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van Galen LG, Orlovich DA, Lord JM, Nilsen AR, Dutoit L, Larcombe MJ. Correlated evolution in an ectomycorrhizal host-symbiont system. THE NEW PHYTOLOGIST 2023; 238:1215-1229. [PMID: 36751898 DOI: 10.1111/nph.18802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.
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Affiliation(s)
- Laura G van Galen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - David A Orlovich
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Janice M Lord
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Andy R Nilsen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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Hackel J, Henkel TW, Moreau P, De Crop E, Verbeken A, Sà M, Buyck B, Neves M, Vasco‐Palacios A, Wartchow F, Schimann H, Carriconde F, Garnica S, Courtecuisse R, Gardes M, Manzi S, Louisanna E, Roy M. Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions. THE NEW PHYTOLOGIST 2022; 236:698-713. [PMID: 35811430 PMCID: PMC9795906 DOI: 10.1111/nph.18365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae. We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia. The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid-Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north-temperate origins and are associated with North Andean uplift and the general north-south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas. Neotropical Russulaceae have multiple biogeographic origins since the mid-Eocene involving dispersal and co-migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.
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Affiliation(s)
- Jan Hackel
- Royal Botanic Gardens, KewRichmond‐upon‐ThamesTW9 3AEUK
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
| | - Terry W. Henkel
- Department of Biological SciencesCalifornia State Polytechnic University, HumboldtArcataCA95521USA
| | - Pierre‐Arthur Moreau
- Faculté de Pharmacie, Laboratoire des Sciences Végétales et Fongiques (LGCgE, ER4)Université de Lille59006LilleFrance
| | - Eske De Crop
- Department of BiologyGhent University9000GentBelgium
| | | | - Mariana Sà
- Centro Universitário de João PessoaPB 58053‐000João PessoaBrazil
| | - Bart Buyck
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne Université, EPHE, Université des Antilles75231Paris cedex 05France
| | - Maria‐Alice Neves
- Departamento de BotânicaUniversidade Federal de Santa CatarinaSC 88040‐900FlorianópolisBrazil
| | - Aída Vasco‐Palacios
- Microbiología Ambiental–School of Microbiology, Laboratory of Taxonomy and Ecology of Fungi–Institute of BiologyUniversity of Antioquia050010MedellínColombia
| | - Felipe Wartchow
- Departamento de Sistemática e EcologiaUniversidade Federal da ParaíbaPB 58051‐970João PessoaBrazil
| | - Heidy Schimann
- UMR Ecologie des Forêts de GuyaneAgroParisTech/CIRAD/CNRS/Université des Antilles/Université de la Guyane/INRA97379Kourou cedexFrench Guiana
| | - Fabian Carriconde
- Institut Agronomique néo‐Calédonien (IAC), Equipe Sol & Végétations (SolVeg)BP1823998848NouméaNew Caledonia
| | - Sigisfredo Garnica
- Instituto de Bioquímica y MicrobiologíaUniversidad Austral de Chile5049000ValdiviaChile
| | - Régis Courtecuisse
- Faculté de Pharmacie, Laboratoire des Sciences Végétales et Fongiques (LGCgE, ER4)Université de Lille59006LilleFrance
| | - Monique Gardes
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
| | - Sophie Manzi
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
| | - Eliane Louisanna
- UMR Ecologie des Forêts de GuyaneAgroParisTech/CIRAD/CNRS/Université des Antilles/Université de la Guyane/INRA97379Kourou cedexFrench Guiana
| | - Mélanie Roy
- Laboratoire Evolution et Diversité Biologique (UMR 5174)Université Toulouse III – Paul Sabatier/CNRS/IRD31062Toulouse cedex 9France
- Instituto Franco‐Argentino para el Estudio del Clima y sus Impactos (UMI IFAECI/CNRS‐CONICET‐UBA‐IRD)Universidad de Buenos AiresC1428EGACiudad Autonoma de Buenos AiresArgentina
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Berckx F, Nguyen TV, Bandong CM, Lin HH, Yamanaka T, Katayama S, Wibberg D, Blom J, Kalinowski J, Tateno M, Simbahan J, Liu CT, Brachmann A, Pawlowski K. A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world. BMC Genomics 2022; 23:602. [PMID: 35986253 PMCID: PMC9392346 DOI: 10.1186/s12864-022-08838-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 01/01/2023] Open
Abstract
It is currently assumed that around 100 million years ago, the common ancestor to the Fabales, Fagales, Rosales and Cucurbitales in Gondwana, developed a root nodule symbiosis with a nitrogen-fixing bacterium. The symbiotic trait evolved first in Frankia cluster-2; thus, strains belonging to this cluster are the best extant representatives of this original symbiont. Most cluster-2 strains could not be cultured to date, except for Frankia coriariae, and therefore many aspects of the symbiosis are still elusive. Based on phylogenetics of cluster-2 metagenome-assembled genomes (MAGs), it has been shown that the genomes of strains originating in Eurasia are highly conserved. These MAGs are more closely related to Frankia cluster-2 in North America than to the single genome available thus far from the southern hemisphere, i.e., from Papua New Guinea. To unravel more biodiversity within Frankia cluster-2 and predict routes of dispersal from Gondwana, we sequenced and analysed the MAGs of Frankia cluster-2 from Coriaria japonica and Coriaria intermedia growing in Japan, Taiwan and the Philippines. Phylogenetic analyses indicate there is a clear split within Frankia cluster-2, separating a continental from an island lineage. Presumably, these lineages already diverged in Gondwana. Based on fossil data on the host plants, we propose that these two lineages dispersed via at least two routes. While the continental lineage reached Eurasia together with their host plants via the Indian subcontinent, the island lineage spread towards Japan with an unknown host plant.
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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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Liu J, Lindstrom AJ, Marler TE, Gong X. Not that young: combining plastid phylogenomic, plate tectonic and fossil evidence indicates a Palaeogene diversification of Cycadaceae. ANNALS OF BOTANY 2022; 129:217-230. [PMID: 34520529 PMCID: PMC8796677 DOI: 10.1093/aob/mcab118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Previous molecular dating studies revealed historical mass extinctions and recent radiations of extant cycads, but debates still exist between palaeobotanists and evolutionary biologists regarding the origin and evolution of Cycadaceae. METHODS Using whole plastomic data, we revisited the phylogeny of this family and found the Palawan endemic Cycas clade was strongly related to all lineages from Southeast Eurasia, coinciding with a plate drift event occurring in the Early Oligocene. By integrating fossil and biogeographical calibrations as well as molecular data from protein-coding genes, we established different calibration schemes and tested competing evolutionary timelines of Cycadaceae. KEY RESULTS We found recent dispersal cannot explain the distribution of Palawan Cycas, yet the scenario including the tectonic calibration yielded a mean crown age of extant Cycadaceae of ~69-43 million years ago by different tree priors, consistent with multiple Palaeogene fossils assigned to this family. Biogeographical analyses incorporating fossil distributions revealed East Asia as the ancestral area of Cycadaceae. CONCLUSIONS Our findings challenge the previously proposed Middle-Late Miocene diversification of cycads and an Indochina origin for Cycadaceae and highlight the importance of combining phylogenetic clades, tectonic events and fossils for rebuilding the evolutionary history of lineages that have undergone massive extinctions.
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Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- For correspondence. Email , or
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
- For correspondence. Email , or
| | - Thomas E Marler
- Western Pacific Tropical Research Center, University of Guam, UOG Station, Mangilao, GU 96923, USA
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- For correspondence. Email , or
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Around the world in 40 million years: Phylogeny and biogeography of Tecomeae (Bignoniaceae). Mol Phylogenet Evol 2021; 166:107335. [PMID: 34757167 DOI: 10.1016/j.ympev.2021.107335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/22/2022]
Abstract
Intercontinental disjunct distributions can arise from vicariance, long distance dispersal, or both. Tecomeae (Bignoniaceae) are a nearly cosmopolitan clade of flowering plants providing us with an excellent opportunity to investigate global distribution patterns. While the tribe contains only about 57 species, it has achieved a distribution that is not only pantropical, but also extends into the temperate zones in both the Northern and Southern hemispheres. This distribution is similar to the distribution of its sister group, a clade of about 750 spp. that includes most remaining taxa in Bignoniaceae. To infer temporal and spatial patterns of dispersal, we generated a phylogeny of Tecomeae by gathering sequence data from chloroplast and nuclear markers for 41 taxa. Fossil calibrations were used to determine divergence times, and ancestral states were reconstructed to infer its biogeographic history. We found support for a South American origin and a crown age of the tribe estimated at ca. 40 Ma. Two dispersal events seem to have happened during the Eocene-Oligocene, one from South America to the Old World, and another from South America to North America. Furthermore, two other dispersal events seem to have taken place during the Miocene, one from North America to Asia, and another from Australia to South America. We suggest that intercontinental dispersal via land bridges and island hopping, as well as sweepstakes of long distance dispersal from the Eocene to the present explain the global distribution of Tecomeae.
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Xue Z, Greimler J, Paun O, Ford KA, Barfuss MHJ, Chiapella JO. The Evolutionary History of New Zealand Deschampsia Is Marked by Long-Distance Dispersal, Endemism, and Hybridization. BIOLOGY 2021; 10:1001. [PMID: 34681100 PMCID: PMC8533413 DOI: 10.3390/biology10101001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022]
Abstract
The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the evolutionary history of three New Zealand endemic Deschampsia species, and how they are related to cosmopolitan D. cespitosa. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the D. cespitosa populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with D. cespitosa lived during the last ten MY. The New Zealand D. cespitosa appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant D. cespitosa of New Zealand. Both data provided strong evidence for hybridization between D. cespitosa and D. chapmanii. Our findings provide evidence for at least two migration events of the genus Deschampsia to New Zealand and hybridization between D. cespitosa and endemic taxa.
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Affiliation(s)
- Zhiqing Xue
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Josef Greimler
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Kerry A. Ford
- Allan Herbarium, Manaaki-Whenua Landcare Research, P.O. Box 69040, Lincoln 7640, New Zealand;
| | - Michael H. J. Barfuss
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, 1030 Vienna, Austria; (O.P.); (M.H.J.B.)
| | - Jorge O. Chiapella
- Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA-CONICET-Universidad Nacional del Comahue), Quintral 1250, Bariloche R8400FRF, Argentina;
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Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: A reanalysis. PLoS One 2021; 16:e0256679. [PMID: 34550988 PMCID: PMC8457462 DOI: 10.1371/journal.pone.0256679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/16/2021] [Indexed: 11/19/2022] Open
Abstract
Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01–63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87–22.85), 24.14 (18.02–30.58), and 21.6 (16.44–27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54–52.22) Ma, compared with 25.16 Ma (18.41–33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.
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Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
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Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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10
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Nguyen TV, Wibberg D, Vigil-Stenman T, Berckx F, Battenberg K, Demchenko KN, Blom J, Fernandez MP, Yamanaka T, Berry AM, Kalinowski J, Brachmann A, Pawlowski K. Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams. Genome Biol Evol 2019; 11:2273-2291. [PMID: 31368478 PMCID: PMC6735867 DOI: 10.1093/gbe/evz153] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 11/14/2022] Open
Abstract
Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.
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Affiliation(s)
- Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | | | - Fede Berckx
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Gießen, Germany
| | - Maria P Fernandez
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université Lyon I, Villeurbanne Cedex, France
| | | | - Alison M Berry
- Department of Plant Sciences, University of California, Davis
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Germany
| | - Andreas Brachmann
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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11
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Markle DF. DRAINAGE EVOLUTION AND FRESHWATER FISH ZOOGEOGRAPHY IN COASTAL OREGON AND WASHINGTON. ACTA ACUST UNITED AC 2019. [DOI: 10.1898/nwn-18-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Douglas F Markle
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331 USA;
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12
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Wallis GP, Jorge F. Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia. Mol Ecol 2018; 27:4368-4396. [DOI: 10.1111/mec.14875] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Fátima Jorge
- Department of Zoology; University of Otago; Dunedin New Zealand
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13
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A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics. Mol Phylogenet Evol 2018; 127:813-822. [DOI: 10.1016/j.ympev.2018.06.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 11/20/2022]
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14
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Bacon CD, Velásquez-Puentes FJ, Hinojosa LF, Schwartz T, Oxelman B, Pfeil B, Arroyo MTK, Wanntorp L, Antonelli A. Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot. PeerJ 2018; 6:e4388. [PMID: 29576938 PMCID: PMC5858603 DOI: 10.7717/peerj.4388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/29/2018] [Indexed: 11/25/2022] Open
Abstract
Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes—the world’s richest and most diverse biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e., páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera, a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, and whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota.
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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), Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Francisco J Velásquez-Puentes
- Laboratório de Biología Molecular (CINBIN), Universidad Industrial de Santander, Bucaramanga, Colombia.,Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Luis Felipe Hinojosa
- Institute of Ecology and Biodiversity, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Thomas Schwartz
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Mary T K Arroyo
- Institute of Ecology and Biodiversity, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Livia Wanntorp
- Department of Phanerogamic Botany, Swedish Museum for Natural History, Stockholm, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.,Gothenburg Botanical Garden, Gothenburg, Sweden.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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15
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Bourguignon T, Tang Q, Ho SYW, Juna F, Wang Z, Arab DA, Cameron SL, Walker J, Rentz D, Evans TA, Lo N. Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics. Mol Biol Evol 2018; 35:970-983. [DOI: 10.1093/molbev/msy013] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Frantisek Juna
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - James Walker
- Department of Agriculture and Water Resources, Cairns, QLD, Australia
| | - David Rentz
- School of Marine and Tropical Biology, James Cook University, Townsville, QLD, Australia
| | - Theodore A Evans
- School of Animal Biology, University of Western Australia, Perth, WA, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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16
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Hamilton FB, Williams DJ, Hardy NB. Five new species of the armored scale genus Andaspis MacGillivray (Hemiptera, Coccomorpha, Diaspididae) from New Caledonia. Zookeys 2017:17-31. [PMID: 29133992 PMCID: PMC5672737 DOI: 10.3897/zookeys.693.13074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/11/2017] [Indexed: 11/12/2022] Open
Abstract
New Caledonia is home to many endemic species of plants and animals. Here, we improve our grasp on that biota by describing five new species of armored scale insects in the genus Andaspis: Andaspis brevicornutasp. n, A. conicasp. n., A. nothofagisp. n., A. novaecaledoniaesp. n., and A. ornatasp. n. Each is known exclusively from collections on southern beeches (Nothofagus spp.) in New Caledonia. A key to the species of Andaspis of New Caledonia is provided.
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Affiliation(s)
- Fredericka B Hamilton
- Auburn University, Department of Entomology and Plant Pathology, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Douglas J Williams
- The Natural History Museum, Department of Life Sciences (Entomology), Cromwell Road, London SW7 5BD, UK
| | - Nate B Hardy
- Auburn University, Department of Entomology and Plant Pathology, 301 Funchess Hall, Auburn, AL 36849, USA
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17
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Heterick BE, Castalanelli M, Shattuck SO. Revision of the ant genus Melophorus (Hymenoptera, Formicidae). Zookeys 2017; 700:1-420. [PMID: 29358897 PMCID: PMC5711039 DOI: 10.3897/zookeys.700.11784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/22/2017] [Indexed: 11/12/2022] Open
Abstract
The fauna of the purely Australian formicine ant genus Melophorus (Hymenoptera: Formicidae) is revised. This project involved integrated morphological and molecular taxonomy using one mitochondrial gene (COI) and four nuclear genes (AA, H3, LR and Wg). Seven major clades were identified and are here designated as the M. aeneovirens, M. anderseni, M. biroi, M. fulvihirtus, M. ludius, M. majeri and M. potteri species-groups. Within these clades, smaller complexes of similar species were also identified and designated species-complexes. The M. ludius species-group was identified purely on molecular grounds, as the morphology of its members is indistinguishable from typical members of the M. biroi species-complex within the M. biroi species-group. Most species-complexes sampled were also found to be monophyletic. Sequencing generally supported monophyly in taxa sampled but some species of the M. fieldi complex and M. biroi were not monophyletic and the implications arising from this are discussed in this monograph. Based on morphology, ninety-three species are recognized, 73 described as new. A further new species (here called 'Species K' [TERC Collection]) is noted in the taxonomic list, but is not described in this work. One species is removed from Melophorus: M. scipio Forel is here placed provisionally in Prolasius. Six species and five subspecies pass into synonymy. Of the full species, M. constans Santschi, M. iridescens (Emery) and M. insularis Wheeler are synonymized under M. aeneovirens (Lowne), M. pillipes Santschi is synonymized under M. turneri Forel, M. marius Forel is synonymized under M. biroi Forel, and M. omniparens Forel is synonymized under M. wheeleri Forel. Of the subspecies, M. iridescens fraudatrix and M. iridescens froggatti Forel are synonymized under M. aeneovirens (Lowne), M. turneri aesopus Forel and M. turneri candidus Santschi are synonymized under M. turneri Forel and M. fieldi propinqua Viehmeyer is synonymized under M. biroi. Camponotus cowlei Froggatt is reinstated as a junior synonym of Melophorus bagoti Lubbock. In addition, the subspecies M. fieldi major Forel, M. ludius sulla Forel and M. turneri perthensis Forel are raised to species. A key to workers of the genus is supplied. A lectotype is designated for M. curtus Forel, M. sulla, and M. turneri.
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Affiliation(s)
- Brian E Heterick
- Curtin University of Technology, GPO Box U1987, Perth WA, Australia, 6845
- Western Australian Museum, Locked Bag 49, Welshpool DC. WA, Australia, 6986
| | | | - Steve O Shattuck
- C/o CSIRO Entomology, P. O. Box 1700, Canberra, Australia, ACT 2601
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18
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Toussaint EFA, Tänzler R, Balke M, Riedel A. Transoceanic origin of microendemic and flightless New Caledonian weevils. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160546. [PMID: 28680653 PMCID: PMC5493895 DOI: 10.1098/rsos.160546] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 05/10/2017] [Indexed: 05/26/2023]
Abstract
The origin of the astonishing New Caledonian biota continues to fuel a heated debate among advocates of a Gondwanan relict scenario and defenders of late oceanic dispersal. Here, we study the origin of New Caledonian Trigonopterus flightless weevils using a multimarker molecular phylogeny. We infer two independent clades of species found in the archipelago. Our dating estimates suggest a Late Miocene origin of both clades long after the re-emergence of New Caledonia about 37 Ma. The estimation of ancestral ranges supports an ancestral origin of the genus in a combined region encompassing Australia and New Guinea with subsequent colonizations of New Caledonia out of New Guinea in the mid-Miocene. The two New Caledonian lineages have had very different evolutionary trajectories. Colonizers belonging to a clade of foliage dwellers greatly diversified, whereas species inhabiting leaf-litter have been less successful.
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Affiliation(s)
| | - Rene Tänzler
- SNSB-Zoological State Collection (ZSM), Münchhausenstrasse 21, 81247 Munich, Germany
| | - Michael Balke
- SNSB-Zoological State Collection (ZSM), Münchhausenstrasse 21, 81247 Munich, Germany
- GeoBioCenter, Ludwig-Maximilians-University, Munich, Germany
| | - Alexander Riedel
- Museum of Natural History Karlsruhe (SMNK), Erbprinzenstrasse 13, 76133 Karlsruhe, Germany
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19
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Peterson KR, Pfister DH, Bell CD. Cophylogeny and biogeography of the fungal parasite Cyttaria and its host Nothofagus, southern beech. Mycologia 2017; 102:1417-25. [DOI: 10.3852/10-048] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Donald H. Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138
| | - Charles D. Bell
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148
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20
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Distribution and Evolution of Mycorrhizal Types and Other Specialised Roots in Australia. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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21
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Liu LX, Li R, Worth JRP, Li X, Li P, Cameron KM, Fu CX. The Complete Chloroplast Genome of Chinese Bayberry ( Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales. FRONTIERS IN PLANT SCIENCE 2017; 8:968. [PMID: 28713393 PMCID: PMC5492642 DOI: 10.3389/fpls.2017.00968] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014-26,069 bp) separated by a large single-copy (LSC) region (88,683-88,809 bp) and a small single-copy (SSC) region (18,676-18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG, and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future research characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.
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Affiliation(s)
- Lu-Xian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan UniversityKaifeng, China
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Rui Li
- Food Inspection and Testing Institute of Henan ProvinceZhengzhou, China
| | - James R. P. Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research InstituteIbaraki, Japan
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
- *Correspondence: Pan Li,
| | | | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
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22
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Tedersoo L. Global Biogeography and Invasions of Ectomycorrhizal Plants: Past, Present and Future. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_20] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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23
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Berger BA, Kriebel R, Spalink D, Sytsma KJ. Divergence times, historical biogeography, and shifts in speciation rates of Myrtales. Mol Phylogenet Evol 2015; 95:116-36. [PMID: 26585030 DOI: 10.1016/j.ympev.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 10/04/2015] [Indexed: 01/22/2023]
Abstract
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.
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Affiliation(s)
- Brent A Berger
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11432, USA; Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Daniel Spalink
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
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24
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A long distance dispersal hypothesis for the Pandanaceae and the origins of the Pandanus tectorius complex. Mol Phylogenet Evol 2015; 83:20-32. [DOI: 10.1016/j.ympev.2014.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 11/23/2022]
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25
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Xiang QP, Wei R, Shao YZ, Yang ZY, Wang XQ, Zhang XC. Phylogenetic relationships, possible ancient hybridization, and biogeographic history of Abies (Pinaceae) based on data from nuclear, plastid, and mitochondrial genomes. Mol Phylogenet Evol 2015; 82 Pt A:1-14. [DOI: 10.1016/j.ympev.2014.10.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 09/30/2014] [Accepted: 10/09/2014] [Indexed: 11/16/2022]
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26
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Sun Y, He X, Glenny D. Transantarctic disjunctions in Schistochilaceae (Marchantiophyta) explained by early extinction events, post-Gondwanan radiations and palaeoclimatic changes. Mol Phylogenet Evol 2014; 76:189-201. [DOI: 10.1016/j.ympev.2014.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 03/03/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
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27
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Morrison DA. The Monkey's Voyage: How Improbable Journeys Shaped the History of Life.—By Alan de Queiroz. Syst Biol 2014. [DOI: 10.1093/sysbio/syu045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- David A. Morrison
- Systematic Biology, Evolutionary Biology Centre, Norbyvägen 18D, 752 36 Uppsala, Sweden
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28
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David-Palma M, Libkind D, Sampaio JP. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Mol Ecol 2014; 23:921-32. [DOI: 10.1111/mec.12642] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Márcia David-Palma
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología; Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA); CONICET - UNComahue; Quintral 1250 (8400), Bariloche Argentina
| | - José Paulo Sampaio
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
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29
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Crisp MD, Cook LG. How Was the Australian Flora Assembled Over the Last 65 Million Years? A Molecular Phylogenetic Perspective. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135910] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael D. Crisp
- Research School of Biology, The Australian National University, Canberra, ACT 2602, Australia;
| | - Lyn G. Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia;
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30
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Friedman M, Keck BP, Dornburg A, Eytan RI, Martin CH, Hulsey CD, Wainwright PC, Near TJ. Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proc Biol Sci 2013; 280:20131733. [PMID: 24048155 PMCID: PMC3779330 DOI: 10.1098/rspb.2013.1733] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/29/2013] [Indexed: 11/21/2022] Open
Abstract
Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (ca 65-57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography.
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Affiliation(s)
- Matt Friedman
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Alex Dornburg
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Ron I. Eytan
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | | | - C. Darrin Hulsey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Peter C. Wainwright
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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Not drowning, (hand)waving? Molecular phylogenetics, biogeography and evolutionary tempo of the ‘Gondwanan’ midge Stictocladius Edwards (Diptera: Chironomidae). Mol Phylogenet Evol 2013; 68:595-603. [DOI: 10.1016/j.ympev.2013.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/21/2013] [Accepted: 04/08/2013] [Indexed: 11/18/2022]
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Bayly MJ, Holmes GD, Forster PI, Cantrill DJ, Ladiges PY. Major clades of Australasian Rutoideae (Rutaceae) based on rbcL and atpB sequences. PLoS One 2013; 8:e72493. [PMID: 23967311 PMCID: PMC3742607 DOI: 10.1371/journal.pone.0072493] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 07/17/2013] [Indexed: 11/18/2022] Open
Abstract
Background Rutaceae subfamily Rutoideae (46 genera, c. 660 species) is diverse in both rainforests and sclerophyll vegetation of Australasia. Australia and New Caledonia are centres of endemism with a number of genera and species distributed disjunctly between the two regions. Our aim was to generate a high-level molecular phylogeny for the Australasian Rutoideae and identify major clades as a framework for assessing morphological and biogeographic patterns and taxonomy. Methodology/Principal Findings Phylogenetic analyses were based on chloroplast genes, rbcL and atpB, for 108 samples (78 new here), including 38 of 46 Australasian genera. Results were integrated with those from other molecular studies to produce a supertree for Rutaceae worldwide, including 115 of 154 genera. Australasian clades are poorly matched with existing tribal classifications, and genera Philotheca and Boronia are not monophyletic. Major sclerophyll lineages in Australia belong to two separate clades, each with an early divergence between rainforest and sclerophyll taxa. Dehiscent fruits with seeds ejected at maturity (often associated with myrmecochory) are inferred as ancestral; derived states include woody capsules with winged seeds, samaras, fleshy drupes, and retention and display of seeds in dehisced fruits (the last two states adaptations to bird dispersal, with multiple origins among rainforest genera). Patterns of relationship and levels of sequence divergence in some taxa, mostly species, with bird-dispersed (Acronychia, Sarcomelicope, Halfordia and Melicope) or winged (Flindersia) seeds are consistent with recent long-distance dispersal between Australia and New Caledonia. Other deeper Australian/New Caledonian divergences, some involving ant-dispersed taxa (e.g., Neoschmidia), suggest older vicariance. Conclusions/Significance This comprehensive molecular phylogeny of the Australasian Rutoideae gives a broad overview of the group’s evolutionary and biogeographic history. Deficiencies of infrafamilial classifications of Rutoideae have long been recognised, and our results provide a basis for taxonomic revision and a necessary framework for more focused studies of genera and species.
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Affiliation(s)
- Michael J Bayly
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia.
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Beaulieu JM, Tank DC, Donoghue MJ. A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana. BMC Evol Biol 2013; 13:80. [PMID: 23565668 PMCID: PMC3636071 DOI: 10.1186/1471-2148-13-80] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 04/02/2013] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND New powerful biogeographic methods have focused attention on long-standing hypotheses regarding the influence of the break-up of Gondwana on the biogeography of Southern Hemisphere plant groups. Studies to date have often concluded that these groups are too young to have been influenced by these ancient continental movements. Here we examine a much larger and older angiosperm clade, the Campanulidae, and infer its biogeographic history by combining Bayesian divergence time information with a likelihood-based biogeographic model focused on the Gondwanan landmasses. RESULTS Our analyses imply that campanulids likely originated in the middle Albian (~105 Ma), and that a substantial portion of the early evolutionary history of campanulids took place in the Southern Hemisphere, despite their greater species richness in the Northern Hemisphere today. We also discovered several disjunctions that show biogeographic and temporal correspondence with the break-up of Gondwana. CONCLUSIONS While it is possible to discern traces of the break-up of Gondwana in clades that are old enough, it will generally be difficult to be confident in continental movement as the prime cause of geographic disjunctions. This follows from the need for the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events to be consistent with the causal hypothesis.
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Affiliation(s)
- Jeremy M Beaulieu
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520-8106, USA
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Blvd, Ste. 106, Knoxville, TN 37996, USA
| | - David C Tank
- College of Natural Resources & Stillinger Herbarium, University of Idaho, 875 Perimeter Drive MS 1133, Moscow, ID 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520-8106, USA
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Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, Cázares E, Kinoshita A, Nouhra ER, Domínguez LS, Tedersoo L, Murat C, Wang Y, Moreno BA, Pfister DH, Nara K, Zambonelli A, Trappe JM, Vilgalys R. Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage. PLoS One 2013; 8:e52765. [PMID: 23300990 PMCID: PMC3534693 DOI: 10.1371/journal.pone.0052765] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/22/2012] [Indexed: 11/18/2022] Open
Abstract
Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes species with socio-economic importance and esteemed culinary attributes. Ecologically, Tuber spp. form obligate mycorrhizal symbioses with diverse species of plant hosts including pines, oaks, poplars, orchids, and commercially important trees such as hazelnut and pecan. Unfortunately, limited geographic sampling and inconclusive phylogenetic relationships have obscured our understanding of their origin, biogeography, and diversification. To address this problem, we present a global sampling of Tuberaceae based on DNA sequence data from four loci for phylogenetic inference and molecular dating. Our well-resolved Tuberaceae phylogeny shows high levels of regional and continental endemism. We also identify a previously unknown epigeous member of the Tuberaceae--the South American cup-fungus Nothojafnea thaxteri (E.K. Cash) Gamundí. Phylogenetic resolution was further improved through the inclusion of a previously unrecognized Southern hemisphere sister group of the Tuberaceae. This morphologically diverse assemblage of species includes truffle (e.g. Gymnohydnotrya spp.) and non-truffle forms that are endemic to Australia and South America. Southern hemisphere taxa appear to have diverged more recently than the Northern hemisphere lineages. Our analysis of the Tuberaceae suggests that Tuber evolved from an epigeous ancestor. Molecular dating estimates Tuberaceae divergence in the late Jurassic (~156 million years ago), with subsequent radiations in the Cretaceous and Paleogene. Intra-continental diversification, limited long-distance dispersal, and ecological adaptations help to explain patterns of truffle evolution and biodiversity.
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Affiliation(s)
- Gregory Bonito
- Deparment of Biology, Duke University, Durham, North Carolina, United States of America.
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Puente-Lelièvre C, Harrington MG, Brown EA, Kuzmina M, Crayn DM. Cenozoic extinction and recolonization in the New Zealand flora: The case of the fleshy-fruited epacrids (Styphelieae, Styphelioideae, Ericaceae). Mol Phylogenet Evol 2013; 66:203-14. [DOI: 10.1016/j.ympev.2012.09.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/07/2012] [Accepted: 09/20/2012] [Indexed: 11/27/2022]
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Wood HM, Matzke NJ, Gillespie RG, Griswold CE. Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders. Syst Biol 2012. [DOI: 10.1093/sysbio/sys092] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Crisp MD, Cook LG. Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes? THE NEW PHYTOLOGIST 2012; 196:681-694. [PMID: 22943495 DOI: 10.1111/j.1469-8137.2012.04298.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 07/25/2012] [Indexed: 05/27/2023]
Abstract
Phylogenetic niche conservatism (PNC) is the tendency of lineages to retain their niche-related traits through speciation events. A recent surge in the availability of well-sampled molecular phylogenies has stimulated phylogenetic approaches to understanding ecological processes at large geographical scales and through macroevolutionary time. We stress that PNC is a pattern, not a process, and is found only in some traits and some lineages. At the simplest level, a pattern of PNC is an inevitable consequence of evolution - descent with modification and divergence of lineages - but several intrinsic causes, including physicochemical, developmental and genetic constraints, can lead directly to a marked pattern of PNC. A pattern of PNC can also be caused indirectly, as a by-product of other causes, such as extinction, dispersal limitation, competition and predation. Recognition of patterns of PNC can contribute to understanding macroevolutionary processes: for example, release from constraint in traits has been hypothesized to trigger adaptive radiations such as that of the angiosperms. Given the multiple causes of patterns of PNC, tests should address explicit questions about hypothesized processes. We conclude that PNC is a scientifically useful concept with applications to the practice of ecological research.
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Affiliation(s)
- Michael D Crisp
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Qld, 4072, Australia
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Thornhill AH, Popple LW, Carter RJ, Ho SY, Crisp MD. Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae. Mol Phylogenet Evol 2012; 63:15-27. [DOI: 10.1016/j.ympev.2011.12.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 11/15/2011] [Accepted: 12/02/2011] [Indexed: 11/26/2022]
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Cruaud A, Jabbour-Zahab R, Genson G, Ungricht S, Rasplus JY. Testing the emergence of New Caledonia: fig wasp mutualism as a case study and a review of evidence. PLoS One 2012; 7:e30941. [PMID: 22383982 PMCID: PMC3285151 DOI: 10.1371/journal.pone.0030941] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/27/2011] [Indexed: 11/18/2022] Open
Abstract
While geologists suggest that New Caledonian main island (Grande Terre) was submerged until ca 37 Ma, biologists are struck by the presence of supposedly Gondwanan groups on the island. Among these groups are the Oreosycea fig trees (Ficus, Moraceae) and their Dolichoris pollinators (Hymenoptera, Agaonidae). These partners are distributed in the Paleotropics and Australasia, suggesting that their presence on New Caledonia could result from Gondwanan vicariance. To test this hypothesis, we obtained mitochondrial and nuclear markers (5.3 kb) from 28 species of Dolichoris, used all available sequences for Oreosycea, and conducted phylogenetic and dating analyses with several calibration strategies. All our analyses ruled out a vicariance scenario suggesting instead that New Caledonian colonization by Dolichoris and Oreosycea involved dispersal across islands from Sundaland ca 45.9-32.0 Ma. Our results show that successful long-distance dispersal of obligate mutualists may happen further suggesting that presence of intimate mutualisms on isolated islands should not be used as a priori evidence for vicariance. Comparing our results to a review of all the published age estimates for New Caledonian plant and animal taxa, we showed that support for a vicariant origin of the island biota is still lacking. Finally, as demonstrating a causal relationship between geology and biology requires independent evidence, we argue that a priori assumptions about vicariance or dispersal should not be used to constrain chronograms. This circular reasoning could lead to under or overestimation of age estimates.
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Affiliation(s)
- Astrid Cruaud
- INRA-UMR Centre de Biologie et de Gestion des Populations, CBGP, INRA/IRD/CIRAD/Montpellier SupAgro, Campus international de Baillarguet, Montferrier-sur Lez, France.
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Nie ZL, Sun H, Manchester SR, Meng Y, Luke Q, Wen J. Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae). BMC Evol Biol 2012; 12:17. [PMID: 22316163 PMCID: PMC3299610 DOI: 10.1186/1471-2148-12-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/08/2012] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the Ampelopsis clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents. RESULTS The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the Ampelopsis clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4-61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9-45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7-22.3 Ma). CONCLUSIONS The global disjunctions in the Ampelopsis clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants.
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Affiliation(s)
- Ze-Long Nie
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Hang Sun
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Steven R Manchester
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ying Meng
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Quentin Luke
- East African Herbarium, National Museums of Kenya, Nairobi 00502, Kenya
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
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Loss-Oliveira L, Aguiar BO, Schrago CG. Testing synchrony in historical biogeography: the case of new world primates and hystricognathi rodents. Evol Bioinform Online 2012; 8:127-37. [PMID: 22346342 PMCID: PMC3273932 DOI: 10.4137/ebo.s9008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The abrupt appearance of primates and hystricognath rodents in early Oligocene deposits of South America has puzzled mastozoologists for decades. Based on the geoclimatic changes that occurred during the Eocene/Oligocene transition period that may have favoured their dispersal, researchers have proposed the hypothesis that these groups arrived in synchrony. Nevertheless, the hypothesis of synchronous origins of platyrrhine and caviomorph in South America has not been explicitly evaluated. Our aim in this work was to apply a formal test for synchronous divergence times to the Platyrrhini and Caviomorpha splits. We have examined a previous work on platyrrhine and hystricognath origins, applied the test to a case where synchrony is known to occur and conducted simulations to show that it is possible to formally test the age of synchronous nodes. We show that the absolute ages of Platyrrhini/Catarrhini and Caviomorpha/Phiomorpha splits depend on data partitioning and that the test applied consistently detected synchronous events when they were known to have happened. The hypothesis that the arrival of primates and hystricognaths to the New World consisted of a unique event cannot be rejected
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Affiliation(s)
- Leticia Loss-Oliveira
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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42
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Premoli AC, Mathiasen P, Cristina Acosta M, Ramos VA. Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be? THE NEW PHYTOLOGIST 2012; 193:261-275. [PMID: 21883239 DOI: 10.1111/j.1469-8137.2011.03861.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
• Here, we performed phylogenetic analyses and estimated the divergence times on mostly sympatric populations of five species within subgenus Nothofagus. We aimed to investigate whether phylogenetic relationships by nuclear internal transcribed spacer (ITS) and phylogeographic patterns by chloroplast DNA (cpDNA) mirror an ancient evolutionary history that was not erased by glacial eras. Extant species are restricted to Patagonia and share a pollen type that was formerly widespread in all southern land masses. Weak reproductive barriers exist among them. • Fifteen cpDNA haplotypes resulted from the analysis of three noncoding regions on 330 individuals with a total alignment of 1794 bp. Nuclear ITS data consisted of 822 bp. We found a deep cpDNA divergence dated 32 Ma at mid-latitudes of Patagonia that predates the phylogenetic divergence of extant taxa. Other more recent breaks by cpDNA occurred towards the north. • Complex paleogeographic features explain the genetic discontinuities. Long-lasting paleobasins and marine ingressions have impeded transoceanic dispersal during range expansion towards lower latitudes under cooler trends since the Oligocene. • Cycles of hybridization-introgression among extant and extinct taxa have resulted in widespread chloroplast capture events. Our data suggest that Nothofagus biogeography will be resolved only if thorough phylogeographic analyses and molecular dating methods are applied using distinct genetic markers.
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Affiliation(s)
- Andrea C Premoli
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional Del Comahue and INIBIOMA-CONICET, Quintral 1250, 8400 Bariloche, Argentina
| | - Paula Mathiasen
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional Del Comahue and INIBIOMA-CONICET, Quintral 1250, 8400 Bariloche, Argentina
| | - M Cristina Acosta
- Laboratorio Ecotono, Centro Regional Universitario Bariloche-Universidad Nacional Del Comahue and INIBIOMA-CONICET, Quintral 1250, 8400 Bariloche, Argentina
| | - Victor A Ramos
- Laboratorio de Tectónica Andina, Departamento de Geología, Universidad de Buenos Aires, Pabellón 2 Ciudad Universitaria, 1428 Buenos Aires, Argentina
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Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM, Murphy DJ, Sniderman JMK, Udovicic F. Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales). Syst Biol 2011; 61:289-313. [DOI: 10.1093/sysbio/syr116] [Citation(s) in RCA: 296] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hervé Sauquet
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS UMR 8079, 91405 Orsay, France
| | - Simon Y. W. Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Maria A. Gandolfo
- L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gregory J. Jordan
- School of Plant Science, University of Tasmania, Private bag 55, Hobart, TAS 7001, Australia
| | - Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA
| | - David J. Cantrill
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
| | - Michael J. Bayly
- School of Botany, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Gillian K. Brown
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
- School of Botany, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Raymond J. Carpenter
- Department of Ecology and Environmental Biology, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Daphne M. Lee
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Daniel J. Murphy
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
| | - J. M. Kale Sniderman
- School of Geography and Environmental Science, Monash University, Melbourne, VIC 3800, Australia
| | - Frank Udovicic
- National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, South Yarra, VIC 3141, Australia
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Amo de Paz G, Cubas P, Divakar PK, Lumbsch HT, Crespo A. Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota) during the Paleogene inferred by Bayesian analysis. PLoS One 2011; 6:e28161. [PMID: 22174775 PMCID: PMC3234259 DOI: 10.1371/journal.pone.0028161] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/02/2011] [Indexed: 11/19/2022] Open
Abstract
There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota) by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these clades. However, our data cannot reject vicariance to explain South America-Australia disjunctions.
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Affiliation(s)
- Guillermo Amo de Paz
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - H. Thorsten Lumbsch
- Department of Botany, The Field Museum, Chicago, Illinois, United States of America
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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Crisp MD, Cook LG. Cenozoic extinctions account for the low diversity of extant gymnosperms compared with angiosperms. THE NEW PHYTOLOGIST 2011; 192:997-1009. [PMID: 21895664 DOI: 10.1111/j.1469-8137.2011.03862.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We test the widely held notion that living gymnosperms are 'ancient' and 'living fossils' by comparing them with their sister group, the angiosperms. This perception derives partly from the lack of gross morphological differences between some Mesozoic gymnosperm fossils and their living relatives (e.g. Ginkgo, cycads and dawn redwood), suggesting that the rate of evolution of gymnosperms has been slow. We estimated the ages and diversification rates of gymnosperm lineages using Bayesian relaxed molecular clock dating calibrated with 21 fossils, based on the phylogenetic analysis of alignments of matK chloroplast DNA (cpDNA) and 26S nuclear ribosomal DNA (nrDNA) sequences, and compared these with published estimates for angiosperms. Gymnosperm crown groups of Cenozoic age are significantly younger than their angiosperm counterparts (median age: 32 Ma vs 50 Ma) and have long unbranched stems, indicating major extinctions in the Cenozoic, in contrast with angiosperms. Surviving gymnosperm genera have diversified more slowly than angiosperms during the Neogene as a result of their higher extinction rate. Compared with angiosperms, living gymnosperm groups are not ancient. The fossil record also indicates that gymnosperms suffered major extinctions when climate changed in the Oligocene and Miocene. Extant gymnosperm groups occupy diverse habitats and some probably survived after making adaptive shifts.
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Affiliation(s)
- Michael D Crisp
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
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Worth JRP, Marthick JR, Jordan GJ, Vaillancourt RE. Low but structured chloroplast diversity in Atherosperma moschatum (Atherospermataceae) suggests bottlenecks in response to the Pleistocene glacials. ANNALS OF BOTANY 2011; 108:1247-1256. [PMID: 21856633 PMCID: PMC3197450 DOI: 10.1093/aob/mcr220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Accepted: 07/04/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS The cool temperate rainforests of Australia were much reduced in range during the cold and dry glacial periods, although genetic evidence indicates that two key rainforest species, Nothofagus cunninghamii and Tasmannia lanceolata, survived within multiple locations and underwent only local range expansions at the end of the Last Glacial. To better understand the glacial response of a co-occurring but wind-dispersed and less cold-tolerant rainforest tree species, Atherosperma moschatum, a chloroplast phylogeographic study was undertaken. METHODS A total of 3294 bp of chloroplast DNA sequence was obtained for 155 samples collected from across the species' range. KEY RESULTS The distribution of six haplotypes observed in A. moschatum was geographically structured with an inferred ancestral haplotype restricted to Tasmania, while three non-overlapping and endemic haplotypes were found on the mainland of south-eastern Australia. Last glacial refugia for A. moschatum are likely to have occurred in at least one location in western Tasmania and in Victoria and within at least two locations in the Great Dividing Range of New South Wales. Nucleotide diversity of A. moschatum was lower (π = 0·00021) than either N. cunninghamii (0·00101) or T. lanceolata (0·00073), and was amongst the lowest recorded for any tree species. CONCLUSIONS This study provides evidence for past bottlenecks having impacted the chloroplast diversity of A. moschatum as a result of the species narrower climatic niche during glacials. This hypothesis is supported by the star-like haplotype network and similar estimated rates of chloroplast DNA substitution for A. moschatum and the two more cold tolerant and co-occurring species that have higher chloroplast diversity, N. cunninghamii and T. lanceolata.
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Affiliation(s)
- James R P Worth
- School of Plant Science, Private Bag 55, University of Tasmania, Hobart 7001, Tasmania, Australia.
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Skrede I, Engh IB, Binder M, Carlsen T, Kauserud H, Bendiksby M. Evolutionary history of Serpulaceae (Basidiomycota): molecular phylogeny, historical biogeography and evidence for a single transition of nutritional mode. BMC Evol Biol 2011; 11:230. [PMID: 21816066 PMCID: PMC3199774 DOI: 10.1186/1471-2148-11-230] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 08/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Serpula (Serpulaceae, Boletales) comprises several saprotrophic (brown rot) taxa, including the aggressive house-infecting dry rot fungus Serpula lacrymans. Recent phylogenetic analyses have indicated that the ectomycorrhiza forming genera Austropaxillus and Gymnopaxillus cluster within Serpula. In this study we use DNA sequence data to investigate phylogenetic relationships, historical biogeography of, and nutritional mode transitions in Serpulaceae. RESULTS Our results corroborate that the two ectomycorrhiza-forming genera, Austropaxillus and Gymnopaxillus, form a monophyletic group nested within the saprotrophic genus Serpula, and that the Serpula species S. lacrymans and S. himantioides constitute the sister group to the Austropaxillus-Gymnopaxillus clade. We found that both vicariance (Beringian) and long distance dispersal events are needed to explain the phylogeny and current distributions of taxa within Serpulaceae. Our results also show that the transition from brown rot to mycorrhiza has happened only once in a monophyletic Serpulaceae, probably between 50 and 22 million years before present. CONCLUSIONS This study supports the growing understanding that the same geographical barriers that limit plant- and animal dispersal also limit the spread of fungi, as a combination of vicariance and long distance dispersal events are needed to explain the present patterns of distribution in Serpulaceae. Our results verify the transition from brown rot to ECM within Serpulaceae between 50 and 22 MyBP.
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Affiliation(s)
- Inger Skrede
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Ingeborg B Engh
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Manfred Binder
- Department of Biology, Clark University, Worcester, Massachusetts 01610, USA
| | - Tor Carlsen
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Håvard Kauserud
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Mika Bendiksby
- National Centre for Biosystematics, Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, N-0318 Oslo, Norway
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Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 2011; 333:762-5. [PMID: 21764756 DOI: 10.1126/science.1205411] [Citation(s) in RCA: 346] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.
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Affiliation(s)
- Daniel C Eastwood
- College of Science, University of Swansea, Singleton Park, Swansea SA2 8PP, UK.
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Lucky A. Molecular phylogeny and biogeography of the spider ants, genus Leptomyrmex Mayr (Hymenoptera: Formicidae). Mol Phylogenet Evol 2011; 59:281-92. [PMID: 21406240 DOI: 10.1016/j.ympev.2011.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 02/17/2011] [Accepted: 03/02/2011] [Indexed: 11/16/2022]
Abstract
This study provides the first phylogenetic reconstruction of the ant genus Leptomyrmex Mayr, a prominent endemic component of rain forest and wet sclerophyll forest in Australia, New Guinea and New Caledonia. Five genes are used to reconstruct phylogeny and estimate of ages of diversification in order to test congruence of the history of nuclear and mitochondrial genes: three protein-coding nuclear genes: arginine kinase (argK, 897 bp), long wavelength rhodopsin (LW Rh, 546 bp) and wingless (Wg, 409 bp), as well as the large subunit ribosomal gene 28S (482 bp) and the mitochondrial gene cytochrome oxidase I (COI, 658 bp). Four different partitioning schemes were tested for optimal resolving power; results show that partitioning by gene, translational pattern and codon position were uniformly favoured over less complex partitions. Nuclear markers showed relatively minor sequence divergence and provided strongly supported topology; phylogeny based solely on mtDNA produced somewhat conflicting topology but offered little power to resolve species complexes. Monophyly of the genus Leptomyrmex was recovered, as was the sister-group relationship of 'micro-' and 'macro-'Leptomyrmex species. Divergence dating analyses estimate that Leptomyrmex arose in the Eocene (stem age ∼ 44 million years ago (ma)), and that the 'macro-' species diverged from the 'micro-' species in the early Oligocene (∼ 31 ma). Diversification of the crown group 'macro-' and 'micro-'Leptomyrmex occurred in the Miocene (∼ 15 ma and 7.9 ma, respectively). New Guinean and New Caledonian lineages appear to have diverged from Australian lineages only recently (∼ 4.7 ma and 10.3 ma, respectively), and the latter clade is inferred to have reached New Caledonia from Australia via long distance dispersal. These results challenge previous hypotheses of Leptomyrmex classification and assumptions about their historical dispersal, but are in agreement with the current knowledge of the geological history of Melanesia.
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Affiliation(s)
- Andrea Lucky
- Department of Entomology, University of California, Davis, CA 95616, USA.
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Krosch MN, Baker AM, Mather PB, Cranston PS. Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae). Mol Phylogenet Evol 2011; 59:458-68. [PMID: 21402162 DOI: 10.1016/j.ympev.2011.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/31/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
Restrictions to effective dispersal and gene flow caused by the fragmentation of ancient supercontinents are considered to have driven diversification and speciation on disjunct landmasses globally. Investigating the role that these processes have played in the development of diversity within and among taxa is crucial to understanding the origins and evolution of regional biotas. Within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae), a group of genera that are distributed across the austral continents (Australia, New Zealand, South America) have been proposed to represent a relict Gondwanan clade. We used a molecular approach to resolve relationships among taxa with the aim to determine the relative roles that vicariance and dispersal may have played in the evolution of this group. Continental biotas did not form monophyletic groups, in accordance with expectations given existing morphological evidence. Patterns of phylogenetic relationships among taxa did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent. Likewise, divergence time estimates, particularly for New Zealand taxa, largely post-dated continental fragmentation and implied instead that several transoceanic dispersal events may have occurred post-vicariance. Passive dispersal of gravid female chironomid adults is the most likely mechanism for transoceanic movement, potentially facilitated by West Wind Drift or anti-cyclone fronts. Estimated timings of divergence among Australian and South American Botryocladius, on the other hand, were congruent with the proposed ages of separation of the two continents from Antarctica. Taken together, these data suggest that a complex relationship between both vicariance and dispersal may explain the evolution of this group. The sampling regime we implemented here was the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly revealed several novel taxa that will require formal description.
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Affiliation(s)
- M N Krosch
- Biogeosciences, Queensland University of Technology, 2 George St., Brisbane 4001, Australia.
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