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AlShamakhi HS, Al-Sadi AM, Cook LG. Evolutionary Relationships of Omani Macrotermes subhyalinus, Macrotermitinae. INSECTS 2024; 15:648. [PMID: 39336616 PMCID: PMC11432140 DOI: 10.3390/insects15090648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 09/30/2024]
Abstract
A study was conducted to investigate the evolutionary relationships of Macrotermes subhyalinus from Oman, in the southeastern part of the Arabian Peninsula. Sequences of the mitochondrial COI and the nuclear large-subunit ribosomal RNA (LSU rRNA, 28S) genes were used to investigate the populations of M. subhyalinus across their distribution in Oman to determine their relationships with other Macrotermes species. Our findings indicate that M. subhyalinus in Oman is a member of an East African clade, distinct from those in West Africa. Analyses of the COI showed that there is base composition bias among the taxa (non-stationarity) that has not been considered in earlier studies. We provide the first report of pseudogene copies of 28S in M. subhyalinus that are differentially amplified.
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Affiliation(s)
| | - Abdullah M Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123, Oman
- College of Agriculture, University of Al Dhaid, Sharjah P.O. Box 27272, United Arab Emirates
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Solovyev VI, Dubatolov VV, Vavilova VY, Kosterin OE. Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00565-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lukicheva S, Mardulyn P. Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles. Mol Ecol 2021; 30:4077-4089. [PMID: 34097806 DOI: 10.1111/mec.16011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023]
Abstract
A large number of genetic variation studies have identified cases of mitochondrial genome introgression in animals, indicating that reproductive barriers among closely related species are often permeable. Because of its sheer size, the impact of hybridization on the evolution of the nuclear genome is more difficult to apprehend. Only a few studies have explored it recently thanks to recent progress in DNA sequencing and genome assembly. Here, we analysed whole-genome sequence variation among multiple individuals of two sister species of leaf beetles inside their hybrid zone, in which asymmetric mitochondrial genome introgression had previously been established. We used a machine learning approach based on computer simulations for training to identify regions of the nuclear genome that were introgressed. We inferred asymmetric introgression of ≈2% of the genome, in the same direction that was observed for the mitochondrial genome. Because a previous study based on a reduced-representation sequencing approach was not able to detect this introgression, we conclude that whole-genome sequencing is necessary when the fraction of the introgressed genome is small. We also analysed the whole-genome sequence of a hybrid individual, demonstrating that hybrids have the capacity to backcross with the species for which virtually no introgression was observed. Our data suggest that one species has recently invaded the range of the other and/or some alleles that where transferred from the invaded into the invading species could be under positive selection and may have favoured the adaptation of the invading species to the Alpine environment.
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Affiliation(s)
- Svitlana Lukicheva
- Evolutionary Biology and Ecology, Interuniversity Institute of Bioinformatics in Brussels - (IB)², Université libre de Bruxelles, Brussels, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Interuniversity Institute of Bioinformatics in Brussels - (IB)², Université libre de Bruxelles, Brussels, Belgium
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Lukicheva S, Flot JF, Mardulyn P. Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species. Genome Biol Evol 2021; 13:6296840. [PMID: 34115123 PMCID: PMC8290105 DOI: 10.1093/gbe/evab134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Coleoptera is the most species-rich insect order, yet is currently underrepresented in genomic databases. An assembly was generated for ca. 1.7 Gb genome of the leaf beetle Gonioctena quinquepunctata by first assembling long-sequence reads (Oxford Nanopore; ± 27-fold coverage) and subsequently polishing the resulting assembly with short sequence reads (Illumina; ± 85-fold coverage). The unusually large size (most Coleoptera species are associated with a reported size below 1 Gb) was at least partially attributed to the presence of a large fraction of repeated elements (73.8%). The final assembly was characterized by an N50 length of 432 kb and a BUSCO score of 95.5%. The heterozygosity rate was ± 0.6%. Automated genome annotation informed by RNA-Seq resulted in 40,568 predicted proteins, which is much larger than the typical range 17,000–23,000 predicted for other Coleoptera. However, no evidence of a genome duplication was detected. This new reference genome will contribute to our understanding of genetic variation in the Coleoptera. Among others, it will also allow exploring reproductive barriers between species, investigating introgression in the nuclear genome, and identifying genes involved in resistance to extreme climate conditions.
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Affiliation(s)
- Svitlana Lukicheva
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Jean-François Flot
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology & Interuniversity Institute of Bioinformatics in Brussels - (IB), Université Libre de Bruxelles (ULB), Brussels, Belgium
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Kastally C, Trasoletti M, Mardulyn P. Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps. J Evol Biol 2019; 32:1406-1417. [DOI: 10.1111/jeb.13538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 08/02/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Chedly Kastally
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Marta Trasoletti
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology Université Libre de Bruxelles Brussels Belgium
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Kastally C, Mardulyn P. Widespread co-occurrence of two distantly related mitochondrial genomes in individuals of the leaf beetle Gonioctena intermedia. Biol Lett 2018; 13:rsbl.2017.0570. [PMID: 29118243 DOI: 10.1098/rsbl.2017.0570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/16/2017] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial genome heteroplasmy-the presence of more than one genomic variant in individuals-is considered only occasional in animals, and most often involves molecules differing only by a few recent mutations. Thanks to new sequencing technologies, a large number of DNA fragments from a single individual can now be sequenced and visualized separately, allowing new insights into intra-individual mitochondrial genome variation. Here, we report evidence from both (i) massive parallel sequencing (MPS) of genomic extracts and (ii) Sanger sequencing of PCR products, for the widespread co-occurrence of two distantly related (greater than 1% nucleotide divergence, excluding the control region) mitochondrial genomes in individuals of a natural population of the leaf beetle Gonioctena intermedia Sanger sequencing of PCR products using universal primers previously failed to identify heteroplasmy in this population. Its occurrence was detected with MPS data and may have important implications for evolutionary studies. It suggests the need to re-evaluate, using MPS techniques, the proportion of animal species displaying heteroplasmy.
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Affiliation(s)
- Chedly Kastally
- Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, avenue Franklin D. Roosevelt 50, 1050 Brussels, Belgium
| | - Patrick Mardulyn
- Department of Evolutionary Biology and Ecology, Université Libre de Bruxelles, avenue Franklin D. Roosevelt 50, 1050 Brussels, Belgium
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Quinzin MC, Normand S, Dellicour S, Svenning JC, Mardulyn P. Glacial survival of trophically linked boreal species in northern Europe. Proc Biol Sci 2017; 284:20162799. [PMID: 28592679 PMCID: PMC5474064 DOI: 10.1098/rspb.2016.2799] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 05/09/2017] [Indexed: 11/12/2022] Open
Abstract
Whether non-arctic species persisted in northern Europe during the Last Glacial Maximum (LGM) is highly debated. Until now, the debate has mostly focused on plants, with little consideration for other groups of organisms, e.g. the numerous plant-dependent insect species. Here, we study the late-Quaternary evolution of the European range of a boreo-montane leaf beetle, Gonioctena intermedia, which feeds exclusively on the boreal and temperate trees Prunus padus and Sorbus aucuparia Using species distribution models, we estimated the congruence between areas of past and present suitable climate for this beetle and its host plants. Then we derived historical hypotheses from the congruent range estimates, and evaluated their compatibility with observed DNA sequence variation at five independent loci. We investigated compatibility using computer simulations of population evolution under various coalescence models. We find strong evidence for range modifications in response to late-Quaternary climate changes, and support for the presence of populations of G. intermedia in northern Europe since the beginning of the last glaciation. The presence of a co-dependent insect in the region through the LGM provides new evidence supporting the glacial survival of cold-tolerant tree species in northern Europe.
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Affiliation(s)
- Maud C Quinzin
- Evolutionary Biology and Ecology, Free University of Brussels (ULB), Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium
| | - Signe Normand
- Dynamic Macroecology, Landscape Dynamics, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903 Birmensdorf, Switzerland
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Simon Dellicour
- Evolutionary Biology and Ecology, Free University of Brussels (ULB), Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium
| | - Jens-Christian Svenning
- Section for Ecoinformatics and Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Free University of Brussels (ULB), Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium
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Evolution of reproductive traits in Cataglyphis desert ants: mating frequency, queen number, and thelytoky. Behav Ecol Sociobiol 2016. [DOI: 10.1007/s00265-016-2144-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Lee CF, Tsai CL, Konstantinov A, Yeh WB. Revision of Mandarella Duvivier from Taiwan, with a new species, new synonymies and identities of highly variable species (Insecta, Chrysomelidae, Galerucinae, Alticini). Zookeys 2016:23-49. [PMID: 27103872 PMCID: PMC4829668 DOI: 10.3897/zookeys.568.7125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 12/21/2015] [Indexed: 12/24/2022] Open
Abstract
Taiwanese species of Mandarella Duvivier are compared on the basis of morphological and molecular evidence. Only three of eleven morphospecies are considered to be valid. Mandarellauenoi (Kimoto, 1969) is transferred from the genus Luperus Geoffroy. Stenoluperustaiwanus Kimoto, 1991 and Stenoluperuskimotoi Döberl, 2001 are synonymized with Mandarellauenoi. Taiwanese records of Stenoluperustibialis Chen, 1942, Stenoluperusnipponensis Laboissière, 1913, and Stenoluperuspotanini (Weise, 1889) were based on misidentifications and represent Mandarellauenoi. The Taiwanese population previously erroneously identified as Stenoluperuspallipes Gressitt and Kimoto, 1963 is here described as a new species, Mandarellatsouisp. n., Stenoluperusesakii Kimoto, 1969, Stenoluperusmatsumurai Takizawa, 1978, and Mandarellataiwanensis Medvedev, 2012 are synonymized with Mandarellaflaviventris (Chen, 1942).
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Affiliation(s)
- Chi-Feng Lee
- Applied Zoology Division, Taiwan Agricultural Research Institute, 189 Chung-Cheng Road, Wufeng, Taichung 41362, TAIWAN
| | - Cheng-Lung Tsai
- Department of Entomology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, TAIWAN
| | | | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, TAIWAN
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Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths. PLoS One 2016; 11:e0148423. [PMID: 26859488 PMCID: PMC4747490 DOI: 10.1371/journal.pone.0148423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 01/18/2016] [Indexed: 01/03/2023] Open
Abstract
The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories.
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Dellicour S, Michez D, Mardulyn P. Comparative phylogeography of five bumblebees: impact of range fragmentation, range size and diet specialization. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12636] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Simon Dellicour
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; av. FD Roosevelt 50 1050 Bruxelles Belgium
| | - Denis Michez
- Laboratory of Zoology; Research Institute of Biosciences; University of Mons; Place du Parc 23 7000 Mons Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; av. FD Roosevelt 50 1050 Bruxelles Belgium
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