-0537-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/10/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Maternal care (egg-nymph guarding behavior) has been recorded in some genera of Acanthosomatidae. However, the origin of the maternal care in the family has remained unclear due to the lack of phylogenetic hypotheses. Another reproductive mode is found in non-caring species whose females smear their eggs before leaving them. They possess pairs of complex organs on the abdominal venter called Pendergrast's organ (PO) and spread the secretion of this organ onto each egg with their hind legs, which is supposed to provide a protective function against enemies. Some authors claim that the absence of PO may be associated with the presence of maternal care. No study, however, has tested this hypothesis of a correlated evolution between the two traits. RESULTS We reconstructed the molecular phylogeny of the subfamily Acanthosomatinae using five genetic markers sequenced from 44 species and one subspecies with and without maternal care. Eight additional species from the other two acanthosomatid subfamilies were included as outgroups. Our results indicated that maternal care has evolved independently at least three times within Acanthosomatinae and once in the outgroup species. Statistical tests for correlated evolution showed that the presence of maternal care is significantly correlated with the secondary loss or reduction of PO. Ancestral state reconstruction for the node of Acanthosoma denticaudum (a non-caring species in which egg smearing with developed POs occurs) and A. firmatum (a caring species with reduced POs) suggested egg smearing was still present in their most recent common ancestor and that maternal care in A. firmatum has evolved relatively recently. CONCLUSIONS We showed that maternal care is an apomorphic trait that has arisen multiple times from the presence of PO within the subfamily Acanthosomatinae. The acquisition of maternal care is correlated with the reduction or loss of PO, which suggests an evolutionary trade-off between the two traits resulting from physiological costs. This prediction also implies that presence of maternal care can be highly expected for those groups lacking behavioral data, which invariably also lack the organ. No secondary loss of maternal care was detected in the present tree. We suggest that the loss of maternal care may be suppressed due to the vulnerability of the PO-free condition, which thus maintains maternal care.
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Affiliation(s)
- Jing-Fu Tsai
- Systematic Entomology, School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
- Department of Biology, National Museum of Natural Science, Taichung, 40427, Taiwan.
| | - Shin-ichi Kudo
- Department of Biology, Naruto University of Education, Naruto, Tokushima, 772-8502, Japan.
| | - Kazunori Yoshizawa
- Systematic Entomology, School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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Gardner AG, Sessa EB, Michener P, Johnson E, Shepherd KA, Howarth DG, Jabaily RS. Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies. Mol Phylogenet Evol 2015; 94:605-617. [PMID: 26463342 DOI: 10.1016/j.ympev.2015.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/18/2015] [Accepted: 10/02/2015] [Indexed: 12/25/2022]
Abstract
Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.
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Affiliation(s)
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Genetics Institute, University of Florida, Gainesville, FL 32607, USA
| | - Pryce Michener
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Eden Johnson
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Kelly A Shepherd
- Western Australian Herbarium, Department of Parks and Wildlife, Kensington, WA 6151, Australia
| | - Dianella G Howarth
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
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Mast AR, Olde PM, Makinson RO, Jones E, Kubes A, Miller ET, Weston PH. Paraphyly changes understanding of timing and tempo of diversification in subtribe Hakeinae (Proteaceae), a giant Australian plant radiation. AMERICAN JOURNAL OF BOTANY 2015; 102:1634-1646. [PMID: 26451040 DOI: 10.3732/ajb.1500195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Subtribe Hakeinae (526 spp.) represents a large Australian plant radiation central to our understanding of that flora's evolution and ecology. It contains Grevillea-the third largest plant genus in Australia and a group inferred to have among the highest diversification rates in the angiosperms. However, we lack a robust phylogenetic framework for understanding subtribe Hakeinae and recognize that Grevillea lacks an unambiguous synapomorphy supporting its monophyly. METHODS We used four plastid and one nuclear DNA region from a taxonomically even sampling of a third of the species to infer a time-calibrated phylogeny of Hakeinae and absolute diversification rates of major clades. We developed the R package addTaxa to add unsampled taxa to the tree for diversification rate inference. KEY RESULTS Grevillea is paraphyletic with respect to Hakea and Finschia. Under most parameter combinations, Hakea contains the major clade with the highest diversification rate in Hakeinae, rather than Grevillea. The crown age of the Grevillea+Hakea+Finschia crown group is about double that of prior estimates. CONCLUSIONS We demonstrate that the paraphyly of Grevillea considerably enlarges the number of Australian descendants from its most recent common ancestor but has also misled investigators who considered a single operational taxonomic unit as adequate to represent the genus for inferences of diversification rate and timing. Our time-calibrated phylogeny can form the basis of future evolutionary, comparative ecology, and biogeography studies involving this large Australian plant radiation, as well as nomenclatural changes.
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Affiliation(s)
- Austin R Mast
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306 USA
| | - Peter M Olde
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, New South Wales, 2000, Australia
| | - Robert O Makinson
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, New South Wales, 2000, Australia
| | - Eric Jones
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306 USA Department of Biology, University of Maine, Machias, Maine 04654 USA
| | - Amanda Kubes
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306 USA
| | - Eliot T Miller
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844 USA
| | - Peter H Weston
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, New South Wales, 2000, Australia
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Williams BRM, Schaefer H, De Sequeira MM, Reyes-Betancort JA, Patiño J, Carine MA. Are there any widespread endemic flowering plant species in Macaronesia? Phylogeography of Ranunculus cortusifolius. AMERICAN JOURNAL OF BOTANY 2015; 102:1736-1746. [PMID: 26453597 DOI: 10.3732/ajb.1500238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Oceanic island endemics typically exhibit very restricted distributions. In Macaronesia, only one endemic angiosperm species, Ranunculus cortusifolius, has a distribution spanning the archipelagos of the Azores, Madeira, and Canaries. Earlier work suggested possible differences between archipelagos and the multiple origins of the species. This paper tests the hypothesis that R. cortusifolius is a single widespread Macaronesian endemic species with a single origin. METHODS Chloroplast (matK-trnK, psbJ-petA) and ITS sequences were generated from across the distribution of R. cortusifolius. Relationships were investigated using Bayesian inference and divergence times estimated using BEAST. Infraspecific variation was investigated using statistical parsimony. The general mixed Yule-coalescent model (GMYC) was further used to identify putative species boundaries based on maternally inherited plastid data. KEY RESULTS The hypothesis of multiple independent origins of R. cortusifolius is rejected. Divergence of the R. cortusifolius lineage from a western Mediterranean sister group in the late Miocene is inferred. Distinct genotypes were resolved within R. cortusifolius that are endemic to the Azores, Madeira, and the Canaries. Four to five putative species were delimited by different versions of the GMYC model. CONCLUSION Ranunculus cortusifolius is the result of a single colonization of Macaronesia. The large distances between archipelagos have been effective barriers to dispersal, promoting allopatric diversification at the molecular level with diversification also evident within the Canaries. Isolation has not been accompanied by marked morphological diversification, which may be explained by the typical association of R. cortusifolius with stable and climatically buffered laurel forest communities.
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Affiliation(s)
- Bethany R M Williams
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD
| | - Hanno Schaefer
- Technische Universitaet Muenchen, Plant Biodiversity, Emil-Ramann Str. 2, D-85354 Freising, Germany
| | | | - J Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Orotava (ICIA), C/ Retama n° 2 38400 Puerto de La Cruz, Tenerife, Spain
| | - Jairo Patiño
- Department of Biology, Ecology and Evolution, Liège University, Bât. B22, Boulevard du Rectorat 27, 4000 Liège, Belgium Departamento de Biología Vegetal, Universidad de La Laguna, C/ Astrofísico Francisco Sánchez, s/n 38071 Tenerife, Spain
| | - Mark A Carine
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD
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Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol Phylogenet Evol 2015; 91:98-122. [DOI: 10.1016/j.ympev.2015.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/01/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
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Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar. Mol Phylogenet Evol 2015; 94:365-82. [PMID: 26432393 DOI: 10.1016/j.ympev.2015.09.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/11/2015] [Accepted: 09/15/2015] [Indexed: 01/05/2023]
Abstract
Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years.
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Pokorny L, Riina R, Mairal M, Meseguer AS, Culshaw V, Cendoya J, Serrano M, Carbajal R, Ortiz S, Heuertz M, Sanmartín I. Living on the edge: timing of Rand Flora disjunctions congruent with ongoing aridification in Africa. Front Genet 2015; 6:154. [PMID: 25983742 PMCID: PMC4416453 DOI: 10.3389/fgene.2015.00154] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/05/2015] [Indexed: 01/16/2023] Open
Abstract
The Rand Flora is a well-known floristic pattern in which unrelated plant lineages show similar disjunct distributions in the continental margins of Africa and adjacent islands—Macaronesia-northwest Africa, Horn of Africa-Southern Arabia, Eastern Africa, and Southern Africa. These lineages are now separated by environmental barriers such as the arid regions of the Sahara and Kalahari Deserts or the tropical lowlands of Central Africa. Alternative explanations for the Rand Flora pattern range from vicariance and climate-driven extinction of a widespread pan-African flora to independent dispersal events and speciation in situ. To provide a temporal framework for this pattern, we used published data from nuclear and chloroplast DNA to estimate the age of disjunction of 17 lineages that span 12 families and nine orders of angiosperms. We further used these estimates to infer diversification rates for Rand Flora disjunct clades in relation to their higher-level encompassing lineages. Our results indicate that most disjunctions fall within the Miocene and Pliocene periods, coinciding with the onset of a major aridification trend, still ongoing, in Africa. Age of disjunctions seemed to be related to the climatic affinities of each Rand Flora lineage, with sub-humid taxa dated earlier (e.g., Sideroxylon) and those with more xeric affinities (e.g., Campylanthus) diverging later. We did not find support for significant decreases in diversification rates in most groups, with the exception of older subtropical lineages (e.g., Sideroxylon, Hypericum, or Canarina), but some lineages (e.g., Cicer, Campylanthus) showed a long temporal gap between stem and crown ages, suggestive of extinction. In all, the Rand Flora pattern seems to fit the definition of biogeographic pseudocongruence, with the pattern arising at different times in response to the increasing aridity of the African continent, with interspersed periods of humidity allowing range expansions.
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Affiliation(s)
| | | | | | - Andrea S Meseguer
- INRA, UMR 1062, Centre de Biologie pour la Gestion des Populations (INRA, IRD, CIRAD, Montpellier SupAgro) Montferrier-sur-Lez, France
| | | | - Jon Cendoya
- Real Jardín Botánico (RJB-CSIC) Madrid, Spain
| | - Miguel Serrano
- Department of Botany, Pharmacy School, University of Santiago de Compostela Santiago de Compostela, Spain
| | - Rodrigo Carbajal
- Department of Botany, Pharmacy School, University of Santiago de Compostela Santiago de Compostela, Spain
| | - Santiago Ortiz
- Department of Botany, Pharmacy School, University of Santiago de Compostela Santiago de Compostela, Spain
| | - Myriam Heuertz
- Forest Research Centre (INIA-CIFOR) Madrid, Spain ; INRA, BIOGECO, UMR 1202 Cestas, France ; University of Bordeaux, BIOGECO, UMR 1202 Talence, France
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Zhang Q, Feild TS, Antonelli A. Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity. AMERICAN JOURNAL OF BOTANY 2015; 102:566-580. [PMID: 25878090 DOI: 10.3732/ajb.1400527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic incongruence between "gene trees" and "species trees" has been widely acknowledged in phylogenetic research. Conflicts may emerge from several processes including paralogy, hybridization, and incomplete lineage sorting. Although phylogenetic incongruence appears common, its impact on many phylogeny-based analyses remains poorly understood. METHODS We examined the occurrence of phylogenetic conflict between nuclear (ribosome ITS) and plastid (rbcL, trnL-F, rpl20-rps12, and rps16 intron) loci in the ancient angiosperm family Chloranthaceae. Then we investigated how phylogenetic conflict bears on taxonomic classification within the family as well as on inferences on biogeographical history, floral evolution, and measures of phylogenetic diversity (PD). KEY RESULTS We found evidence for significant phylogenetic incongruence between plastid and nuclear data in the genus Hedyosmum. Within Hedyosmum, our results did not support previous subgeneric classification of the genus. Division of sections within subgenus Tafalla was supported by the ITS data but not by the plastid data set. As a consequence, we showed that inferring the evolution of key floral characters and geographical history within Hedyosmum depends on the phylogenetic data used. Both data sets yielded similar PD measures across genera, but we found contrasting PD measures in Hedyosmum, even after correcting for rate heterogeneity. CONCLUSIONS Our study demonstrated that phylogenetic conflict not only affects the inference of organismal relationships but also impacts our understanding of biogeographical history, morphological evolution, and phylogenetic diversity.
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Affiliation(s)
- Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences 541006, Guilin, China
| | - Taylor S Feild
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Alexandre Antonelli
- Gothenburg Botanical Garden and Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
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Cardoso D, São-Mateus WM, da Cruz DT, Zartman CE, Komura DL, Kite G, Prenner G, Wieringa JJ, Clark A, Lewis G, Pennington RT, de Queiroz LP. Filling in the gaps of the papilionoid legume phylogeny: The enigmatic Amazonian genus Petaladenium is a new branch of the early-diverging Amburaneae clade. Mol Phylogenet Evol 2015; 84:112-24. [DOI: 10.1016/j.ympev.2014.12.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/20/2014] [Accepted: 12/27/2014] [Indexed: 11/28/2022]
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Cappa JJ, Yetter C, Fakra S, Cappa PJ, DeTar R, Landes C, Pilon-Smits EAH, Simmons MP. Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis. THE NEW PHYTOLOGIST 2015; 205:583-95. [PMID: 25262627 DOI: 10.1111/nph.13071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/07/2014] [Indexed: 05/20/2023]
Abstract
Past studies have identified herbivory as a likely selection pressure for the evolution of hyperaccumulation, but few have tested the origin(s) of hyperaccumulation in a phylogenetic context. We focused on the evolutionary history of selenium (Se) hyperaccumulation in Stanleya (Brassicaceae). Multiple accessions were collected for all Stanleya taxa and two outgroup species. We sequenced four nuclear gene regions and performed a phylogenetic analysis. Ancestral reconstruction was used to predict the states for Se-related traits in a parsimony framework. Furthermore, we tested the taxa for Se localization and speciation using X-ray microprobe analyses. True hyperaccumulation was found in three taxa within the S. pinnata/bipinnata clade. Tolerance to hyperaccumulator Se concentrations was found in several taxa across the phylogeny, including the hyperaccumulators. X-ray analysis revealed two distinct patterns of leaf Se localization across the genus: marginal and vascular. All taxa accumulated predominantly (65-96%) organic Se with the C-Se-C configuration. These results give insight into the evolution of Se hyperaccumulation in Stanleya and suggest that Se tolerance and the capacity to produce organic Se are likely prerequisites for Se hyperaccumulation in Stanleya.
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Affiliation(s)
- Jennifer J Cappa
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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Simmons MP. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Mol Phylogenet Evol 2014; 74:1-14. [DOI: 10.1016/j.ympev.2014.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 01/30/2014] [Accepted: 01/30/2014] [Indexed: 11/16/2022]
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Wynns JT, Lange CBA. A comparison of 16 DNA regions for use as phylogenetic markers in the pleurocarpous moss genus Plagiothecium (Hypnales). AMERICAN JOURNAL OF BOTANY 2014; 101:652-669. [PMID: 24699540 DOI: 10.3732/ajb.1300269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Within the Hypnales-the most derived and species-rich order of pleurocarpous mosses - phylogenies at or below the family level often show poor resolution. In preparation for a phylogeny of the genus Plagiothecium, we wished to identify the DNA markers best suited for evolutionary reconstruction in this group of hypnalean pleurocarps. METHODS For each of 25 collections of Plagiothecium and associated taxa, 16 DNA regions were sequenced: nuclear ITS and 26S, and plastid rps4, rps4-trnL, trnL-F, trnK (matK)-psbA, psbA-trnH, trnM-V, trnD-T, rbcL, atpB-rbcL, psbT-H, rpoC1 exon 2 (partial), the trnG intron, the rpl16 intron and the plastid ribosomal spacer DNA (cpITS). Each region was evaluated on the basis of its ability to resolve clades, the amount of homoplasy present in the data set, and the relative ease of obtaining the data. Descriptive statistics for each region are given. KEY RESULTS Under-utilized plastid markers for bryophytes such as trnK-psbA, rps4-trnL, and trnD-T outperformed more traditional markers such as trnL-F and rps4. Individual plastid topologies were similar, suggesting that only a limited amount of plastid data are needed to recover a backbone phylogeny. Adding a small amount of nuclear ribosomal data to a large plastid matrix restructured the recovered topology, emphasizing the importance of sampling multiple genomes and the need for new low-copy nuclear markers in bryophyte systematics. CONCLUSIONS Future genus-level phylogenies of pleurocarpous mosses should target under-utilized plastid markers such as trnK-psbA and rps4-trnL in conjunction with low-copy nuclear markers.
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Affiliation(s)
- Justin T Wynns
- Section for Organismal Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Rolighedsvej 21, DK-1958 Frederiksberg, Denmark
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Chaowasku T, Thomas DC, van der Ham RWJM, Smets EF, Mols JB, Chatrou LW. A plastid DNA phylogeny of tribe Miliuseae: insights into relationships and character evolution in one of the most recalcitrant major clades of Annonaceae. AMERICAN JOURNAL OF BOTANY 2014; 101:691-709. [PMID: 24688057 DOI: 10.3732/ajb.1300403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Tribe Miliuseae (∼25 genera and ∼510 species) includes a substantial part of the species and generic diversity in the pantropical flowering-plant family Annonaceae (∼108 genera and ∼2400 species). Previous molecular phylogenetic analyses have failed to resolve the backbone phylogeny of the tribe, impeding biogeographical and evolutionary studies. We use a dense generic taxon sample (∼89% of generic diversity in Miliuseae) and plastid DNA sequence data (∼7 kb) to clarify the phylogenetic relationships of and within the tribe. METHODS Parsimony and Bayesian phylogenetic reconstructions and ancestral character-state reconstructions of several reproductive characters were performed. KEY RESULTS Dendrokingstoniae, Monocarpieae, and Miliuseae are recovered in a strongly supported clade, and each tribe is strongly supported as monophyletic. Miliuseae are characterized by a synapomorphic cryptoaperturate/disulculate pollen apertural system. Stenanona is shown to be nested within the paraphyletic genus Desmopsis. The only Neotropical clade (Sapranthus, Tridimeris, Desmopsis, and Stenanona) in the predominantly Asian Miliuseae is shown to be closely related to an undescribed genus from continental Southeast Asia and the Indo-Malayan and Austral-Pacific genus Meiogyne. Ancestral character-state reconstructions of several reproductive characters that are diagnostically important at the generic level indicate a considerable degree of homoplasy. CONCLUSIONS The results improve our understanding of the relationships of and within Miliuseae, but parts of the backbone of the phylogeny remain poorly supported. Additional data from variable nuclear markers or reduced-genome-representation approaches seem to be required to further resolve relationships within this recalcitrant clade.
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Affiliation(s)
- Tanawat Chaowasku
- Naturalis Biodiversity Center (section NHN), Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
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Bissinger K, Khoshravesh R, Kotrade JP, Oakley J, Sage TL, Sage RF, Hartmann HEK, Kadereit G. Gisekia (Gisekiaceae): phylogenetic relationships, biogeography, and ecophysiology of a poorly known C₄ lineage in the Caryophyllales. AMERICAN JOURNAL OF BOTANY 2014; 101:499-509. [PMID: 24638165 DOI: 10.3732/ajb.1300279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Gisekiaceae are a monogeneric family of the core Caryophyllales distributed in arid regions of Africa and Asia. The only widespread species of the genus, Gisekia pharnaceoides, performs C4 photosynthesis based on CO2 compensation point measurements. This study investigates the C4 syndrome and its evolution in Gisekia. The infrageneric relationships, distribution and bioclimatic preferences of Gisekia are also investigated. METHODS Leaf gas exchange characteristics, activity of Rubisco and major C4 cycle enzymes, and ultrastructural characteristics of mesophyll and bundle sheath cells are studied for Gisekia pharnaceoides. δ(13)C values and leaf anatomy are analyzed for all species. A dated molecular phylogeny of 39 accessions representing all species of Gisekiaceae and 14 representatives of closely related core Caryophyllales families is generated using four cp markers and ITS. The precise current distribution and bioclimatic niche of Gisekia is assessed on the basis of 520 georeferenced specimen localities. KEY RESULTS All traditionally recognized species of Gisekia are C4 plants with atriplicoid Kranz anatomy. Gisekia pharnaceoides uses the NAD-ME biochemical type. The molecular phylogeny demonstrated two East African clades nested within South African clades, demonstrating migration along the arid areas of eastern Africa during the Late Miocene/Pliocene Epochs. Most traditionally defined species are polyphyletic. CONCLUSIONS Gisekia represents an isolated C4 lineage within core Caryophyllales dating back to the Miocene Epoch and probably spread along the African arid corridor from a South African center of origin. The seven currently recognized species should be treated as one polymorphic species or species complex, Gisekia pharnaceoides agg.
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Affiliation(s)
- Kerstin Bissinger
- Institut für Allgemeine und Spezielle Botanik, Anselm-Franz-von Bentzel weg 9a, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
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Büsse S, Hörnschemeyer T. The thorax musculature of Anisoptera (Insecta: Odonata) nymphs and its evolutionary relevance. BMC Evol Biol 2013; 13:237. [PMID: 24180622 PMCID: PMC4228402 DOI: 10.1186/1471-2148-13-237] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/29/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Among the winged insects (Pterygota) the Odonata (dragon- and damselflies) are special for several reasons. They are strictly aerial predators showing remarkable flight abilities and their thorax morphology differs significantly from that of other Pterygota in terms of the arrangement and number of muscles. Even within one individual the musculature is significantly different between the nymphal and adult stage. RESULTS Here we present a comparative morphological investigation of the thoracic musculature of dragonfly (Anisoptera) nymphs. We investigated representatives of the Libellulidae, Aeshnidae and Cordulegasteridae and found 71 muscles: 19 muscles in the prothorax, 26 in the mesothorax and 27 in the metathorax. Nine of these muscles were previously unknown in Odonata, and for seven muscles no homologous muscles could be identified in the neopteran thorax. CONCLUSION Our results support and extend the homology hypotheses for the thoracic musculatures of Odonata and Neoptera, thus supplementing our understanding of the evolution of Pterygota and providing additional characters for phylogenetic analyses comprising all subgroups of Pterygota.
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Affiliation(s)
- Sebastian Büsse
- Department of Morphology, Systematic & Evolutionary Biology, J-F-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, Göttingen, Germany
| | - Thomas Hörnschemeyer
- Department of Morphology, Systematic & Evolutionary Biology, J-F-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, Göttingen, Germany
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