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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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Sullivan JP, Hopkins CD, Pirro S, Peterson R, Chakona A, Mutizwa TI, Mukweze Mulelenu C, Alqahtani FH, Vreven E, Dillman CB. Mitogenome recovered from a 19 th Century holotype by shotgun sequencing supplies a generic name for an orphaned clade of African weakly electric fishes (Osteoglossomorpha, Mormyridae). Zookeys 2022; 1129:163-196. [PMID: 36761845 PMCID: PMC9836601 DOI: 10.3897/zookeys.1129.90287] [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: 07/13/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Heteromormyrus Steindachner, 1866, a genus of Mormyridae (Teleostei: Osteoglossomorpha), has been monotypic since the description of Heteromormyruspauciradiatus (Steindacher, 1866) from a single specimen. No type locality other than "Angola" was given and almost no specimens have been subsequently identified to this species. In order to investigate the relationship of this taxon to fresh specimens collected in Angola and elsewhere, whole genome paired-end sequencing of DNA extracted from the holotype specimen of Heteromormyruspauciradiatus was performed and a nearly complete mitogenome assembled from the sequences obtained. Comparison of cytochrome oxidase I and cytochrome b sequences from this mitogenome to sequences from recently collected material reveal that Heteromormyruspauciradiatus is closely related to specimens identified as Hippopotamyrusansorgii (Boulenger, 1905), Hippopotamyrusszaboi Kramer, van der Bank & Wink, 2004, Hippopotamyruslongilateralis Kramer & Swartz, 2010, as well as to several undescribed forms from subequatorial Africa collectively referred to in the literature as the "Hippopotamyrusansorgii species complex" and colloquially known as "slender stonebashers." Previous molecular phylogenetic work has shown that these species are not close relatives of Hippopotamyruscastor Pappenheim, 1906, the type species of genus Hippopotamyrus Pappenheim, 1906 from Cameroon, and are thus misclassified. Hippopotamyrusansorgii species complex taxa and another species shown to have been misclassified, Paramormyropstavernei (Poll, 1972), are placed in genus Heteromormyrus and one genetic lineage from the Kwanza and Lucala rivers of Angola are identified as conspecific Heteromormyruspauciradiatus. Three additional new combinations and a synonymy in Mormyridae are introduced. The morphological characteristics and geographical distribution of the genus Heteromormyrus are reviewed. The electric organ discharges (EODs) of Heteromormyrus species are to be treated in a separate study.
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Affiliation(s)
- John P. Sullivan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA,Cornell University Museum of Vertebrates, Ithaca, New York, USA
| | - Carl D. Hopkins
- Cornell University Museum of Vertebrates, Ithaca, New York, USA,Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
| | | | - Rose Peterson
- The George Washington University, Washington, D.C., USA
| | - Albert Chakona
- NRF-South African Institute for Aquatic Biodiversity, Makhanda, South Africa,Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Tadiwa I. Mutizwa
- NRF-South African Institute for Aquatic Biodiversity, Makhanda, South Africa,Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Christian Mukweze Mulelenu
- Département de Zootechnie, Faculté des Sciences Agronomiques, Université de Kolwezi, Kolwezi, Democratic Republic of the Congo,Département de Gestion des Ressources Naturelles Renouvelables, Unité de recherche en Biodiversité et Exploitation durable des Zones Humides, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo,Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit, Leuven, Belgium,Zoology Department, Ichthyology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Fahad H. Alqahtani
- National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Emmanuel Vreven
- Laboratory of Biodiversity and Evolutionary Genomics, Katholieke Universiteit, Leuven, Belgium,Zoology Department, Ichthyology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Casey B. Dillman
- Cornell University Museum of Vertebrates, Ithaca, New York, USA,Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, USA
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Castañeda-Rico S, Edwards CW, Hawkins MTR, Maldonado JE. Museomics and the holotype of a critically endangered cricetid rodent provide key evidence of an undescribed genus. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.
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Integrative Taxonomy within Eremias multiocellata Complex (Sauria, Lacertidae) from the Western Part of Range: Evidence from Historical DNA. Genes (Basel) 2022; 13:genes13060941. [PMID: 35741703 PMCID: PMC9222255 DOI: 10.3390/genes13060941] [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: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
The Kokshaal racerunner, Eremias kokshaaliensis Eremchenko et Panfilov, 1999, together with other central Asian racerunner species, is included in the Eremias multiocellata complex. In the present work, for the first time, the results of the analysis of historical mitochondrial DNA (barcode) are presented and the taxonomic status and preliminary phylogenetic relationships within the complex are specified. We present, for the first time, the results of the molecular analysis using historical DNA recovered from specimens of several species of this complex (paratypes of the Kokshaal racerunner and historical collections of the Kashgar racerunner E. buechneri from Kashgaria) using DNA barcoding.
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