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Song N, Wang MM, Huang WC, Wu ZY, Shao R, Yin XM. Phylogeny and evolution of hemipteran insects based on expanded genomic and transcriptomic data. BMC Biol 2024; 22:190. [PMID: 39218865 PMCID: PMC11367992 DOI: 10.1186/s12915-024-01991-1] [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: 04/14/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Hemiptera is the fifth species-rich order of insects and the most species-rich order of hemimetabolous insects, including numerous insect species that are of agricultural or medical significance. Despite much effort and recent advance in inferring the Hemiptera phylogeny, some high-level relationships among superfamilies remain controversial. RESULTS We sequenced the genomes of 64 hemipteran species from 15 superfamilies and the transcriptomes of two additional scale insect species, integrating them with existing genomic and transcriptomic data to conduct a comprehensive phylogenetic analysis of Hemiptera. Our datasets comprise an average of 1625 nuclear loci of 315 species across 27 superfamilies of Hemiptera. Our analyses supported Cicadoidea and Cercopoidea as sister groups, with Membracoidea typically positioned as the sister to Cicadoidea + Cercopoidea. In most analyses, Aleyrodoidea was recovered as the sister group of all other Sternorrhyncha. A sister-group relationship was supported between Coccoidea and Aphidoidea + Phylloxeroidea. These relationships were further supported by four-cluster likelihood mapping analyses across diverse datasets. Our ancestral state reconstruction indicates phytophagy as the primary feeding strategy for Hemiptera as a whole. However, predation likely represents an ancestral state for Heteroptera, with several phytophagous lineages having evolved from predatory ancestors. Certain lineages, like Lygaeoidea, have undergone a reversal transition from phytophagy to predation. Our divergence time estimation placed the diversification of hemipterans to be between 60 and 150 million years ago. CONCLUSIONS By expanding phylogenomic taxon sampling, we clarified the superfamily relationships within the infraorder Cicadomorpha. Our phylogenetic analyses supported the sister-group relationship between the superfamilies Cicadoidea and Cercopoidea, and the superfamily Membracoidea as the sister to Cicadoidea + Cercopoidea. Our divergence time estimation supported the close association of hemipteran diversification with the evolutionary success and adaptive radiation of angiosperms during the Cretaceous period.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, Henan Agricultural University, Zhengzhou, Henan, China
- Centre for Bioinnovation and School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, 4556, QLD, Australia
| | - Miao-Miao Wang
- College of Plant Protection, Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wei-Chao Huang
- Hangzhou Xiaoshan Airport Customs, Hangzhou, Zhejiang, China
| | - Zhi-Yi Wu
- Zhejiang Academy of Science & Technology for Inspection & Quarantine, Hangzhou, Zhejiang, China
| | - Renfu Shao
- Centre for Bioinnovation and School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, 4556, QLD, Australia.
| | - Xin-Ming Yin
- College of Plant Protection, Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, Henan Agricultural University, Zhengzhou, Henan, China.
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2
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Liu D, Cui J, Liu Y, Niu M, Wang F, Zhao Q, Cai B, Zhang H, Wei J. Ultraconserved elements from transcriptome and genome data provide insight into the phylogenomics of Sternorrhyncha (Insecta: Hemiptera). Cladistics 2024. [PMID: 38808591 DOI: 10.1111/cla.12585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.
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Affiliation(s)
- Dajun Liu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, 034000, China
| | - Jinyu Cui
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Yubo Liu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Minmin Niu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Fang Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
| | - Bo Cai
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, No. 9 West Haixiu Road, Haikou, 570311, China
| | - Hufang Zhang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, 034000, China
| | - Jiufeng Wei
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China
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3
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Bossert S, Pauly A, Danforth BN, Orr MC, Murray EA. Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae). Mol Ecol Resour 2024; 24:e13925. [PMID: 38183389 DOI: 10.1111/1755-0998.13925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024]
Abstract
Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.
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Affiliation(s)
- Silas Bossert
- Department of Entomology, Washington State University, Pullman, Washington, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alain Pauly
- Royal Belgian Institute of Natural Sciences, O.D. Taxonomy and Phylogeny, Brussels, Belgium
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, Washington, USA
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4
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Paz-Sedano S, Moles J, Smirnoff D, Gosliner TM, Pola M. A combined phylogenetic strategy illuminates the evolution of Goniodorididae nudibranchs (Mollusca, Gastropoda, Heterobranchia). Mol Phylogenet Evol 2024; 192:107990. [PMID: 38072142 DOI: 10.1016/j.ympev.2023.107990] [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: 08/16/2023] [Revised: 10/27/2023] [Accepted: 12/07/2023] [Indexed: 01/08/2024]
Abstract
Goniodorididae is a family of small dorid nudibranchs distributed worldwide that feed on entoprocts, ascidians, and bryozoans. The evolutionary relationships between its taxa have been uncertain due to the limited taxa available for phylogenetic analyses; some genera being paraphyletic. The family includes a remarkable number of synonymized genera in which the species richness is unequally distributed, while some genera have dozens of species others are monospecific. Some clades are very uniform morphologically while others are considered highly variable. To increase backbone phylogenetic resolution a target enrichment approach of ultra-conserved elements was aimed at representative Goniodorididae species for the first time. Additionally, we increase species representation by including mitochondrial markers cytochrome c oxidase subunit I and ribosomal RNA 16S as well as nuclear Histone 3 and ribosomal RNA 18S from 109 Goniodorididae species, out of approximately 160 currently valid species. Maximum likelihood and Bayesian inference analyses were performed to infer the phylogeny of the family. As a result, two subfamilies and eleven genera were elucidated. The synonymized genera Bermudella, Cargoa, and Ceratodoris are here resurrected and a new genus, Naisdoris gen. nov., is described. The clades included taxa with shared prey preference, showing that trophic behavior could have driven species evolution and morphological uniqueness within the family Goniodorididae.
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Affiliation(s)
- Sofía Paz-Sedano
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain.
| | - Juan Moles
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Dimitri Smirnoff
- Department of Invertebrate Zoology, California Academy of Sciences, San Francisco, CA, USA
| | - Terrence M Gosliner
- Department of Invertebrate Zoology, California Academy of Sciences, San Francisco, CA, USA
| | - Marta Pola
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Madrid, Spain; Biodiversity and Global Change Research Center (CIBC-UAM), Campus of International Excellence UAM + CSIC, Madrid, Spain
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Friedrich M. Parallel Losses of Blue Opsin Correlate with Compensatory Neofunctionalization of UV-Opsin Gene Duplicates in Aphids and Planthoppers. INSECTS 2023; 14:774. [PMID: 37754742 PMCID: PMC10531960 DOI: 10.3390/insects14090774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Expanding on previous efforts to survey the visual opsin repertoires of the Hemiptera, this study confirms that homologs of the UV- and LW-opsin subfamilies are conserved in all Hemiptera, while the B-opsin subfamily is missing from the Heteroptera and subgroups of the Sternorrhyncha and Auchenorrhyncha, i.e., aphids (Aphidoidea) and planthoppers (Fulgoroidea), respectively. Unlike in the Heteroptera, which are characterized by multiple independent expansions of the LW-opsin subfamily, the lack of B-opsin correlates with the presence of tandem-duplicated UV-opsins in aphids and planthoppers. Available data on organismal wavelength sensitivities and retinal gene expression patterns lead to the conclusion that, in both groups, one UV-opsin paralog shifted from ancestral UV peak sensitivity to derived blue sensitivity, likely compensating for the lost B-opsin. Two parallel bona fide tuning site substitutions compare to 18 non-corresponding amino acid replacements in the blue-shifted UV-opsin paralogs of aphids and planthoppers. Most notably, while the aphid blue-shifted UV-opsin clade is characterized by a replacement substitution at one of the best-documented UV/blue tuning sites (Rhodopsin site 90), the planthopper blue-shifted UV-opsin paralogs retained the ancestral lysine at this position. Combined, the new findings identify aphid and planthopper UV-opsins as a new valuable data sample for studying adaptive opsin evolution.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA;
- Department of Ophthalmological, Visual, and Anatomical Sciences, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA
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6
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Forthman M, Gordon ERL, Kimball RT. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). ROYAL SOCIETY OPEN SCIENCE 2023; 10:230307. [PMID: 37388308 PMCID: PMC10300676 DOI: 10.1098/rsos.230307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023]
Abstract
Target capture is widely used in phylogenomic, ecological and functional genomic studies. Bait sets that allow capture from a diversity of species can be advantageous, but high-sequence divergence from baits can limit yields. Currently, only four experimental comparisons of a critical target capture parameter, hybridization temperature, have been published. These have been in vertebrates, where bait divergences are typically low, and none include invertebrates where bait-target divergences may be higher. Most invertebrate capture studies use a fixed, high hybridization temperature to maximize the proportion of on-target data, but many report low locus recovery. Using leaf-footed bugs (Hemiptera: Coreoidea), we investigate the effect of hybridization temperature on capture success of ultraconserved elements targeted by (i) baits developed from divergent hemipteran genomes and (ii) baits developed from less divergent coreoid transcriptomes. Lower temperatures generally resulted in more contigs and improved recovery of targets despite a lower proportion of on-target reads, lower read depth and more putative paralogues. Hybridization temperatures had less of an effect when using transcriptome-derived baits, which is probably due to lower bait-target divergences and greater bait tiling density. Thus, accommodating low hybridization temperatures during target capture can provide a cost-effective, widely applicable solution to improve invertebrate locus recovery.
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Affiliation(s)
- Michael Forthman
- California State Collection of Arthropods, Plant Pest Diagnostics Branch, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- Entomology and Nematology Department, University of Florida, 1881 Natural Area Drive, Gainesville, FL 32611, USA
| | - Eric R. L. Gordon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA
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7
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Forthman M, Downie C, Miller CW, Kimball RT. Evolution of stridulatory mechanisms: vibroacoustic communication may be common in leaf-footed bugs and allies (Heteroptera: Coreoidea). ROYAL SOCIETY OPEN SCIENCE 2023; 10:221348. [PMID: 37122949 PMCID: PMC10130729 DOI: 10.1098/rsos.221348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/07/2023] [Indexed: 05/03/2023]
Abstract
Intra- and interspecific communication is crucial to fitness via its role in facilitating mating, territoriality and defence. Yet, the evolution of animal communication systems is puzzling-how do they originate and change over time? Studying stridulatory morphology provides a tractable opportunity to deduce the origin and diversification of a communication mechanism. Stridulation occurs when two sclerotized structures rub together to produce vibratory and acoustic (vibroacoustic) signals, such as a cricket 'chirp'. We investigated the evolution of stridulatory mechanisms in the superfamily Coreoidea (Hemiptera: Heteroptera), a group of insects known for elaborate male fighting behaviours and enlarged hindlegs. We surveyed a large sampling of taxa and used a phylogenomic dataset to investigate the evolution of stridulatory mechanisms. We identified four mechanisms, with at least five evolutionary gains. One mechanism, occurring only in male Harmostini (Rhopalidae), is described for the first time. Some stridulatory mechanisms appear to be non-homoplastic apomorphies within Rhopalidae, while others are homoplastic or potentially homoplastic within Coreidae and Alydidae, respectively. We detected no losses of these mechanisms once evolved, suggesting they are adaptive. Our work sets the stage for further behavioural, evolutionary and ecological studies to better understand the context in which these traits evolve and change.
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Affiliation(s)
- Michael Forthman
- California State Collection of Arthropods, Plant Pest Diagnostics Branch, California Department of Food & Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- Entomology & Nematology Department, University of Florida, 1881 Natural Area Drive, Gainesville, FL 32611, USA
| | | | - Christine W. Miller
- Entomology & Nematology Department, University of Florida, 1881 Natural Area Drive, Gainesville, FL 32611, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA
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8
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Liu D, Niu M, Lu Y, Wei J, Zhang H. Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.984396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Scale insects (Coccoidea) are morphologically specialized members of the order Hemiptera, with 56 families recognized to date. However, the phylogenetic relationships within and among families are poorly resolved. In this study, to further characterize the phylogenetic relationships among scale insects, an ultraconserved element (UCE) probe set was designed specifically for Coccoidea based on three low-coverage whole genome sequences along with three publicly available genomes. An in silico test including eight additional genomes was performed to evaluate the effectiveness of the probe set. Most scale insect lineages were recovered by the phylogenetic analysis. This study recovered the monophyly of neococcoids. The newly developed UCE probe set has the potential to reshape and improve our understanding of the phylogenetic relationships within and among families of scale insects at the genome level.
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New Cretaceous Bugs from Northeastern China Imply the Systematic Position of Pachymeridiidae (Hemiptera: Heteroptera). INSECTS 2022; 13:insects13080689. [PMID: 36005314 PMCID: PMC9408836 DOI: 10.3390/insects13080689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/27/2023]
Abstract
Varicapitatus sinuolatus gen. et sp. nov. is described from the Yixian Formation of Northeastern China. Based on the new specimens, this study discusses the morphological characteristics and taxonomic position of Pachymeridiidae: Pachymeridiidae belongs to Pentatomomorpha and is more closely related to Lygaeoidea. In Heteroptera, the costal fracture of the forewing is a homoplastic characteristic, already evolved independently several times among most taxa before the Early Cretaceous. The pulvillus under the claw in Pentatomomorpha is also a homoplastic characteristic. In Pachymeridiidae, the forewing costal fracture and absence of pulvillus can be recognized as an independent evolution or convergence, implying that pachymeridiids may have different flight and crawling behaviors distinct from other Pentatomomorpha groups.
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Dong X, Wang K, Tang Z, Zhang Y, Yi W, Xue H, Zheng C, Bu W. Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21878. [PMID: 35181948 DOI: 10.1002/arch.21878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/23/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Coreoidea (Insecta: Hemiptera: Heteroptera) is a widely distributed and agriculturally important bugs. However, the phylogeny of Coreoidea lacked consensus on higher-level relationships and several studies by comparative morphological characters and molecular data suggested the non-monophyly of two families: Coreidae and Alydidae. The mitochondrial genome (mitogenome) has long been thought to be a significant marker to understand phylogenetic relationships, but the mitogenome in Alydidae is scarce to date. In the present study, we gathered the mitogenomes of 28 species from four families of Coreoidea excluding Hyocephalidae (Alydidae, Coreidae, Rhopalidae, and Stenocephalidae), including four newly sequenced mitogenomes of Alydidae, and conducted mitogenomic organization and phylogenetic studies. We used maximum likelihood and Bayesian inference methods to infer the higher-level phylogeny from the perspective of mitogenomes, primarily to investigate the phylogenetic relationship betweeen Coreidae and Alydidae. We add evidence that neither Alydidae nor Coreidae are monophyletic based on mitogenomes. Newly sequenced mitogenomes of Alydidae have traditional gene structure and gene rearrangement was not found. Alydinae was always recovered as closely related to Pseudophloeinae of the coreid subfamily with high support. The placement of the coreid subfamily Hydarinae and alydid subfamily Micrelytrinae are unstable depending on approach used. In terms of the length and nucleotide composition of the protein coding genes in mitogenomes, Pseudophloeinae and Hydarinae of coreid were more similar to Alydidae. The unsettled classification issues of Coreidae and Alydidae by mitogenomes were demonstrated in this work, indicating that further study is needed.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zechen Tang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yaoyao Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenbo Yi
- Department of Biology, Xinzhou Teachers University, Xinzhou, Shanxi, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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11
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Weyna A, Bourouina L, Galtier N, Romiguier J. Detection of F1 hybrids from single-genome data reveals frequent hybridization in Hymenoptera and particularly ants. Mol Biol Evol 2022; 39:6562163. [PMID: 35363317 PMCID: PMC9021736 DOI: 10.1093/molbev/msac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybridization occupies a central role in many fundamental evolutionary processes, such as speciation or adaptation. Yet, despite its pivotal importance in evolution, little is known about the actual prevalence and distribution of current hybridization across the tree of life. Here we develop and implement a new statistical method enabling the detection of F1 hybrids from single-individual genome sequencing data. Using simulations and sequencing data from known hybrid systems, we first demonstrate the specificity of the method, and identify its statistical limits. Next, we showcase the method by applying it to available sequencing data from more than 1,500 species of Arthropods, including Hymenoptera, Hemiptera, Coleoptera, Diptera, and Archnida. Among these taxa, we find Hymenoptera, and especially ants, to display the highest number of candidate F1 hybrids, suggesting higher rates of recent hybridization between previously isolated gene pools in these groups. The prevalence of F1 hybrids was heterogeneously distributed across ants, with taxa including many candidates tending to harbor specific ecological and life-history traits. This work shows how large-scale genomic comparative studies of recent hybridization can be implemented, uncovering the determinants of first-generation hybridization across whole taxa.
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Affiliation(s)
- Arthur Weyna
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
| | - Lucille Bourouina
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
| | - Jonathan Romiguier
- Institut des Sciences de l'Evolution (UMR 5554), University of Montpellier, CNRS
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12
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Ye F, Kment P, Rédei D, Luo JY, Wang YH, Kuechler SM, Zhang WW, Chen PP, Wu HY, Wu YZ, Sun XY, Ding L, Wang YR, Xie Q. Diversification of the phytophagous lineages of true bugs (Insecta: Hemiptera: Heteroptera) shortly after that of the flowering plants. Cladistics 2022; 38:403-428. [PMID: 35349192 DOI: 10.1111/cla.12501] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 12/20/2022] Open
Abstract
More than 95% of phytophagous true bug (Hemiptera: Heteroptera) species belong to four superfamilies: Miroidea (Cimicomorpha), Pentatomoidea, Coreoidea, and Lygaeoidea (all Pentatomomorpha). These iconic groups of highly diverse, overwhelmingly phytophagous insects include several economically prominent agricultural and silvicultural pest species, though their evolutionary history has not yet been well resolved. In particular, superfamily- and family-level phylogenetic relationships of these four lineages have remained controversial, and the divergence times of some crucial nodes for phytophagous true bugs have hitherto been little known, which hampers a better understanding of the evolutionary processes and patterns of phytophagous insects. In the present study, we used 150 species and concatenated nuclear and mitochondrial protein-coding genes and rRNA genes to infer the phylogenetic relationships within the Terheteroptera (Cimicomorpha + Pentatomomorpha) and estimated their divergence times. Our results support the monophyly of Cimicomorpha, Pentatomomorpha, Miroidea, Pentatomoidea, Pyrrhocoroidea, Coreoidea, and Lygaeoidea. The phylogenetic relationships across phytophagous lineages are largely congruent at deep nodes across the analyses based on different datasets and tree-reconstructing methods with just a few exceptions. Estimated divergence times and ancestral state reconstructions for feeding habit indicate that phytophagous true bugs explosively radiated in the Early Cretaceous-shortly after the angiosperm radiation-with the subsequent diversification of the most speciose clades (Mirinae, Pentatomidae, Coreinae, and Rhyparochromidae) in the Late Cretaceous.
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Affiliation(s)
- Fei Ye
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Petr Kment
- Department of Entomology, National Museum, Praha, Czech Republic
| | | | - Jiu-Yang Luo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yan-Hui Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Stefan M Kuechler
- Department of Animal Ecology II, University of Bayreuth, Bayreuth, Germany
| | | | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis, Leiden, Netherlands
| | - Hao-Yang Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Xiao-Ya Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Lu Ding
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yue-Ran Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiang Xie
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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13
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Phylogenomic analysis with improved taxon sampling corroborates an Alydidae + Hydarinae + Pseudophloeinae clade (Heteroptera: Coreoidea: Alydidae, Coreidae). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00548-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Chen D, Hosner PA, Dittmann DL, O'Neill JP, Birks SM, Braun EL, Kimball RT. Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements. BMC Ecol Evol 2021; 21:209. [PMID: 34809586 PMCID: PMC8609756 DOI: 10.1186/s12862-021-01935-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results. RESULTS In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different "gene shopping" schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree. CONCLUSIONS We provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL, USA
- Natural History Museum of Denmark and Center for Global Mountain Biodiversity, University of Copenhagen, Copenhagen, Denmark
| | - Donna L Dittmann
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - John P O'Neill
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Sharon M Birks
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
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15
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White ND, Batz ZA, Braun EL, Braun MJ, Carleton KL, Kimball RT, Swaroop A. A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution. Mol Ecol Resour 2021; 22:587-601. [PMID: 34652059 DOI: 10.1111/1755-0998.13496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.
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Affiliation(s)
- Noor D White
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA
| | - Zachary A Batz
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Karen L Carleton
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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16
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Miller CD, Forthman M, Miller CW, Kimball RT. Extracting ‘legacy loci’ from an invertebrate sequence capture data set. ZOOL SCR 2021. [DOI: 10.1111/zsc.12513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Caroline D. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
| | - Michael Forthman
- Department of Entomology & Nematology University of Florida Gainesville FL USA
- California State Collection of Arthropods Plant Pest Diagnostics Branch California Department of Food & Agriculture Sacramento CA USA
| | - Christine W. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
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17
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Cruaud A, Delvare G, Nidelet S, Sauné L, Ratnasingham S, Chartois M, Blaimer BB, Gates M, Brady SG, Faure S, van Noort S, Rossi JP, Rasplus JY. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics 2021; 37:1-35. [PMID: 34478176 DOI: 10.1111/cla.12416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2020] [Indexed: 11/30/2022] Open
Abstract
Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.
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Affiliation(s)
- Astrid Cruaud
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gérard Delvare
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.,UMR CBGP, CIRAD, F-34398, Montpellier, France
| | - Sabine Nidelet
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Laure Sauné
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Marguerite Chartois
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Michael Gates
- USDA, ARS, SEL, c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Seán G Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sariana Faure
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, PO Box 61, Cape Town, 8000, South Africa.,Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Pierre Rossi
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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18
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Cumming RT, Tirant SL. Drawing the Excalibur bug from the stone: adding credibility to the double-edged sword hypothesis of coreid evolution (Hemiptera, Coreidae). Zookeys 2021; 1043:117-131. [PMID: 34163298 PMCID: PMC8217075 DOI: 10.3897/zookeys.1043.67730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/22/2021] [Indexed: 12/02/2022] Open
Abstract
A new genus and species of exaggerated antennae Coreidae is described from Myanmar amber of the Late Cretaceous (Cenomanian stage). Ferriantennaexcaliburgen. et sp. nov. appears related to another Cretaceous coreid with exaggerated antennae, Magnusantenna Du & Chen, 2021, but can be differentiated by the fourth antennal segment which is short and paddle-like, the undulating shape of the pronotum and mesonotum, and the shorter and thicker legs. The new coreid, with elaborately formed antennae and simple hind legs instead of the typical extant coreid morphology with simple antennae and elaborately formed hind legs, begs the question: why were the elaborate features of the antennae lost in favor of ornate hind legs? Features that are large and showy are at higher risk of being attacked by predators or stuck in a poor molt and subjected to autotomy and are therefore lost at a higher rate than simple appendages. We hypothesize that because elaborate antennae play an additional significant sensory role compared to elaborate hind legs, that evolutionarily it is more costly to have elaborate antennae versus elaborate hind legs. Thus, through the millenia, as coreid evolution experimented with elaborate/ornate features, those on the antennae were likely selected against in favor of ornate hind legs.
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Affiliation(s)
- Royce T Cumming
- Montreal Insectarium, 4581 rue Sherbrooke est, Montréal , H1X 2B2, Québec, Canada Montreal Insectarium Montréal Canada.,Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA American Museum of Natural History New York United States of America.,Biology, Graduate Center, City University of New York, NY, USA City University of New York New York United States of America
| | - Stéphane Le Tirant
- Montreal Insectarium, 4581 rue Sherbrooke est, Montréal , H1X 2B2, Québec, Canada Montreal Insectarium Montréal Canada
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19
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Knyshov A, Gordon ERL, Weirauch C. New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics. PeerJ 2021; 9:e11019. [PMID: 33850647 PMCID: PMC8019319 DOI: 10.7717/peerj.11019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/06/2021] [Indexed: 01/03/2023] Open
Abstract
Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate goal of generating a phylogeny. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, which may increase rates of false positive results. Many tools are also difficult to install and may lack adequate user resources. Here, we describe a program that uses freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance compared to other commonly used bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, and on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated or unannotated, low or high depth shotgun, and target capture assemblies as well or better than other software as assessed by recovering the most genes with maximal coverage and with a low rate of false positives throughout all datasets. When assessing this combination of criteria, ALiBaSeq is frequently the best evaluated tool for gathering the most comprehensive and accurate phylogenetic alignments on all types of data tested. The software (implemented in Python), tutorials, and manual are freely available at https://github.com/AlexKnyshov/alibaseq.
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Affiliation(s)
- Alexander Knyshov
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Eric R L Gordon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Christiane Weirauch
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
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20
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Comprehensive phylogeny of Myrmecocystus honey ants highlights cryptic diversity and infers evolution during aridification of the American Southwest. Mol Phylogenet Evol 2020; 155:107036. [PMID: 33278587 DOI: 10.1016/j.ympev.2020.107036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 11/22/2022]
Abstract
The New World ant genus Myrmecocystus Wesmael, 1838 (Formicidae: Formicinae: Lasiini) is endemic to arid and semi-arid habitats of the western United States and Mexico. Several intriguing life history traits have been described for the genus, the best-known of which are replete workers, that store liquified food in their largely expanded crops and are colloquially referred to as "honeypots". Despite their interesting biology and ecological importance for arid ecosystems, the evolutionary history of Myrmecocystus ants is largely unknown and the current taxonomy presents an unsatisfactory systematic framework. We use ultraconserved elements to infer the evolutionary history of Myrmecocystus ants and provide a comprehensive, dated phylogenetic framework that clarifies the molecular systematics within the genus with high statistical support, reveals cryptic diversity, and reconstructs ancestral foraging activity. Using maximum likelihood, Bayesian and species tree approaches on a data set of 134 ingroup specimens (including samples from natural history collections and type material), we recover largely identical topologies that leave the position of only few clades uncertain and cover the intra- and interspecific variation of 28 of the 29 described and six undescribed species. In addition to traditional support values, such as bootstrap and posterior probability, we quantify genealogical concordance to estimate the effects of conflicting evolutionary histories on phylogenetic inference. Our analyses reveal that the current taxonomic classification of the genus is inconsistent with the molecular phylogenetic inference, and we identify cryptic diversity in seven species. Divergence dating suggests that the split between Myrmecocystus and its sister taxon Lasius occurred in the early Miocene. Crown group Myrmecocystus started diversifying about 14.08 Ma ago when the gradual aridification of the southwestern United States and northern Mexico led to formation of the American deserts and to adaptive radiations of many desert taxa.
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21
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Kieran TJ. Ultraconserved element bait set for trypanosomatida target enrichment and phylogenetics. Exp Parasitol 2020; 219:108015. [PMID: 33031787 DOI: 10.1016/j.exppara.2020.108015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Lack of knowledge of taxonomic biodiversity and reliable genetic markers in Trypanosomatidae limit our understanding of their phylogenetic relationships. Ultraconserved elements (UCEs) have improved phylogenetic analyses and inferences in many vertebrate and invertebrate taxa. However, it is unknown whether protozoans have these markers, their abundance, and if these could be reliably used for phylogenetics. In this study I design a target enrichment bait set for UCE loci for this group. In silico testing showed good loci recovery rates across 63 taxa and produced consistent, highly supported phylogenetic trees. This bait set adds a new resource of useful genetic markers for Trypanosomatidae phylogenetics.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, 206 Environmental Health Science Building, Athens, GA, 30602, USA.
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22
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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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23
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Drohojowska J, Szwedo J, Żyła D, Huang DY, Müller P. Fossils reshape the Sternorrhyncha evolutionary tree (Insecta, Hemiptera). Sci Rep 2020; 10:11390. [PMID: 32647332 PMCID: PMC7347605 DOI: 10.1038/s41598-020-68220-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 11/17/2022] Open
Abstract
The Sternorrhyncha, which comprise about 18,700 described recent species, is a suborder of the Hemiptera, one of big five most diverse insect orders. In the modern fauna, these tiny phytophages comprise insects of great ecological and economic importance, like aphids (Aphidomorpha), scale insects (Coccidomorpha), whiteflies (Aleyrodomorpha) and psyllids (Psylloidea). Their evolutionary history can be traced back to the Late Carboniferous, but the early stages of their evolution and diversification is poorly understood, with two known extinct groups-Pincombeomorpha and Naibiomorpha variously placed in classifications and relationships hypotheses. Most of the recent Sternorrhyncha groups radiated rapidly during the Cretaceous. Here we report the new finding of very specialised sternorrhynchans found as inclusions in mid-Cretaceous amber from Kachin state (northern Myanmar), which represent another extinct lineage within this hemipteran suborder. These fossils, proposed to be placed in a new infraorder, are revealed to be related to whiteflies and psyllids. We present, also for the first time, the results of phylogenetic analyses covering extinct and extant lineages of the Sternorrhyncha.
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Affiliation(s)
- Jowita Drohojowska
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, 9, Bankowa St., 40-007 Katowice, Poland
| | - Jacek Szwedo
- Laboratory of Evolutionary Entomology and Museum of Amber Inclusions, Department of Invertebrate Zoology and Parasitology, University of Gdańsk, 59, Wita Stwosza St., 80-308 Gdańsk, Poland
| | - Dagmara Żyła
- Laboratory of Evolutionary Entomology and Museum of Amber Inclusions, Department of Invertebrate Zoology and Parasitology, University of Gdańsk, 59, Wita Stwosza St., 80-308 Gdańsk, Poland
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA USA
| | - Di-Ying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Patrick Müller
- Kaeshofen, Germany
- Amber Study Group, c/o Geological-Palaeontological Museum of the University of Hamburg, Bundesstraße 55, 20146 Hamburg, Germany
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24
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Kieran TJ, Bayona-Vásquez NJ, Varian CP, Saldaña A, Samudio F, Calzada JE, Gottdenker NL, Glenn TC. Population genetics of two chromatic morphs of the Chagas disease vector Rhodnius pallescens Barber, 1932 in Panamá. INFECTION GENETICS AND EVOLUTION 2020; 84:104369. [PMID: 32442632 DOI: 10.1016/j.meegid.2020.104369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022]
Abstract
Rhodnius pallescens is the principal vector of Chagas disease in Panama. Recently a dark chromatic morph has been discovered in the highlands of Veraguas Province. Limited genetic studies have been conducted with regards to the population structure and dispersal potential of Triatominae vectors, particularly in R. pallescens. Next generation sequencing methods such as RADseq and complete mitochondrial DNA (mtDNA) genome sequencing have great potential for examining vector biology across space and time. Here we utilize a RADseq method (3RAD), along with complete mtDNA sequencing, to examine the population structure of the two chromatic morpho types of R. pallescens in Panama. We sequenced 105 R. pallescens samples from five localities in Panama. We generated a 2216 SNP dataset and 6 complete mtDNA genomes. RADseq showed significant differentiation among the five localities (FCT = 0.695; P = .004), but most of this was between localities with the dark vs. light chromatic morphs (Veraguas vs. Panama Oeste). The mtDNA genomes showed a 97-98% similarity between dark and light chromatic morphs across all genes and a 502 bp insert in light morphs. Thus, both the RADseq and mtDNA data showed highly differentiated clades with essentially no gene flow between the dark and light chromatic morphs from Veraguas and central Panama respectively. We discuss the growing evidence showing clear distinctions between these two morpho types with the possibility that these are separate species, an area of research that requires further investigation. Finally, we discuss the cost-effectiveness of 3RAD which is a third of the cost compared to other RADseq methods used recently in Chagas disease vector research.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, The University of Georgia, Athens, GA, USA
| | - Christina P Varian
- Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA; Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama; Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Facultad de Medicina, Universidad de Panamá, Panama
| | - Franklyn Samudio
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Nicole L Gottdenker
- Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA; Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA; Odum School of Ecology, The University of Georgia, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, The University of Georgia, Athens, GA, USA; Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA.
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25
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Emberts Z, St Mary CM, Howard CC, Forthman M, Bateman PW, Somjee U, Hwang WS, Li D, Kimball RT, Miller CW. The evolution of autotomy in leaf-footed bugs. Evolution 2020; 74:897-910. [PMID: 32267543 PMCID: PMC7317576 DOI: 10.1111/evo.13948] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/24/2020] [Indexed: 01/04/2023]
Abstract
Sacrificing body parts is one of many behaviors that animals use to escape predation. This trait, termed autotomy, is classically associated with lizards. However, several other taxa also autotomize, and this trait has independently evolved multiple times throughout Animalia. Despite having multiple origins and being an iconic antipredatory trait, much remains unknown about the evolution of autotomy. Here, we combine morphological, behavioral, and genomic data to investigate the evolution of autotomy within leaf-footed bugs and allies (Insecta: Hemiptera: Coreidae + Alydidae). We found that the ancestor of leaf-footed bugs autotomized and did so slowly; rapid autotomy (<2 min) then arose multiple times. The ancestor likely used slow autotomy to reduce the cost of injury or to escape nonpredatory entrapment but could not use autotomy to escape predation. This result suggests that autotomy to escape predation is a co-opted benefit (i.e., exaptation), revealing one way that sacrificing a limb to escape predation may arise. In addition to identifying the origins of rapid autotomy, we also show that across species variation in the rates of autotomy can be explained by body size, distance from the equator, and enlargement of the autotomizable appendage.
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Affiliation(s)
- Zachary Emberts
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Colette M St Mary
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Cody Coyotee Howard
- Department of Biology, University of Florida, Gainesville, Florida, 32611.,Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611
| | - Michael Forthman
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611
| | - Philip W Bateman
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6845, Australia
| | - Ummat Somjee
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, 117377, Singapore
| | - Daiqin Li
- Department of Biological Science, National University of Singapore, Singapore, 117543, Singapore
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, 32611
| | - Christine W Miller
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611
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26
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Johnson KP. Putting the genome in insect phylogenomics. CURRENT OPINION IN INSECT SCIENCE 2019; 36:111-117. [PMID: 31546095 DOI: 10.1016/j.cois.2019.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/02/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
Next-generation sequencing technologies provide a substantial increase in the size of molecular phylogenetic datasets that can be obtained for studies of insect systematics. Several new genome reduction approaches are leveraging these technologies to generate large phylogenomic datasets: targeted amplicon sequencing, target capture, and transcriptome sequencing. Although cost effective, these approaches provide limited data for questions outside of phylogenetics. For many groups of insects, sequencing the entire genome at modest coverage is feasible. Using these genomic reads, an automated Target Restricted Assembly Method (aTRAM) can use the results of blast searches to assemble thousands of single copy ortholog genes across a group of interest. These locally assembled genes can then be compiled into very large phylogenomic datasets. These genomic libraries have the advantage in that they also contain reads from the mitochondrial genome and symbiont genomes, as well the entire insect genome, and can be leveraged for additional studies beyond phylogenetics.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820 USA.
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27
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Kulkarni S, Wood H, Lloyd M, Hormiga G. Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae). Mol Ecol Resour 2019; 20:185-203. [PMID: 31599100 DOI: 10.1111/1755-0998.13099] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/11/2019] [Accepted: 09/24/2019] [Indexed: 11/29/2022]
Abstract
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target-capture methods, using the previously designed arachnid-specific probe set, can target a maximum of about 1,000 loci. Here, we develop a specialized target-capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the 'spider-specific' probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe set includes UCEs from the previously designed Arachnida probe set. The new 'spider-specific' probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The 'spider-specific' probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider-specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using maximum likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g. UCE data suggest monophyly of 'symphytognathoids'). Our preferred hypothesis based on topology tests, suggests monophyly of the 'symphytognathoids' (the miniature orb weavers), which in previous studies has only been supported by a combination of morphological and behavioural characters.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Hannah Wood
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Michael Lloyd
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA.,The Jackson Laboratory, Bar Harbor, ME, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
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28
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Simon C, Gordon ERL, Moulds MS, Cole JA, Haji D, Lemmon AR, Lemmon EM, Kortyna M, Nazario K, Wade EJ, Meister RC, Goemans G, Chiswell SM, Pessacq P, Veloso C, McCutcheon JP, Łukasik P. Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.
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Affiliation(s)
- Chris Simon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Eric R L Gordon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - M S Moulds
- Australian Museum Research Institute, Sydney, NSW, Australia
| | - Jeffrey A Cole
- Natural Sciences Division, Pasadena City College, Pasadena, CA, USA
| | - Diler Haji
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | - Michelle Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katherine Nazario
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Elizabeth J Wade
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Department of Natural Sciences and Mathematics, Curry College, Milton, MA, USA
| | - Russell C Meister
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Geert Goemans
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | | | - Pablo Pessacq
- Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas, Esquel, Chubut, Argentina
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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29
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Glenn TC, Nilsen RA, Kieran TJ, Sanders JG, Bayona-Vásquez NJ, Finger JW, Pierson TW, Bentley KE, Hoffberg SL, Louha S, Garcia-De Leon FJ, del Rio Portilla MA, Reed KD, Anderson JL, Meece JK, Aggrey SE, Rekaya R, Alabady M, Belanger M, Winker K, Faircloth BC. Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ 2019; 7:e7755. [PMID: 31616586 PMCID: PMC6791352 DOI: 10.7717/peerj.7755] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/26/2019] [Indexed: 01/02/2023] Open
Abstract
Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in (i.e., getting the smallest possible amount of data from a run); and (3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 × 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: (1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and (2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent Adapterama papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Roger A. Nilsen
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Small Animal Medicine, College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Jon G. Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, United States of America
- Current affiliation: Cornell Institute for Host—Microbe Interaction and Disease, Cornell University, Ithaca, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Francisco J. Garcia-De Leon
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, SC, Instituto Politécnico Nacional, La Paz, Mexico
| | | | - Kurt D. Reed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Jennifer L. Anderson
- Integrated Research and Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, United States of America
| | - Jennifer K. Meece
- Integrated Research and Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, United States of America
| | - Samuel E. Aggrey
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Poultry Science, University of Georgia, Athens, GA, United States of America
| | - Romdhane Rekaya
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
| | - Magdy Alabady
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
| | - Myriam Belanger
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
| | - Kevin Winker
- University of Alaska Museum, Fairbanks, AK, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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30
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Forthman M, Miller CW, Kimball RT. Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic. ZOOL SCR 2019. [DOI: 10.1111/zsc.12353] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michael Forthman
- Entomology & Nematology Department University of Florida Gainesville Florida
| | - Christine W. Miller
- Entomology & Nematology Department University of Florida Gainesville Florida
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