1
|
Fan Z, Gao C, Lin L. Phylogeographical and population genetics of Polyspora sweet in China provides insights into its phylogenetic evolution and subtropical dispersal. BMC PLANT BIOLOGY 2024; 24:89. [PMID: 38317071 PMCID: PMC10845455 DOI: 10.1186/s12870-024-04783-5] [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: 11/17/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Geological movements and climatic fluctuations stand as pivotal catalysts driving speciation and phylogenetic evolution. The genus Polyspora Sweet (Theaceae), prominently found across the Malay Archipelagos and Indochina Peninsula in tropical Asia, exhibits its northernmost distribution in China. In this study, we investigated the evolutionary and biogeographical history of the genus Polyspora in China, shedding light on the mechanisms by which these species respond to ancient geological and climatic fluctuations. METHODS Phylogenetic relationships of 32 representative species of Theaceae were reconstructed based on the chloroplast genome and ribosome 18-26 S rRNA datasets. Species divergence time was estimated using molecular clock and five fossil calibration. The phylogeography and population genetics in 379 individuals from 32 populations of eight species were analyzed using chloroplast gene sequences (trnH-psbA, rpoB-trnC and petN-psbM), revealing the glacial refugia of each species, and exploring the causes of the phylogeographic patterns. RESULTS We found that Chinese Polyspora species diverged in the middle Miocene, showing a tropical-subtropical divergence order. A total of 52 haplotypes were identified by the combined chloroplast sequences. Chinese Polyspora exhibited a distinct phylogeographical structure, which could be divided into two clades and eight genealogical subdivisions. The divergence between the two clades occurred approximately 20.67 Ma. Analysis of molecular variance revealed that the genetic variation mainly occurred between species (77.91%). At the species level, Polyspora axillaris consists of three lineages, while P. speciosa had two lineages. The major lineages of Chinese Polyspora diverged between 12 and 15 Ma during the middle to late Miocene. The peak period of haplotype differentiation in each species occurred around the transition from the last interglacial to the last glacial period, approximately 6 Ma ago. CONCLUSION The primary geographical distribution pattern of Chinese Polyspora was established prior to the last glacial maximum, and the population historical dynamics were relatively stable. The geological and climatic turbulence during the Quaternary glacial period had minimal impact on the distribution pattern of the genus. The genus coped with Quaternary climate turbulence by glacial in situ survival in multiple refuges. The Sino-Vietnam border and Nanling corridor might be the genetic mixing center of Polyspora.
Collapse
Affiliation(s)
- Zhifeng Fan
- City College, Kunming University of Science and Technology, Kunming, 650093, China.
| | - Can Gao
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, China
| | - Lifang Lin
- Hot Spring Sub-district Office, Anning Municipal People's Government, Kunming, 650300, China.
| |
Collapse
|
2
|
Hasan AMM, Cremaschi P, Wetterskog D, Jayaram A, Wong SQ, Williams S, Pasam A, Trigos A, Trujillo B, Grist E, Friedrich S, Vainauskas O, Parry M, Ismail M, Devlies W, Wingate A, Linch M, Naceur-Lombardelli C, Swanton C, Jamal-Hanjani M, Lise S, Sandhu S, Attard G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nat Commun 2023; 14:4823. [PMID: 37563129 PMCID: PMC10415299 DOI: 10.1038/s41467-023-40315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories.
Collapse
Affiliation(s)
| | | | | | - Anuradha Jayaram
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Scott Williams
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Blanca Trujillo
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Emily Grist
- University College London Cancer Institute, London, UK
| | | | | | - Marina Parry
- University College London Cancer Institute, London, UK
| | | | - Wout Devlies
- University College London Cancer Institute, London, UK
| | - Anna Wingate
- University College London Cancer Institute, London, UK
| | - Mark Linch
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Stefano Lise
- University College London Cancer Institute, London, UK
| | | | - Gerhardt Attard
- University College London Cancer Institute, London, UK.
- University College London Hospitals, London, UK.
| |
Collapse
|
3
|
Gamboa M, Serrana J, Takemon Y, Monaghan MT, Watanabe K. Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species. Oecologia 2023; 201:513-524. [PMID: 36680607 DOI: 10.1007/s00442-023-05321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.
Collapse
Affiliation(s)
- Maribet Gamboa
- Department of Ecology, Universidad Católica de La Santísima Concepción, Concepción, Chile.
| | - Joeselle Serrana
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Center Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Yasuhiro Takemon
- Water Resources Research Center, Disaster Prevention Research Institute, Kyoto University, Gokasho, Uji, 6110011, Japan
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
- Institut Für Biologie, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195, Berlin, Germany
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Center Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| |
Collapse
|
4
|
Belluardo F, Jesus Muñoz-Pajares A, Miralles A, Silvestro D, Cocca W, Mihaja Ratsoavina F, Villa A, Roberts SH, Mezzasalma M, Zizka A, Antonelli A, Crottini A. Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae). Mol Phylogenet Evol 2023; 178:107635. [PMID: 36208694 DOI: 10.1016/j.ympev.2022.107635] [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: 03/23/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
Collapse
Affiliation(s)
- Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
| | - A Jesus Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Genética, Universidad de Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
| | - Aurélien Miralles
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Ch. du Musée 10, 1700 Fribourg, Switzerland; Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Walter Cocca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Domaine Sciences et Technologies, Université d'Antananarivo, B.P. 906, 101 Antananarivo, Madagascar
| | - Andrea Villa
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Spain
| | - Sam Hyde Roberts
- SEED Madagascar, Unit 7, Beethoven Street 1A, W10 4LG London, UK; Oxford Brookes University, Headington Campus, 0X3 0BP Oxford, UK; Operation Wallacea, Wallace House, Old Bolingbroke, PE23 4EX Spilsby, UK
| | - Marcello Mezzasalma
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden; Royal Botanic Gardens, Kew, TW9 3AE Richmond, UK; Department of Biology, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| |
Collapse
|
5
|
The phylogeography of some soil-feeding termites shaped by the Andes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00594-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
6
|
Keates C, Conradie W, Dalu T, Dondofema F, Riddel ES, Wasserman RJ. Phylogenetic placement of the enigmatic Floodplain water snake, Lycodonomorphus obscuriventris FitzSimons, 1964. KOEDOE: AFRICAN PROTECTED AREA CONSERVATION AND SCIENCE 2022. [DOI: 10.4102/koedoe.v64i1.1698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Lycodonomorphus is a genus of lamprophiid water snake endemic in Africa. Although widespread, abundant and presumably an important component of many aquatic and semi-aquatic food webs, these snakes are poorly understood taxonomically, particularly from a phylogenetic perspective. With only four of the nine species currently sequenced, this study attempts to improve our understanding of the evolutionary relationships within the genus through the phylogenetic placement of one of the most elusive species, Lycodonomorphus obscuriventris. Collected in the Ramsar declared Makuleke Wetlands in northern Kruger National Park (South Africa), the sample used in this study not only yielded the first DNA sequences for the taxon but also represented the most northerly South African record, bridging the gap between the southern and northern populations. The snake was sequenced for three partial mitochondrial genes (16S, Cyt-b, ND4) and one partial nuclear gene (c-mos) and phylogenetically placed, relative to the rest of the genus, using maximum likelihood (ML) and Bayesian inference (BI). Sequence divergences between sister taxa were also estimated using pairwise distance analysis. The concatenated phylogenetic reconstruction yielded similar topological structuring when compared to phylogenies from past articles, with both the ML and BI algorithms recovering strong support for L. obscuriventris as sister to a clade comprising of L. whytii + L. laevissimus + L. rufulus. The phylogenetic placement, albeit based on a single sample, challenges the original placement (morphological) of L. obscuriventris as sub-specific within L. whytii, suggesting that multiple species concepts should be considered when delineating species within this group.Conservation implications: Prior to the discovery of the new record, the global distribution of L. obscuriventris was characterised by two disjunct populations. The new record bridges the distribution gap between these two populations, rendering the distribution continuous. This bodes well for the species as there is likely no barrier to gene flow, thereby buffering the species from localised threats given the more expansive distribution. Furthermore, given that the specimen was sampled from the Kruger National Park, the species is likely to be well-protected as much of its distribution within South Africa seems to fall within protected areas.
Collapse
|
7
|
Xu Y, Jiang J, Lin X, Shi W, Cao C. Identification of Diverse Viruses Associated with Grasshoppers Unveils Parallel Relationship Between Host Phylogeny and Virome Composition. Virus Evol 2022; 8:veac057. [PMID: 35821717 PMCID: PMC9271882 DOI: 10.1093/ve/veac057] [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: 11/19/2021] [Revised: 06/02/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Grasshoppers (Orthoptera: Acridoidea) are one of the most dangerous agricultural pests. Environmentally benign microbial pesticides are increasingly desirable for controlling grasshopper outbreaks in fragile ecosystems. However, little is known about natural pathogens infecting this pest. Here we profile the rich viral communities in forty-five grasshopper species and report 302 viruses, including 231 novel species. Most of the identified viruses are related to other insect viruses, and small RNA sequencing indicates that some are targeted by host antiviral RNA interference (RNAi) pathway. Our analysis of relationships between host phylogeny and virus diversity suggests that the composition of viromes is closely allied with host evolution. Overall, this study is a first extensive exploration of viruses in grasshoppers and provides a valuable comparative dataset of both academic and applied interest.
Collapse
Affiliation(s)
- Yao Xu
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Jingyi Jiang
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Xiaoju Lin
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Wangpeng Shi
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Chuan Cao
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| |
Collapse
|
8
|
Etchegaray E, Dechaud C, Barbier J, Naville M, Volff JN. Diversity of Harbinger-like Transposons in Teleost Fish Genomes. Animals (Basel) 2022; 12:ani12111429. [PMID: 35681893 PMCID: PMC9179366 DOI: 10.3390/ani12111429] [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: 04/13/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The study of transposable elements, which are repeated DNA sequences that can insert into new locations in genomes, is of particular interest to genome evolution, as they are sources of mutations but also of new regulatory and coding sequences. Teleost fish are a species-rich clade presenting a high diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger-like DNA transposons, which are widespread from plants to vertebrates but absent from mammalian genomes. These elements code for both a transposase and a Myb-like protein. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish. While Harbinger transposons might have been present in a common ancestor of all the fish species studied, ISL2EU elements were possibly gained by horizontal transfer at the base of teleost fish. Transposase and Myb-like protein phylogenies of Harbinger transposons indicated unique origins of the association between both genes and suggests recombination was rare between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish. Abstract Harbinger elements are DNA transposons that are widespread from plants to vertebrates but absent from mammalian genomes. Among vertebrates, teleost fish are the clade presenting not only the largest number of species but also the highest diversity of transposable elements, both quantitatively and qualitatively, making them a very attractive group to investigate the evolution of mobile sequences. We studied Harbinger DNA transposons and the distantly related ISL2EU elements in fish, focusing on representative teleost species compared to the spotted gar, the coelacanth, the elephant shark and the amphioxus. We observed high variability in the genomic composition of Harbinger-like sequences in teleost fish, as they covered 0.002–0.14% of the genome, when present. While Harbinger transposons might have been present in a common ancestor of all the fish species studied here, with secondary loss in elephant shark, our results suggests that ISL2EU elements were gained by horizontal transfer at the base of teleost fish 200–300 million years ago, and that there was secondary loss in a common ancestor of pufferfishes and stickleback. Harbinger transposons code for a transposase and a Myb-like protein. We reconstructed and compared molecular phylogenies of both proteins to get insights into the evolution of Harbinger transposons in fish. Transposase and Myb-like protein phylogenies showed global congruent evolution, indicating unique origin of the association between both genes and suggesting rare recombination between transposon sublineages. Finally, we report one case of Harbinger horizontal transfer between divergent fish species and the transcriptional activity of both Harbinger and ISL2EU transposons in teleost fish. There was male-biased expression in the gonads of the medaka fish.
Collapse
|
9
|
Kadej M, Zając K, Gutowski JM, Jaworski T, Plewa R, Ruta R, Sikora K, Smolis A, Magoga G, Montagna M, Eckelt A, Birkemoe T, Bonacci T, Brandmayr P, Heibl C, Cizek L, Algis Davenis S, Fuchs L, Horak J, Kapla A, Kulijer D, Merkl O, Müller J, Noordijk J, Saluk S, Sverdrup-Thygeson A, Vrezec A, Kajtoch Ł. Disentangling phylogenetic relations and biogeographic history within the Cucujus haematodes species group (Coleoptera: Cucujidae). Mol Phylogenet Evol 2022; 173:107527. [DOI: 10.1016/j.ympev.2022.107527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
|
10
|
Kambayashi C, Kakehashi R, Sato Y, Mizuno H, Tanabe H, Rakotoarison A, Künzel S, Furuno N, Ohshima K, Kumazawa Y, Nagy ZT, Mori A, Allison A, Donnellan SC, Ota H, Hoso M, Yanagida T, Sato H, Vences M, Kurabayashi A. Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey. Mol Biol Evol 2022; 39:6563207. [PMID: 35417559 PMCID: PMC9007160 DOI: 10.1093/molbev/msac052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.
Collapse
Affiliation(s)
- Chiaki Kambayashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Ryosuke Kakehashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Yusuke Sato
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
| | | | - Hideyuki Tanabe
- School of Advanced Sciences, The Graduate University for Advanced Studies, SOKENDAI, Kanagawa, Japan
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Nobuaki Furuno
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
| | - Kazuhiko Ohshima
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | | | | | - Akira Mori
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | | | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, and Museum of Nature and Human Activities, Hyogo, Japan
| | - Masaki Hoso
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tetsuya Yanagida
- Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Sato
- Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Atsushi Kurabayashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, Japan.,Amphibian Research Center, Hiroshima University, Hiroshima, Japan.,Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| |
Collapse
|
11
|
Lobon-Rovira J, Conradie W, Pinto PV, Keates C, Edwards S, Plessis ADU, Branch WR. Systematic revision of Afrogecko ansorgii (Boulenger, 1907) (Sauria: Gekkonidae) from western Angola. Zootaxa 2022; 5124:401-430. [PMID: 35391113 DOI: 10.11646/zootaxa.5124.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 11/04/2022]
Abstract
Here we provide the first phylogenetic analysis that include Afrogecko ansorgii and a detailed morphological comparison with other species of leaf-toed geckos. For this purpose, we used two mitochondrial (16S, ND2) and four nuclear (RAG1, RAG2, CMOS, PDC) genes to produce a robust phylogenetic reconstruction. This allowed us to show that A. ansorgii is not related as previously believed to circum-Indian Ocean leaf-toed geckos and is rather more closely related to other Malagasy leaf-toed geckos. Additionally, we explore and compare osteological variation in A. ansorgii skulls through High Resolution X-ray Computed Tomography with previously published material. This allowed us to describe herein a new genus, Bauerius gen. nov., and additionally provide a detailed redescription of the species (including the first description of male material), supplementing the limited original description and type series, which consisted of only two females.
Collapse
Affiliation(s)
- Javier Lobon-Rovira
- CIBIO, Centro de Investigao em Biodiversidade e Recursos Genticos, InBIO Laboratrio Associado, Campus de Vairo, Universidade do Porto, 4485-661 Vairo, Portugal. 2Departamento de Biologia, Faculdade de Cincias, Universidade do Porto, 4099-002 Porto, Portugal. 3BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairo, 4485-661 Vairo, Portugal..
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Beach Road, Humewood, Port Elizabeth, 6013, South Africa. Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa. .
| | - Pedro Vaz Pinto
- CIBIO, Centro de Investigao em Biodiversidade e Recursos Genticos, InBIO Laboratrio Associado, Campus de Vairo, Universidade do Porto, 4485-661 Vairo, Portugal. BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairo, 4485-661 Vairo, Portugal. Fundao Kissama, Rua Joquim Kapango, 49 1 Luanda, Angola..
| | - Chad Keates
- Zoology and Entomology Molecular Lab (ZEML), Department of Zoology and Entomology, Rhodes University, Makhanda, 6140, South Africa. .
| | - Shelley Edwards
- Zoology and Entomology Molecular Lab (ZEML), Department of Zoology and Entomology, Rhodes University, Makhanda, 6140, South Africa..
| | - Anton DU Plessis
- Physics Department, Stellenbosch University, Stellenbosch, 7602, South Africa. CT Scanner Facility, Stellenbosch University, Stellenbosch, 7602, South Africa..
| | - William R Branch
- Port Elizabeth Museum (Bayworld), Beach Road, Humewood, Port Elizabeth, 6013, South Africa. .
| |
Collapse
|
12
|
Orr RJS, Di Martino E, Ramsfjell MH, Gordon DP, Berning B, Chowdhury I, Craig S, Cumming RL, Figuerola B, Florence W, Harmelin JG, Hirose M, Huang D, Jain SS, Jenkins HL, Kotenko ON, Kuklinski P, Lee HE, Madurell T, McCann L, Mello HL, Obst M, Ostrovsky AN, Paulay G, Porter JS, Shunatova NN, Smith AM, Souto-Derungs J, Vieira LM, Voje KL, Waeschenbach A, Zágoršek K, Warnock RCM, Liow LH. Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny. SCIENCE ADVANCES 2022; 8:eabm7452. [PMID: 35353568 PMCID: PMC8967238 DOI: 10.1126/sciadv.abm7452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.
Collapse
Affiliation(s)
| | | | | | - Dennis P. Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Björn Berning
- Geoscience Collections, Oberösterreichische Landes-Kultur GmbH, Linz, Austria
| | - Ismael Chowdhury
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Sean Craig
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | | | | | - Wayne Florence
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa
| | - Jean-Georges Harmelin
- Station marine d’Endoume, OSU Pytheas, MIO, GIS Posidonie, Université Aix-Marseille, Marseille, France
| | - Masato Hirose
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sudhanshi S. Jain
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Helen L. Jenkins
- Marine Biological Association of the UK, Plymouth, UK
- Natural History Museum, London, UK
| | - Olga N. Kotenko
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Piotr Kuklinski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Hannah E. Lee
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | | | - Linda McCann
- Smithsonian Environmental Research Center, TIburon, CA, USA
| | | | - Matthias Obst
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Andrew N. Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, University of Vienna, Vienna, Austria
| | - Gustav Paulay
- Florida Museum of Natural History, Gainesville, FL, USA
| | - Joanne S. Porter
- International Centre for Island Technology, Heriot-Watt University, Stromness, UK
| | - Natalia N. Shunatova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Javier Souto-Derungs
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, University of Vienna, Vienna, Austria
| | - Leandro M. Vieira
- Natural History Museum, London, UK
- Department of Zoology, Universidade Federal de Pernambuco, Recife, Brazil
| | - Kjetil L. Voje
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Kamil Zágoršek
- Department of Geography, Technical University of Liberec, Liberec, Czech Republic
| | - Rachel C. M. Warnock
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
13
|
Exchangeable and sampling-consistent distributions on rooted binary trees. J Appl Probab 2022. [DOI: 10.1017/jpr.2021.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling-consistent and exchangeable distributions on n-leaf phylogenetic trees is a polytope. We use this polytope to show that the set of all exchangeable and sampling-consistent distributions on four-leaf phylogenetic trees is exactly Aldous’ beta-splitting model, and give a description of some of the vertices for the polytope of distributions on five leaves. We also introduce a new semialgebraic set of exchangeable and sampling consistent models we call the multinomial model and use it to characterize the set of exchangeable and sampling-consistent distributions. Using this new model, we obtain a finite de Finetti-type theorem for rooted binary trees in the style of Diaconis’ theorem on finite exchangeable sequences.
Collapse
|
14
|
Tinsley CR, Jacques N, Lucas M, Grondin C, Legras JL, Casaregola S. Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the Yeast Geotrichum candidum. Microorganisms 2022; 10:103. [PMID: 35056553 PMCID: PMC8780849 DOI: 10.3390/microorganisms10010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/01/2023] Open
Abstract
Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five clades, of which one contained only environmental isolates, two were composed almost entirely of dairy isolates, and two others contained a mixture of dairy, environmental, and miscellaneous food isolates. In order to provide a simple method to uniquely type G. candidum strains, and in addition to permit investigation of the population structure at a fine level, we describe here a molecular analysis using a set of twelve highly discriminating microsatellite-like markers. The present study consolidates the previously suggested division between dairy and environmental strains, and in addition distinguishes a specifically European group of environmental strains. This analysis permitted the discrimination of 72 genotypes from the collection of 80 isolates, while retaining the underlying meaningful phylogenetic relation between groups of strains.
Collapse
Affiliation(s)
- Colin R. Tinsley
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
- Unité Microbiologie et Génétique Moléculaire, Department des Sciences de la Vie et Santé, AgroParisTech, 16 Rue Claude Bernard, 75005 Paris, France
| | - Noémie Jacques
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| | - Marine Lucas
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| | - Cécile Grondin
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France
| | - Jean-Luc Legras
- SPO, Université de Montpellier, INRAE, Institut Agro, 34000 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.R.T.); (N.J.); (M.L.); (C.G.); (S.C.)
| |
Collapse
|
15
|
Brito KL, Oliveira AR, Alexandrino AO, Dias U, Dias Z. An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes. Algorithms Mol Biol 2021; 16:24. [PMID: 34965857 PMCID: PMC8717661 DOI: 10.1186/s13015-021-00203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the genetic content or the arrangement of elements from the genome. Reversal and transposition are two of the most studied genome rearrangement events. A reversal inverts a segment of a genome while a transposition swaps two consecutive segments. Initial studies in the area considered only the order of the genes. Recent works have incorporated other genetic information in the model. In particular, the information regarding the size of intergenic regions, which are structures between each pair of genes and in the extremities of a linear genome. RESULTS AND CONCLUSIONS In this work, we investigate the SORTING BY INTERGENIC REVERSALS AND TRANSPOSITIONS problem on genomes sharing the same set of genes, considering the cases where the orientation of genes is known and unknown. Besides, we explored a variant of the problem, which generalizes the transposition event. As a result, we present an approximation algorithm that guarantees an approximation factor of 4 for both cases considering the reversal and transposition (classic definition) events, an improvement from the 4.5-approximation previously known for the scenario where the orientation of the genes is unknown. We also present a 3-approximation algorithm by incorporating the generalized transposition event, and we propose a greedy strategy to improve the performance of the algorithms. We performed practical tests adopting simulated data which indicated that the algorithms, in both cases, tend to perform better when compared with the best-known algorithms for the problem. Lastly, we conducted experiments using real genomes to demonstrate the applicability of the algorithms.
Collapse
|
16
|
Baptista NL, Pinto PV, Keates C, Edwards S, Rdel MO, Conradie W. A new species of red toad, Schismaderma Smith, 1849 (Anura: Bufonidae), from central Angola. Zootaxa 2021; 5081:301-332. [PMID: 35391006 DOI: 10.11646/zootaxa.5081.3.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Indexed: 11/04/2022]
Abstract
A new species of red toad, from the previously monotypic genus Schismaderma, is described. The new species was found in Malanje Province, and seems endemic to central Angola, occurring approximately 500 km west of the closest known records of Schismaderma carens. Unusual adult colouration and geographical distance to remaining S. carens populations suggested specific differentiation. In an integrative approach, we compared the red toads from central Angola with S. carens from across the entire range, including molecular data, morphology of adults and tadpoles, and male advertisement calls. Phylogenetic analysis based on mitochondrial (12S, 16S, COI) and nuclear (CXCR4, RAG1) markers, retrieved the Angolan clade as monophyletic, and revealed intra-specific substructuring among the remaining Schismaderma. Genetic distances supported specific differentiation of the central Angolan material compared with other S. carens. Adults from the new Angolan species have bolder ventral patterning and smaller body size than S. carens. No obvious differences were detected between the tadpoles and the advertisement calls of the two Schismaderma species. This discovery adds to the knowledge of the herpetofauna of the Angolan Miombo woodlands, a poorly understood ecoregion, and likely more biodiverse than previously assumed. The result of past river basin dynamics in central Angola likely led to the evolution of this new species of Schismaderma.
Collapse
Affiliation(s)
- Ninda L Baptista
- CIBIO-InBIO, Centro de Investigao em Biodiversidade e Recursos Genticos, Laboratrio Associado, Universidade do Porto, Campus Agrrio de Vairo, Rua Padre Armando Quintas, 4485-661 Vairo, Portugal. Departamento de Biologia, Faculdade de Cincias, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Pedro Vaz Pinto
- CIBIO-InBIO, Centro de Investigao em Biodiversidade e Recursos Genticos, Laboratrio Associado, Universidade do Porto, Campus Agrrio de Vairo, Rua Padre Armando Quintas, 4485-661 Vairo, Portugal. Fundao Kissama, Luanda, Angola.
| | - Chad Keates
- Zoology and Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa 8South African Institute for Aquatic Biodiversity (SAIAB), Makhanda, South Africa.
| | - Shelley Edwards
- Zoology and Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa.
| | - Mark-Oliver Rdel
- Museum fr NaturkundeLeibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany. Berlin-Brandenburg Institute of Advanced Biodiversity ResearchBBIB, Altensteinstr. 34, 14195 Berlin, Germany .
| | - Werner Conradie
- South African Institute for Aquatic Biodiversity (SAIAB), Makhanda, South Africa.
| |
Collapse
|
17
|
Siqueira G, Brito KL, Dias U, Dias Z. Heuristics for Genome Rearrangement Distance With Replicated Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2094-2108. [PMID: 34232886 DOI: 10.1109/tcbb.2021.3095021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In comparative genomics, one goal is to find similarities between genomes of different organisms. Comparisons using genome features like genes, gene order, and regulatory sequences are carried out with this purpose in mind. Genome rearrangements are mutational events that affect large extensions of the genome. They are responsible for creating extant species with conserved genes in different positions across genomes. Close species - from an evolutionary point of view - tend to have the same set of genes or share most of them. When we consider gene order to compare two genomes, it is possible to use a parsimony criterion to estimate how close the species are. We are interested in the shortest sequence of genome rearrangements capable of transforming one genome into the other, which is named rearrangement distance. Reversal is one of the most studied genome rearrangements events. This event acts in a segment of the genome, inverting the position and the orientation of genes in it. Transposition is another widely studied event. This event swaps the position of two consecutive segments of the genome. When the genome has no gene repetition, a common approach is to map it as a permutation such that each element represents a conserved block. When genomes have replicated genes, this mapping is usually performed using strings. The number of replicas depends on the organisms being compared, but in many scenarios, it tends to be small. In this work, we study the rearrangement distance between genomes with replicated genes considering that the orientation of genes is unknown. We present four heuristics for the problem of genome rearrangement distance with replicated genes. We carry out experiments considering the exclusive use of the reversals or transpositions events, as well as the version in which both events are allowed. We developed a database of simulated genomes and compared our results with other algorithms from the literature. The experiments showed that our heuristics with more sophisticated rules presented a better performance than the known algorithms to estimate the evolutionary distance between genomes with replicated genes. In order to validate the application of our algorithms in real data, we construct a phylogenetic tree based on the distance provided by our algorithm and compare it with a know tree from the literature.
Collapse
|
18
|
Oliveira AR, Jean G, Fertin G, Brito KL, Dias U, Dias Z. Sorting Permutations by Intergenic Operations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2080-2093. [PMID: 33945484 DOI: 10.1109/tcbb.2021.3077418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions, can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal, which inverts a sequence of genes, and the transposition, which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms, with factors 3.5 and 2.5, considering two distinct definitions for the problem. We also investigate the signed reversal and transposition distance between two genomes considering their intergenic regions. This second problem is called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms, with factors 3 and 2.5. We check how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data.
Collapse
|
19
|
de Carvalho J, Beale M, Hagen F, Fisher M, Kano R, Bonifaz A, Toriello C, Negroni R, Rego RDM, Gremião I, Pereira S, de Camargo Z, Rodrigues A. Trends in the molecular epidemiology and population genetics of emerging Sporothrix species. Stud Mycol 2021; 100:100129. [PMID: 35027980 PMCID: PMC8693333 DOI: 10.1016/j.simyco.2021.100129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Sporothrix (Ophiostomatales) comprises species that are pathogenic to humans and other mammals as well as environmental fungi. Developments in molecular phylogeny have changed our perceptions about the epidemiology, host-association, and virulence of Sporothrix. The classical agent of sporotrichosis, Sporothrix schenckii, now comprises several species nested in a clinical clade with S. brasiliensis, S. globosa, and S. luriei. To gain a more precise view of outbreaks dynamics, structure, and origin of genetic variation within and among populations of Sporothrix, we applied three sets of discriminatory AFLP markers (#3 EcoRI-GA/MseI-TT, #5 EcoRI-GA/MseI-AG, and #6 EcoRI-TA/MseI-AA) and mating-type analysis to a large collection of human, animal and environmental isolates spanning the major endemic areas. A total of 451 polymorphic loci were amplified in vitro from 188 samples, and revealed high polymorphism information content (PIC = 0.1765-0.2253), marker index (MI = 0.0001-0.0002), effective multiplex ratio (E = 15.1720-23.5591), resolving power (Rp = 26.1075-40.2795), discriminating power (D = 0.9766-0.9879), expected heterozygosity (H = 0.1957-0.2588), and mean heterozygosity (Havp = 0.000007-0.000009), demonstrating the effectiveness of AFLP markers to speciate Sporothrix. Analysis using the program structure indicated three genetic clusters matching S. brasiliensis (population 1), S. schenckii (population 2), and S. globosa (population 3), with the presence of patterns of admixture amongst all populations. AMOVA revealed highly structured clusters (PhiPT = 0.458-0.484, P < 0.0001), with roughly equivalent genetic variability within (46-48 %) and between (52-54 %) populations. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for S. schenckii (χ2 = 2.522; P = 0.1122), supporting random mating. In contrast, skewed distributions were found for S. globosa (χ2 = 9.529; P = 0.0020) with a predominance of MAT1-1 isolates, and regional differences were highlighted for S. brasiliensis with the overwhelming occurrence of MAT1-2 in Rio de Janeiro (χ2 = 14.222; P = 0.0002) and Pernambuco (χ2 = 7.364; P = 0.0067), in comparison to a higher prevalence of MAT1-1 in the Rio Grande do Sul (χ2 = 7.364; P = 0.0067). Epidemiological trends reveal the geographic expansion of cat-transmitted sporotrichosis due to S. brasiliensis via founder effect. These data support Rio de Janeiro as the centre of origin that has led to the spread of this disease to other regions in Brazil. Our ability to reconstruct the source, spread, and evolution of the ongoing outbreaks from molecular data provides high-quality information for decision-making aimed at mitigating the progression of the disease. Other uses include surveillance, rapid diagnosis, case connectivity, and guiding access to appropriate antifungal treatment.
Collapse
Affiliation(s)
- J.A. de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - M.A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - F. Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - M.C. Fisher
- MRC Center for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - R. Kano
- Department of Veterinary Dermatology, Nihon University College of Bioresource Sciences, Fujisawa, Kanagawa, Japan
| | - A. Bonifaz
- Dermatology Service, Mycology Department, Hospital General de México, "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - C. Toriello
- Departamento de Microbiología-Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), 04510, Mexico City, Mexico
| | - R. Negroni
- Mycology Unit of the Infectious Diseases Hospital F.J. Muñiz, Reference Center of Mycology of Buenos Aires City, Buenos Aires, Argentina
| | - R.S. de M. Rego
- Mycology Division, Associate Pathologists of Pernambuco, Recife, Brazil
| | - I.D.F. Gremião
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - S.A. Pereira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Z.P. de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| |
Collapse
|
20
|
Roberto T, de Carvalho J, Beale M, Hagen F, Fisher M, Hahn R, de Camargo Z, Rodrigues A. Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers. Stud Mycol 2021; 100:100131. [PMID: 34934463 PMCID: PMC8645518 DOI: 10.1016/j.simyco.2021.100131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of Paracoccidioides propagules from the environment. The main agents include members of the P. brasiliensis complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and P. lutzii. DNA-sequencing of protein-coding loci (e.g., GP43, ARF, and TUB1) is the reference method for recognizing Paracoccidioides species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within Paracoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping Paracoccidioides species. The bioinformatic analysis generated 144 in silico AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were used in vitro to genotype 165 Paracoccidioides isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers in vitro (67-87 fragments), the values of polymorphism information content (PIC = 0.3345-0.3456), marker index (MI = 0.0018), effective multiplex ratio (E = 44.6788-60.3818), resolving power (Rp = 22.3152-34.3152), discriminating power (D = 0.5183-0.5553), expected heterozygosity (H = 0.4247-0.4443), and mean heterozygosity (H avp = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciate Paracoccidioides and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among P. brasiliensis complex and P. lutzii (PhiPT = 0.651-0.658, P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for P. brasiliensis s. str. (χ2 = 1.025; P = 0.3113), P. venezuelensis (χ2 = 0.692; P = 0.4054), and P. lutzii (χ2 = 0.027; P = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for P. americana (χ2 = 8.909; P = 0.0028) and P. restrepiensis (χ2 = 4.571; P = 0.0325) with a preponderance of MAT1-1. Geographical distributions confirmed that P. americana, P. restrepiensis, and P. lutzii are more widespread than previously thought. P. brasiliensis s. str. is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology of Paracoccidioides species, guiding disease-control strategies to mitigate PCM.
Collapse
Affiliation(s)
- T.N. Roberto
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - J.A. de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - M.A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - F. Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - M.C. Fisher
- MRC Center for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - R.C. Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, 78060900, Brazil
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá, 78048902, Brazil
| | - Z.P. de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| |
Collapse
|
21
|
Orr RJS, Di Martino E, Gordon DP, Ramsfjell MH, Mello HL, Smith AM, Liow LH. A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution. Mol Phylogenet Evol 2021; 161:107172. [PMID: 33813020 DOI: 10.1016/j.ympev.2021.107172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, and 17 genes (2 nuclear and 15 mitochondrial) we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified body-wall layer in ascus-bearing cheilostomes) and ask if its presence has any bearing on the diversification rates of cheilostomes.
Collapse
Affiliation(s)
- R J S Orr
- Natural History Museum, University of Oslo, Oslo, Norway.
| | - E Di Martino
- Natural History Museum, University of Oslo, Oslo, Norway
| | - D P Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - M H Ramsfjell
- Natural History Museum, University of Oslo, Oslo, Norway
| | - H L Mello
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - A M Smith
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - L H Liow
- Natural History Museum, University of Oslo, Oslo, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
22
|
Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil ( Lens culinaris Medik.). PLANTS 2020; 10:plants10010015. [PMID: 33374129 PMCID: PMC7823456 DOI: 10.3390/plants10010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.
Collapse
|
23
|
Conradie W, Keates C, Lobón-Rovira J, Pinto PV, Verburgt L, Baptista NL, Harvey J, Júlio T. New insights into the taxonomic status, distribution and natural history of De Witte’s Clicking Frog (Kassinula wittei Laurent, 1940). AFRICAN ZOOLOGY 2020. [DOI: 10.1080/15627020.2020.1821771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Werner Conradie
- Port Elizabeth Museum, Humewood, South Africa
- School of Natural Resource Management, George Campus, Nelson Mandela University, George, South Africa
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
| | - Chad Keates
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Javier Lobón-Rovira
- CIBIO/InBio Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro Vaz Pinto
- CIBIO/InBio Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Fundação Kissama, Luanda, Angola
- Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola
| | - Luke Verburgt
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Ninda L Baptista
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- CIBIO/InBio Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola
| | | | - Timóteo Júlio
- National Geographic Okavango Wilderness Project, Wild Bird Trust, South Africa
- Fundação Kissama, Luanda, Angola
| |
Collapse
|
24
|
Xiao G, Tang G, Wang C. Congruence Amidst Discordance between Sequence and Protein-Content Based Phylogenies of Fungi. J Fungi (Basel) 2020; 6:jof6030134. [PMID: 32823730 PMCID: PMC7559059 DOI: 10.3390/jof6030134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022] Open
Abstract
Amid the genomic data explosion, phylogenomic analysis has resolved the tree of life of different organisms, including fungi. Genome-wide clustering has also been conducted based on gene content data that can lighten the issue of the unequal evolutionary rate of genes. In this study, using different fungal species as models, we performed phylogenomic and protein-content (PC)-based clustering analysis. The obtained sequence tree reflects the phylogenetic trajectory of examined fungal species. However, 15 PC-based trees constructed from the Pfam matrices of the whole genomes, four protein families, and ten subcellular locations largely failed to resolve the speciation relationship of cross-phylum fungal species. However, lifestyle and taxonomic associations were more or less evident between closely related fungal species from PC-based trees. Pairwise congruence tests indicated that a varied level of congruent or discordant relationships were observed between sequence- and PC-based trees, and among PC-based trees. It was intriguing to find that a few protein family and subcellular PC-based trees were more topologically similar to the phylogenomic tree than was the whole genome PC-based phylogeny. In particular, a most significant level of congruence was observed between sequence- and cell wall PC-based trees. Cophylogenetic analysis conducted in this study may benefit the prediction of the magnitude of evolutionary conservation, interactive associations, or networking between different family or subcellular proteins.
Collapse
Affiliation(s)
- Guohua Xiao
- School of Computer Science, Fudan University, Shanghai 200433, China;
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Guirong Tang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Chengshu Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
- CAS Center for Excellence in Biotic interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Correspondence:
| |
Collapse
|
25
|
Prieto JAF, Rodríguez JMA, Sanna M, Cires E. Phylogeographical patterns of Campanula gr. arvatica, an endemic group of the Cantabrian mountains (NW Iberian Peninsula), based on plastid and nuclear DNA polymorphisms. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1783715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- José Antonio Fernández Prieto
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Área de Botánica, C/Catedrático Rodrigo Uría s/n, Oviedo, 33071, Spain
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
| | - Jose M. Arjona Rodríguez
- Field Crops Program, IRTA (Institute for Food and Agricultural Research and Technology), Rovira Roure, Lleida, 191, 25198, Spain
| | - Mauro Sanna
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
| | - Eduardo Cires
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Área de Botánica, C/Catedrático Rodrigo Uría s/n, Oviedo, 33071, Spain
- Instituto de Recursos Naturales y Ordenación del Territorio (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, Mieres, 33600, Spain
- Instituto Universitario de Biotecnología de Asturias, Campus El Cristo, Edificio Santiago Gascón 2a planta, Oviedo, 33006, Spain
| |
Collapse
|
26
|
Li Y, Ruta M, Wills MA. Craniodental and Postcranial Characters of Non-Avian Dinosauria Often Imply Different Trees. Syst Biol 2020; 69:638-659. [PMID: 31769837 PMCID: PMC7302058 DOI: 10.1093/sysbio/syz077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 12/28/2022] Open
Abstract
Despite the increasing importance of molecular sequence data, morphology still makes an important contribution to resolving the phylogeny of many groups, and is the only source of data for most fossils. Most systematists sample morphological characters as broadly as possible on the principle of total evidence. However, it is not uncommon for sampling to be focused on particular aspects of anatomy, either because characters therein are believed to be more informative, or because preservation biases restrict what is available. Empirically, the optimal trees from partitions of morphological data sets often represent significantly different hypotheses of relationships. Previous work on hard-part versus soft-part characters across animal phyla revealed significant differences in about a half of sampled studies. Similarly, studies of the craniodental versus postcranial characters of vertebrates revealed significantly different trees in about one-third of cases, with the highest rates observed in non-avian dinosaurs. We test whether this is a generality here with a much larger sample of 81 published data matrices across all major dinosaur groups. Using the incongruence length difference test and two variants of the incongruence relationship difference test, we found significant incongruence in about 50% of cases. Incongruence is not uniformly distributed across major dinosaur clades, being highest (63%) in Theropoda and lowest (25%) in Thyreophora. As in previous studies, our partition tests show some sensitivity to matrix dimensions and the amount and distribution of missing entries. Levels of homoplasy and retained synapomorphy are similar between partitions, such that incongruence must partly reflect differences in patterns of homoplasy between partitions, which may itself be a function of modularity and mosaic evolution. Finally, we implement new tests to determine which partition yields trees most similar to those from the entire matrix. Despite no bias across dinosaurs overall, there are striking differences between major groups. The craniodental characters of Ornithischia and the postcranial characters of Saurischia yield trees most similar to the "total evidence" trees derived from the entire matrix. Trees from these same character partitions also tend to be most stratigraphically congruent: a mutual consilience suggesting that those partitions yield more accurate trees. [Dinosauria; homoplasy; partition homogeneity.].
Collapse
Affiliation(s)
- Yimeng Li
- Department of Biology & Biochemistry, The Milner Centre for Evolution, The University of Bath, The Avenue, Claverton Down, Bath BA2 7AY, UK
| | - Marcello Ruta
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln LN6 7DL, UK
| | - Matthew A Wills
- Department of Biology & Biochemistry, The Milner Centre for Evolution, The University of Bath, The Avenue, Claverton Down, Bath BA2 7AY, UK
| |
Collapse
|
27
|
de Carvalho JA, Hagen F, Fisher MC, de Camargo ZP, Rodrigues AM. Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species. PLoS Negl Trop Dis 2020; 14:e0008330. [PMID: 32609739 PMCID: PMC7329091 DOI: 10.1371/journal.pntd.0008330] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/27/2020] [Indexed: 11/19/2022] Open
Abstract
Sporotrichosis is a chronic subcutaneous mycosis caused by Sporothrix species, of which the main aetiological agents are S. brasiliensis, S. schenckii, and S. globosa. Infection occurs after a traumatic inoculation of Sporothrix propagules in mammals' skin and can follow either a classic route through traumatic inoculation by plant debris (e.g., S. schenckii and S. globosa) or an alternative route through zoonotic transmission from animals (e.g., S. brasiliensis). Epizootics followed by a zoonotic route occur in Brazil, with Rio de Janeiro as the epicenter of a recent cat-transmitted epidemic. DNA-based markers are needed to explore the epidemiology of these Sporothrix expansions using molecular methods. This paper reports the use of amplified-fragment-length polymorphisms (AFLP) to assess the degree of intraspecific variability among Sporothrix species. We used whole-genome sequences from Sporothrix species to generate 2,304 virtual AFLP fingerprints. In silico screening highlighted 6 primer pair combinations to be tested in vitro. The protocol was used to genotype 27 medically relevant Sporothrix. Based on the overall scored AFLP markers (97-137 fragments), the values of polymorphism information content (PIC = 0.2552-0.3113), marker index (MI = 0.002-0.0039), effective multiplex ratio (E = 17.8519-35.2222), resolving power (Rp = 33.6296-63.1852), discriminating power (D = 0.9291-0.9662), expected heterozygosity (H = 0.3003-0.3857), and mean heterozygosity (Havp = 0.0001) demonstrated the utility of these primer combinations for discriminating Sporothrix. AFLP markers revealed cryptic diversity in species previously thought to be the most prevalent clonal type, such as S. brasiliensis, responsible for cat-transmitted sporotrichosis, and S. globosa responsible for large sapronosis outbreaks in Asia. Three combinations (#3 EcoRI-FAM-GA/MseI-TT, #5 EcoRI-FAM-GA/MseI-AG, and #6 EcoRI-FAM-TA/MseI-AA) provide the best diversity indices and lowest error rates. These methods make it easier to track routes of disease transmission during epizooties and zoonosis, and our DNA fingerprint assay can be further transferred between laboratories to give insights into the ecology and evolution of pathogenic Sporothrix species and to inform management and mitigation strategies to tackle the advance of sporotrichosis.
Collapse
Affiliation(s)
- Jamile Ambrósio de Carvalho
- Departament of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, Peoples Republic of China
| | - Matthew C. Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Zoilo Pires de Camargo
- Departament of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| |
Collapse
|
28
|
Sun DL, Gao YZ, Ge XY, Shi ZL, Zhou NY. Special Features of Bat Microbiota Differ From Those of Terrestrial Mammals. Front Microbiol 2020; 11:1040. [PMID: 32582057 PMCID: PMC7284282 DOI: 10.3389/fmicb.2020.01040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Bats (order Chiroptera) are one of the most diverse and widely distributed group of mammals with a close relationship to humans. Over the past few decades, a number of studies have been performed on bat viruses; in contrast, bacterial pathogens carried by bats were largely neglected. As more bacterial pathogens are being identified from bats, the need to study their natural microbiota is becoming urgent. In the current study, fecal samples of four bat species from different locations of China were analyzed for their microbiota composition. Together with the results of others, we concluded that bat microbiota is most commonly dominated by Firmicutes and Proteobacteria; the strict anaerobic phylum Bacteroidetes, which is dominant in other terrestrial mammals, especially humans and mice, is relatively rare in bats. This phenomenon was interpreted as a result of a highly specified gastrointestinal tract in adaptation to the flying lifestyle of bats. Further comparative study implied that bat microbiota resemble those of the order Carnivora. To discover potential bacterial pathogens, a database was generated containing the 16S rRNA gene sequences of known bacterial pathogens. Potential bacterial pathogens belonging to 12 genera were detected such as Salmonella, Shigella, and Yersinia, among which some have been previously reported in bats. This study demonstrated high resolution and repeatability in detecting organisms of rare existence, and the results could be used as guidance for future bacterial pathogen isolation.
Collapse
Affiliation(s)
- Dong-Lei Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Zhou Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Yi Ge
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,College of Biology, Hunan University, Changsha, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ning-Yi Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
29
|
Hayati M, Chindelevitch L. Computing the distribution of the Robinson-Foulds distance. Comput Biol Chem 2020; 87:107284. [PMID: 32599459 DOI: 10.1016/j.compbiolchem.2020.107284] [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: 02/17/2020] [Accepted: 05/09/2020] [Indexed: 11/22/2022]
Abstract
With the exponential growth of genome databases, the importance of phylogenetics has increased dramatically over the past years. Studying phylogenetic trees enables us not only to understand how genes, genomes, and species evolve, but also helps us predict how they might change in future. One of the crucial aspects of phylogenetics is the comparison of two or more phylogenetic trees. There are different metrics for computing the dissimilarity between a pair of trees. The Robinson-Foulds (RF) distance is one of the widely used metrics on the space of labeled trees. The distribution of the RF distance from a given tree has been studied before, but the fastest known algorithm for computing this distribution is a slow, albeit polynomial-time, O(l5) algorithm. In this paper, we modify the dynamic programming algorithm for computing the distribution of this distance for a given tree by leveraging the number-theoretic transform (NTT), and improve the running time from O(l5) to O(l3logl), where l is the number of tips of the tree. In addition to its practical usefulness, our method represents a theoretical novelty, as it is, to our knowledge, one of the rare applications of the number-theoretic transform for solving a computational biology problem.
Collapse
Affiliation(s)
- Maryam Hayati
- Simon Fraser University, Department of Computing Science, add8888 University Avenue, Burnaby, BC V5A 1S6, Canada
| | - Leonid Chindelevitch
- Simon Fraser University, Department of Computing Science, add8888 University Avenue, Burnaby, BC V5A 1S6, Canada.
| |
Collapse
|
30
|
Bansal MS. Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance. Algorithms Mol Biol 2020; 15:6. [PMID: 32313549 PMCID: PMC7155338 DOI: 10.1186/s13015-020-00166-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We consider two fundamental computational problems that arise when comparing phylogenetic trees, rooted or unrooted, with non-identical leaf sets. The first problem arises when comparing two trees where the leaf set of one tree is a proper subset of the other. The second problem arises when the two trees to be compared have only partially overlapping leaf sets. The traditional approach to handling these problems is to first restrict the two trees to their common leaf set. An alternative approach that has shown promise is to first complete the trees by adding missing leaves, so that the resulting trees have identical leaf sets. This requires the computation of an optimal completion that minimizes the distance between the two resulting trees over all possible completions. RESULTS We provide optimal linear-time algorithms for both completion problems under the widely-used Robinson-Foulds (RF) distance measure. Our algorithm for the first problem improves the time complexity of the current fastest algorithm from quadratic (in the size of the two trees) to linear. No algorithms have yet been proposed for the more general second problem where both trees have missing leaves. We advance the study of this general problem by proposing a useful restricted version of the general problem and providing optimal linear-time algorithms for the restricted version. Our experimental results on biological data sets suggest that completion-based RF distances can be very different compared to traditional RF distances.
Collapse
|
31
|
Rodrigues A, Beale M, Hagen F, Fisher M, Terra P, de Hoog S, Brilhante R, de Aguiar Cordeiro R, de Souza Collares Maia Castelo-Branco D, Rocha M, Sidrim J, de Camargo Z. The global epidemiology of emerging Histoplasma species in recent years. Stud Mycol 2020; 97:100095. [PMID: 33335607 PMCID: PMC7714791 DOI: 10.1016/j.simyco.2020.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histoplasmosis is a serious infectious disease in humans caused by Histoplasma spp. (Onygenales), whose natural reservoirs are thought to be soil enriched with bird and bat guano. The true global burden of histoplasmosis is underestimated and frequently the pulmonary manifestations are misdiagnosed as tuberculosis. Molecular data on epidemiology of Histoplasma are still scarce, even though there is increasing recognition of histoplasmosis in recent years in areas distant from the traditional endemic regions in the Americas. We used multi-locus sequence data from protein coding loci (ADP-ribosylation factor, H antigen precursor, and delta-9 fatty acid desaturase), DNA barcoding (ITS1/2+5.8s), AFLP markers and mating type analysis to determine the genetic diversity, population structure and recognise the existence of different phylogenetic species among 436 isolates of Histoplasma obtained globally. Our study describes new phylogenetic species and the molecular characteristics of Histoplasma lineages causing outbreaks with a high number of severe outcomes in Northeast Brazil between 2011 and 2015. Genetic diversity levels provide evidence for recombination, common ancestry and clustering of Brazilian isolates at different geographic scales with the emergence of LAm C, a new genotype assigned to a separate population cluster in Northeast Brazil that exhibited low diversity indicative of isolation. The global survey revealed that the high genetic variability among Brazilian isolates along with the presence of divergent cryptic species and/or genotypes may support the hypothesis of Brazil being the center of dispersion of Histoplasma in South America, possibly with the contribution of migratory hosts such as birds and bats. Outside Brazil, the predominant species depends on the region. We confirm that histoplasmosis has significantly broadened its area of occurrence, an important feature of emerging pathogens. From a practical point of view, our data point to the emergence of histoplasmosis caused by a plethora of genotypes, and will enable epidemiological analysis focused on understanding the processes that lead to histoplasmosis. Further, the description of this diversity opens avenues for comparative genomic studies, which will allow progress toward a consensus taxonomy, improve understanding of the presence of hybrids in natural populations of medically relevant fungi, test reproductive barriers and to explore the significance of this variation.
Collapse
Affiliation(s)
- A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, 04023-062, Brazil
- Correspondence: A.M. Rodrigues; Z.P. de Camargo
| | - M.A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - M.C. Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - P.P.D. Terra
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, 04023-062, Brazil
| | - S. de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.S.N. Brilhante
- Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - R. de Aguiar Cordeiro
- Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - M.F.G. Rocha
- Postgraduate Program in Veterinary Science, State University of Ceará, Fortaleza, Ceará, Brazil
| | - J.J.C. Sidrim
- Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Z.P. de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, 04023-062, Brazil
- Correspondence: A.M. Rodrigues; Z.P. de Camargo
| |
Collapse
|
32
|
Orr RJS, Haugen MN, Berning B, Bock P, Cumming RL, Florence WK, Hirose M, Di Martino E, Ramsfjell MH, Sannum MM, Smith AM, Vieira LM, Waeschenbach A, Liow LH. A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae. BMC Evol Biol 2019; 19:235. [PMID: 31881939 PMCID: PMC6935126 DOI: 10.1186/s12862-019-1563-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders. RESULTS We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level. CONCLUSIONS We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.
Collapse
Affiliation(s)
| | - Marianne N Haugen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Björn Berning
- Geoscience Collections, Upper Austrian State Museum, Linz, Austria
| | - Philip Bock
- Museum Victoria, Melbourne, Victoria, Australia
| | | | - Wayne K Florence
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa
| | - Masato Hirose
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | | | | | - Maja M Sannum
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Abigail M Smith
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Leandro M Vieira
- Department of Zoology, Universidade Federal de Pernambuco, Recife, Brazil
| | | | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway.
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
33
|
Keates C, Conradie W, Greenbaum E, Edwards S. A snake in the grass: Genetic structuring of the widespread African grass snake (
Psammophylax
Fitzinger 1843), with the description of a new genus and a new species. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chad Keates
- Zoology and Entomology Molecular Lab Department of Zoology and Entomology Rhodes University Grahamstown South Africa
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld) Humewood South Africa
- School of Natural Resource Management Nelson Mandela University George Campus George South Africa
- National Geographic Okavango Wilderness Project, Wild Bird Trust Hogsback South Africa
| | - Eli Greenbaum
- Department of Biological Sciences University of Texas at El Paso El Paso TX USA
| | - Shelley Edwards
- Zoology and Entomology Molecular Lab Department of Zoology and Entomology Rhodes University Grahamstown South Africa
| |
Collapse
|
34
|
de Vienne DM. Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence. Mol Biol Evol 2019; 36:174-176. [PMID: 30351416 DOI: 10.1093/molbev/msy196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Evolutionary Biologists are often faced with the need to compare phylogenetic trees. One popular method consists in visualizing the trees face to face with links connecting matching taxa. These tanglegrams are optimized beforehand so that the number of lines crossing (the entanglement) is minimal. This representation is implicitly justified by the expectation that the level of entanglement is correlated with the level of similarity (or congruence) between the trees compared. Using simulations, I show that this correlation is actually very weak, which should preclude the use of such technique for getting insight into the level of congruence between trees.
Collapse
Affiliation(s)
- Damien M de Vienne
- Laboratoire de Biométrie et Biologie Evolutive UMR5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
| |
Collapse
|
35
|
Poli A, Bovio E, Verkley G, Prigione V, Varese GC. Elbamycellarosea gen. et sp. nov. (Juncigenaceae, Torpedosporales) isolated from the Mediterranean Sea. MycoKeys 2019; 55:15-28. [PMID: 31274984 PMCID: PMC6595004 DOI: 10.3897/mycokeys.55.35522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/16/2019] [Indexed: 11/17/2022] Open
Abstract
Elbamycellarosea sp. nov., introduced in the new genus Elbamycella, was collected in the Mediterranean Sea in association with the seagrass Posidoniaoceanica and with the brown alga Padinapavonica. The affiliation of the new taxon to the family Juncigenaceae is supported by both morphology and phylogenetic inference based on a combined nrSSU and nrLSU sequence dataset. Maximum-likelihood and Bayesian phylogeny proved Elbamycella gen. nov. as a distinct genus within Juncigenaceae. The new genus has been compared with closely related genera and is characterised by a unique suite of characters, such as ascospores with polar appendages and peculiar shape and dimension of ascomata and asci.
Collapse
Affiliation(s)
- Anna Poli
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Torino, Viale Mattioli 25, 10125 Torino, ItalyUniversity of TorinoTorinoItaly
| | - Elena Bovio
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Torino, Viale Mattioli 25, 10125 Torino, ItalyUniversity of TorinoTorinoItaly
| | - Gerard Verkley
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT Utrecht, The NetherlandsWesterdijk Fungal Biodiversity InstituteUtrechtNetherlands
| | - Valeria Prigione
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Torino, Viale Mattioli 25, 10125 Torino, ItalyUniversity of TorinoTorinoItaly
| | - Giovanna Cristina Varese
- Department of Life Sciences and Systems Biology, Mycotheca Universitatis Taurinensis (MUT), University of Torino, Viale Mattioli 25, 10125 Torino, ItalyUniversity of TorinoTorinoItaly
| |
Collapse
|
36
|
Brinkworth AR, Sansom R, Wills MA. Phylogenetic incongruence and homoplasy in the appendages and bodies of arthropods: why broad character sampling is best. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Notwithstanding the rapidly increasing sampling density of molecular sequence data, morphological characters still make an important contribution to our understanding of the evolutionary relationships of arthropod groups. In many clades, characters relating to the number and morphological specialization of appendages are ascribed particular phylogenetic significance and may be preferentially sampled. However, previous studies have shown that partitions of morphological character matrices often imply significantly different phylogenies. Here, we ask whether a similar incongruence is observed in the appendage and non-appendage characters of arthropods. We apply tree length (incongruence length difference, ILD) and tree distance (incongruence relationship difference, IRD) tests to these partitions in an empirical sample of 53 published neontological datasets for arthropods. We find significant incongruence about one time in five: more often than expected, but markedly less often than in previous partition studies. We also find similar levels of homoplasy in limb and non-limb characters, both in terms of internal consistency and consistency relative to molecular trees. Taken together, these findings imply that sampled limb and non-limb characters are of similar phylogenetic utility and quality, and that a total evidence approach to their analysis is preferable.
Collapse
Affiliation(s)
- Andrew R Brinkworth
- The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, Claverton Down, Bath, UK
| | - Robert Sansom
- School of Earth and Environmental Science, The University of Manchester, Manchester, UK
| | - Matthew A Wills
- The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, Claverton Down, Bath, UK
| |
Collapse
|
37
|
Multilocus Sequence Analysis Reveals Three Distinct Populations of " Candidatus Phytoplasma palmicola" with a Specific Geographical Distribution on the African Continent. Appl Environ Microbiol 2019; 85:AEM.02716-18. [PMID: 30770404 PMCID: PMC6450020 DOI: 10.1128/aem.02716-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/05/2019] [Indexed: 12/15/2022] Open
Abstract
Coconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme (MLST) for tracking epidemics of “Ca. Phytoplasma palmicola,” which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of “Ca. Phytoplasma palmicola” with low intrapopulation diversity. The reasons for the observed strong geographic patterns remain to be established but could result from the lethality of CLYD and the dominance of short-distance insect-mediated transmission. To sustain epidemiological studies on coconut lethal yellowing disease (CLYD), a devastating disease in Africa caused by a phytoplasma, we developed a multilocus sequence typing (MLST) scheme for “Candidatus Phytoplasma palmicola” based on eight housekeeping genes. At the continental level, eight different sequence types were identified among 132 “Candidatus Phytoplasma palmicola”-infected coconuts collected in Ghana, Nigeria, and Mozambique, where CLYD epidemics are still very active. “Candidatus Phytoplasma palmicola” appeared to be a bacterium that is subject to strong bottlenecks, reducing the fixation of positively selected beneficial mutations into the bacterial population. This phenomenon, as well as a limited plant host range, might explain the observed country-specific distribution of the eight haplotypes. As an alternative means to increase fitness, bacteria can also undergo genetic exchange; however, no evidence for such recombination events was found for “Candidatus Phytoplasma palmicola.” The implications for CLYD epidemiology and prophylactic control are discussed. The usefulness of seven housekeeping genes to investigate the genetic diversity in the genus “Candidatus Phytoplasma” is underlined. IMPORTANCE Coconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme (MLST) for tracking epidemics of “Ca. Phytoplasma palmicola,” which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of “Ca. Phytoplasma palmicola” with low intrapopulation diversity. The reasons for the observed strong geographic patterns remain to be established but could result from the lethality of CLYD and the dominance of short-distance insect-mediated transmission.
Collapse
|
38
|
Puigbò P, Wolf YI, Koonin EV. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life. Methods Mol Biol 2019; 1910:241-269. [PMID: 31278667 DOI: 10.1007/978-1-4939-9074-0_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the boot-split distance (BSD) method is introduced as an extension of the previously developed split distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting treelike and netlike evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the applications methods used to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."
Collapse
Affiliation(s)
- Pere Puigbò
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.,Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
39
|
Adams RH, Castoe TA. Supergene validation: A model-based protocol for assessing the accuracy of non-model-based supergene methods. MethodsX 2019; 6:2181-2188. [PMID: 31667118 PMCID: PMC6812401 DOI: 10.1016/j.mex.2019.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
Genome-scale species tree inference is largely restricted to heuristic approaches that use estimated gene trees to reconstruct species-level relationships. Central to these heuristic species tree methods is the assumption that the gene trees are estimated without error. To increase the accuracy of input gene trees used to infer species trees, several techniques have recently been developed for constructing longer “supergenes” that represent sets of loci inferred to share the same genealogical history. While these supergene methods are designed to increase the amount of data for gene tree estimation by concatenating several loci into “supergenes” to increase gene tree accuracy, no formal protocols have been proposed to validate this key “supergene” concatenation step. In a recent study, we developed several supergene validation strategies for assessing the accuracy of a popular supergene method: the so-called “statistical binning” pipeline. In this article, we describe a more generalizable and model-based “supergene validation” protocol for assessing the accuracy of supergenes and supergene methods using model-based tests of phylogenetic congruency. Supergenes are validated by adopting model-based tests of topological congruence These model-based procedures out preform non-model based methods for supergene construction The results of this protocol can be used to assess the overall performance of a supergene method across a phylogenomic dataset
Collapse
|
40
|
Epidemiological and genetic analysis of Avian avulavirus-1 in Israel reveals parallel circulating strains and a new sub-genotype within genotype VI. INFECTION GENETICS AND EVOLUTION 2018; 66:159-170. [DOI: 10.1016/j.meegid.2018.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/08/2018] [Accepted: 09/17/2018] [Indexed: 11/23/2022]
|
41
|
Orr RJS, Zhao S, Klaveness D, Yabuki A, Ikeda K, Makoto WM, Shalchian-Tabrizi K. Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution. BMC Evol Biol 2018; 18:115. [PMID: 30021531 PMCID: PMC6052632 DOI: 10.1186/s12862-018-1224-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/29/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The class Diphyllatea belongs to a group of enigmatic unicellular eukaryotes that play a key role in reconstructing the morphological innovation and diversification of early eukaryotic evolution. Despite its evolutionary significance, very little is known about the phylogeny and species diversity of Diphyllatea. Only three species have described morphology, being taxonomically divided by flagella number, two or four, and cell size. Currently, one 18S rRNA Diphyllatea sequence is available, with environmental sequencing surveys reporting only a single partial sequence from a Diphyllatea-like organism. Accordingly, geographical distribution of Diphyllatea based on molecular data is limited, despite morphological data suggesting the class has a global distribution. We here present a first attempt to understand species distribution, diversity and higher order structure of Diphyllatea. RESULTS We cultured 11 new strains, characterised these morphologically and amplified their rRNA for a combined 18S-28S rRNA phylogeny. We sampled environmental DNA from multiple sites and designed new Diphyllatea-specific PCR primers for long-read PacBio RSII technology. Near full-length 18S rRNA sequences from environmental DNA, in addition to supplementary Diphyllatea sequence data mined from public databases, resolved the phylogeny into three deeply branching and distinct clades (Diphy I - III). Of these, the Diphy III clade is entirely novel, and in congruence with Diphy II, composed of species morphologically consistent with the earlier described Collodictyon triciliatum. The phylogenetic split between the Diphy I and Diphy II + III clades corresponds with a morphological division of Diphyllatea into bi- and quadriflagellate cell forms. CONCLUSIONS This altered flagella composition must have occurred early in the diversification of Diphyllatea and may represent one of the earliest known morphological transitions among eukaryotes. Further, the substantial increase in molecular data presented here confirms Diphyllatea has a global distribution, seemingly restricted to freshwater habitats. Altogether, the results reveal the advantage of combining a group-specific PCR approach and long-read high-throughput amplicon sequencing in surveying enigmatic eukaryote lineages. Lastly, our study shows the capacity of PacBio RS when targeting a protist class for increasing phylogenetic resolution.
Collapse
Affiliation(s)
- Russell J. S. Orr
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
| | - Sen Zhao
- Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Medical Faculty, Center for Cancer Biomedicine, University of Oslo University Hospital, Oslo, Norway
| | - Dag Klaveness
- Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061 Japan
| | - Keiji Ikeda
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Watanabe M. Makoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Kamran Shalchian-Tabrizi
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
| |
Collapse
|
42
|
Co-speciation in bedbug Wolbachia parallel the pattern in nematode hosts. Sci Rep 2018; 8:8797. [PMID: 29891919 PMCID: PMC5995804 DOI: 10.1038/s41598-018-25545-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/27/2018] [Indexed: 01/30/2023] Open
Abstract
Wolbachia bacteria, vertically transmitted intracellular endosymbionts, are associated with two major host taxa in which they show strikingly different symbiotic modes. In some taxa of filarial nematodes, where Wolbachia are strictly obligately beneficial to the host, they show complete within- and among-species prevalence as well as co-phylogeny with their hosts. In arthropods, Wolbachia usually are parasitic; if beneficial effects occurs, they can be facultative or obligate, related to host reproduction. In arthropods, the prevalence of Wolbachia varies within and among taxa, and no co-speciation events are known. However, one arthropod species, the common bedbug Cimex lectularius was recently found to be dependent on the provision of biotin and riboflavin by Wolbachia, representing a unique case of Wolbachia providing nutritional and obligate benefits to an arthropod host, perhaps even in a mutualistic manner. Using the presence of presumably functional biotin gene copies, our study demonstrates that the obligate relationship is maintained at least in 10 out of 15 species of the genera Cimex and Paracimex. The remaining five species harboured Wolbachia as well, demonstrating the first known case of 100% prevalence of Wolbachia among higher arthropod taxa. Moreover, we show the predicted co-cladogenesis between Wolbachia and their bedbug hosts, also as the first described case of Wolbachia co-speciation in arthropods.
Collapse
|
43
|
Brynildsrud O, Tysnes KR, Robertson LJ, Debenham JJ. Giardia duodenalis in primates: Classification and host specificity based on phylogenetic analysis of sequence data. Zoonoses Public Health 2018; 65:637-647. [PMID: 29654656 DOI: 10.1111/zph.12470] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 01/19/2023]
Abstract
Giardia duodenalis colonizes the gastrointestinal tract of a wide range of hosts, including humans and other primates. It is grouped into eight different Assemblages and, beyond that, into a number of sub-Assemblages, defined ad hoc on the basis of genetic differences; these various groups are often considered to be associated with a specific restricted host range. The aim of this study was to use publicly available genotyping data to investigate the relatedness of human and non-human primate (NHP) Giardia isolates in order to evaluate the usefulness of current taxonomic classification and to assess whether there is potential for zoonotic transmission between humans and NHP. Our final data set consisted of sequence data from 165 isolates, 111 from NHP and 54 from humans. Assemblages were well defined, but sub-Assemblages across Assemblage B were not resolved. Although sub-Assemblages AI and AII were resolved, the terms were not found to capture any useful molecular or host/deme properties. In the phylogenetic tree, NHP isolates were scattered among human isolates across Assemblages A and B, and were even found in Assemblage E. We conclude that there does not appear to be significant molecular distinction between human and NHP Giardia isolates across these four molecular markers. Thus, on the basis of these markers, we cannot exclude a risk for zoonotic and anthropozoonotic transmission of Assemblages A and B isolates, irrespective of sub-Assemblage classification. We further evaluated the relative merit of the four genes used in genotyping studies. The tpi, gdh and bg genes gave relatively congruent tree topologies, but the SSU gene did not resolve Assemblages according to the current classification. Future genotyping efforts should aim for multilocus or whole-genome approaches and, in particular, use of the SSU gene as the sole marker should be avoided when possible.
Collapse
Affiliation(s)
- O Brynildsrud
- Department of Infectious Disease Modelling and Epidemiology, Norwegian Institute of Public Health (FHI), Oslo, Norway
| | - K R Tysnes
- Faculty of Veterinary Medicine, Department Food Safety and Infection Biology, The Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - L J Robertson
- Faculty of Veterinary Medicine, Department Food Safety and Infection Biology, The Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - J J Debenham
- Faculty of Veterinary Medicine, Department of Companion Animal Clinical Sciences, The Norwegian University of Life Sciences (NMBU), Oslo, Norway
| |
Collapse
|
44
|
Yahiaoui N, Chéron JJ, Ravelomanantsoa S, Hamza AA, Petrousse B, Jeetah R, Jaufeerally-Fakim Y, Félicité J, Fillâtre J, Hostachy B, Guérin F, Cellier G, Prior P, Poussier S. Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands. FRONTIERS IN PLANT SCIENCE 2017; 8:2139. [PMID: 29312394 PMCID: PMC5742265 DOI: 10.3389/fpls.2017.02139] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/04/2017] [Indexed: 05/21/2023]
Abstract
Epidemiological surveillance of plant pathogens based on genotyping methods is mandatory to improve disease management strategies. In the Southwest Indian Ocean (SWIO) islands, bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) is hampering the production of many sustainable and cash crops. To thoroughly analyze the genetic diversity of the RSSC in the SWIO, we performed a wide sampling survey (in Comoros, Mauritius, Reunion, Rodrigues, and Seychelles) that yielded 1,704 isolates from 129 plots, mainly from solanaceous crops. Classification of the isolates to the four major RSSC phylogenetic groups, named phylotypes, showed that 87% were phylotype I, representing the most prevalent strain in each of the SWIO islands. Additionally, 9.7% were phylotype II, and 3.3% were phylotype III; however, these isolates were found only in Reunion. Phylotype IV (2 isolates), known to be restricted to Indonesia-Australia-Japan, was reported in Mauritius, representing the first report of this group in the SWIO. Partial endoglucanase (egl) sequencing, based on the selection of 145 isolates covering the geographic and host diversity in the SWIO (also including strains from Mayotte and Madagascar), revealed 14 sequevars with Reunion and Mauritius displaying the highest sequevar diversity. Through a multilocus sequence analysis (MLSA) scheme based on the partial sequencing of 6 housekeeping genes (gdhA, gyrB, rplB, leuS, adk, and mutS) and 1 virulence-associated gene (egl), we inferred the phylogenetic relationships between these 145 SWIO isolates and 90 worldwide RSSC reference strains. Phylotype I was the most recombinogenic, although recombination events were detected among all phylotypes. A multilocus sequence typing (MLST) scheme identified 29 sequence types (STs) with variable geographic distributions in the SWIO. The outstanding epidemiologic feature was STI-13 (sequevar I-31), which was overrepresented in the SWIO and obviously reflected a lineage strongly adapted to the SWIO environment. A goeBURST analysis identified eight clonal complexes (CCs) including SWIO isolates, four CCs being geographically restricted to the SWIO, and four CCs being widespread beyond the SWIO. This work, which highlights notable genetic links between African and SWIO strains, provides a basis for the epidemiological surveillance of RSSC and will contribute to BW management in the SWIO.
Collapse
Affiliation(s)
- Noura Yahiaoui
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, France
- Anses, National Plant Health Laboratory, Tropical Pests and Diseases Unit, Saint-Pierre, France
- Université de la Réunion, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, France
| | - Jean-Jacques Chéron
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, France
| | | | - Azali A. Hamza
- Institut National de Recherche pour l'Agriculture, la Pêche et l'Environnement, Moroni, Comoros
| | | | - Rajan Jeetah
- Food and Agricultural Research and Extension Institute, Curepipe, Mauritius
| | | | | | - Jacques Fillâtre
- Association Réunionnaise pour la Modernisation de l'Economie Fruitière, Légumière et HORticole, Saint-Pierre, France
| | - Bruno Hostachy
- Anses, National Plant Health Laboratory, Tropical Pests and Diseases Unit, Saint-Pierre, France
| | - Fabien Guérin
- Université de la Réunion, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, France
| | - Gilles Cellier
- Anses, National Plant Health Laboratory, Tropical Pests and Diseases Unit, Saint-Pierre, France
| | - Philippe Prior
- Institut National de la Recherche Agronomique, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, France
| | - Stéphane Poussier
- Université de la Réunion, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, France
| |
Collapse
|
45
|
Russo L, Miller AD, Tooker J, Bjornstad ON, Shea K. Quantitative evolutionary patterns in bipartite networks: Vicariance, phylogenetic tracking or diffuse co‐evolution? Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12914] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura Russo
- Department of Biology Pennsylvania State University University Park PA USA
- Department of Botany Trinity College Dublin Dublin 2 Ireland
| | - Adam D. Miller
- Department of Biology Pennsylvania State University University Park PA USA
| | - John Tooker
- Department of Entomology Pennsylvania State University University Park PA USA
| | - Ottar N. Bjornstad
- Department of Biology Pennsylvania State University University Park PA USA
- Department of Entomology Pennsylvania State University University Park PA USA
| | - Katriona Shea
- Department of Biology Pennsylvania State University University Park PA USA
| |
Collapse
|
46
|
Yu XQ, Gao LM, Soltis DE, Soltis PS, Yang JB, Fang L, Yang SX, Li DZ. Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family. THE NEW PHYTOLOGIST 2017; 215:1235-1248. [PMID: 28695680 DOI: 10.1111/nph.14683] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/04/2017] [Indexed: 05/22/2023]
Abstract
Subtropical evergreen broadleaved forests (EBLFs) inhabit large areas of East Asia. Although paleovegetation reconstructions have revealed that the subtropical EBLFs existed in Southwest China during the Miocene, the historical construction of these forests remains poorly known. Here, we used the tea family (Theaceae), a characteristic component of the subtropical EBLFs, to gain new insights into the assembly of this important biome. Using a robust phylogenetic framework of Theaceae based on plastome and nuclear ribosomal DNA sequence data, the temporal history of the family was reconstructed. Data from other characteristic components of subtropical EBLFs, including Fagaceae, Lauraceae and Magnoliaceae, were also integrated. Most of the essential elements of the subtropical EBLFs appear to have originated around the Oligocene-Miocene (O-M) boundary. However, small woody lineages (e.g. Camellia, Hartia) from Theaceae were dated to the late Miocene. Accelerated net diversification rates within Theaceae were also detected near the O-M transition period and the late Miocene. Our results suggest that two independent intensifications of the East Asian summer monsoon (EASM) around the O-M boundary and the late Miocene may have facilitated the historical assembly of the subtropical EBLFs in East Asia.
Collapse
Affiliation(s)
- Xiang-Qin Yu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Liang Fang
- College of Life Sciences, Jiujiang University, Jiujiang, Jiangxi, 332000, China
| | - Shi-Xiong Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| |
Collapse
|
47
|
Dexter KG, Lavin M, Torke BM, Twyford AD, Kursar TA, Coley PD, Drake C, Hollands R, Pennington RT. Dispersal assembly of rain forest tree communities across the Amazon basin. Proc Natl Acad Sci U S A 2017; 114:2645-2650. [PMID: 28213498 PMCID: PMC5347625 DOI: 10.1073/pnas.1613655114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.
Collapse
Affiliation(s)
- Kyle G Dexter
- School of GeoSciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom;
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Mathew Lavin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717
| | - Benjamin M Torke
- Institute of Systematic Botany, New York Botanical Garden, Bronx, NY 10458
| | - Alex D Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Thomas A Kursar
- Biology Department, University of Utah, Salt Lake City, UT 84112
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Phyllis D Coley
- Biology Department, University of Utah, Salt Lake City, UT 84112
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Camila Drake
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Ruth Hollands
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | | |
Collapse
|
48
|
Bláha M, Patoka J, Kozák P, Kouba A. Unrecognized diversity in New Guinean crayfish species (Decapoda, Parastacidae): The evidence from molecular data. Integr Zool 2017; 11:457-468. [PMID: 27264730 DOI: 10.1111/1749-4877.12211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The phylogenetic relationships among imported ornamental crayfish belonging to the genus Cherax were inferred from a combined dataset of 3 mitochondrial genes (COI, 16S and 12S) and by comparison with available GenBank sequences of 14 Cherax species. Furthermore, the concordance of previously described species obtained from a wholesaler (Cherax boesemani, C. holthuisi and C. peknyi) with available GenBank sequences was verified based on COI with special respect to comparison with sequences assigned as Cherax species. Recently described species C. gherardiae, C. pulcher and C. subterigneus belong to the northern group of Cherax species. Comparison and analysis with other GenBank COI sequences show previously unreported diversity of New Guinean species, suggesting 5 putative new species. Surprisingly, species assigned to the subgenus Astaconephrops do not form a monophyletic clade; this subgenus should be reappraised relative to the purported typical morphological characteristic of the uncalcified patch on male chelae. Increasing importation of crayfish underscores the importance of accurate species identification. Use of basic molecular methods is a necessary requisite for documenting occurrence, abundance and population trends of target species. Consequently, it helps to support eventual conservation decision-making by stakeholders.
Collapse
Affiliation(s)
- Martin Bláha
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Praha, Czech Republic
| | - Pavel Kozák
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| |
Collapse
|
49
|
Karamipour N, Mehrabadi M, Fathipour Y. Gammaproteobacteria as essential primary symbionts in the striped shield bug, Graphosoma Lineatum (Hemiptera: Pentatomidae). Sci Rep 2016; 6:33168. [PMID: 27609055 PMCID: PMC5016839 DOI: 10.1038/srep33168] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/16/2016] [Indexed: 11/21/2022] Open
Abstract
Many members of suborder Heteroptra harbor heritable symbiotic bacteria. Here we characterize the gut symbiotic bacterium in Graphosoma lineatum (Hemiptera: Pentatomidae) by using molecular phylogeny, real-time PCR analysis as well as light and electron microscopy observations. The microscopy observations revealed the presence of a large number of rod-shaped bacterial cells in the crypts. A very high prevalence (98 to 100%) of the symbiont infection was found in the insect populations that strongly supports an intimate association between these two organisms. Real-time PCR analysis also showed that the Gammaproteobacteria dominated the crypts. The sequences of 16sr RNA and groEL genes of symbiont showed high levels of similarity (93 to 95%) to Pantoea agglomeranse and Erwinia herbicola Gammaproteobacteria. Phylogenetic analyses placed G. lineatum symbiont in a well-defined branch, divergent from other stink bug bacterial symbionts. Co-evolutionary analysis showed lack of host-symbiont phylogenetic congruence. Surface sterilization of eggs resulted in increased pre-adult stage in the offspring (aposymbionts) in comparison to the normal. Also, fecundity, longevity, and adult stage were significantly decreased in the aposymbionts. Therefore, it seems that the symbiont might play a vital function in the host biology, in which host optimal development depends on the symbiont.
Collapse
Affiliation(s)
- Naeime Karamipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Yaghoub Fathipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
50
|
Rousse P, Quicke DLJ, Matthee CA, Lefeuvre P, van Noort S. A molecular and morphological reassessment of the phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pascal Rousse
- Natural History Department; Iziko South African Museum; PO Box 61 Cape Town 8000 South Africa
- Department of Botany and Zoology; Evolutionary Genomics Group; Stellenbosch University; Private Bag X1 Stellenbosch 7602 South Africa
| | - Donald L. J. Quicke
- Faculty of Science; Chulalongkorn University; 254 Phayathai Road Pathumwan Bangkok Thailand
| | - Conrad A. Matthee
- Department of Botany and Zoology; Evolutionary Genomics Group; Stellenbosch University; Private Bag X1 Stellenbosch 7602 South Africa
| | - Pierre Lefeuvre
- Cirad; UMR PVBMT; 7 Chemin Ligne Paradis 97410 St Pierre France
| | - Simon van Noort
- Natural History Department; Iziko South African Museum; PO Box 61 Cape Town 8000 South Africa
- Department of Biological Sciences; University of Cape Town; Private Bag Rondebosch 7701 South Africa
| |
Collapse
|