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Lyra ML, Kirchhof S, Goutte S, Kassie A, Boissinot S. Crossing the Rift valley: using complete mitogenomes to infer the diversification and biogeographic history of ethiopian highlands Ptychadena (anura: Ptychadenidae). Front Genet 2023; 14:1215715. [PMID: 37600664 PMCID: PMC10434514 DOI: 10.3389/fgene.2023.1215715] [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: 05/02/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
The Ethiopian Highlands are considered a biodiversity hotspot, harboring a high number of endemic species. Some of the endemic species probably diversified in situ; this is, for example, the case of a monophyletic clade containing 12 known species of grass frogs of the genus Ptychadena. The different species occur at elevations ranging from 1,500 to above 3,400 m and constitute excellent models to study the process of diversification in the highlands as well as adaptations to high elevations. In this study, we sampled 294 specimens across the distribution of this clade and used complete mitogenomes and genome-wide SNP data to better understand how landscape features influenced the population structure and dispersal of these grass frogs across time and space. Using phylogenetic inference, population structure analyses, and biogeographic reconstructions, we found that the species complex probably first diversified on the south-east side of the Great Rift Valley. Later on, species dispersed to the north-west side, where more recent diversification occurred. We further demonstrate that Ptychadena species have dispersed across the Great Rift Valley at different times. Our analyses allowed for a more complete understanding of the contribution of geological events, biogeographic barriers and climatic changes as drivers of species diversification and adaptation in this important biogeographic region.
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Affiliation(s)
- M. L. Lyra
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - S. Kirchhof
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - S. Goutte
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - A. Kassie
- Animal Biodiversity Directorate, Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia
- Department of Zoological Sciences, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - S. Boissinot
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Kassie Teme A, Bekele Simegn A, Afework Bogale B. Species composition and distribution of endemic frog species of Keffa, southwest Ethiopia. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Reyes-Velasco J, Goutte* S, Freilich X, Boissinot S. Mitogenomics of historical type specimens clarifies the taxonomy of Ethiopian Ptychadena Boulenger, 1917 (Anura, Ptychadenidae). Zookeys 2021; 1070:135-149. [PMID: 34819775 PMCID: PMC8604866 DOI: 10.3897/zookeys.1070.66598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 09/07/2021] [Indexed: 11/12/2022] Open
Abstract
The taxonomy of the Ptychadenaneumanni species complex, a radiation of grass frogs inhabiting the Ethiopian highlands, has puzzled scientists for decades because of the morphological resemblance among its members. Whilst molecular phylogenetic methods allowed the discovery of several species in recent years, assigning pre-existing and new names to clades was challenged by the unavailability of molecular data for century-old type specimens. We used Illumina short reads to sequence the mitochondrial DNA of type specimens in this group, as well as ddRAD-seq analyses to resolve taxonomic uncertainties surrounding the P.neumanni species complex. The phylogenetic reconstruction revealed recurrent confusion between Ptychadenaerlangeri (Ahl, 1924) and P.neumanni (Ahl, 1924) in the literature. The phylogeny also established that P.largeni Perret, 1994 represents a junior synonym of P.erlangeri (Ahl, 1924) and distinguished between two small species, P.nana Perret, 1994, restricted to the Arussi Plateau, and P.robeensis Goutte, Reyes-Velasco, Freilich, Kassie & Boissinot, 2021, which inhabits the Bale Mountains. The phylogenetic analyses of mitochondrial DNA from type specimens also corroborate the validity of seven recently described species within the group. Our study shows how modern molecular tools applied to historical type specimens can help resolve long-standing taxonomic issues in cryptic species complexes.
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Affiliation(s)
- Jacobo Reyes-Velasco
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAENew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Sandra Goutte*
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAENew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Xenia Freilich
- Department of Biology, Queens College, City University of New York, Flushing, NY, USACity University of New YorkFlushingUnited States of America
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAENew York University Abu DhabiAbu DhabiUnited Arab Emirates
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Box EK, Cleveland CA, Subramaniam K, Waltzek TB, Yabsley MJ. Molecular Confirmation of Ranavirus Infection in Amphibians From Chad, Africa. Front Vet Sci 2021; 8:733939. [PMID: 34604370 PMCID: PMC8481899 DOI: 10.3389/fvets.2021.733939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/16/2021] [Indexed: 11/22/2022] Open
Abstract
Ranaviruses are DNA viruses (Family Iridoviridae; Subfamily Alphairidovirinae) and ranaviral disease is considered an emerging infectious disease of ectothermic vertebrates. Ranavirus infection can have varying pathological effects on infected amphibians, reptiles, and fish, most notably causing significant mortality events and population declines. Despite having a broad global range with reports from six continents, only a single incidental finding in Xenopus longipes from mainland Africa (Cameroon) is known and lacks molecular confirmation. Thus, there is a considerable knowledge gap concerning ranaviruses in Africa. We opportunistically obtained tissue samples from 160 amphibians representing five genera (Hoplobatrachus, Hylarana, Ptychadena, Pyxicephalus, and Xenopus) and two turtles (Pelomedusa sp.) from Chad, Africa. Samples were tested for ranavirus infection using a conventional PCR assay targeting the major capsid protein (MCP). A total of 25/160 (16%) frogs tested positive including 15/87 (17%) Hoplobatrachus occipitalis, 10/58 (17%) Ptychadena spp., 0/3 Pyxicephalus spp., 0/9 Xenopus spp., and 0/3 Hylarana spp. One of two turtles tested positive. Partial MCP gene sequences indicated all samples were >98% similar to several frog virus 3 (FV3)-like sequences. Additional gene targets (DNA polymerase [DNApol], ribonucleotide reductase alpha [RNR- α], ribonucleotide reductase beta subunit [RNR- β]) were sequenced to provide further detailed classification of the virus. Sequences of individual gene targets indicate that the ranavirus detected in frogs in Chad is most similar to tiger frog virus (TFV), a FV3-like virus previously isolated from diseased amphibians cultured in China and Thailand. Full genome sequencing of one sample indicates that the Chad frog virus (CFV) is a well-supported sister group to the TFVs previously determined from Asia. This work represents the first molecular confirmation of ranaviruses from Africa and is a first step in comparing ranavirus phylogeography on a local and global scale.
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Affiliation(s)
- Erin K Box
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Christopher A Cleveland
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Michael J Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
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Goutte S, Reyes-Velasco J, Freilich X, Kassie A, Boissinot S. Taxonomic revision of grass frogs (Ptychadenidae, Ptychadena) endemic to the Ethiopian highlands. Zookeys 2021; 1016:77-141. [PMID: 33628080 PMCID: PMC7892535 DOI: 10.3897/zookeys.1016.59699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/20/2020] [Indexed: 12/03/2022] Open
Abstract
Frogs of the genus Ptychadena that inhabit the Ethiopian highlands serve as a model system to understand biogeography, diversification, and adaptations to high elevations. Despite recent studies focusing on the systematics of this group, the taxonomy of the Ptychadenaneumanni species complex remains only partially resolved, owing largely to the morphological resemblance of its members. Here, the taxonomy of this historically problematic group of frogs is revised by integrating morphological and molecular analyses on both century-old type specimens and more recently collected material. Based on these multiple lines of evidence, the P.neumanni species complex is shown to be more speciose than previously thought and four new species are described. With the aim of clarifying and stabilizing the taxonomy of the group, six species are also re-described and morphological and acoustic identification keys are provided. This study also establishes species distribution maps and reveals important differences in range size between the members of the P.neumanni complex, calling for adapted conservation measures across the Ethiopian highlands.
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Affiliation(s)
- Sandra Goutte
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAE New York University Abu Dhabi Abu Dhabi United Arab Emirates
| | - Jacobo Reyes-Velasco
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAE New York University Abu Dhabi Abu Dhabi United Arab Emirates
| | - Xenia Freilich
- Department of Biology, Queens College, City University of New York, Flushing, New York, USA City University of New York New York United States of America
| | - Abeje Kassie
- Ethiopian Biodiversity Institute, Addis Ababa, Ethiopia Ethiopian Biodiversity Institute Addis Ababa Ethiopia.,Addis Ababa University, Addis Ababa, Ethiopia Addis Ababa University Addis Ababa Ethiopia
| | - Stephane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, UAE New York University Abu Dhabi Abu Dhabi United Arab Emirates
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Asefa M, Cao M, He Y, Mekonnen E, Song X, Yang J. Ethiopian vegetation types, climate and topography. PLANT DIVERSITY 2020; 42:302-311. [PMID: 33094201 PMCID: PMC7567763 DOI: 10.1016/j.pld.2020.04.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Ethiopia is land of geographical contrasts with elevations that range from 125 m below sea level in the Danakil Depression to 4533 m above sea level in the Semien Mountains, a world heritage site. The diverse climate of various ecological regions of the country has driven the establishment of diverse vegetation, which range from Afroalpine vegetation in the mountains to the arid and semi-arid vegetation type in the lowlands. The formation of Ethiopian vegetation is highly connected to the climate and geological history of the country. Highland uplift and rift formation due to volcanic forces formed novel habitats with different topography and climatic conditions that have ultimately become drivers for vegetation diversification. Due to Ethiopia's connection with the temperate biome in the north and the Arabian Peninsula during the dry glacial period, the biotic assemblage of Ethiopian highlands consists of both Afrotropical and palearctic biota. In general, eight distinct vegetation types have been identified in Ethiopia, based mainly on elevation and climate gradients. These vegetation types host their own unique species, but also share several common species. Some of the vegetation types are identified as centers of endemism and have subsequently been identified globally as the East African Afromontane hotspot. Ethiopia is biologically rich, with more than 6500 vascular plant species. Of these species, 12% are endemic mainly due to geographical isolation and unique climatic conditions. However, researchers have yet to extensively investigate the ecology, phenology, as well as the evolutionary, genetics, and conservation status of Ethiopian vegetations at community and species level over space and time. This lack of research is a barrier to achieving the goal of zero global plant extinctions. Taxa extinction risk assessment has not been extensively carried out for majority of Ethiopian species. Detailed research is needed to explore how vegetation and species respond to rapidly growing environmental change. Currently, human-induced climate change and habitat fragmentation are severely threatening the country's biodiversity, and the consequences of these effects have not been studied at large. Furthermore, we still lack scientific evidence on how micro- and macro-ecological and evolutionary processes have been shaping vegetation structures in this climatically, topographically, and geologically diverse country. These gaps in our knowledge represent an opportunity for ecologists, geneticists, evolutionary biologists, conservation biologists, and other experts to investigate the biodiversity status and the complex ecological processes involved in structuring vegetation dynamics so as to help take effective conservation actions.
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Affiliation(s)
- Mengesha Asefa
- CAS, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Yunnan, China
- Department of Biology, College of Natural and Computational Sciences, University of Gondar, 196, Gondar, Ethiopia
| | - Min Cao
- CAS, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Yunnan, China
| | - Yunyun He
- CAS, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Yunnan, China
| | - Ewuketu Mekonnen
- CAS, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Yunnan, China
| | - Xiaoyang Song
- CAS, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Yunnan, China
| | - Jie Yang
- CAS, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Yunnan, China
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Reyes-Velasco J, Manthey JD, Freilich X, Boissinot S. Diversification of African tree frogs (genusLeptopelis) in the highlands of Ethiopia. Mol Ecol 2018; 27:2256-2270. [DOI: 10.1111/mec.14573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 02/25/2018] [Accepted: 03/12/2018] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Xenia Freilich
- Department of Biology; Queens College; City University of New York; Flushing NY USA
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Reyes-Velasco J, Manthey JD, Bourgeois Y, Freilich X, Boissinot S. Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. PLoS One 2018; 13:e0190440. [PMID: 29389966 PMCID: PMC5794058 DOI: 10.1371/journal.pone.0190440] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/14/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon's range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot. We used thousands of genome-wide SNPs obtained from double digest restriction site associated DNA sequencing (ddRAD-seq) in populations of the Ptychadena neumanni species complex from the Ethiopian highlands in order to infer their phylogenetic relationships and genetic structure, as well as to study their demographic history. Our genome-wide phylogenetic study supports the existence of approximately 13 lineages clustered into 3 species groups. Our phylogenetic and phylogeographic reconstructions suggest that those endemic lineages diversified in allopatry, and subsequently specialized to different habitats and elevations. Demographic analyses point to a continuous decrease in the population size across the majority of lineages and populations during the Pleistocene, which is consistent with a continuous period of aridification that East Africa experienced since the Pliocene. We discuss the taxonomic implications of our analyses and, in particular, we warn against the recent practice to solely use Bayesian species delimitation methods when proposing taxonomic changes.
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Affiliation(s)
| | - Joseph D. Manthey
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Yann Bourgeois
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Xenia Freilich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States of America
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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Smith ML, Noonan BP, Colston TJ. Correction to 'The role of climatic and geological events in generating diversity in Ethiopian grass frogs (genus Ptychadena)'. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171389. [PMID: 29134107 PMCID: PMC5666290 DOI: 10.1098/rsos.171389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
[This corrects the article DOI: 10.1098/rsos.170021.].
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