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Skojec C, Earl C, Couch CD, Masonick P, Kawahara AY. Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris). PeerJ 2024; 12:e17365. [PMID: 38827314 PMCID: PMC11144400 DOI: 10.7717/peerj.17365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/18/2024] [Indexed: 06/04/2024] Open
Abstract
The saturniid moth genus Automeris includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. Automeris moths are cryptically colored, with forewings that resemble dead leaves, and conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within Automeris and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of Automeris to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, Pseudautomeris and Leucanella, as well as a morphologically distinct genus, Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to assemble a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports Automeris as a paraphyletic genus, with Leucanella and Pseudautomeris nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of Automeris biology, including geographical distribution patterns, potential drivers of speciation, and ecological adaptations such as antipredator defense mechanisms.
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Affiliation(s)
- Chelsea Skojec
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Chandra Earl
- Bishop Museum, Bernice Pauahi, Honolulu, HI, United States of America
| | - Christian D. Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Paul Masonick
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
- Department of Biology, University of Florida, Gainesville, FL, United States of America
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Nunes R, Storer C, Doleck T, Kawahara AY, Pierce NE, Lohman DJ. Predictors of sequence capture in a large-scale anchored phylogenomics project. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.943361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.
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Cobb NS, Gall LF, Zaspel JM, Dowdy NJ, McCabe LM, Kawahara AY. Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 2019; 7:e8086. [PMID: 31788358 PMCID: PMC6882419 DOI: 10.7717/peerj.8086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a "vast hidden treasure trove" of biodiversity -95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation's decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.
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Affiliation(s)
- Neil S. Cobb
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Lawrence F. Gall
- Entomology Division, Yale Peabody Museum of Natural History, New Haven, CT, United States of America
| | - Jennifer M. Zaspel
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nicolas J. Dowdy
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States of America
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States of America
| | - Lindsie M. McCabe
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
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Hamilton CA, St Laurent RA, Dexter K, Kitching IJ, Breinholt JW, Zwick A, Timmermans MJTN, Barber JR, Kawahara AY. Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives. BMC Evol Biol 2019; 19:182. [PMID: 31533606 PMCID: PMC6751749 DOI: 10.1186/s12862-019-1505-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. RESULTS The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). CONCLUSIONS Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
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Affiliation(s)
- C A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844, USA.
| | - R A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - K Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - I J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - J W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- RAPiD Genomics, 747 SW 2nd Avenue #314, Gainesville, FL, 32601, USA
| | - A Zwick
- Australian National Insect Collection, CSIRO, Clunies Ross St, Acton, ACT, Canberra, 2601, Australia
| | - M J T N Timmermans
- Department of Natural Sciences, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - J R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - A Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
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Anchored hybrid enrichment phylogenomics resolves the backbone of erebine moths. Mol Phylogenet Evol 2018; 131:99-105. [PMID: 30391315 DOI: 10.1016/j.ympev.2018.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/26/2018] [Accepted: 10/30/2018] [Indexed: 12/19/2022]
Abstract
The subfamily Erebinae (Lepidoptera, Erebidae) includes approximately 10,000 species with many still undescribed. It is one of the most diverse clades within the moth superfamily Noctuoidea and encompasses a diversity of ecological habits. Erebine caterpillars feed on a broad range of host plants including several economically important crops. Adults possess a unique array of adaptations for predator defense, including some of the most sensitive hearing organs (tympana) across the Lepidoptera and striking wing coloration to startle visual predators. Despite the relevance of these moths to agriculture and ecological research, a robust phylogenetic framework is lacking. Here we used anchored hybrid enrichment, a relatively new approach in phylogenomics, to resolve relationships among the subfamily. Using the recently developed Lep1 anchored hybrid enrichment probe set, 658 gene fragments with an average length of 320 bp were captured from an exemplar set of 75 erebine species, representing 73 genera and 23 tribes. While the total number of erebine tribes is not firmly established, this represents at least 75% of known tribal level diversity. Anchored hybrid enrichment data were partitioned by locus and by codon position for maximum likelihood phylogenetic analysis and coalescent-based species-tree approaches. Results from our study provided strong nodal support (BP ≥ 95) for nearly all nodes in the partitioned ML tree, solidifying many relationships that were previously uncertain or moderately supported based on morphology or a smaller number of gene fragments. Likelihood analyses confidently resolved the placement of Acantholipini as a sister tribe to Sypnini and all other Erebinae. The remaining tribes were placed in a single, strongly supported clade split into two major subclades. Additionally, 25 tropical species that did not have previous tribal assignments are confidently placed on the phylogeny. Statistical comparisons with Shimodaira-Hasegawa (SH) tests found that our maximum likelihood trees were significantly more likely than alternative hypotheses. This study demonstrates the utility of anchored phylogenomics for resolving relationships within subfamilies of Lepidoptera.
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Toussaint EFA, Breinholt JW, Earl C, Warren AD, Brower AVZ, Yago M, Dexter KM, Espeland M, Pierce NE, Lohman DJ, Kawahara AY. Anchored phylogenomics illuminates the skipper butterfly tree of life. BMC Evol Biol 2018; 18:101. [PMID: 29921227 PMCID: PMC6011192 DOI: 10.1186/s12862-018-1216-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 06/07/2018] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. This is especially true for skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. METHODS To infer a robust phylogenomic hypothesis for Hesperiidae, we sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers. Molecular datasets were analyzed using maximum-likelihood, parsimony and coalescent multi-species phylogenetic methods. RESULTS All analyses converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic trees with strong nodal support at nearly all nodes and all taxonomic levels. Our results support Coeliadinae as the sister group to the remaining skippers, the monotypic Euschemoninae as the sister group to all other subfamilies but Coeliadinae, and the monophyly of Eudaminae plus Pyrginae. Within Pyrginae, Celaenorrhinini and Tagiadini are sister groups, the Neotropical firetips, Pyrrhopygini, are sister to all other tribes but Celaenorrhinini and Tagiadini. Achlyodini is recovered as the sister group to Carcharodini, and Erynnini as sister group to Pyrgini. Within the grass skippers (Hesperiinae), there is strong support for the monophyly of Aeromachini plus remaining Hesperiinae. The giant skippers (Agathymus and Megathymus) once classified as a subfamily, are recovered as monophyletic with strong support, but are deeply nested within Hesperiinae. CONCLUSIONS Anchored Hybrid Enrichment sequencing resulted in a large amount of data that built the foundation for a new, robust evolutionary tree of skippers. The newly inferred phylogenetic tree resolves long-standing systematic issues and changes our understanding of the skipper tree of life. These resultsenhance understanding of the evolution of one of the most species-rich butterfly families.
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Affiliation(s)
- Emmanuel F A Toussaint
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- , RAPiD Genomics 747 SW 2nd Avenue IMB#14, Gainesville, FL, 32601, USA
| | - Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Andrew D Warren
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Andrew V Z Brower
- Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Masaya Yago
- The University Museum, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kelly M Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Marianne Espeland
- Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer Allee 160, 53113, Bonn, Germany
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, New York, NY, 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, 10016, USA
- Entomology Section, National Museum of the Philippines, 1000, Manila, Philippines
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
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Kawahara AY, Breinholt JW, Espeland M, Storer C, Plotkin D, Dexter KM, Toussaint EFA, St Laurent RA, Brehm G, Vargas S, Forero D, Pierce NE, Lohman DJ. Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set. Mol Phylogenet Evol 2018; 127:600-605. [PMID: 29902572 DOI: 10.1016/j.ympev.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/25/2018] [Accepted: 06/02/2018] [Indexed: 11/28/2022]
Abstract
The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A new, target capture, anchored hybrid enrichment probe set ('BUTTERFLY2.0') was developed to infer relationships of hedylids and some of their butterfly relatives. The probe set includes 13 genes that have historically been used in butterfly phylogenetics. Our dataset comprised of up to 10,898 aligned base pairs from 22 hedylid species and 19 outgroups. Eleven of the thirteen loci were successfully captured from all samples, and the remaining loci were captured from ≥94% of samples. The inferred phylogeny was consistent with recent molecular studies by placing Hedylidae sister to Hesperiidae, and the tree had robust support for 80% of nodes. Our results are also consistent with morphological studies, with Macrosoma tipulata as the sister species to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved once from diurnality in Hedylidae, and demonstrate that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family. The BUTTERFLY2.0 probe set includes standard butterfly phylogenetics markers, captures sequences from decades-old museum specimens, and is a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life.
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Affiliation(s)
- Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; RAPiD Genomics, 747 SW 2nd Avenue, IMB#14, Gainesville, FL 32601, USA
| | - Marianne Espeland
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer Allee 160, Bonn 53113, Germany
| | - Caroline Storer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - David Plotkin
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA
| | - Kelly M Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Ryan A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Gunnar Brehm
- Institute of Zoology and Evolutionary Biology with Phyletic Museum, Friedrich-Schiller-University Jena, Jena 07743, Germany
| | - Sergio Vargas
- Laboratorio de Entomología, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Dimitri Forero
- Laboratorio de Entomología, Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - David J Lohman
- Biology Department, City College of New York, New York, NY 10031, USA; Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA; Entomology Section, National Museum of the Philippines, Manila 1000, Philippines
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8
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Espeland M, Breinholt J, Willmott KR, Warren AD, Vila R, Toussaint EF, Maunsell SC, Aduse-Poku K, Talavera G, Eastwood R, Jarzyna MA, Guralnick R, Lohman DJ, Pierce NE, Kawahara AY. A Comprehensive and Dated Phylogenomic Analysis of Butterflies. Curr Biol 2018; 28:770-778.e5. [DOI: 10.1016/j.cub.2018.01.061] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/21/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022]
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Breinholt JW, Earl C, Lemmon AR, Lemmon EM, Xiao L, Kawahara AY. Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics. Syst Biol 2018; 67:78-93. [PMID: 28472519 DOI: 10.1093/sysbio/syx048] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/28/2017] [Indexed: 11/12/2022] Open
Abstract
The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.
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Affiliation(s)
- Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,RAPiD Genomics, Gainesville, FL 32601, USA
| | - Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Lei Xiao
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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Abstract
With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.
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Affiliation(s)
- Andrew Edward Z Short
- Department of Ecology and Evolutionary Biology; and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA;
| | - Torsten Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA;
| | - Corrie S Moreau
- Department of Science and Education, Field Museum of Natural History, Chicago, Illinois 60605, USA;
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11
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Novák M, Jakubec P, Qubaiová J, Šuláková H, Růžička J. Revisited larval morphology of Thanatophilus rugosus (Coleoptera: Silphidae). Int J Legal Med 2017; 132:939-954. [DOI: 10.1007/s00414-017-1764-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/12/2017] [Indexed: 10/18/2022]
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12
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Schmidt O, Hausmann A, Cancian de Araujo B, Sutrisno H, Peggie D, Schmidt S. A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys). Biodivers Data J 2017; 5:e20006. [PMID: 29134041 PMCID: PMC5676197 DOI: 10.3897/bdj.5.e20006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology - Indonesian Institute of Sciences (RCB-LIPI, Bogor).
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Affiliation(s)
- Olga Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | - Axel Hausmann
- SNSB - Zoologische Staatssammlung München, Munich, Germany
| | | | - Hari Sutrisno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djunijanti Peggie
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Stefan Schmidt
- SNSB - Zoologische Staatssammlung München, Munich, Germany
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