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Chou MH, Chu IH, Lau D, Huang JP. Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: a case study on. INVERTEBR SYST 2022. [DOI: 10.1071/is22011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Alpha taxonomy is fundamental for many biological fields. Delineation of the species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets, and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the Cylindera pseudocylindriformis complex. We discuss the association between genetic divergence and microhabitat specialisation, and further corroborate that C. subtilis sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can occur at a small geographic scale, even in a winged insect like tiger beetles. Our results also indicated that there may still be undocumented species diversity of Taiwanese Cylindera remaining to be discovered. ZooBank LSID: urn:lsid:zoobank.org:pub:9DEC1432-365C-4872-8D06-73B95F30624F
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Fuentes-López A, Pedreño Sala A, Romera E, Galián J. DNA-based and taxonomic identification of forensically important Sarcophagidae (Diptera) in southeastern Spain. Sci Justice 2021; 61:150-159. [PMID: 33736847 DOI: 10.1016/j.scijus.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/21/2020] [Accepted: 11/07/2020] [Indexed: 12/16/2022]
Abstract
Studying dipterans at the scene of a death can provide essential information for interpreting the evidence and help to reconstruct the events happened to a corpse in the past. Molecular tools have been employed for identification at specific levels in the cases of cryptic species or poorly conserved specimens. Identification of specimens is essential in forensic entomology since each species has a specific growth rate, which determines the calculation of the minimum post mortem interval (minPMI). In addition, phylogeographic reconstruction within a species can help to differentiate the haplotypes from a geographic area, thereby helping to clarify the possible relocation of a corpse. The morphological identification of Sarcophagidae species is often difficult, especially for the females. This is an important Diptera family since some of its species are among the first to reach a corpse, especially in warm areas. In this study, we compared the sarcophagids found in human corpses in forensic cases in Alicante (southeast of Spain) with specimens collected from baited traps in the same area and surrounding provinces. In total, 189 specimens were collected, comprising 72 from forensic cases and 117 from baited traps. Molecular identification was conducted by sequencing the cox1 mitochondrial gene and analyzing the sequences using ABGD, GMYC, and BIN species delimitation methods. The median joining algorithm in the PopART program was used to construct phylogeographic networks. Eight species in the family Sarcophagidae were identified. The most widely collected species were Sarcophaga argyrostoma and Sarcophaga tibialis. The haplotype networks obtained for these species did not indicate a clear geographic distribution of haplotypes. The S. argyrostoma samples from Alcoy were clearly isolated. The results demonstrated that this method is useful for identifying Sarcophagidae samples in forensic investigations and it can be employed for minPMI estimation.
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Affiliation(s)
- Alberto Fuentes-López
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Región de Murcia, Spain.
| | - Aarón Pedreño Sala
- Brigada Provincial de Policía Científica, Comisaría Provincial de Policía Nacional de Alicante, Alicante 03007, Comunitat Valenciana, Spain.
| | - Elena Romera
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Región de Murcia, Spain.
| | - José Galián
- Departamento de Zoología y Antropología Física, Campus Mare Nostrum, Universidad de Murcia, Campus de Espinardo, 30100 Región de Murcia, Spain.
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Fuentes-López A, Rebelo MT, Romera E, López-López A, Galián J. Genetic diversity of Calliphora vicina (Diptera: Calliphoridae) in the Iberian Peninsula based on cox1, 16S and ITS2 sequences. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The study of Diptera at the scene of a crime can provide essential information for the interpretation of evidence. Phylogeographic reconstruction could help differentiate haplotypes of a dipteran species in a geographical area, clarifying, for example, the details of a possible relocation of a corpse. In addition, inferring the ancestral areas of distribution helps to understand the current status of the species and its biogeographic history. One of the most important species in forensic entomology is Calliphora vicina Rovineau-Desvoidy, 1830 (Diptera: Calliphoridae). The aim of this work is to increase our knowledge of this species in the Iberian Peninsula using 464 specimens from Spain and Portugal. These samples were identified using morphological keys and by molecular methods using fragments of the cox1, 16S and ITS2 genes. The phylogeographic history of these populations was inferred from haplotype networks and the reconstruction of ancestral areas of distribution. The molecular results corroborated the morphological identifications of the samples. Phylogeographic networks showed no geographical structure, as haplotypes are shared among almost all populations. reconstruct ancestral state in phylogenies analyses showed a high rate of movement among populations, possibly related to human activity. These results suggest that this species had a very rapid and recent spatial and demographic expansion throughout the Iberian Peninsula.
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Affiliation(s)
- Alberto Fuentes-López
- Departamento de Zoología y Antropología Física (Área de Biología Animal), Universidad de Murcia, Campus Mare Nostrum, Murcia, Spain
| | - María Teresa Rebelo
- Departamento de Biología Animal/Centro de Estudos do Ambiente e do Mar, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Elena Romera
- Departamento de Zoología y Antropología Física (Área de Biología Animal), Universidad de Murcia, Campus Mare Nostrum, Murcia, Spain
| | - Alejandro López-López
- Departamento de Zoología y Antropología Física (Área de Biología Animal), Universidad de Murcia, Campus Mare Nostrum, Murcia, Spain
- Área de Zoología, Departamento de Agroquímica y Medio Ambiente, Universidad Miguel Hernández de Elche, Elche, Spain
| | - José Galián
- Departamento de Zoología y Antropología Física (Área de Biología Animal), Universidad de Murcia, Campus Mare Nostrum, Murcia, Spain
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Torres‐Mantelet N, Galián J, León‐Quinto T, López‐López A. Glacial refuges and cryptic speciation in a Southern Palearctic tiger beetle (Coleoptera: Cicindelidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - José Galián
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia Spain
| | - Trinidad León‐Quinto
- Área de Zoología Universidad Miguel Hernández de Elche Alicante Spain
- Instituto de Bioingeniería Universidad Miguel Hernández de Elche Alicante Spain
| | - Alejandro López‐López
- Área de Zoología Universidad Miguel Hernández de Elche Alicante Spain
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia Spain
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Chou MH, Yeh WB. Delineation of two new, highly similar species of Taiwanese Cylindera tiger beetles (Coleoptera, Carabidae, Cicindelinae) based on morphological and molecular evidence. Zookeys 2019; 875:31-62. [PMID: 31572044 PMCID: PMC6751220 DOI: 10.3897/zookeys.875.37856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/11/2019] [Indexed: 11/12/2022] Open
Abstract
Tiger beetles have been recognized primarily based on morphological characters. However, the variations of elytral maculation and coloration sometimes lead to misjudgment in species classification and the overlooking of the existence of cryptic species. Recently, specimens of two endemic species of Taiwanese Cylindera, C.sauteri and C.pseudocylindriformis, exhibit morphologically recognizable forms, indicating that some undescribed species may exist. To clarify their taxonomic status, morphological characteristics including male genitalia were examined and two mitochondrial genes, COI and 16S rDNA, and one nuclear 28S rDNA were analyzed. Molecular phylogenetic inferences indicated that both forms in both species are reciprocally monophyletic. Moreover, molecular dating showed the forms diverged approximately 1.3 million years ago. Two new species, Cylinderaooasp. nov. and Cylinderaautumnalissp. nov., are thereby described. The main recognizable characteristics separating C.ooasp. nov. from C.sauteri are the lack of a triangular spot at the middle edge of elytron and the elongated but not rounded subapical spot. For C.autumnalissp. nov., the apical lunula near the elytral suture is thickened but not linear and slender, and its elytra are more metallic brownish than those of C.pseudocylindriformis. Although their aedeagi characteristics are not distinctive, the body size of the proposed two new species is different. Field observation revealed that niche utilization would be relevant for differentiating these closely related species.
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Affiliation(s)
- Ming-Hsun Chou
- Department of Entomology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan National Chung Hsing University Taichung Taiwan
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Graham MR, Myers EA, Kaiser RC, Fet V. Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia. ZOOL SCR 2019. [DOI: 10.1111/zsc.12381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington DC USA
| | - Ronald C. Kaiser
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | - Victor Fet
- Department of Biological Sciences Marshall University Huntington WV USA
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Renner MAM, Heslewood MM, Patzak SDF, Schäfer-Verwimp A, Heinrichs J. By how much do we underestimate species diversity of liverworts using morphological evidence? An example from Australasian Plagiochila (Plagiochilaceae: Jungermanniopsida). Mol Phylogenet Evol 2016; 107:576-593. [PMID: 28007566 DOI: 10.1016/j.ympev.2016.12.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/24/2022]
Abstract
As a framework for revisionary study of the leafy liverwort Plagiochila in Australia, two methods for species delimitation on molecular sequence data, General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) were applied to a dataset including 265 individuals from Australia, New Zealand, and the Pacific. Groups returned by GMYC and ABGD were incongruent in some lineages, and ABGD tended to lump groups. This may reflect underlying heterogeneity in the history of diversification within different lineages of Plagiochila. GMYC from trees calculated using three different molecular clocks were compared, in some lineages different primary species hypotheses were returned by analyses of trees estimated under different clock models, suggesting clock model selection should be a routine component of phylogeny reconstruction for tree-based species delimitation methods, such as GMYC. Our results suggest that a minimum of 71 Plagiochilaceae species occur in Australasia, 16 more than currently accepted for the region, comprising 8 undetermined species and 8 synonyms requiring reinstatement. Despite modern taxonomic investigation over a four decade period, (1) real diversity is 29% higher than currently recognized; and (2) 12 of 33, or 36%, of currently accepted and previously untested Australasian species have circumscription issues, including polyphyly, paraphyly, internal phylogenetic structure, or combinations of two or more of these issues. These both reflect the many challenges associated with grouping decisions based solely on morphological data in morphologically simple yet polymorphic plant lineages. Our results highlight again the critical need for combined molecular-morphological datasets as a basis for resolving robust species hypotheses in species-rich bryophyte lineages.
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Affiliation(s)
- Matt A M Renner
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, NSW 2000, Australia.
| | - Margaret M Heslewood
- Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, NSW 2000, Australia
| | - Simon D F Patzak
- Ludwig Maximilian University, Faculty of Biology, Department of Biology and Geobio-Center, Menzinger Straβe 67, D-80638 Munich, Germany
| | | | - Jochen Heinrichs
- Ludwig Maximilian University, Faculty of Biology, Department of Biology and Geobio-Center, Menzinger Straβe 67, D-80638 Munich, Germany
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Oliver PM, McDonald PJ. Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160018. [PMID: 27853534 PMCID: PMC5098959 DOI: 10.1098/rsos.160018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cincta has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa-often ecologically specialized forms-that show evidence of having persisted since earlier intensification of aridity in the late Miocene.
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Affiliation(s)
- Paul M. Oliver
- Division of Evolution, Ecology and Genetics, Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Building 116, Daley Road, Acton, Australian Capital Territory 2601, Australia
| | - Peter J. McDonald
- Flora and Fauna Division, Department of Land Resource Management, Alice Springs, Northern Territory 0870, Australia
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Characterisation and expression analysis of UBC9 and UBS27 genes in developing gonads of cicindelids (Coleoptera: Cicindelidae). Comp Biochem Physiol B Biochem Mol Biol 2016; 202:75-82. [PMID: 27524263 DOI: 10.1016/j.cbpb.2016.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/03/2016] [Accepted: 08/09/2016] [Indexed: 11/22/2022]
Abstract
Ubiquitin and small ubiquitin-like modifiers (SUMO) are post-translational modifiers essential in a variety of cellular processes, including gametogenesis. SUMO-conjugating enzyme (UBC9) and the ubiquitin ribosomal fusion protein UBS27 have been characterised in several model species. However, their expression in coleopteran remains unstudied. In this study, UBC9 and UBS27 genes have been characterised in the tiger beetle Cicindela campestris for the first time. Bioinformatic analysis showed that the Cc-UBC9 gene encoded a 159 amino acid protein with a predicted molecular weight of 18.18kDa, and the Cc-UBS27 gene encoded a 156 amino acid protein with a predicted molecular weight of 17.71kDa. Selection analyses carried out in several cicindelid species revealed that both genes were affected by purifying selection. Real time quantitative PCR analysis demonstrated that Cc-UBC9 and Cc-UBS27 were expressed in different tissues. The highest expression on both genes was found in the ovary and testis, and there were differential expression levels between immature and mature stages of testis development. The expression patterns of Cc-UBC9 and Cc-UBS27 suggest that these genes play important roles in gametogenesis in C. campestris. This information is relevant to better understand the reproductive process in cicindelids and the function of ubiquitin and small ubiquitin-related modifier genes in the Coleoptera.
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