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Shi BY, Pan D, Zhang KQ, Gu TY, Yeo DCJ, Ng PKL, Cumberlidge N, Sun HY. Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China. Mol Phylogenet Evol 2024; 190:107955. [PMID: 37898294 DOI: 10.1016/j.ympev.2023.107955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
The numerous naturally-fragmented sky islands (SIs) in the Hengduan Mountains Region (HMR) of southwestern China constitute discontinuous landscapes where montane habitats are isolated by dry-hot valleys which have fostered exceptional species diversification and endemicity. However, studies documenting the crucial role of SI on the speciation dynamics of native freshwater organisms are scarce. Here we used a novel set of comprehensive genetic markers (24 nuclear DNA sequences and complete mitogenomes), morphological characters, and biogeographical information to reveal the evolutionary history and speciation mechanisms of a group of small-bodied montane potamids in the genus Tenuipotamon. Our results provide a robustly supported phylogeny, and suggest that the vicariance events of these montane crabs correlate well with the emergence of SIs due to the uplift of the HMR during the Late Oligocene. Furthermore, ancestrally, mountain ridges provided corridors for the dispersal of these montane crabs that led to the colonization of moist montane-specific habitats, aided by past climatic conditions that were the crucial determinants of their evolutionary history. The present results illustrated that the mechanisms isolating SIs are reinforced by the harsh-dry isolating climatic features of dry-hot valleys separating SIs and continue to affect local diversification. This offers insights into the causes of the high biodiversity and endemism shown by the freshwater crabs of the HMR-SIs in southwestern China.
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Affiliation(s)
- Bo-Yang Shi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Kang-Qin Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tian-Yu Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Darren C J Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Republic of Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Neil Cumberlidge
- Department of Biology, Northern Michigan University, Marquette, MI 49855, USA
| | - Hong-Ying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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2
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Poorani J. An illustrated guide to the lady beetles (Coleoptera: Coccinellidae) of the Indian Subcontinent. Part II. Tribe Chilocorini. Zootaxa 2023; 5378:1-108. [PMID: 38220796 DOI: 10.11646/zootaxa.5378.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 01/16/2024]
Abstract
An illustrated guide to the lady beetles of the tribe Chilocorini (Coleoptera: Coccinellidae: Coccinellinae) of the Indian region is presented. Brief diagnostic accounts of six genera and 31 species are given with supporting illustrations of the diagnostic characters, including genitalia, wherever possible. Details of distribution, host insects / plant associations, and seasonal occurrences are provided for the first time based on extensive collections, label data and published literature. Chilocorus keralensis sp. n. is described from the Western Ghats, South India. Brumoides lineatus sensu Kapur 1967, recorded from the Andaman Islands, is found to be distinct from B. lineatus Weise 1885, and described and illustrated as B. andamanensis sp. n. Phaenochilus indicus Miyatake, 1970 and P. flaviceps Miyatake, 1970 are transferred to Chilocorus Leach (comb. n.) following the latest phylogenetic generic classification of Chilocorini. Three species, Chilocorus albomarginalis (Li & Wang), Chilocorus nigricaeruleus Li & Wang and Chilocorus yunlongensis Cao & Xiao, all originally described from China, are added to the Indian fauna of Chilocorini based on material examined from the north-eastern Indian states of Assam, Meghalaya, and Manipur, respectively. For nine species, illustrations of the life stages are included to facilitate their field identification. A key to the genera and an updated and revised checklist of the Chilocorini of the Indian subcontinent are also provided.
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Affiliation(s)
- J Poorani
- ICAR-National Research Centre for Banana; Thogamalai Road; Thayanur Post; Tiruchirappalli 620102; Tamil Nadu; India.
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3
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Li J, Han G, Tian X, Liang D, Zhang P. UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics. Mol Biol Evol 2023; 40:msad230. [PMID: 37832226 PMCID: PMC10630340 DOI: 10.1093/molbev/msad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.
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Affiliation(s)
- JiaXuan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - GuangCheng Han
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiao Tian
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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4
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Laslo M, Just J, Angelini DR. Theme and variation in the evolution of insect sex determination. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:162-181. [PMID: 35239250 PMCID: PMC10078687 DOI: 10.1002/jez.b.23125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022]
Abstract
The development of dimorphic adult sexes is a critical process for most animals, one that is subject to intense selection. Work in vertebrate and insect model species has revealed that sex determination mechanisms vary widely among animal groups. However, this variation is not uniform, with a limited number of conserved factors. Therefore, sex determination offers an excellent context to consider themes and variations in gene network evolution. Here we review the literature describing sex determination in diverse insects. We have screened public genomic sequence databases for orthologs and duplicates of 25 genes involved in insect sex determination, identifying patterns of presence and absence. These genes and a 3.5 reference set of 43 others were used to infer phylogenies and compared to accepted organismal relationships to examine patterns of congruence and divergence. The function of candidate genes for roles in sex determination (virilizer, female-lethal-2-d, transformer-2) and sex chromosome dosage compensation (male specific lethal-1, msl-2, msl-3) were tested using RNA interference in the milkweed bug, Oncopeltus fasciatus. None of these candidate genes exhibited conserved roles in these processes. Amidst this variation we wish to highlight the following themes for the evolution of sex determination: (1) Unique features within taxa influence network evolution. (2) Their position in the network influences a component's evolution. Our analyses also suggest an inverse association of protein sequence conservation with functional conservation.
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Affiliation(s)
- Mara Laslo
- Department of Cell Biology, Curriculum Fellows ProgramHarvard Medical School25 Shattuck StBostonMassachusettsUSA
| | - Josefine Just
- Department of Organismic and Evolutionary BiologyHarvard University26 Oxford StCambridgeMassachusettsUSA
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
| | - David R. Angelini
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
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5
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Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Bouchard P, Huang D, Pisani D, Donoghue PCJ. Integrated phylogenomics and fossil data illuminate the evolution of beetles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211771. [PMID: 35345430 PMCID: PMC8941382 DOI: 10.1098/rsos.211771] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/15/2022] [Indexed: 05/03/2023]
Abstract
Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.
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Affiliation(s)
- Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Erik Tihelka
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mattia Giacomelli
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - John F. Lawrence
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Robin Kundrata
- Department of Zoology, Faculty of Science, Palacký University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Shûhei Yamamoto
- Hokkaido University Museum, Hokkaido University, Kita 8, Nishi 5, Kita-ku, Sapporo 060-0808, Japan
| | - Margaret K. Thayer
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Richard A. B. Leschen
- Manaaki Whenua Landcare Research, New Zealand Arthropod Collection, Private Bag 92170, Auckland, New Zealand
| | - Matthew L. Gimmel
- Invertebrate Zoology Department, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, CA 93105, USA
| | - Liang Lü
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Patrice Bouchard
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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6
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Che L, Zhang P, Deng S, Escalona HE, Wang X, Li Y, Pang H, Vandenberg N, Ślipiński A, Tomaszewska W, Liang D. New insights into the phylogeny and evolution of lady beetles (Coleoptera: Coccinellidae) by extensive sampling of genes and species. Mol Phylogenet Evol 2021; 156:107045. [PMID: 33352317 DOI: 10.1016/j.ympev.2020.107045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/30/2020] [Accepted: 12/14/2020] [Indexed: 01/09/2023]
Abstract
Ladybirds (family Coccinellidae) are one of the most diverse groups of beetles and globally comprise over 6000 species. Despite their scientific and economic significance, the taxonomy of Coccinellidae remains unstable, and we still know little about their evolutionary history. By using a small number of genes, previous phylogenetic analyses have not reliably resolved the relationships among major ladybird lineages. In this study, we sequenced 94 nuclear protein-coding genes for 214 species of Coccinellidae and 14 outgroups, covering 90 genera and 35 tribes. We found that nucleotide compositional heterogeneity is present among ladybird tribes so that phylogenetic inference at the amino acid level is more reliable than at the DNA level. Based on the maximum likelihood analyses of the amino acid dataset, we recognize three subfamilies in Coccinellidae: Microweiseinae, Monocoryninae stat. nov., and Coccinellinae. The subfamily relationships are strongly supported as (Microweiseinae, (Monocoryninae stat. nov., Coccinellinae)). The tribes of ladybirds are mostly monophyletic, except Ortaliini, Sticholotidini, Scymnini, and Coccidulini. The phylogenetic relationships among tribes of Coccinellinae are still not well resolved, with many nodes weakly supported. Our divergence time analysis suggests that the crown group of extant lady beetles arose in the Early Cretaceous ~ 143 million years ago (Mya) and experienced a rapid diversification during the Late Cretaceous (120-70 Mya). We hypothesize that the boom of angiosperms in the Late Cretaceous promoted the diversification of herbivorous Sternorrhyncha insects, especially aphids, which in turn drove the rapid radiation of predatory lady beetles. In summary, our work provides a comprehensive time-calibrated phylogeny of Coccinellidae that provides a sound framework for revising their classification and understanding the origin of their biodiversity.
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Affiliation(s)
- LiHeng Che
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - ShaoHong Deng
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Hermes E Escalona
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Xingmin Wang
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Department of Entomology, South China Agricultural University, Guangzhou, China
| | - Yun Li
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Hong Pang
- School of Ecology, Sun Yat-Sen University, Shenzhen, China
| | - Natalia Vandenberg
- Systematic Entomology Lab, Agricultural Research Service, USDA c/o National Museum of Natural History, Smithsonian Institution, P. O. Box 37012, MRC-168, Washington, DC 20013-7012, USA
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Wioletta Tomaszewska
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland.
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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7
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Sex-Specific Wolbachia Infection Patterns in Populations of Polygraphus proximus Blandford (Coleoptera; Curculionidae: Scolytinae). INSECTS 2020; 11:insects11080547. [PMID: 32824858 PMCID: PMC7469224 DOI: 10.3390/insects11080547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 12/02/2022]
Abstract
Simple Summary Wolbachia bacteria are the most common symbionts of insects. These bacteria are ordinarily transmitted via oocyte cytoplasm from mother to progeny, like mitochondria, and are sporadically transmitted from one species to another. The Wolbachia symbionts have evolved to be parasitic (feminization of genetic males, male-killing, parthenogenesis, and cytoplasmic incompatibility) or/and mutualistic (increasing lifespan and fecundity, providing vitamins and nutrients, defending against viruses and parasites). Here we have studied Wolbachia infection in populations of four-eyed fir bark beetle Polygraphusproximus, which is one of the most dangerous pests of Siberian fir forests. A high rate of the only wProx Wolbachia strain in P.proximus populations was found in a vastly studied territory. Surprisingly, females were more often harboring Wolbachia than males. Besides, a comparison of the Wolbachia density in individuals has revealed that females contain much more Wolbachia symbionts than males. We suppose that the difference in infection status, as well as the difference in Wolbachia load between males and females within a population, can be found in some other Wolbachia–host associations. Abstract Wolbachia symbionts are maternally inherited bacteria that are widely distributed among Arthropoda hosts. Wolbachia influence their host biology in diverse ways. They may induce reproductive abnormalities, protect hosts against pathogens and parasites, or benefit hosts through metabolic provisioning. The progeny of an infected female are ordinarily infected with Wolbachia; however, Wolbachia have no future in male host progeny because they cannot transmit the symbiont to the next generation. Here, we analyze native and invasive populations of the four-eyed fir bark beetle (Polygraphus proximus) for Wolbachia prevalence and symbiont genetic diversity. This species is a dangerous pest of Siberian fir (Abies sibirica) forests. The native range of P. proximus includes the territories of the Russian Far East, Japan, Korea, and Northeast China, whereas its invasive range includes West Siberia, with further expansion westward. Surprisingly, we revealed a difference in the patterns of Wolbachia prevalence for males and females. Infection rate and Wolbachia titers were higher in females than in males. ST-533, the only haplotype of Wolbachia supergroup B, was associated with a minimum of three out of the five described mitochondrial haplotypes.
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8
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Owen CL, Stern DB, Hilton SK, Crandall KA. Hemiptera phylogenomic resources: Tree‐based orthology prediction and conserved exon identification. Mol Ecol Resour 2020; 20:1346-1360. [DOI: 10.1111/1755-0998.13180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/02/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Christopher L. Owen
- Computational Biology Institute George Washington University Washington DC USA
- Systematic Entomology Laboratory USDA‐ARS Beltsville MD USA
| | - David B. Stern
- Computational Biology Institute George Washington University Washington DC USA
- Department of Integrative Biology University of Wisconsin ‐ Madison Madison WI USA
| | - Sarah K. Hilton
- Computational Biology Institute George Washington University Washington DC USA
- Department of Genome Sciences University of Washington Washington DC USA
| | - Keith A. Crandall
- Computational Biology Institute George Washington University Washington DC USA
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9
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Huang W, Xie X, Peng F, Liang X, Wang X, Chen X. Optimizing the widely used nuclear protein-coding gene primers in beetle phylogenies and their application in the genus Sasajiscymnus Vandenberg (Coleoptera: Coccinellidae). Ecol Evol 2020; 10:7731-7738. [PMID: 32760560 PMCID: PMC7391345 DOI: 10.1002/ece3.6497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/10/2020] [Accepted: 06/02/2020] [Indexed: 11/26/2022] Open
Abstract
Advances in genomic biology and the increasing availability of genomic resources allow developing hundreds of nuclear protein-coding (NPC) markers, which can be used in phylogenetic research. However, for low taxonomic levels, it may be more practical to select a handful of suitable molecular loci for phylogenetic inference. Unfortunately, the presence of degenerate primers of NPC markers can be a major impediment, as the amplification success rate is low and they tend to amplify nontargeted regions. In this study, we optimized five NPC fragments widely used in beetle phylogenetics (i.e., two parts of carbamoyl-phosphate synthetase: CADXM and CADMC, Topoisomerase, Wingless and Pepck) by reducing the degenerate site of primers and the length of target genes slightly. These five NPC fragments and 6 other molecular loci were amplified to test the monophyly of the coccinellid genus Sasajiscymnus Vandenberg. The analysis of our molecular data set clearly supported the genus Sasajiscymnus may be monophyletic but confirmation with an extended sampling is required. A fossil-calibrated chronogram was generated by BEAST, indicating an origin of the genus at the end of the Cretaceous (77.87 Myr). Furthermore, a phylogenetic informativeness profile was generated to compare the phylogenetic properties of each gene more explicitly. The results showed that COI provides the strongest phylogenetic signal among all the genes, but Pepck, Topoisomerase, CADXM and CADMC are also relatively informative. Our results provide insight into the evolution of the genus Sasajiscymnus, and also enrich the molecular data resources for further study.
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Affiliation(s)
- Weidong Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiufeng Xie
- Guangdong Agriculture Industry Business Polytechnic CollegeGuangzhouChina
| | - Feng Peng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xinyue Liang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xingmin Wang
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiaosheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
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10
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Li W, Chen B, Huo L, Chen X, Wang X. New records and checklist of Chilocorini (Coleoptera: Coccinellidae) from China. Biodivers Data J 2020; 8:e51092. [PMID: 32665761 PMCID: PMC7329919 DOI: 10.3897/bdj.8.e51092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/10/2020] [Indexed: 12/03/2022] Open
Abstract
Background China is one of the countries with the greatest species diversity of Chilocorini (Coleoptera: Coccinellidae), including nearly forty-five percent of the known genera and fourteen percent of all described species in this tribe. Recently, we discovered three species previously not recorded in China. New information In this study, three species Priscibrumusuropygialis (Mulsant, 1853), Priscibrumusdisjunctus Canepari, 1997 and Brumusoctosignatus (Gebler, 1830) are documented for the first time in China. Brumusoctosignatus is the first member of the genus Brumus Mulsant, 1850 recorded in China. Detailed descriptions, illustrations and distributions of these three species are provided. A checklist of Chinese Chilocorini is also given.
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Affiliation(s)
- Wenjing Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou China
| | - Bingxu Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences Guangzhou China
| | - Lizhi Huo
- Key Laboratory of Bio-Pesticide Innovation and Application, Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province; Engineering Research Center of Biological Control, Ministry of Education & Guangdong Province, South China Agricultural University, Guangzhou, China Key Laboratory of Bio-Pesticide Innovation and Application, Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province; Engineering Research Center of Biological Control, Ministry of Education & Guangdong Province, South China Agricultural University Guangzhou China
| | - Xiaosheng Chen
- Key Laboratory of Bio-Pesticide Innovation and Application, Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province; Engineering Research Center of Biological Control, Ministry of Education & Guangdong Province, South China Agricultural University, Guangzhou, China Key Laboratory of Bio-Pesticide Innovation and Application, Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province; Engineering Research Center of Biological Control, Ministry of Education & Guangdong Province, South China Agricultural University Guangzhou China
| | - Xingmin Wang
- Key Laboratory of Bio-Pesticide Innovation and Application, Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province; Engineering Research Center of Biological Control, Ministry of Education & Guangdong Province, South China Agricultural University, Guangzhou, China Key Laboratory of Bio-Pesticide Innovation and Application, Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province; Engineering Research Center of Biological Control, Ministry of Education & Guangdong Province, South China Agricultural University Guangzhou China
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11
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Gäde G, Šimek P, Marco HG. Structural diversity of adipokinetic hormones in the hyperdiverse coleopteran Cucujiformia. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 102:e21611. [PMID: 31471923 DOI: 10.1002/arch.21611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Seventeen species of the coleopteran series Cucujiformia are investigated for the presence and sequence of putative adipokinetic hormones (AKHs). Cucujiformia includes species from the major superfamilies, that is, Chrysomeloidea, Curculionoidea, Cucujoidea, and Tenebrionoidea. The clade Phytophaga in which the Chrysomeloidea and Curculionoidea reside, harbor very detrimental species for agriculture and forestry. Thus, this study aims not only to demonstrate the structural biodiversity of AKHs in these beetle species and possible evolutionary trends but also to determine whether the AKHs from harmful pest species can be used as lead substances for a future putative insecticide that is harmless to beneficial insects. Sequence analysis of AKHs is achieved by liquid chromatography coupled to mass spectrometry. Most of the investigated species contain AKH octapeptides in their corpora cardiaca, although previously published work also found a few decapeptides, which we comment on. The signature and sole AKH in cerambycidae Chrysomeloidea and Curculionoidea is Peram-CAH-I (pEVNFSPNW amide), which is also found in the majority of chrysomelidae Chrysomeloidea and in the one investigated species of Cucujoidea albeit in a few cases associated with a second AKH which can be either Peram-CAH-II (pELTFTPNW amide), Emppe-AKH (pEVNFTPNW amide), or Micvi-CC (pEINFTPNW amide). The most often encountered AKH in Tenebrionoidea, family Meloidae as well as family Tenebrionidae, is Tenmo-HrTH (pELNFSPNW amide) followed by Pyrap-AKH (pELNFTPNW amide) and a Tenmo-HrTH extended decapeptide (in Meloidae). Finally, we examine AKH sequences from 43 species of cucujiform beetles, including the superfamily Coccinelloidea for a possible lead compound for producing a cucujiform-specific pesticide.
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Affiliation(s)
- Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Petr Šimek
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
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12
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Peris D, Rust J. Cretaceous beetles (Insecta: Coleoptera) in amber: the palaeoecology of this most diverse group of insects. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Beetles, the most successful group of invertebrates on Earth, have a worldwide distribution and an outstanding fossil record. In addition, they are well known as inclusions in fossil resin. In historical studies of fossil material, specimens were often named and described without placing the taxa in an ecological context. However, the research philosophy for fossil beetles has changed over the past few years. In this article, we summarize the palaeoecological interpretations of fossil beetles from Cretaceous ambers, which includes species from 69 families, most of which were described during the last 3 years. By analysing current habits of those families, we argue that saproxylicity was the most common feeding strategy for these fossil beetles. More specifically, fungivorous species appear to dominate. In contrast, we find only anecdotal evidence for the presence of wood-boring groups, and it is thus necessary to identify alternative abiotic or biotic processes that are responsible for the copious resin production at this time. Finally, the recent description of some beetles as gymnosperm pollinators during the Cretaceous lends more weight to the importance of amber studies in addressing the role of beetles in the evolution of pollination strategies.
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Affiliation(s)
- David Peris
- Institut für Geowissenschaften und Meteorologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jes Rust
- Institut für Geowissenschaften und Meteorologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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13
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Gustafson GT, Alexander A, Sproul JS, Pflug JM, Maddison DR, Short AEZ. Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecol Evol 2019; 9:6933-6948. [PMID: 31312430 PMCID: PMC6617817 DOI: 10.1002/ece3.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/10/2023] Open
Abstract
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.
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Affiliation(s)
- Grey T Gustafson
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.,Biodiversity Institute University of Kansas Lawrence Kansas
| | - Alana Alexander
- Biodiversity Institute University of Kansas Lawrence Kansas.,Department of Anatomy, School of Biomedical Sciences University of Otago Dunedin New Zealand
| | - John S Sproul
- Department of Integrative Biology Oregon State University Corvallis Oregon.,Department of Biology University of Rochester Rochester New York
| | - James M Pflug
- Department of Integrative Biology Oregon State University Corvallis Oregon
| | - David R Maddison
- Department of Integrative Biology Oregon State University Corvallis Oregon
| | - Andrew E Z Short
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.,Biodiversity Institute University of Kansas Lawrence Kansas
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14
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Zhang Y, Deng S, Liang D, Zhang P. Sequence capture across large phylogenetic scales by using pooled PCR-generated baits: A case study of Lepidoptera. Mol Ecol Resour 2019; 19:1037-1051. [PMID: 31012219 DOI: 10.1111/1755-0998.13026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/03/2019] [Accepted: 04/16/2019] [Indexed: 11/30/2022]
Abstract
Sequence capture across large phylogenetic scales is not easy because hybridization capture is only effective when the genetic distance between the bait and target is small. Here, we propose a simple but effective strategy to tackle this issue: pooling DNA from a number of selected representative species of different clades to prepare PCR-generated baits to minimize the genetic distance between the bait and target. To demonstrate the utility of this strategy, we newly developed a set of universal nuclear markers (including 94 nuclear protein-coding genes) for Lepidoptera, a superdiverse insect group. We used a DNA pool from six lepidopteran species (representing six superfamilies) to prepare PCR baits for the 94 markers. These homemade PCR baits were used to capture sequence data from 43 species of 17 lepidopteran families, and 94% of the target loci were recovered. We constructed two data sets from the obtained data (one containing ~90 kb target coding sequences and the other containing ~120 kb target + flanking coding sequences). Both data sets yielded highly similar and well-resolved trees with 90% of nodes having >95% bootstrap support. Our capture experiment indicated that using DNA mixtures pooled from different clade-representative species of Lepidoptera to prepare PCR baits can reliably capture a large number of targeted nuclear markers across different Lepidoptera lineages. We hope that this newly developed nuclear marker set will serve as a new phylogenetic tool for Lepidoptera phylogenetics, and the PCR bait preparation strategy can facilitate the application of sequence capture techniques by researchers to accelerate data collection.
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Affiliation(s)
- Yuan Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
| | - Shaohong Deng
- State Key Laboratory of Biocontrol, School of Life Sciences, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, China
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15
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Luo D, Li Y, Zhao Q, Zhao L, Ludwig A, Peng Z. Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers. Genes (Basel) 2019; 10:E38. [PMID: 30634684 PMCID: PMC6356338 DOI: 10.3390/genes10010038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 11/16/2022] Open
Abstract
Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called "living fossil" species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.
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Affiliation(s)
- Dehuai Luo
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Lianpeng Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany.
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China.
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16
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Liu Y, Liu S, Yeh CF, Zhang N, Chen G, Que P, Dong L, Li SH. The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies. Sci Rep 2018; 8:15723. [PMID: 30356056 PMCID: PMC6200822 DOI: 10.1038/s41598-018-33646-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/21/2018] [Indexed: 11/24/2022] Open
Abstract
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Simin Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chia-Fen Yeh
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Nan Zhang
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Guoling Chen
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Pinjia Que
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China.
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17
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Zhang SQ, Che LH, Li Y, Dan Liang, Pang H, Ślipiński A, Zhang P. Evolutionary history of Coleoptera revealed by extensive sampling of genes and species. Nat Commun 2018; 9:205. [PMID: 29335414 PMCID: PMC5768713 DOI: 10.1038/s41467-017-02644-4] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/15/2017] [Indexed: 01/04/2023] Open
Abstract
Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic. The species-poor Nosodendridae is robustly recovered in a novel position sister to Staphyliniformia, Bostrichiformia, and Cucujiformia. Our divergence time analyses suggest that the crown group of extant beetles occurred ~297 million years ago (Mya) and that ~64% of families originated in the Cretaceous. Most of the herbivorous families experienced a significant increase in diversification rate during the Cretaceous, thus suggesting that the rise of angiosperms in the Cretaceous may have been an 'evolutionary impetus' driving the hyperdiversity of herbivorous beetles.
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Affiliation(s)
- Shao-Qian Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Li-Heng Che
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yun Li
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia.
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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18
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Li J, He C, Guo P, Zhang P, Liang D. A workflow of massive identification and application of intron markers using snakes as a model. Ecol Evol 2017; 7:10042-10055. [PMID: 29238535 PMCID: PMC5723593 DOI: 10.1002/ece3.3525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/27/2017] [Accepted: 10/02/2017] [Indexed: 11/29/2022] Open
Abstract
Relative to the commonly used mitochondrial and nuclear protein-coding genes, the noncoding intron sequences are a promising source of informative markers that have the potential to resolve difficult phylogenetic nodes such as rapid radiations and recent divergences. Yet many issues exist in the use of intron markers, which prevent their extensive application as conventional markers. We used the diverse group of snakes as an example to try paving the way for massive identification and application of intron markers. We performed a series of bioinformatics screenings which identified appropriate introns between single-copy and conserved exons from two snake genomes, adding particular constraints on sequence length variability and sequence variability. A total of 1,273 candidate intron loci were retrieved. Primers for nested polymerase chain reaction (PCR) were designed for over a hundred candidates and tested in 16 snake representatives. 96 intron markers were developed that could be amplified across a broad range of snake taxa with high PCR successful rates. The markers were then applied to 49 snake samples. The large number of amplicons was subjected to next-generation sequencing (NGS). An analytic strategy was developed to accurately recover the amplicon sequences, and approximately, 76% of the marker sequences were recovered. The average p-distances of the intron markers at interfamily, intergenus, interspecies, and intraspecies levels were .168, .052, .015, and .004, respectively, suggesting that they were useful to study snake relationships of different evolutionary depths. A snake phylogeny was constructed with the intron markers, which produced concordant results with robust support at both interfamily and intragenus levels. The intron markers provide a convenient way to explore the signals in the noncoding regions to address the controversies on the snake tree. Our improved strategy of genome screening is effective and can be applied to other animal groups. NGS coupled with appropriate sequence processing can greatly facilitate the extensive application of molecular markers.
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Affiliation(s)
- Jiang‐Ni Li
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Chong He
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Peng Guo
- College of Life Sciences and Food EngineeringYibin UniversityYibinChina
| | - Peng Zhang
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Dan Liang
- State Key Laboratory of BiocontrolCollege of Ecology and EvolutionSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
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