1
|
Sato H. The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes. THE NEW PHYTOLOGIST 2024; 241:444-460. [PMID: 37292019 DOI: 10.1111/nph.19055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
Ectomycorrhizal (EcM) symbiosis, a ubiquitous plant-fungus interaction in forests, evolved in parallel in fungi. Why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification remains unclear. This study aimed to reveal the driving mechanism of the evolutionary diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. The historical character transitions of trophic state and fruitbody form were estimated based on phylogenies inferred from fragments of 89 single-copy genes. Moreover, five analyses were used to estimate the net diversification rates (speciation rate minus extinction rate). The results indicate that the unidirectional evolution of EcM symbiosis occurred 27 times, ranging in date from the Early Triassic to the Early Paleogene. The increased diversification rates appeared to occur intensively at the stem of EcM fungal clades diverging in the Late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. By contrast, the evolution of fruitbody form was not strongly linked with the increased diversification rates. These findings suggest that the evolution of EcM symbiosis in the Late Cretaceous, supposedly with coevolving EcM angiosperms, was the key drive of the explosive diversification in Agaricomycetes.
Collapse
Affiliation(s)
- Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan
| |
Collapse
|
2
|
Narváez-Barandica JC, Quintero-Galvis JF, Aguirre-Pabón JC, Castro LR, Betancur R, Acero Pizarro A. A Comparative Phylogeography of Three Marine Species with Different PLD Modes Reveals Two Genetic Breaks across the Southern Caribbean Sea. Animals (Basel) 2023; 13:2528. [PMID: 37570336 PMCID: PMC10417521 DOI: 10.3390/ani13152528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/02/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
The comparative phylogeography of marine species with contrasting dispersal potential across the southern Caribbean Sea was evaluated by the presence of two putative barriers: the Magdalena River plume (MRP) and the combination of the absence of a rocky bottom and the almost permanent upwelling in the La Guajira Peninsula (ARB + PUG). Three species with varying biological and ecological characteristics (i.e., dispersal potentials) that inhabit shallow rocky bottoms were selected: Cittarium pica (PLD < 6 days), Acanthemblemaria rivasi (PLD < 22 days), and Nerita tessellata (PLD > 60 days). We generated a set of SNPs for the three species using the ddRad-seq technique. Samples of each species were collected in five locations from Capurganá to La Guajira. For the first time, evidence of a phylogeographic break caused by the MRP is provided, mainly for A. rivasi (AMOVA: ΦCT = 0.420). The ARB + PUG barrier causes another break for A. rivasi (ΦCT = 0.406) and C. pica (ΦCT = 0.224). Three populations (K = 3) were identified for A. rivasi and C. pica, while N. tessellata presented one population (K = 1). The Mantel correlogram indicated that A. rivasi and C. pica fit the hierarchical population model, and only the A. rivasi and C. pica comparisons showed phylogeographic congruence. Our results demonstrate how the biological traits of these three species and the biogeographic barriers have influenced their phylogeographic structure.
Collapse
Affiliation(s)
- Juan Carlos Narváez-Barandica
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Julián F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile;
| | - Juan Carlos Aguirre-Pabón
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Lyda R. Castro
- Centro de Genética y Biología Molecular, Universidad del Magdalena, Carrera 32 No 22–08, Santa Marta 470004, Colombia; (J.C.A.-P.); (L.R.C.)
| | - Ricardo Betancur
- Biology Department, University of Oklahoma, Norman, OK 73019, USA;
| | - Arturo Acero Pizarro
- Instituto de Estudios en Ciencias del Mar (CECIMAR), Universidad Nacional de Colombia sede Caribe, Santa Marta 470006, Colombia;
| |
Collapse
|
3
|
Romeiro-Brito M, Khan G, Perez MF, Zappi DC, Taylor NP, Olsthoorn G, Franco FF, Moraes EM. Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. AMERICAN JOURNAL OF BOTANY 2023; 110:1-17. [PMID: 36708517 DOI: 10.1002/ajb2.16134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.
Collapse
Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky-University Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
| | - Manolo F Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília (UNB), PO Box 04457, Brasília, DF, 70910-970, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, The Alameda, PO Box 843, GX11 1AA, Gibraltar
| | | | - Fernando F Franco
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Sorocaba, SP, 18052-780, Brazil
| |
Collapse
|
4
|
Garavaglia M, Muzlera A, Valverde C. Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas. Mol Phylogenet Evol 2023; 179:107663. [PMID: 36372354 DOI: 10.1016/j.ympev.2022.107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.
Collapse
Affiliation(s)
- Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Andrés Muzlera
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina.
| |
Collapse
|
5
|
Devarajan AK, Truu M, Gopalasubramaniam SK, Muthukrishanan G, Truu J. Application of data integration for rice bacterial strain selection by combining their osmotic stress response and plant growth-promoting traits. Front Microbiol 2022; 13:1058772. [PMID: 36590400 PMCID: PMC9797599 DOI: 10.3389/fmicb.2022.1058772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Agricultural application of plant-beneficial bacteria to improve crop yield and alleviate the stress caused by environmental conditions, pests, and pathogens is gaining popularity. However, before using these bacterial strains in plant experiments, their environmental stress responses and plant health improvement potential should be examined. In this study, we explored the applicability of three unsupervised machine learning-based data integration methods, including principal component analysis (PCA) of concatenated data, multiple co-inertia analysis (MCIA), and multiple kernel learning (MKL), to select osmotic stress-tolerant plant growth-promoting (PGP) bacterial strains isolated from the rice phyllosphere. The studied datasets consisted of direct and indirect PGP activity measurements and osmotic stress responses of eight bacterial strains previously isolated from the phyllosphere of drought-tolerant rice cultivar. The production of phytohormones, such as indole-acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA), and cytokinin, were used as direct PGP traits, whereas the production of hydrogen cyanide and siderophore and antagonistic activity against the foliar pathogens Pyricularia oryzae and Helminthosporium oryzae were evaluated as measures of indirect PGP activity. The strains were subjected to a range of osmotic stress levels by adding PEG 6000 (0, 11, 21, and 32.6%) to their growth medium. The results of the osmotic stress response experiments showed that all bacterial strains accumulated endogenous proline and glycine betaine (GB) and exhibited an increase in growth, when osmotic stress levels were increased to a specific degree, while the production of IAA and GA considerably decreased. The three applied data integration methods did not provide a similar grouping of the strains. Especially deviant was the ordination of microbial strains based on the PCA of concatenated data. However, all three data integration methods indicated that the strains Bacillus altitudinis PB46 and B. megaterium PB50 shared high similarity in PGP traits and osmotic stress response. Overall, our results indicate that data integration methods complement the single-table data analysis approach and improve the selection process for PGP microbial strains.
Collapse
Affiliation(s)
- Arun Kumar Devarajan
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia,*Correspondence: Arun Kumar Devarajan,
| | - Marika Truu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Sabarinathan Kuttalingam Gopalasubramaniam
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Tuticorin, India,Sabarinathan Kuttalingam Gopalasubramaniam,
| | - Gomathy Muthukrishanan
- Department of Soil Science and Agricultural Chemistry, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Tuticorin, India
| | - Jaak Truu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| |
Collapse
|
6
|
Geography and language divergence: The case of Andic languages. PLoS One 2022; 17:e0265460. [PMID: 35617249 PMCID: PMC9135239 DOI: 10.1371/journal.pone.0265460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/02/2022] [Indexed: 11/19/2022] Open
Abstract
We study the correlation between phylogenetic and geographic distances for the languages of the Andic branch of the East Caucasian (Nakh-Daghestanian) language family. For several alternative phylogenies, we find that geographic distances correlate with linguistic divergence. Notably, qualitative classifications show a better fit with geography than cognacy-based phylogenies. We interpret this result as follows: The better fit may be due to implicit geographic bias in qualitative classifications. We conclude that approaches to classification other than those based on cognacy run a risk to implicitly include geography and geography-related factors as one basis of genealogical classifications.
Collapse
|
7
|
Cruz-Laufer AJ, Pariselle A, Jorissen MWP, Muterezi Bukinga F, Al Assadi A, Van Steenberge M, Koblmüller S, Sturmbauer C, Smeets K, Huyse T, Artois T, Vanhove MPM. Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes. Cladistics 2022; 38:465-512. [PMID: 35488795 DOI: 10.1111/cla.12506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.
Collapse
Affiliation(s)
- Armando J Cruz-Laufer
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Antoine Pariselle
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France.,Faculty of Sciences, Laboratory "Biodiversity, Ecology and Genome", Research Centre "Plant and Microbial Biotechnology, Biodiversity and Environment", Mohammed V University, Rabat, Morocco
| | - Michiel W P Jorissen
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium.,Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Fidel Muterezi Bukinga
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo
| | - Anwar Al Assadi
- Fraunhofer Institute for Manufacturing Engineering and Automation IPA, Nobelstraße 12, Stuttgart, 70569, Germany
| | - Maarten Van Steenberge
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium.,Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, B-1000, Belgium
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Karen Smeets
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Tine Huyse
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Tom Artois
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Maarten P M Vanhove
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| |
Collapse
|
8
|
Kmentová N, Cruz-Laufer AJ, Pariselle A, Smeets K, Artois T, Vanhove MPM. Dactylogyridae 2022: a meta-analysis of phylogenetic studies and generic diagnoses of parasitic flatworms using published genetic and morphological data. Int J Parasitol 2022; 52:427-457. [PMID: 35245493 DOI: 10.1016/j.ijpara.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022]
Abstract
Dactylogyridae is one of the most studied families of parasitic flatworms with more than 1000 species and 166 genera described to date including ecto- and endoparasites. Dactylogyrid monogeneans were suggested as model organisms for host-parasite macroevolutionary and biogeographical studies due to the scientific and economic importance of some of their host lineages. Consequently, an array of phylogenetic research into different dactylogyrid lineages has been produced over the past years but the last family-wide study was published 16 years ago. Here, we provide a meta-analysis of the phylogenetic relationships of Dactylogyridae including representatives of all genera with available molecular data (n=67). First, we investigate the systematic informativeness of morphological characters widely used to diagnose dactylogyrid genera through a parsimony analysis of the characters, character mapping, and phylogenetic comparative methods. Second, we provide an overview of the current state of the systematics of the family and its subfamilies, and summarise potentially poly- and paraphyletic genera. Third, we elaborate on the implications of taxonomic, citation, and confirmation bias in past studies. Fourth, we discuss host range, biogeographical, and freshwater-marine patterns. We found two well-supported macroclades which we assigned to the subfamilies Dactylogyrinae and Ancyrocephalinae. These subfamilies further include 16 well-supported clades with only a few synapomorphies that could be deduced from generic diagnoses in the literature. Furthermore, few morphological characters considered systematically informative at the genus level display a strong phylogenetic signal. However, the parsimony analysis suggests that these characters provide little information on the relationships between genera. We conclude that a strong taxonomic bias and low coverage of DNA sequences and regions limit knowledge on morphological and biogeographical evolutionary patterns that can be inferred from these results. We propose addressing potential citation and confirmation biases through a 'level playing field' multiple sequence alignment as provided by this study.
Collapse
Affiliation(s)
- Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic; Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium.
| | - Armando J Cruz-Laufer
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Antoine Pariselle
- ISEM, CNRS, Université de Montpellier, IRD, Montpellier, France; Laboratory "Biodiversity, Ecology and Genome", Mohammed V University in Rabat, Faculty of Sciences, 4 avenue Ibn Batouta, BP 1014, Rabat, Morocco
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic; Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| |
Collapse
|
9
|
Post-natal conservation of human blood and marrow-specific CD34+ hematopoietic phenotypes. Exp Hematol 2022; 109:18-26. [DOI: 10.1016/j.exphem.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/18/2022]
|
10
|
de Aguiar JCC, Domingues MV, Silva W, Ceccarelli PS, Adriano EA, Soares GB. Morphology and molecular phylogeny of Pauciconfibuloides amazonica gen. n. sp. n. (Platyhelminthes, Monogenoidea) parasitizing the Amazonian croaker Plagioscion squamosissimus. Parasitol Int 2021; 87:102489. [PMID: 34737075 DOI: 10.1016/j.parint.2021.102489] [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: 07/04/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 10/20/2022]
Abstract
An integrative study was performed to understand the phylogenetic relationships of an undescribed, freshwater species of microcotylid parasitizing Plagioscion squamosissimus from the Amazon River Basin. Based on morphological and molecular analysis (18S rDNA and partial 28S rDNA genes), a new genus is proposed to accommodate this new species, Pauciconfibuloides amazonica gen. n. sp. n. The new genus is closely related to Protastomicrocotylinae and Pauciconfibula by sharing the vagina, male copulatory organ, and genital atrium all unarmed. However, Pauciconfibuloides gen. n. can be distinguished from those taxa by the prostatic system and position of the vaginal pore. Molecular phylogenetic inference suggests a sister relationship with species of Polylabris (Prostatomicrocotylinae), but to date, there are no available 18S or 28S rDNA sequences of Pauciconfibula to be compared. This is the first report of a microcotylid parasitizing a freshwater sciaenid from South America.
Collapse
Affiliation(s)
- Julio Cesar Cenci de Aguiar
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, 255, CEP 13083-862 Campinas, São Paulo, Brazil; Sistema de Ensino, Campanha Nacional de Escolas da Comunidade (CNEC), Rua Frei Paulino, 530, Nossa Sra. da Abadia, CEP 38025-180 Uberaba, Minas Gerais, Brazil.
| | - Marcus Vinicius Domingues
- Instituto de Estudos Costeiros, Universidade Federal do Pará (UFPA), Travessa Leandro Ribeiro, s/n, Aldeia, CEP 68600-000 Bragança, Pará, Brazil
| | - Willian Silva
- Departamento de Medicina Veterinária, Centro Universitário da Fundação de Ensino Octávio Bastos (UNIFEOB), Av. Dr. Otávio da Silva Bastos, 2439, Jardim Nova São Joao, São João da Boa Vista CEP 13874-149, São Paulo, Brazil
| | - Paulo Sérgio Ceccarelli
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Aquática Continental, Instituto Chico Mendes de Conservação da Biodiversidade (CEPTA/ICMBio), Rodovia Prefeito Euberto Nemésio Pereira de Godoy, km 6,5, CEP 13630-970 Pirassununga, São Paulo, Brazil
| | - Edson Aparecido Adriano
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo (UNIFESP), Rua Professor Arthur Riedel, 275, Jardim Eldorado, CEP 09972-270 Diadema, São Paulo, Brazil
| | - Geusivam Barbosa Soares
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, 255, CEP 13083-862 Campinas, São Paulo, Brazil
| |
Collapse
|
11
|
Shipunov A, Fernández-Alonso JL, Hassemer G, Alp S, Lee HJ, Pay K. Molecular and Morphological Data Improve the Classification of Plantagineae (Lamiales). PLANTS (BASEL, SWITZERLAND) 2021; 10:2299. [PMID: 34834664 PMCID: PMC8625185 DOI: 10.3390/plants10112299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The tribe Plantagineae (Lamiales) is a group of plants with worldwide distribution, notorious for its complicated taxonomy and still unresolved natural history. We describe the result of a broadly sampled phylogenetic study of tribe. The expanded sampling dataset is based on the trnL-F spacer, rbcL, and ITS2 markers across all three included genera (Aragoa, Littorella and Plantago) and makes this the most comprehensive study to date. The other dataset uses five markers and provides remarkably good resolution throughout the tree, including support for all of the major clades. In addition to the molecular phylogeny, a morphology database of 114 binary characters was assembled to provide comparison with the molecular phylogeny and to develop a means to assign species not sampled in the molecular analysis to their most closely related species that were sampled. Based on the molecular phylogeny and the assignment algorithm to place unsampled species, a key to sections is presented, and a revised classification of the tribe is provided. We also include the description of new species from North America.
Collapse
Affiliation(s)
- Alexey Shipunov
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | | | - Gustavo Hassemer
- Três Lagoas Campus, Federal University of Mato Grosso do Sul, Três Lagoas CEP 79610-100, Brazil;
| | - Sean Alp
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | - Hye Ji Lee
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| | - Kyle Pay
- Department of Biology, Minot State University, Minot, ND 58707, USA; (S.A.); (H.J.L.); (K.P.)
| |
Collapse
|
12
|
Sîrbu I, Benedek AM, Sîrbu M. Variation partitioning in double-constrained multivariate analyses: linking communities, environment, space, functional traits, and ecological niches. Oecologia 2021; 197:43-59. [PMID: 34379198 PMCID: PMC8445867 DOI: 10.1007/s00442-021-05006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/21/2021] [Indexed: 11/25/2022]
Abstract
Constrained multivariate analysis is a common tool for linking ecological communities to environment. The follow-up is the development of the double-constrained correspondence analysis (dc-CA), integrating traits as species-related predictors. Further, methods have been proposed to integrate information on phylogenetic relationships and space variability. We expand this framework, proposing a dc-CA-based algorithm for decomposing variation in community structure and testing the simple and conditional effects of four sets of predictors: environment characteristics and space configuration as predictors related to sites, while traits and niche (dis)similarities as species-related predictors. In our approach, ecological niches differ from traits in that the latter are distinguished by and characterize the individual level, while niches are measured on the species level, and when compared, they are characteristics of communities and should be used as separate predictors. The novelties of this approach are the introduction of new niche parameters, niche dissimilarities, synthetic niche-based diversity which we related to environmental features, the development of an algorithm for the full variation decomposition and testing of the community–environment–niche–traits–space (CENTS) space by dc-CAs with and without covariates, and new types of diagrams for the results. Applying these methods to a dataset on freshwater mollusks, we learned that niche predictors may be as important as traits in explaining community structure and are not redundant, overweighting the environmental and spatial predictors. Our algorithm opens new pathways for developing integrative methods linking life, environment, and other predictors, both in theoretical and practical applications, including assessment of human impact on habitats and ecological systems.
Collapse
Affiliation(s)
- Ioan Sîrbu
- Faculty of Sciences, Lucian Blaga University of Sibiu, 5-7 Dr. I. Ratiu St., 550012, Sibiu, Romania.
| | - Ana Maria Benedek
- Faculty of Sciences, Lucian Blaga University of Sibiu, 5-7 Dr. I. Ratiu St., 550012, Sibiu, Romania
| | - Monica Sîrbu
- Andrei Șaguna National Pedagogical College, 2 Aleea Turnu Roșu St., 550361, Sibiu, Romania
| |
Collapse
|
13
|
Boluda CG, Rico VJ, Naciri Y, Hawksworth DL, Scheidegger C. Phylogeographic reconstructions can be biased by ancestral shared alleles: The case of the polymorphic lichen Bryoria fuscescens in Europe and North Africa. Mol Ecol 2021; 30:4845-4865. [PMID: 34252241 DOI: 10.1111/mec.16078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 11/26/2022]
Abstract
Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.
Collapse
Affiliation(s)
- Carlos G Boluda
- Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques and Université de Genève, Chambésy, Switzerland
| | - Víctor J Rico
- Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Yamama Naciri
- Laboratoire de Systématique Végétale et Biodiversité, Conservatoire et Jardin botaniques and Université de Genève, Chambésy, Switzerland
| | - David L Hawksworth
- Department of Life Sciences, The Natural History Museum, London, UK.,Comparative Fungal Biology, Royal Botanic Gardens, Kew, UK
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| |
Collapse
|
14
|
Bakkes DK, Ropiquet A, Chitimia-Dobler L, Matloa DE, Apanaskevich DA, Horak IG, Mans BJ, Matthee CA. Adaptive radiation and speciation in Rhipicephalus ticks: A medley of novel hosts, nested predator-prey food webs, off-host periods and dispersal along temperature variation gradients. Mol Phylogenet Evol 2021; 162:107178. [PMID: 33892098 DOI: 10.1016/j.ympev.2021.107178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 01/22/2023]
Abstract
Rhipicephalus are a species-diverse genus of ticks, mainly distributed in the Afrotropics with some species in the Palearctic and Oriental regions. Current taxonomic consensus comprise nine informal species groups/lineages based on immature morphology. This work integrates biogeographic, ecological and molecular lines of evidence to better understand Rhipicephalus evolution. Phylogenetic analysis based on four genes (12S, 16S, 28S-D2 and COI) recovered five distinct clades with nine descendant clades that are generally congruent with current taxonomy, with some exceptions. Historical biogeography is inferred from molecular divergence times, ancestral distribution areas, host-use and climate niches of four phylogenetically significant bioclimatic variables (isothermality, annual, seasonal and diurnal temperature range). Novel hosts enabled host-linked dispersal events into new environments, and ticks exploited new hosts through nested predator-prey connections in food webs. Diversification was further induced by climate niche partitioning along gradients in temperature range during off-host periods. Ancestral climate niche estimates corroborated dispersal events by indicating hypothetical ancestors moved into environments with different annual and seasonal temperature ranges along latitudinal gradients. Host size for immature and adult life stages was important for dispersal and subsequent diversification rates. Clades that utilise large, mobile hosts (ungulates and carnivores) early in development have wider geographic ranges but slower diversification rates, and those utilising small, less mobile hosts (rodents, lagomorphs and afroinsectivores) early in development have smaller ranges but higher diversification rates. These findings suggest diversification is driven by a complex set of factors linked to both host-associations (host size, ranges and mobility) and climate niche partitioning along annual and seasonal temperature range gradients that vary with latitude. Moreover, competitive interactions can reinforce these processes and drive speciation. Off-host periods facilitate adaptive radiation by enabling host switches along nested predator-prey connections in food webs, but at the cost of environmental exposure that partitions niches among dispersing progenitors, disrupting geneflow and driving diversification. As such, the evolution and ecological niches of Rhipicephalus are characterised by trade-offs between on- and off-host periods, and these trade-offs interact with nested predator-prey connections in food webs, host-use at different life stages, as well as gradients in annual and seasonal temperature ranges to drive adaptive radiation and speciation.
Collapse
Affiliation(s)
- Deon K Bakkes
- Gertrud Theiler Tick Museum - Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria 0110, South Africa; Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
| | - Anne Ropiquet
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; Middlesex University, Department of Natural Sciences- Faculty of Science and Technology, London NW4 4BT, United Kingdom
| | | | - Dikeledi E Matloa
- Gertrud Theiler Tick Museum - Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria 0110, South Africa
| | - Dmitry A Apanaskevich
- United States National Tick Collection, the James H. Oliver, Jr. Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA 30460-8042, USA; Biology Department, Georgia Southern University, Statesboro, GA 30460, USA; Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Ivan G Horak
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Ben J Mans
- Gertrud Theiler Tick Museum - Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria 0110, South Africa; Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa; Department of Life and Consumer Sciences, University of South Africa, South Africa
| | - Conrad A Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| |
Collapse
|
15
|
Keeley ER, Loxterman JL, Matsaw SL, Njoroge ZM, Seiler MB, Seiler SM. Morphological and genetic concordance of cutthroat trout ( Oncorhynchus clarkii) diversification from western North America. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cutthroat trout (Oncorhynchus clarkii (Richardson, 1836)) is one of the most widely distributed species of freshwater fish in western North America. Occupying a diverse range of habitats, they exhibit significant phenotypic variability that is often recognized by intraspecific taxonomy. Recent molecular phylogenies have described phylogenetic diversification across cutthroat trout populations, but no study has provided a range-wide morphological comparison of taxonomic divisions. In this study, we used linear- and geometric-based morphometrics to determine if phylogenetic and subspecies divisions correspond to morphological variation in cutthroat trout, using replicate populations from throughout the geographic range of the species. Our data indicate significant morphological divergence of intraspecific categories in some, but not all, cutthroat trout subspecies. We also compare morphological distance measures with distance measures of mtDNA sequence divergence. DNA sequence divergence was positively correlated with morphological distance measures, indicating that morphologically more similar subspecies have lower sequence divergence in comparison to morphologically distant subspecies. Given these results, integrating both approaches to describing intraspecific variation may be necessary for developing a comprehensive conservation plan in wide-ranging species.
Collapse
Affiliation(s)
- Ernest R. Keeley
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | - Janet L. Loxterman
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | - Sammy L. Matsaw
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | - Zacharia M. Njoroge
- Department of Biological Sciences, Mail Stop 8007, Idaho State University, Pocatello, ID 83209, USA
| | | | - Steven M. Seiler
- Department of Biology, Lock Haven University, Lock Haven, PA 17745, USA
| |
Collapse
|
16
|
Cardoso YP, Jardim de Queiroz L, Bahechar IA, Posadas PE, Montoya-Burgos JI. Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin. Sci Rep 2021; 11:5073. [PMID: 33658600 PMCID: PMC7930046 DOI: 10.1038/s41598-021-83464-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 01/05/2021] [Indexed: 01/31/2023] Open
Abstract
Distribution history of the widespread Neotropical genus Hypostomus was studied to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny, ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distribution analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene. Dispersal to other rivers of La Plata Basin started about 8 Mya, followed by habitat shifts and an increased rate of cladogenesis. Amazonian Hypostomus species colonized La Plata Basin several times in the Middle Miocene, probably via the Upper Paraná and the Paraguay rivers that acted as dispersal corridors. During the Miocene, La Plata Basin experienced marine incursions, and geomorphological and climatic changes that reconfigured its drainage pattern, driving dispersal and diversification of Hypostomus. The Miocene marine incursion was a strong barrier and its retraction triggered Hypostomus dispersal, increased speciation rate and ecological diversification. The timing of hydrogeological changes in La Plata Basin coincides well with Hypostomus cladogenetic events, indicating that the history of this basin has acted on the diversification of its biota.
Collapse
Affiliation(s)
- Yamila P Cardoso
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Paseo del Bosque S/N, B1900FWA, La Plata, Buenos Aires, Argentina.
| | - Luiz Jardim de Queiroz
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Ilham A Bahechar
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Paula E Posadas
- Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Paseo del Bosque S/N, B1900FWA, La Plata, Buenos Aires, Argentina
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| |
Collapse
|
17
|
Villalobos-Cid M, Salinas F, Inostroza-Ponta M. Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence. J Bioinform Comput Biol 2020; 18:2050040. [PMID: 33155874 DOI: 10.1142/s0219720020500407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Phylogenetic inference proposes an evolutionary hypothesis for a group of taxa which is usually represented as a phylogenetic tree. The use of several distinct biological evidence has shown to produce more resolved phylogenies than single evidence approaches. Currently, two conflicting paradigms are applied to combine biological evidence: taxonomic congruence (TC) and total evidence (TE). Although the literature recommends the application of these paradigms depending on the congruence of the input data, the resultant evolutionary hypotheses could vary according to the strategy used to combine the biological evidence biasing the resultant topologies of the trees. In this work, we evaluate the ability of different strategies associated with both paradigms to produce integrated evolutionary hypotheses by considering different features of the data: missing biological evidence, diversity among sequences, complexity, and congruence. Using datasets from the literature, we compare the resultant trees with reference hypotheses obtained by applying two inference criteria: maximum parsimony and likelihood. The results show that methods associated with TE paradigm are more robust compared to TC methods, obtaining trees with more similar topologies in relation to reference trees. These results are obtained regardless of (1) the features of the data, (2) the estimated evolutionary rates, and (3) the criteria used to infer the reference evolutionary hypotheses.
Collapse
Affiliation(s)
- Manuel Villalobos-Cid
- Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Avenida Ecuador #3659, Estación Central 9170124, Chile
| | - Francisco Salinas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Mario Inostroza-Ponta
- Departamento de Ingeniería Informática, Universidad de Santiago de Chile, Avenida Ecuador #3659, Estación Central 9170124, Chile
| |
Collapse
|
18
|
Sato H, Ohta R, Murakami N. Molecular prospecting for cryptic species of the Hypholoma fasciculare complex: toward the effective and practical delimitation of cryptic macrofungal species. Sci Rep 2020; 10:13224. [PMID: 32764692 PMCID: PMC7413530 DOI: 10.1038/s41598-020-70166-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/24/2020] [Indexed: 11/11/2022] Open
Abstract
Many macrofungal cryptic species remain unidentified. A possible solution is to increase the number of loci analyzed and use rigorous statistics for macrofungal species delimitation. To validate this assumption, cryptic species of the Hypholoma fasciculare complex, a group of common wood-decomposing fungi, were attempted to be delineated. Massively parallel sequencing of mitochondrial ribosomal RNA (mt_rRNA), nuclear ribosomal internal transcribed spacer (ITS) region, and 24 single-copy genes were performed for 96 specimens collected in Japan. Then, the species boundaries were inferred using comparative gene genealogies (mt_rRNA vs. ITS), Bayesian Poisson tree process (bPTP) model for the phylogeny of concatenated nuclear sequences, and analysis of molecular variance (AMOVA) for single nucleotide polymorphisms. In both the mt_rRNA and ITS phylogenies, the H. fasciculare complex was not divided into well-supported clades. Nevertheless, based on the bPTP, two mitochondrial haplotypes were inferred to represent distinct species (H. fasciculare and H. subviride). The results of AMOVA also indicated that the differentiation of nuclear loci can be explained mostly by differences between haplotype. These results suggest that it is necessary to increase the number of target loci to 20 or more and use both phylogeny-based and population genetics-based statistics for the accurate delimitation of macrofungal species.
Collapse
Affiliation(s)
- Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Ryoma Ohta
- Makino Herbarium, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| | - Noriaki Murakami
- Makino Herbarium, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| |
Collapse
|
19
|
Abstract
AbstractChaetothyriales is an ascomycetous order within Eurotiomycetes. The order is particularly known through the black yeasts and filamentous relatives that cause opportunistic infections in humans. All species in the order are consistently melanized. Ecology and habitats of species are highly diverse, and often rather extreme in terms of exposition and toxicity. Families are defined on the basis of evolutionary history, which is reconstructed by time of divergence and concepts of comparative biology using stochastical character mapping and a multi-rate Brownian motion model to reconstruct ecological ancestral character states. Ancestry is hypothesized to be with a rock-inhabiting life style. Ecological disparity increased significantly in late Jurassic, probably due to expansion of cytochromes followed by colonization of vacant ecospaces. Dramatic diversification took place subsequently, but at a low level of innovation resulting in strong niche conservatism for extant taxa. Families are ecologically different in degrees of specialization. One of the clades has adapted ant domatia, which are rich in hydrocarbons. In derived families, similar processes have enabled survival in domesticated environments rich in creosote and toxic hydrocarbons, and this ability might also explain the pronounced infectious ability of vertebrate hosts observed in these families. Conventional systems of morphological classification poorly correspond with recent phylogenetic data. Species are hypothesized to have low competitive ability against neighboring microbes, which interferes with their laboratory isolation on routine media. The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods, novel taxonomic entities being introduced at a regular pace. Our study comprises all available species sequenced to date for LSU and ITS, and a nomenclatural overview is provided. A limited number of species could not be assigned to any extant family.
Collapse
|
20
|
Discordant evolution of mitochondrial and nuclear yeast genomes at population level. BMC Biol 2020; 18:49. [PMID: 32393264 PMCID: PMC7216626 DOI: 10.1186/s12915-020-00786-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
Background Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. Results In contrast with pre-whole genome duplication fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with a weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked intron variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer the expected growth defect in fermentable rich media. Conclusions Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.
Collapse
|
21
|
Villalobos-Cid M, Salinas F, Kessi-Pérez EI, De Chiara M, Liti G, Inostroza-Ponta M, Martínez C. Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae. Microorganisms 2019; 8:E32. [PMID: 31877949 PMCID: PMC7022669 DOI: 10.3390/microorganisms8010032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/04/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Massive sequencing projects executed in Saccharomyces cerevisiae have revealed in detail its population structure. The recent "1002 yeast genomes project" has become the most complete catalogue of yeast genetic diversity and a powerful resource to analyse the evolutionary history of genes affecting specific phenotypes. In this work, we selected 22 nitrogen associated genes and analysed the sequence information from the 1011 strains of the "1002 yeast genomes project". We constructed a total evidence (TE) phylogenetic tree using concatenated information, which showed a 27% topology similarity with the reference (REF) tree of the "1002 yeast genomes project". We also generated individual phylogenetic trees for each gene and compared their topologies, identifying genes with similar topologies (suggesting a shared evolutionary history). Furthermore, we pruned the constructed phylogenetic trees to compare the REF tree topology versus the TE tree and the individual genes trees, considering each phylogenetic cluster/subcluster within the population, observing genes with cluster/subcluster topologies of high similarity to the REF tree. Finally, we used the pruned versions of the phylogenetic trees to compare four strains considered as representatives of S. cerevisiae clean lineages, observing for 15 genes that its cluster topologies match 100% the REF tree, supporting that these strains represent main lineages of yeast population. Altogether, our results showed the potential of tree topologies comparison for exploring the evolutionary history of a specific group of genes.
Collapse
Affiliation(s)
- Manuel Villalobos-Cid
- Departamento de Ingeniería Informática, Facultad de Ingeniería, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Francisco Salinas
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago 7500574, Chile
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile (UACH), Valdivia 5110566, Chile
| | - Eduardo I. Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | | | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, 06107 Nice, France
| | - Mario Inostroza-Ponta
- Departamento de Ingeniería Informática, Facultad de Ingeniería, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| |
Collapse
|
22
|
Parra PP, Aime MC. New species of Bannoa described from the tropics and the first report of the genus in South America. Mycologia 2019; 111:953-964. [PMID: 31634053 DOI: 10.1080/00275514.2019.1647397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The genus Bannoa consists of four described species associated with dead leaves in southwestern Japan. In this study, we describe three new species, Bannoa guamensis, B. rosea, and B. tropicalis, from the South Pacific island of Guam and Guyana in South America. Isolates were obtained from surfaces of diseased and healthy leaves of plants in the Euphorbiaceae, Asteraceae, and Poaceae. DNA sequences from four gene regions, including nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S), nuc 18S rDNA (18S), and a portion of tef1, which encodes translation elongation factor 1-alpha, were produced for phylogenetic analysis. Intercompatibility tests were performed, and subsequent development of clamp connections and basidia were documented for B. tropicalis. Potential life history strategies and association with diseased leaves, including rust-infected leaves, were evaluated across the genus. This is the first report of a species of Bannoa from South America.
Collapse
Affiliation(s)
- Pedro Pablo Parra
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| |
Collapse
|
23
|
Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi ( Bryoria sect. Implexae, Parmeliaceae). PERSOONIA 2019; 42:75-100. [PMID: 31551615 PMCID: PMC6712543 DOI: 10.3767/persoonia.2019.42.04] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/18/2018] [Indexed: 01/07/2023]
Abstract
In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.
Collapse
|
24
|
Sato H, Toju H. Timing of evolutionary innovation: scenarios of evolutionary diversification in a species-rich fungal clade, Boletales. THE NEW PHYTOLOGIST 2019; 222:1924-1935. [PMID: 30664238 DOI: 10.1111/nph.15698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Acquisition of mutualistic symbiosis could provide hosts and/or symbionts with novel ecological opportunities for evolutionary diversification. Such a mechanism is one of the major components of coevolutionary diversification. However, whether the origin of mycorrhizal symbiosis promotes diversification in fungi still requires clarification. Here, we aimed to reveal evolutionary diversification in a clade comprising ectomycorrhizal (ECM) fungi. Based on a phylogenic tree inferred from the sequences of 87 single-copy genes, we reconstructed the origins of ECM symbiosis in a species-rich basidiomycetous order, Boletales. High-resolution phylogeny of Boletales revealed that ECM symbiosis independently evolved from non-ECM states at least four times in the group. Among them, only the second most recent event, occurring in the clade of Boletaceae, was inferred to involve an almost synchronous rapid diversification and rapid transition from non-ECM to ECM symbiosis. Our results contradict the hypothesis of evolutionary priority effect, which postulates the greatest ecological opportunities in the oldest lineages. Therefore, the novel resources that had not been pre-empted by the old ECM fungal lineages - supposedly the coevolving angiosperm hosts - could be available for the young ECM fungal lineages, which resulted in evolutionary diversification occurring only in the young ECM fungal lineages.
Collapse
Affiliation(s)
- Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, 509-3, 2-chome, Hirano, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| |
Collapse
|
25
|
A topological view of human CD34 + cell state trajectories from integrated single-cell output and proteomic data. Blood 2019; 133:927-939. [PMID: 30622121 DOI: 10.1182/blood-2018-10-878025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/23/2018] [Indexed: 12/11/2022] Open
Abstract
Recent advances in single-cell molecular analytical methods and clonal growth assays are enabling more refined models of human hematopoietic lineage restriction processes to be conceptualized. Here, we report the results of integrating single-cell proteome measurements with clonally determined lymphoid, neutrophilic/monocytic, and/or erythroid progeny outputs from >1000 index-sorted CD34+ human cord blood cells in short-term cultures with and without stromal cells. Surface phenotypes of functionally examined cells were individually mapped onto a molecular landscape of the entire CD34+ compartment constructed from single-cell mass cytometric measurements of 14 cell surface markers, 20 signaling/cell cycle proteins, and 6 transcription factors in ∼300 000 cells. This analysis showed that conventionally defined subsets of CD34+ cord blood cells are heterogeneous in their functional properties, transcription factor content, and signaling activities. Importantly, this molecular heterogeneity was reduced but not eliminated in phenotypes that were found to display highly restricted lineage outputs. Integration of the complete proteomic and functional data sets obtained revealed a continuous probabilistic topology of change that includes a multiplicity of lineage restriction trajectories. Each of these reflects progressive but variable changes in the levels of specific signaling intermediates and transcription factors but shared features of decreasing quiescence. Taken together, our results suggest a model in which increasingly narrowed hematopoietic output capabilities in neonatal CD34+ cord blood cells are determined by a history of external stimulation in combination with innately programmed cell state changes.
Collapse
|
26
|
López-Rubio A, Suaza-Vasco JD, Solari S, Gutiérez-Builes L, Porter C, Uribe SI. Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar & Knab 1913, based on mitochondrial and nuclear ribosomal genes. INFECTION GENETICS AND EVOLUTION 2018; 67:183-190. [PMID: 30395997 DOI: 10.1016/j.meegid.2018.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/10/2018] [Accepted: 10/20/2018] [Indexed: 12/30/2022]
Abstract
Three mitochondrial regions and a fragment of a large nuclear ribosomal subunit was used to study the evolutionary patterns of An. neivai, a mosquito inhabiting mangroves and tropical forest in the lowland and coastal areas of the Yucatan Peninsula through the Pacific Ecuadorian coast. This species exhibits epidemiological importance regarding Malaria transmission in natural ecosystems, particularly in rural areas of the Pacific Colombian coast. The results based on phylogenetic networks and Bayesian inference showed no robust evidence supporting the existence of previously suggested cryptic species. Diversification patterns in geographically widespread species such as this one, are complex and therefore could impact malaria control strategies. Further studies focused on behavior, morphology, and phylogenomics will improve the understanding of the evolutionary patterns within An. neivai and its role as a disease vector.
Collapse
Affiliation(s)
- Andrés López-Rubio
- Universidad Nacional de Colombia - Medellín, Facultad de Ciencias - Escuela de Biociencias, Grupo de Investigación en Sistemática Molecular, Carrera 65 59A-110, Medellín 050034, Colombia.
| | - Juan David Suaza-Vasco
- Universidad Nacional de Colombia - Medellín, Facultad de Ciencias - Escuela de Biociencias, Grupo de Investigación en Sistemática Molecular, Carrera 65 59A-110, Medellín 050034, Colombia
| | - Sergio Solari
- Instituto de Biología, Grupo de Mastozoología, Universidad de Antioquia, Calle 70 52-21, Medellín, Colombia
| | - Lina Gutiérez-Builes
- Escuela de Ciencias de la Salud, Facultad de Medicina, Grupo de Biología de Sistemas, Universidad Pontificia Bolivariana, Calle 78B 72A-109, Medellín, Colombia
| | - Charles Porter
- Universidad Nacional de Colombia - Medellín, Facultad de Ciencias - Escuela de Biociencias, Grupo de Investigación en Sistemática Molecular, Carrera 65 59A-110, Medellín 050034, Colombia
| | - Sandra I Uribe
- Universidad Nacional de Colombia - Medellín, Facultad de Ciencias - Escuela de Biociencias, Grupo de Investigación en Sistemática Molecular, Carrera 65 59A-110, Medellín 050034, Colombia
| |
Collapse
|
27
|
Fonseca LHM, Lohmann LG. Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae). Mol Phylogenet Evol 2018; 123:1-15. [DOI: 10.1016/j.ympev.2018.01.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 01/25/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
|
28
|
Alkhamis MA, Gallardo C, Jurado C, Soler A, Arias M, Sánchez-Vizcaíno JM. Phylodynamics and evolutionary epidemiology of African swine fever p72-CVR genes in Eurasia and Africa. PLoS One 2018; 13:e0192565. [PMID: 29489860 PMCID: PMC5831051 DOI: 10.1371/journal.pone.0192565] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72 and the central variable region of isolates collected between 1960 and 2015. We used Bayesian phylodynamic models to reconstruct the evolutionary history of the virus, to identify virus population demographics and to quantify dispersal patterns between host species. Results suggest that ASFV exhibited a significantly high evolutionary rate and population growth through time since its divergence in the 18th century from East Africa, with no signs of decline till recent years. This increase corresponds to the growing pig trade activities between continents during the 19th century, and may be attributed to an evolutionary drift that resulted from either continuous circulation or maintenance of the virus within Africa and Eurasia. Furthermore, results implicate wild suids as the ancestral host species (root state posterior probability = 0.87) for ASFV in the early 1700s in Africa. Moreover, results indicate the transmission cycle between wild suids and pigs is an important cycle for ASFV spread and maintenance in pig populations, while ticks are an important natural reservoir that can facilitate ASFV spread and maintenance in wild swine populations. We illustrated the prospects of phylodynamic methods in improving risk-based surveillance, support of effective animal health policies, and epidemic preparedness in countries at high risk of ASFV incursion.
Collapse
Affiliation(s)
- Moh A Alkhamis
- Faculty of Public Heath, Health Sciences Centre, Kuwait University, Kuwait City, Kuwait
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Carmina Gallardo
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Cristina Jurado
- VISAVET Health Surveillance Centre and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Alejandro Soler
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Marisa Arias
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - José M Sánchez-Vizcaíno
- VISAVET Health Surveillance Centre and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| |
Collapse
|
29
|
Mardones M, Trampe-Jaschik T, Oster S, Elliott M, Urbina H, Schmitt I, Piepenbring M. Phylogeny of the order Phyllachorales ( Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci. PERSOONIA 2017; 39:74-90. [PMID: 29503471 PMCID: PMC5832958 DOI: 10.3767/persoonia.2017.39.04] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/01/2017] [Indexed: 11/25/2022]
Abstract
The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.
Collapse
Affiliation(s)
- M. Mardones
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
- Escuela de Biología, Universidad de Costa Rica, San Pedro, 11501 San José, Costa Rica
| | - T. Trampe-Jaschik
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | - S. Oster
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | - M. Elliott
- Department of Plant Pathology, University of Florida – IFAS, Fort Lauderdale Research and Education Center, Davie, FL-33314, USA
| | - H. Urbina
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN-47907, USA
| | - I. Schmitt
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - M. Piepenbring
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Biologicum, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| |
Collapse
|
30
|
Franco FF, Jojima CL, Perez MF, Zappi DC, Taylor N, Moraes EM. The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti. Ecol Evol 2017; 7:9281-9293. [PMID: 29187968 PMCID: PMC5696397 DOI: 10.1002/ece3.3458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/07/2017] [Accepted: 08/11/2017] [Indexed: 01/15/2023] Open
Abstract
In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.
Collapse
Affiliation(s)
- Fernando Faria Franco
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Cecília Leiko Jojima
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Manolo Fernandez Perez
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Daniela Cristina Zappi
- Museu Paraense Emilio GoeldiCoord. Botânica/Instituto Tecnológico ValeBelém do ParáBrazil
| | | | - Evandro Marsola Moraes
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| |
Collapse
|
31
|
Shen C, Dupont CL, Hopkinson BM. The diversity of CO2-concentrating mechanisms in marine diatoms as inferred from their genetic content. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3937-3948. [PMID: 28510761 PMCID: PMC5853954 DOI: 10.1093/jxb/erx163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/24/2017] [Indexed: 05/24/2023]
Abstract
Marine diatoms are one of the most ecologically significant primary producers in the ocean. Most diatoms use a CO2-concentrating mechanism (CCM) to overcome the scarcity of CO2 in the ocean and limitations of the carbon-fixing enzyme Rubisco. However, the CCMs in model diatoms differ substantially in their genetic make-up and structural organization. To assess the extent of CCM diversity in marine diatoms more generally, we analyzed genome and transcriptome data from 31 diatom strains to identify putative CCM genes, examine the overall CCM architecture, and study CCM development in the context of the evolutionary history of these diatoms. Key CCM genes [carbonic anhydrases (CAs) and solute carrier 4 (SLC4) bicarbonate transporters] identified in the diatoms were placed into groups of likely orthologs by sequence similarity (OrthoMCL) and phylogenetic methods. These analyses indicated that diatoms seem to share similar HCO3- transporters, but possess a variety of CAs that have either undergone extensive diversification within the diatom lineage or have been acquired through horizontal gene transfer. Hierarchical clustering of the diatom species based on their CCM gene content suggests that CCM development is largely congruent with evolution of diatom species, despite some notable differences in CCM genes even among closely related species.
Collapse
Affiliation(s)
- Chen Shen
- Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, China
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | | | - Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| |
Collapse
|
32
|
Singh G, Dal Grande F, Divakar PK, Otte J, Crespo A, Schmitt I. Fungal-algal association patterns in lichen symbiosis linked to macroclimate. THE NEW PHYTOLOGIST 2017; 214:317-329. [PMID: 27918622 DOI: 10.1111/nph.14366] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Both macroclimate and evolutionary events may influence symbiont association and diversity patterns. Here we assess how climatic factors and evolutionary events shape fungal-algal association patterns in the widely distributed lichen-forming fungal genus Protoparmelia. Multilocus phylogenies of fungal and algal partners were generated using 174 specimens. Coalescent-based species delimitation analysis suggested that 23 fungal hosts are associating with 20 algal species. Principal component analysis (PCA) was performed to infer how fungal-algal association patterns varied with climate. Fungi associated with one to three algal partners whereas algae accepted one to five fungal partners. Both fungi and algae were more specific, associating with fewer partners, in the warmer climates. Interaction with more than one partner was more frequent in cooler climates for both the partners. Cophylogenetic analyses suggest congruent fungal-algal phylogenies. Host switch was a more common event in warm climates, whereas failure of the photobiont to diverge with its fungal host was more frequent in cooler climates. We conclude that both environmental factors and evolutionary events drive fungal and algal evolution in Protoparmelia. The processes leading to phylogenetic congruence of fungi and algae are different in different macrohabitats in our study system. Hence, closely related species inhabiting diverse habitats may follow different evolutionary pathways.
Collapse
Affiliation(s)
- Garima Singh
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Pradeep K Divakar
- Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal, s/n, Ciudad Universitaria, E-28040, Madrid, Spain
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Ana Crespo
- Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal, s/n, Ciudad Universitaria, E-28040, Madrid, Spain
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| |
Collapse
|
33
|
Guillin EA, de Oliveira LO, Grijalba PE, Gottlieb AM. Genetic entanglement between Cercospora species associating soybean purple seed stain. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1289-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
34
|
Neilson J, Lagüe M, Thomson S, Aurousseau F, Murphy AM, Bizimungu B, Deveaux V, Bègue Y, Jacobs JME, Tai HH. Gene expression profiles predictive of cold-induced sweetening in potato. Funct Integr Genomics 2017; 17:459-476. [PMID: 28236275 DOI: 10.1007/s10142-017-0549-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/18/2017] [Accepted: 01/30/2017] [Indexed: 10/24/2022]
Abstract
Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS. A distance matrix for potato clones based on glucose levels after cold storage was constructed and compared to distance matrices constructed using RNA-seq gene expression data. Congruence between glucose and gene expression distance matrices was tested for each gene. Correlation between glucose and gene expression was also tested. Seventy-three genes were found that had significant p values in the congruence and correlation tests. Twelve genes from the list of 73 genes also had a high correlation between glucose and gene expression as measured by Nanostring nCounter. The gene annotations indicated functions in protein degradation, nematode resistance, auxin transport, and gibberellin response. These 12 genes were used to build models for prediction of CIS using multiple linear regression. Nine linear models were constructed that used different combinations of the 12 genes. An F-box protein, cellulose synthase, and a putative Lax auxin transporter gene were most frequently used. The findings of this study demonstrate the utility of gene expression profiles in predictive diagnostics for severity of CIS.
Collapse
Affiliation(s)
- Jonathan Neilson
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
| | - M Lagüe
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - S Thomson
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - F Aurousseau
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - A M Murphy
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - B Bizimungu
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - V Deveaux
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - Y Bègue
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - J M E Jacobs
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - H H Tai
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| |
Collapse
|
35
|
Wang C, Shikano T, Persat H, Merilä J. Phylogeography and historical introgression in smoothtail nine-spined sticklebacks, Pungitius laevis (Gasterosteiformes: Gasterosteidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
36
|
Rosser NL, Thomas L, Stankowski S, Richards ZT, Kennington WJ, Johnson MS. Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora. Proc Biol Sci 2017; 284:20162182. [PMID: 28077772 PMCID: PMC5247495 DOI: 10.1098/rspb.2016.2182] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC, provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.
Collapse
Affiliation(s)
- Natalie L Rosser
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Luke Thomas
- School of Plant Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Zoe T Richards
- Department of Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, Australia
| | - W Jason Kennington
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael S Johnson
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| |
Collapse
|
37
|
Sánchez-García M, Henkel TW, Aime MC, Smith ME, Matheny PB. Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics. Fungal Biol 2016; 120:1540-1553. [PMID: 27890090 DOI: 10.1016/j.funbio.2016.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 11/25/2022]
Abstract
A new genus and three new species of Agaricales are described from the Pakaraima Mountains of Guyana in the central Guiana Shield. All three of these new species fruit on the ground in association with species of the ectomycorrhizal (ECM) tree genus Dicymbe (Fabaceae subfam. Caesalpinioideae) and one species has been shown to form ectomycorrhizas. Multi-locus molecular phylogenetic analyses place Guyanagarika gen. nov. within the Catathelasma clade, a lineage in the suborder Tricholomatineae of the Agaricales. We formally recognize this 'Catathelasma clade' as an expanded family Catathelasmataceae that includes the genera Callistosporium, Catathelasma, Guyanagarika, Macrocybe, Pleurocollybia, and Pseudolaccaria. Within the Catathelasmataceae, Catathelasma and Guyanagarika represent independent origins of the ectomycorrhizal habit. Guyanagarika is the first documented case of an ECM Agaricales genus known only from the Neotropics.
Collapse
Affiliation(s)
- Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, USA
| | - Mary Catherine Aime
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Patrick Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
38
|
Abstract
Many areas of research in ecology and evolutionary biology depend on the quantification of dietary niche width. For herbivorous insects, diet breadth has most often been measured as simply the number and type of host plant taxa attacked. We propose an index of host range (which we refer to as "ordinated diet breadth") based on observed associations between plants and insects, and the calculation of multivariate distances among plants in ordination space. Similarities and distances are calculated based on host association and, in this context, potentially encompass multiple properties of plants, including phytochemistry, phenology, and other plant traits. This approach can distinguish between herbivores that utilize suites of hosts that are commonly used together and herbivores that attack unusual host combinations, and thus have a relatively broad diet breadth. For illustration, we use a data set of nymphalid butterfly host records, and compare taxonomic and ordinated host range. For a large number of butterfly taxa, we find that host use is clustered in multivariate space with respect to associations observed across all of the butterfly taxa. Applications are discussed, including a hypothesis test of nonrandom host association, and prediction of shifts and expansions of diet breadth.
Collapse
|
39
|
Chriki-Adeeb R, Chriki A. Estimating Divergence Times and Substitution Rates in Rhizobia. Evol Bioinform Online 2016; 12:87-97. [PMID: 27168719 PMCID: PMC4856229 DOI: 10.4137/ebo.s39070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/22/2016] [Accepted: 03/26/2016] [Indexed: 11/05/2022] Open
Abstract
Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth-death, birth-death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes.
Collapse
Affiliation(s)
- Rim Chriki-Adeeb
- Département de Biologie, Laboratoire de Génétique, Faculté des Sciences de Bizerte, Jarzouna, Tunisie
| | - Ali Chriki
- Département de Biologie, Laboratoire de Génétique, Faculté des Sciences de Bizerte, Jarzouna, Tunisie
| |
Collapse
|
40
|
Dowie NJ, Grubisha LC, Trowbridge SM, Klooster MR, Miller SL. Variability of ecological and autotrophic host specificity in a mycoheterotrophic system: Pterospora andromedea and associated fungal and conifer hosts. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
41
|
Gohli J, Selvarajah T, Kirkendall LR, Jordal BH. Globally distributed Xyleborus species reveal recurrent intercontinental dispersal in a landscape of ancient worldwide distributions. BMC Evol Biol 2016; 16:37. [PMID: 26877088 PMCID: PMC4753646 DOI: 10.1186/s12862-016-0610-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Invasive species can have devastating effects on native ecosystems and therefore impose a significant threat to human welfare. The introduction rate of invasive species has accelerated dramatically in recent times due to human activity (anthropogenic effects), with a steadily growing pool of widespread tramp species. We present an in-depth analysis of four pantropical species of Xyleborus ambrosia beetles (Xyleborus volvulus, Xyleborus perforans, Xyleborus ferrugineus, and Xyleborus affinis) with similar ecology (fungus cultivation in dead wood), reproductive biology (permanent inbreeding) and genetic system (haplodiploidy). The unique combination of reproductive traits and broad host plant usage pre-adapts these beetles for colonizing of new areas. RESULTS We found that all four species were broadly distributed long before human-assisted dispersal became common, and that the impact of anthropogenic effects varied among the species. For X. volvulus, X. perforans, and X. affinis there was evidence of ancient establishment in numerous regions, but also of abundant recent introductions into previously colonized areas. For X. ferrugineus, we found clear biogeographical structuring of old clades, but little evidence for recent successful introductions. CONCLUSIONS Our results indicate that current human-aided transoceanic dispersal has strongly affected the genetic makeup of three of the species in this study. However, current biogeographical patterns of all four species are equally, if not more strongly, influenced by ancient establishment on different continents.
Collapse
Affiliation(s)
- Jostein Gohli
- Natural History Collections, University Museum of Bergen, University of Bergen, P.O. box 7800, 5020, Bergen, Norway.
| | - Tina Selvarajah
- Department of Biology, University of Bergen, P.O. box 7800, 5020, Bergen, Norway
| | | | - Bjarte H Jordal
- Natural History Collections, University Museum of Bergen, University of Bergen, P.O. box 7800, 5020, Bergen, Norway
| |
Collapse
|
42
|
Fiset J, Tessier N, Millien V, Lapointe FJ. Phylogeographic Structure of the White-Footed Mouse and the Deer Mouse, Two Lyme Disease Reservoir Hosts in Québec. PLoS One 2015; 10:e0144112. [PMID: 26633555 PMCID: PMC4669108 DOI: 10.1371/journal.pone.0144112] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 11/13/2015] [Indexed: 12/01/2022] Open
Abstract
Modification of a species range is one of many consequences of climate change and is driving the emergence of Lyme disease in eastern Canada. The primary reservoir host of the bacteria responsible for Lyme disease, Borrelia burgdorferi, is the white-footed mouse (Peromyscus leucopus), whose range is rapidly shifting north into southern Québec. The deer mouse, P. maniculatus, is occurring over most Québec province and is a less competent host for B. burgdorferi. Here, we compared the phylogeographic structure of both Peromyscus species in Québec. Using a combination of multiple mitochondrial DNA markers and phylogeographic methods, we detected an ongoing and rapid expansion of P. leucopus, while P. maniculatus appears more stable. Haplotype and populations networks indicated that populations of P. maniculatus exhibit more genetic structure than P. leucopus across the study area. Furthermore, significant and consistent genetic divergences between populations of the two species on both sides of the St. Lawrence River suggest that distinct lineages of P. leucopus and P. maniculatus with different ancestral origins colonized Southern Québec following the Last Glacial Maximum. The phylogeographic structure of pathogens is expected to mirror the structure observed in their reservoir hosts. As different strains of Borrelia burgdorferi may be associated with different levels of pathogenicity and immune responses of their hosts, our results are helpful at better understanding the pattern of spread of Lyme disease in a zone of emergence, and associated risk for human populations.
Collapse
Affiliation(s)
- Jessica Fiset
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Nathalie Tessier
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
- Ministère des Forêts, de la Faune et des Parcs, Longueuil, Québec, Canada
| | - Virginie Millien
- Redpath Museum, McGill University, Montréal, Québec, Canada
- * E-mail:
| | | |
Collapse
|
43
|
Carvalho JC, Cardoso P, Rigal F, Triantis KA, Borges PAV. Modeling directional spatio-temporal processes in island biogeography. Ecol Evol 2015; 5:4671-82. [PMID: 26668731 PMCID: PMC4670066 DOI: 10.1002/ece3.1632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/28/2015] [Accepted: 07/09/2015] [Indexed: 12/02/2022] Open
Abstract
A key challenge in island biogeography is to quantity the role of dispersal in shaping biodiversity patterns among the islands of a given archipelago. Here, we propose such a framework. Dispersal within oceanic archipelagos may be conceptualized as a spatio‐temporal process dependent on: (1) the spatial distribution of islands, because the probability of successful dispersal is inversely related to the spatial distance between islands and (2) the chronological sequence of island formation that determines the directional asymmetry of dispersal (hypothesized to be predominantly from older to younger islands). From these premises, directional network models may be constructed, representing putative connections among islands. These models may be translated to eigenfunctions in order to be incorporated into statistical analysis. The framework was tested with 12 datasets from the Hawaii, Azores, and Canaries. The explanatory power of directional network models for explaining species composition patterns, assessed by the Jaccard dissimilarity index, was compared with simpler time‐isolation models. The amount of variation explained by the network models ranged from 5.5% (for Coleoptera in Hawaii) to 60.2% (for Pteridophytes in Canary Islands). In relation to the four studied taxa, the variation explained by network models was higher for Pteridophytes in the three archipelagos. By the contrary, small fractions of explained variation were observed for Coleoptera (5.5%) and Araneae (8.6%) in Hawaii. Time‐isolation models were, in general, not statistical significant and explained less variation than the equivalent directional network models for all the datasets. Directional network models provide a way for evaluating the spatio‐temporal signature of species dispersal. The method allows building scenarios against which hypotheses about dispersal within archipelagos may be tested. The new framework may help to uncover the pathways via which species have colonized the islands of a given archipelago and to understand the origins of insular biodiversity.
Collapse
Affiliation(s)
- José C Carvalho
- CE3C - Centre for Ecology Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias 9700-042 Angra do Heroísmo Açores Portugal ; Department of Biology CBMA - Centre for Molecular and Environmental Biology University of Minho 4710-087 Braga Portugal
| | - Pedro Cardoso
- CE3C - Centre for Ecology Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias 9700-042 Angra do Heroísmo Açores Portugal ; Finnish Museum of Natural History University of Helsinki P.O. Box 17, 00014 Helsinki Finland
| | - François Rigal
- CE3C - Centre for Ecology Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias 9700-042 Angra do Heroísmo Açores Portugal
| | - Kostas A Triantis
- CE3C - Centre for Ecology Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias 9700-042 Angra do Heroísmo Açores Portugal ; Department of Ecology and Taxonomy Faculty of Biology National and Kapodistrian University Athens GR-15784 Greece ; Conservation Biogeography and Macroecology Programme School of Geography and the Environment University of Oxford, South Parks Road Oxford OX1 3QY UK
| | - Paulo A V Borges
- CE3C - Centre for Ecology Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias 9700-042 Angra do Heroísmo Açores Portugal
| |
Collapse
|
44
|
Molecular Phylogenetic Analysis of Ballistoconidium-Forming Yeasts in Trichosporonales (Tremellomycetes): A Proposal for Takashimella gen. nov. and Cryptotrichosporon tibetense sp. nov. PLoS One 2015. [PMID: 26200459 PMCID: PMC4511645 DOI: 10.1371/journal.pone.0132653] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bullera species in the Trichosporonales (Tremellomycetes, Agaricomycotina) are phylogenetically distinct from Bullera alba (teleomorph: Bulleromyces albus), the type species of Bullera that belongs to Tremellales. In the present study, the three Bullera species, namely Bullera formosensis, Bullera koratensis and Bullera lagerstroemiae, and Cryptococcus tepidarius belonging to the Trichosporonales are transferred into a new genus Takashimella gen. nov. (MycoBank No. MB 810672) based on sequence analysis of the small subunit (SSU) rRNA gene, the D1/D2 domains of large subunit (LSU) rRNA gene and the ITS+5.8S rRNA gene sequences. In addition, the genus Cryptotrichosporon is emended to accommodate a novel ballistoconidium-forming species of the Trichosporonales, which is named as Cryptotrichosporon tibetense (type strain CGMCC 2.02614T = CBS 10455T). The MycoBank number of this new species is MB 810688.
Collapse
|
45
|
Sundaram M, Willoughby JR, Lichti NI, Steele MA, Swihart RK. Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions. PLoS One 2015; 10:e0130942. [PMID: 26110828 PMCID: PMC4482146 DOI: 10.1371/journal.pone.0130942] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27–73%), and combined effects of seed traits and phylogeny of hardwood trees (5–55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 “global” axes of traits that were phylogenetically autocorrelated at the family and genus level and a third “local” axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30–76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.
Collapse
Affiliation(s)
- Mekala Sundaram
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
| | - Janna R. Willoughby
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Nathanael I. Lichti
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Michael A. Steele
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Robert K. Swihart
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| |
Collapse
|
46
|
Boyle EE, Adamowicz SJ. Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes. PLoS One 2015; 10:e0126662. [PMID: 26110886 PMCID: PMC4481530 DOI: 10.1371/journal.pone.0126662] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/04/2015] [Indexed: 12/02/2022] Open
Abstract
Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.
Collapse
Affiliation(s)
- Elizabeth E. Boyle
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, Ontario, N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, Ontario, N1G 2W1, Canada
- * E-mail:
| |
Collapse
|
47
|
Hendrickx F, Backeljau T, Dekoninck W, Van Belleghem SM, Vandomme V, Vangestel C. Persistent inter- and intraspecific gene exchange within a parallel radiation of caterpillar hunter beetles (Calosomasp.) from the Galápagos. Mol Ecol 2015; 24:3107-21. [DOI: 10.1111/mec.13233] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - Wouter Dekoninck
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
| | - Steven M. Van Belleghem
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Viki Vandomme
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| |
Collapse
|
48
|
Núñez-Zapata J, Cubas P, Hawksworth DL, Crespo A. Biogeography and Genetic Structure in Populations of a Widespread Lichen (Parmelina tiliacea, Parmeliaceae, Ascomycota). PLoS One 2015; 10:e0126981. [PMID: 25961726 PMCID: PMC4427293 DOI: 10.1371/journal.pone.0126981] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/09/2015] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity and population structure of the foliose lichenized fungus Parmelina tiliacea has been analyzed through its geographical range, including samples from Macaronesia (Canary Islands), the Mediterranean, and Eurosiberia. DNA sequences from the nuclear ribosomal internal transcribed spacer, the mitochondrial large subunit ribosomal RNA gene, and the translation elongation factor 1-α were used as molecular markers. The haplotypes of the three markers and the molecular variance analyses of multilocus haplotypes showed the highest diversity in the Canary Islands, while restricted haplotypes occurred at high frequencies in Mediterranean coastal samples. The multilocus haplotypes formed three unevenly distributed clusters (clusters 1-3). In the Canary Islands all the haplotypes were present in a similar proportion, while the coastal Mediterranean sites had almost exclusively haplotypes of cluster 3; cluster 2 predominated in inland Mediterranean sites; and cluster 1 was more abundant in central and northern Europe (Eurosiberian area). The distribution of clusters is partially explained by climatic factors, and its interaction with local spatial structure, but much of the variation remains unexplained. The high frequency of individuals in the Canary Islands with haplotypes shared with other areas suggests that could be a refugium of genetic diversity, and the high frequency of individuals of the Mediterranean coastal sites with restricted haplotypes indicates that gene flow to contiguous areas may be restricted. This is significant for the selection of areas for conservation purposes, as those with most genetic variation may reflect historical factors and biological properties of the species.
Collapse
Affiliation(s)
- Jano Núñez-Zapata
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
- * E-mail:
| | - David L. Hawksworth
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
49
|
Singh G, Dal Grande F, Divakar PK, Otte J, Leavitt SD, Szczepanska K, Crespo A, Rico VJ, Aptroot A, Cáceres MEDS, Lumbsch HT, Schmitt I. Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota). PLoS One 2015; 10:e0124625. [PMID: 25932996 PMCID: PMC4416777 DOI: 10.1371/journal.pone.0124625] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
Collapse
Affiliation(s)
- Garima Singh
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Grüneburgplatz 1, 60323, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- * E-mail: (GS); (IS)
| | - Francesco Dal Grande
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - Jürgen Otte
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Steven D. Leavitt
- Science & Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, United States of America
| | - Katarzyna Szczepanska
- Department of Botany and Plant Ecology, Wroclaw University of Environmental and Life Sciences, pl. Grunwaldzki 24a, 50-363, Wroclaw, Poland
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - Víctor J. Rico
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Plaza de Ramon y Cajal s/n, E-28040, Madrid, Spain
| | - André Aptroot
- Advice Bureau for Bryology and Lichenology Herbarium, Soest, The Netherlands
| | | | - H. Thorsten Lumbsch
- Science & Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, United States of America
| | - Imke Schmitt
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität, Grüneburgplatz 1, 60323, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- * E-mail: (GS); (IS)
| |
Collapse
|
50
|
Tambong JT, Xu R, Kaneza CA, Nshogozabahizi JC. An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea. Evol Bioinform Online 2014; 10:115-25. [PMID: 25125967 PMCID: PMC4125426 DOI: 10.4137/ebo.s15738] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/15/2014] [Accepted: 05/20/2014] [Indexed: 01/14/2023] Open
Abstract
Partial sequences of six core genes (fusA, gyrB, leuS, pyrG, rlpB, and rpoB) of 37 strains of Pantoea species were analyzed in order to obtain a comprehensive view regarding the phylogenetic relationships within the Pantoea genus and compare tree topologies to identify gene(s) for reliable species and subspecies differentiation. All genes used in this study were effective at species-level delineation, but the internal nodes represented conflicting common ancestors in fusA- and pyrG-based phylogenies. Concatenated gene phylogeny gave the expected DNA relatedness, underscoring the significance of a multilocus sequence analysis. Pairwise comparison of topological distances and percent similarities indicated a significant differential influence of individual genes on the concatenated tree topology. leuS- and fusA-inferred phylogenies exhibited, respectively, the lowest (4) and highest (52) topological distances to the concatenated tree. These correlated well with high (96.3%) and low (64.4%) percent similarities of leuS- and fusA-inferred tree topologies to the concatenated tree, respectively. We conclude that the concatenated tree topology is strongly influenced by the gene with the highest number of polymorphic and non-synonymous sites in the absence of significant recombination events.
Collapse
Affiliation(s)
- James T Tambong
- Laboratory of Bacteriology, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada
| | - Renlin Xu
- Laboratory of Bacteriology, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada
| | - Cynthia-Anne Kaneza
- Laboratory of Bacteriology, Agriculture and Agri-Food Canada, Ottawa, Ontario Canada
| | | |
Collapse
|