1
|
Li S, Zhu Y, Xu Z, Chen L, Wang W, Cheng Z. The phylogeny and divergence time of Ophiocordyceps sinensis and its host insects based on elongation factor 1 alpha. Arch Microbiol 2023; 205:98. [PMID: 36853446 DOI: 10.1007/s00203-023-03444-9] [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: 06/09/2022] [Revised: 09/18/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
Ophiocordyceps sinensis Berk. is a fungal parasite that parasitizes the larvae of Hepialidae and is endemic to the Qinghai-Tibet Plateau (QTP). The phylogeny and divergence time of O. sinensis and its host insects were analyzed for 137 individuals from 48 O. sinensis populations based on the elongation factor 1 alpha (EF-1α) gene. Lower nucleotide variation, with only 7 and 16 EF-1α haplotypes, was detected in O. sinensis and its host insects, respectively. The isolated and broad distribution patterns coexisted in both O. sinensis and its host insects on the QTP. The divergence time estimates show that O. sinensis and its host insects originated later than 14.33 million years (Myr) and earlier than 23.60 Myr in the Miocene period, and the major differentiation occurred later than 4 Myr. Their origin and differentiation match well with the second and third uplifts of the QTP, respectively. The host insects from the O. sinensis populations distributed around Qinghai Lake are inferred as an ancient and relict species that has survived various geological events of the QTP. It is suitable to estimate the divergence times of both O. sinensis and its host insects from the same individuals using one gene: EF-1α. Our findings of the origin, phylogeny, and evolution of the endemic species also support the epoch of geological events on the QTP.
Collapse
Affiliation(s)
- Shan Li
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Yunguo Zhu
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Zixian Xu
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Lingling Chen
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Wenqian Wang
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Zhou Cheng
- School of Life Science and Technology, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China.
| |
Collapse
|
2
|
Eberle J, Dimitrov D, Valdez-Mondragón A, Huber BA. Microhabitat change drives diversification in pholcid spiders. BMC Evol Biol 2018; 18:141. [PMID: 30231864 PMCID: PMC6145181 DOI: 10.1186/s12862-018-1244-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/16/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera. RESULTS Assessments of ancestral microhabitat revealed frequent evolutionary change. In particular, within the largest subfamily Pholcinae, numerous changes from near-ground habitats towards leaves and back were found. In general, taxa occupying leaves and large sheltered spaces had higher diversification rates than ground-dwelling taxa. Shifts in speciation rate were found in leaf- and space-dwelling taxa. CONCLUSIONS Our analyses result in one of the most comprehensive phylogenies available for a major spider family and provide a framework for any subsequent studies of pholcid spider biology. Diversification analyses strongly suggest that microhabitat is an important factor influencing diversification patterns in pholcid spiders.
Collapse
Affiliation(s)
- Jonas Eberle
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
| | - Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
- Department of Natural History, University Museum of Bergen, University of Bergen, PO Box 7800, NO-5020 Bergen, Norway
| | - Alejandro Valdez-Mondragón
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
- Instituto de Biologia UNAM, sede Tlaxcala. Contiguo FES-Zaragoza Campus III, Ex Fábrica San Manuel de Morcom s/n, San Miguel Contla, Municipio de Santa Cruz Tlaxcala, C.P, 90640 Tlaxcala, Mexico
| | - Bernhard A. Huber
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
| |
Collapse
|
3
|
Ebrahimi S, Bordbar A, Parvizi P. Genetic dynamics in the sand fly (Diptera: Psychodidae) nuclear and mitochondrial genotypes: evidence for vector adaptation at the border of Iran with Iraq. Parasit Vectors 2016; 9:319. [PMID: 27260204 PMCID: PMC4893242 DOI: 10.1186/s13071-016-1603-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/23/2016] [Indexed: 11/30/2022] Open
Abstract
Background Our investigation uses nucleotide variations of the genera Phlebotomus and Sergentomyia using the EF-1α and Cyt b genotype regions to describe the sand fly fauna and genetic aspects collected at war-torn sites of the Khuzestan boundary between Iraq and Iran. Methods All sand fly species were characterized using molecular genetics. The field work was conducted in six districts including 24 locations in remote areas for three years at the peak of sand fly activity during cutaneous leishmaniasis (CL) transmission seasons. The distribution of CL vectors was determined based on the climatic regionalization using the kriging method in ArcGIS model. DNA of sand fly pools were screened via polymerase chain reaction (PCR) using neutrality (Tajima’s D) and neutral allele frequency (Fu’s Fs) tests to measure the effect of randomly evolving DNA sequence on the genetic diversity of sand fly populations in response to habitat fragmentation and landscape modification. Results Among the 1213 specimens, ten species were identified based on morphology. The non-native species Phlebotomus sergenti was unequivocally found for the first time in the studied regions. Nucleotide substitutions of sand fly sequences varied most in the most disrupted districts (Dashte-Azadegan and Abadan; disparity index test: P < 0.05). The haplotypes of Cyt b from the subgenus Sergentomyia and P. papatasi revealed more heterogeneity (Tajima’s D > +2) than P. alexandri (D > +1), which suggests widespread heteroplasmic mitochondrial DNA mutations in the same mtDNA gene among different sand fly species. Subgenus Sintonius exhibited greater fitness (D = 0) and (neutrality test; P > 0.05) no evidence of selection. The sequence of the nuclear gene EF-1α indicated similar nucleotide differences, as observed for the Cyt b gene, in all sand fly species, but lower levels of polymorphisms (D > +1) were observed compared with the mitochondrial Cyt b gene (D > +2) in the subgenus Sergentomyia. Conclusion Our findings describe random nucleotide diversity in the Phlebotomus and Sergentomyia population gene pools due to recent anthropogenic influence. A phylogenetic analysis showed that the closely related species are positioned in monophyletic clades, except for the subgenus Sergentomyia and P. sergenti, and highlights the importance of haplotype variations for the development of adaptability.
Collapse
Affiliation(s)
- Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ali Bordbar
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran. .,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
4
|
Daniels SR, Dambire C, Klaus S, Sharma PP. Unmasking alpha diversity, cladogenesis and biogeographical patterning in an ancient panarthropod lineage (Onychophora: Peripatopsidae:Opisthopatus cinctipes) with the description of five novel species. Cladistics 2016; 32:506-537. [DOI: 10.1111/cla.12154] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 12/15/2022] Open
Affiliation(s)
- Savel R. Daniels
- Department of Botany and Zoology; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - Charlene Dambire
- Department of Botany and Zoology; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| | - Sebastian Klaus
- Department of Ecology and Evolution; J. W. Goethe-University; Biologicum D-60435 Frankfurt am Main Germany
| | - Prashant P. Sharma
- Department of Zoology; University of Wisconsin-Madison; Madison WI 53706 USA
| |
Collapse
|
5
|
Richart CH, Hayashi CY, Hedin M. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Mol Phylogenet Evol 2015; 95:171-82. [PMID: 26691642 DOI: 10.1016/j.ympev.2015.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/16/2015] [Accepted: 11/13/2015] [Indexed: 11/19/2022]
Abstract
Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.
Collapse
Affiliation(s)
- Casey H Richart
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA; Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| |
Collapse
|
6
|
Abstract
Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group's biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.
Collapse
Affiliation(s)
- Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138;
| | | |
Collapse
|
7
|
Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, Giribet G. Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal. Mol Biol Evol 2014; 31:2963-84. [DOI: 10.1093/molbev/msu235] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
8
|
Groh SS, Giribet G. Polyphyly of
C
addoidea, reinstatement of the family
A
cropsopilionidae in
D
yspnoi, and a revised classification system of
P
alpatores (
A
rachnida,
O
piliones). Cladistics 2014; 31:277-290. [DOI: 10.1111/cla.12087] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2014] [Indexed: 12/01/2022] Open
Affiliation(s)
- Sebastian S. Groh
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University 26 Oxford Street Cambridge MA 02138USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University 26 Oxford Street Cambridge MA 02138USA
| |
Collapse
|
9
|
Riesgo A, Andrade SCS, Sharma PP, Novo M, Pérez-Porro AR, Vahtera V, González VL, Kawauchi GY, Giribet G. Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Front Zool 2012; 9:33. [PMID: 23190771 PMCID: PMC3538665 DOI: 10.1186/1742-9994-9-33] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/08/2012] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED INTRODUCTION Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa. RESULTS cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature. CONCLUSIONS We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry.
Collapse
Affiliation(s)
- Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Centro de Estudios Avanzados de Blanes, CSIC, c/ Accés a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain
| | - Sónia C S Andrade
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Prashant P Sharma
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Marta Novo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Current address: Cardiff School of Biosciences, Cardiff University, BIOSI 1, Museum Avenue, Cardiff, CF10 3TL, UK
| | - Alicia R Pérez-Porro
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Centro de Estudios Avanzados de Blanes, CSIC, c/ Accés a la Cala St. Francesc 14, Blanes, Girona, 17300, Spain
| | - Varpu Vahtera
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Current address: Finnish Museum of Natural History, Zoology Unit, Pohjoinen Rautatiekatu 13, 00014 University of Helsinki, Helsinki, Finland
| | - Vanessa L González
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gisele Y Kawauchi
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| |
Collapse
|