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Zhang Y, De Meyer M, Virgilio M, Feng S, Badji K, Li Z. Phylogenomic resolution of the Ceratitis FARQ complex (Diptera: Tephritidae). Mol Phylogenet Evol 2021; 161:107160. [PMID: 33794396 DOI: 10.1016/j.ympev.2021.107160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
The Ceratitis FARQ complex (formerly FAR complex) includes four frugivorous tephritids, Ceratitis fasciventris, C. anonae, C. rosa and C. quilicii, the latter two causing important agricultural losses in Africa. Although FARQ species can be identified on the basis of subtle morphological differences, they cannot be resolved as monophyletic when trying phylogenetic tree reconstructions based on mitochondrial or nuclear gene fragments except for microsatellites. In this study, we used mitogenome and genome-wide SNPs to investigate the phylogenetic relationship within the complex as well as between all four Ceratitis subgenera. The analysis of 13 species supported the monophyly of the Ceratitis subgenera Ceratitis, Ceratalaspis, Pardalaspis, and recovered Pterandrus as paraphyletic but could not properly resolve species within the FARQ complex. Conversely, gene and species tree reconstructions based on 785,484 genome-wide SNPs could consistently resolve the FARQ taxa and provide insights into their phylogenetic relationships. Gene flow was detected by TreeMix analysis from C. quilicii to C. fasciventris, suggesting the existence of introgression events in the FARQ complex. Our results suggest that genome-wide SNPs represent a suitable tool for the molecular diagnosis of FARQ species and could possibly be used to develop rapid diagnostic methods or to trace the origins of intercepted samples.
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Affiliation(s)
- Yue Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Marc De Meyer
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium.
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Invertebrates Section and JEMU, Tervuren B3080, Belgium.
| | - Shiqian Feng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Kemo Badji
- Crop Protection Directorate, Dakar, Senegal.
| | - Zhihong Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon. DIVERSITY 2020. [DOI: 10.3390/d12110428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.
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Alström P, van Linschooten J, Donald PF, Sundev G, Mohammadi Z, Ghorbani F, Shafaeipour A, van den Berg A, Robb M, Aliabadian M, Wei C, Lei F, Oxelman B, Olsson U. Multiple species delimitation approaches applied to the avian lark genus Alaudala. Mol Phylogenet Evol 2020; 154:106994. [PMID: 33250446 DOI: 10.1016/j.ympev.2020.106994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.
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Affiliation(s)
- Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jip van Linschooten
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Paul F Donald
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, P.O. Box 537, Ulaanbaatar 210646a, Ulaanbaatar, Mongolia
| | - Zeinolabedin Mohammadi
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Fatemeh Ghorbani
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Arya Shafaeipour
- Department of Biology, Faculty of Science, Yasouj University, Yasouj, Iran
| | - Arnoud van den Berg
- The Sound Approach, c/o Duinlustparkweg 98, 2082 EG Santpoort-Zuid, the Netherlands
| | - Magnus Robb
- The Sound Approach, c/o Rua Dr Pedro Almeida Lima 6, 2710-122 Sintra, Portugal
| | - Mansour Aliabadian
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Chentao Wei
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bengt Oxelman
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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Ghorbani F, Aliabadian M, Zhang R, Irestedt M, Hao Y, Sundev G, Lei F, Ma M, Olsson U, Alström P. Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark (
Alaudala rufescens
) — Sand Lark (
A. raytal
) species complex (Aves, Passeriformes) reveal cryptic diversity. ZOOL SCR 2020. [DOI: 10.1111/zsc.12422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fatemeh Ghorbani
- Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
- Zoological Innovations Research Department Institute of Applied Zoology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society Ulaanbaatar Mongolia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Ming Ma
- Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Xinjiang China
| | - Urban Olsson
- Systematics and Biodiversity Department of Biology and Environmental Sciences University of Gothenburg Göteborg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
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Gwee CY, Eaton JA, Garg KM, Alström P, Van Balen S(B, Hutchinson RO, Prawiradilaga DM, Le MH, Rheindt FE. Cryptic diversity in Cyornis (Aves: Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - James A Eaton
- Birdtour Asia Ltd, Littleover, Derby, United Kingdom
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | | | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor, Indonesia
| | - Manh Hung Le
- Graduated University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Caugiay, Hanoi, Vietnam
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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Dupuis J, Brunet B, Bird H, Lumley L, Fagua G, Boyle B, Levesque R, Cusson M, Powell J, Sperling F. Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol Phylogenet Evol 2017; 111:158-168. [DOI: 10.1016/j.ympev.2017.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 01/02/2023]
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