Xenopus fraseri: Mr. Fraser, where did your frog come from?
Autoři:
Ben J. Evans aff001; Marie-Theres Gansauge aff002; Edward L. Stanley aff003; Benjamin L. S. Furman aff001; Caroline M. S. Cauret aff001; Caleb Ofori-Boateng aff005; Václav Gvoždík aff006; Jeffrey W. Streicher aff008; Eli Greenbaum aff009; Richard C. Tinsley aff010; Matthias Meyer aff002; David C. Blackburn aff003
Působiště autorů:
Department of Biology, McMaster University, Hamilton, ON, Canada
aff001; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
aff002; Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
aff003; Department of Zoology, Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
aff004; Forestry Research Institute of Ghana, Kumasi, Ghana
aff005; Institute of Vertebrate Biology of the Czech Academy of Sciences, Czech Republic
aff006; Department of Zoology, National Museum, Prague, Czech Republic
aff007; Department of Life Sciences, The Natural History Museum, London, United Kingdom
aff008; Department of Biological Sciences, University of Texas at El Paso, El Paso, United States of America
aff009; School of Biological Sciences, University of Bristol, Bristol, United Kingdom
aff010
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0220892
Souhrn
A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these challenges. To illustrate this, we used modern approaches to tackle a centuries-old taxonomic enigma presented by Fraser’s Clawed Frog, Xenopus fraseri, including whether X. fraseri is different from other species, and if so, where it is situated geographically and phylogenetically. To facilitate these inferences, we used high-resolution techniques to examine morphological variation, and we generated and analyzed complete mitochondrial genome sequences from all Xenopus species, including >150-year-old type specimens. Our results demonstrate that X. fraseri is indeed distinct from other species, firmly place this species within a phylogenetic context, and identify its minimal geographic distribution in northern Ghana and northern Cameroon. These data also permit novel phylogenetic resolution into this intensively studied and biomedically important group. Xenopus fraseri was formerly thought to be a rainforest endemic placed alongside species in the amieti species group; in fact this species occurs in arid habitat on the borderlands of the Sahel, and is the smallest member of the muelleri species group. This study illustrates that the taxonomic enigma of Fraser’s frog was a combined consequence of sparse collection records, interspecies conservation and intraspecific polymorphism in external anatomy, and type specimens with unusual morphology.
Klíčová slova:
Biology and life sciences – Biochemistry – Bioenergetics – Energy-producing organelles – Mitochondria – Nucleic acids – Forms of DNA – Mitochondrial DNA – Cell biology – Cellular structures and organelles – Organisms – Eukaryota – Animals – Vertebrates – Amphibians – Frogs – Xenopus – Genetics – DNA – Genomics – Animal genomics – Amphibian genomics – Genome analysis – Population genetics – Phylogeography – Biogeography – Evolutionary biology – Evolutionary systematics – Phylogenetics – Phylogenetic analysis – Population biology – Taxonomy – Computational biology – Research and analysis methods – Animal studies – Experimental organism systems – Model organisms – Animal models – Database and informatics methods – Bioinformatics – Sequence analysis – DNA sequence analysis – Ecology and environmental sciences – Earth sciences – Geography – Computer and information sciences – Data management
Zdroje
1. Boulenger GA. On a collection of batrachians and reptiles made in South Africa by Mr. C. H. B. Grant, and presented to the British Museum by Mr. C. D. Rudd. Proceedings of the Zoological Society of London. 1905;1905:248–55.
2. Evans BJ, Carter TF, Greenbaum E, Gvoždík V, Kelley DB, McLaughlin PJ, et al. Genetics, morphology, adverstisement calls, and historical records distinguish six new polyploid species of African clawed frog (Xenopus, Pipidae) from West and Central Africa. PLoS One. 2015;10(12):e0142823. doi: 10.1371/journal.pone.0142823 26672747
3. Kobel HR, Loumont C, Tinsley RC. The extant species. In: Tinsley RC, Kobel HR, editors. The Biology of Xenopus. Oxford: Clarendon Press; 1996. p. 9–33.
4. Conlon JM, Mechkarska M, Kolodziejek J, Nowotny N, Coquet L, Leprince J, et al. Host-defense peptides from skin secretions of Fraser's clawed frog Xenopus fraseri (Pipidae): Further insight into the evolutionary history of the Xenopodinae. Comparative Biochemistry and Physiology, Part D Genomics Proteomics. 2014;12:45–52. doi: 10.1016/j.cbd.2014.10.001 25463057
5. Evans BJ. Genome evolution and speciation genetics of allopolyploid clawed frogs (Xenopus and Silurana). Front Biosci. 2008;13:4687–706. 18508539
6. Evans BJ, Carter TF, Hanner R, Tobias ML, Kelley DB, Hanner R, et al. A new species of clawed frog (genus Xenopus), from the Itombwe Plateau, Democratic Republic of the Congo: Implications for DNA barcodes and biodiversity conservation. Zootaxa. 2008;1780:55–68.
7. Evans BJ, Greenbaum E, Kusamba C, Carter TF, Tobias ML, Mendel SA, et al. Description of a new octoploid frog species (Anura: Pipidae: Xenopus) from the Democratic Republic of the Congo, with a discussion of the biogeography of African clawed frogs in the Albertine Rift. J Zool, Lond. 2011;283:276–90.
8. Evans BJ, Kelley DB, Tinsley RC, Melnick DJ, Cannatella DC. A mitochondrial DNA phylogeny of clawed frogs: Phylogeography on sub-Saharan Africa and implications for polyploid evolution. Mol Phylogenet Evol. 2004;33:197–213. 15324848
9. Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016;538(7625):336–43. doi: 10.1038/nature19840 27762356; PubMed Central PMCID: PMC5313049.
10. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kaptonov V, et al. The genome of the western clawed frog Xenopus tropicalis. Science. 2010;328:633–6. doi: 10.1126/science.1183670 20431018
11. Tandon P, Conlon F, Furlow JD, Horb ME. Expanding the genetic toolkit in Xenopus: Approaches and opportunities for human disease modeling. Dev Biol. 2016;426(2):325–35. doi: 10.1016/j.ydbio.2016.04.009 27109192.
12. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–52. doi: 10.1038/nbt.1883 21572440; PubMed Central PMCID: PMC3571712.
13. Katoh K, Standley SM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. MBE. 2013;30:772–80.
14. Minh BQ, Nguyen MA, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 2013;30(5):1188–95. doi: 10.1093/molbev/mst024 23418397; PubMed Central PMCID: PMC3670741.
15. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74. doi: 10.1093/molbev/msu300 25371430; PubMed Central PMCID: PMC4271533.
16. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. MBE. 2012;29:1969–73.
17. Feng YJ, Blackburn DC, Liang D, Hillis DM, Wake DB, Cannatella DC, et al. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary. PNAS. 2017;114(29):E5864–E70. doi: 10.1073/pnas.1704632114 28673970; PubMed Central PMCID: PMC5530686.
18. Rambaut A, Drummond AJ. Tracer v1.5, Available from http://beast.bio.ed.ac.uk/Tracer. 2007.
19. Haramoto Y, Oshima T, Takahashi S, Asashima M, Ito Y, Kurabayashi A. Complete mitochondrial genome of “Xenopus tropicalis” Asashima line (Anura: Pipidae), a possible undescribed species. Mitochondrial DNA. 2016;6(27):3341–3.
20. Evans BJ, Cannatella DC, Melnick DJ. Understanding the origins of areas of endemism in phylogeographic analyses: a reply to Bridle et al. Evolution. 2004;58(6):1397–400.
21. Evans BJ, Kelley DB, Melnick DJ, Cannatella DC. Evolution of RAG-1 in polyploid clawed frogs. MBE. 2005;22(5):1193–207.
22. Irwin DE. Phylogeographic breaks without geographic barriers to gene flow. Evolution. 2002;56(12):2383–94. 12583579
23. Furman BL, Bewick AJ, Harrison TL, Greenbaum E, Gvozdik V, Kusamba C, et al. Pan-African phylogeography of a model organism, the African clawed frog 'Xenopus laevis'. Mol Ecol. 2015;24(4):909–25. doi: 10.1111/mec.13076 25583226.
24. Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winkley K, et al. Cryptic species as a window on diversity and conservation. TREE. 2006;22(3):148–55. 17129636
25. Furman BLS, Evans BJ. Sequential turnovers of sex chromosomes in African clawed frogs (Xenopus) suggest some genomic regions are good at sex determination. G3. 2016;6:3625–33. doi: 10.1534/g3.116.033423 27605520
26. Yoshimoto S, Okada E, Umemoto H, Tamura K, Uno Y, Nishida-Umehara C, et al. A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis. PNAS. 2008;105(7):2469–74. doi: 10.1073/pnas.0712244105 18268317
27. Bewick AJ, Anderson DW, Evans BJ. Evolution of the closely related, sex-related genes DM-W and DMRT1 in African clawed frogs (Xenopus). Evolution. 2011;65(3):698–712. doi: 10.1111/j.1558-5646.2010.01163.x 21044062
28. Tinsley RC, Loumont C, Kobel HR. Geographical distribution and ecology. In: Tinsley RC, Kobel HR, editors. The Biology of Xenopus. Oxford: Clarendon Press; 1996. p. 35–59.
Článek vyšel v časopise
PLOS One
2019 Číslo 9
- S diagnostikou Parkinsonovy nemoci může nově pomoci AI nástroj pro hodnocení mrkacího reflexu
- Je libo čepici místo mozkového implantátu?
- Pomůže v budoucnu s triáží na pohotovostech umělá inteligence?
- AI může chirurgům poskytnout cenná data i zpětnou vazbu v reálném čase
- Nová metoda odlišení nádorové tkáně může zpřesnit resekci glioblastomů
Nejčtenější v tomto čísle
- Graviola (Annona muricata) attenuates behavioural alterations and testicular oxidative stress induced by streptozotocin in diabetic rats
- CH(II), a cerebroprotein hydrolysate, exhibits potential neuro-protective effect on Alzheimer’s disease
- Comparison between Aptima Assays (Hologic) and the Allplex STI Essential Assay (Seegene) for the diagnosis of Sexually transmitted infections
- Assessment of glucose-6-phosphate dehydrogenase activity using CareStart G6PD rapid diagnostic test and associated genetic variants in Plasmodium vivax malaria endemic setting in Mauritania
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy