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Yang H, Li T, Dang K, Bu W. Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). BMC Genomics 2018; 19:264. [PMID: 29669515 PMCID: PMC5907366 DOI: 10.1186/s12864-018-4650-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 04/08/2018] [Indexed: 01/24/2023] Open
Abstract
Background Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above. Results Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably, the value of Ka/Ks ratios of all PCGs is less than 1, indicating that these genes are likely evolving under purifying selection. Conclusions Our results demonstrate that mt-genomes have sites with strong phylogenetic signals for the inference of higher-level phylogeny of Cimicomorpha. Consequently, bioinformatic approaches to removing sites with weak phylogenetic signals in mt-genome without relying on an a priori tree topology would greatly improve this field. Electronic supplementary material The online version of this article (10.1186/s12864-018-4650-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huanhuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China.
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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Zhang Z, An M, Miao J, Gu Z, Liu C, Zhong B. The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution. BMC PLANT BIOLOGY 2018; 18:53. [PMID: 29614974 PMCID: PMC5883279 DOI: 10.1186/s12870-018-1273-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/27/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The ice alga Chlamydomonas sp. ICE-L is the main contributor to primary productivity in Antarctic sea ice ecosystems and is well adapted to the extremely harsh environment. However, the adaptive mechanism of Chlamydomonas sp. ICE-L to sea-ice environment remains unclear. To study the adaptive strategies in Chlamydomonas sp. ICE-L, we investigated the molecular evolution of chloroplast photosynthetic genes that are essential for the accumulation of carbohydrate and energy living in Antarctic sea ice. RESULTS The 60 chloroplast protein-coding genes of Chlamydomonas sp. ICE-L were obtained, and the branch-site test detected significant signatures of positive selection on atpB, psaB, and rbcL genes in Chlamydomonas sp. ICE-L associated with the photosynthetic machinery. These positively selected genes were further identified as being under convergent evolution between Chlamydomonas sp. ICE-L and the halotolerant alga Dunaliella salina. CONCLUSIONS Our study provides evidence that the phototrophic component of Chlamydomonas sp. ICE-L exhibits adaptive evolution under extreme environment. The positive Darwinian selection operates on the chloroplast protein-coding genes of Antarctic ice algae adapted to extreme environment following functional-specific and lineages-specific patterns. In addition, three positively selected genes with convergent substitutions in Chlamydomonas sp. ICE-L were identified, and the adaptive modifications in these genes were in functionally important regions of the proteins. Our study provides a foundation for future experiments on the biochemical and physiological impacts of photosynthetic genes in green algae.
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Affiliation(s)
- Zhenhua Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Meiling An
- Medical College, Qingdao University, Qingdao, China
| | - Jinlai Miao
- Medical College, Qingdao University, Qingdao, China
- Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Zhiqiang Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Bojian Zhong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
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53
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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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54
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Ballarin F, Li S. Diversification in tropics and subtropics following the mid-Miocene climate change: A case study of the spider genus Nesticella. GLOBAL CHANGE BIOLOGY 2018; 24:e577-e591. [PMID: 29055169 DOI: 10.1111/gcb.13958] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/22/2017] [Accepted: 09/27/2017] [Indexed: 06/07/2023]
Abstract
Caves may offer suitable refugia for troglophilic invertebrates during periods of unfavourable climatic conditions because of their stable microclimates. As a consequence, allopatric divergence from their epigean counterparts may occur, leading to formation of truly hypogean communities (the Climatic Relict Hypothesis). Unlike the well-studied effects of Pleistocene glaciations, we know little about how ancient climate changes drove the development of cave-dwelling organisms living at both middle and lower latitudes. We investigate the evolutionary history of the troglophilic spider genus Nesticella (Araneae, Nesticidae) in relation to Asian Neogene (23-2.6 Ma) climatic changes. Our analyses discern clear differences in the evolution of the two main clades of Nesticella, which occur in temperate/subtropical and tropical latitudes. Eastern Asian Nesticella gradually evolved greater sedentariness and a strict subterranean lifestyle starting from the middle Miocene Epoch (~15-14 Ma) in conjunction with the progressive deterioration of the climate and vegetational shifts. Caves appear to have acted as refugia because of their internally uniform temperature and humidity, which allowed these spiders to survive increasing external seasonality and habitat loss. In contrast, a uniform accumulation of lineages, long-lasting times for dispersals and the lack of a comparable habitat shifting characterized the tropical lineage. This difference in pattern likely owes to the mild effects of climate change at low latitudes and the consequent lack of strong climatic drivers in tropical environments. Thus, the mid-Miocene climatic shift appears to be the major evolutionary force shaping the ecological differences between Asian troglophilic invertebrates and the driver of the permanent hypogean communities in middle latitudes.
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Affiliation(s)
- Francesco Ballarin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
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55
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Scott Chialvo CH, Chialvo P, Holland JD, Anderson TJ, Breinholt JW, Kawahara AY, Zhou X, Liu S, Zaspel JM. A phylogenomic analysis of lichen-feeding tiger moths uncovers evolutionary origins of host chemical sequestration. Mol Phylogenet Evol 2017; 121:23-34. [PMID: 29274497 DOI: 10.1016/j.ympev.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Host species utilize a variety of defenses to deter feeding, including secondary chemicals. Some phytophagous insects have evolved tolerance to these chemical defenses, and can sequester secondary defense compounds for use against their own predators and parasitoids. While numerous studies have examined plant-insect interactions, little is known about lichen-insect interactions. Our study focused on reconstructing the evolution of lichen phenolic sequestration in the tiger moth tribe Lithosiini (Lepidoptera: Erebidae: Arctiinae), the most diverse lineage of lichen-feeding moths, with 3000 described species. We built an RNA-Seq dataset and examined the adult metabolome for the presence of lichen-derived phenolics. Using the transcriptomic dataset, we recover a well-resolved phylogeny of the Lithosiini, and determine that the metabolomes within species are more similar than those among species. Results from an initial ancestral state reconstruction suggest that the ability to sequester phenolics produced by a single chemical pathway preceded generalist sequestration of phenolics produced by multiple chemical pathways. We conclude that phenolics are consistently and selectively sequestered within Lithosiini. Furthermore, sequestration of compounds from a single chemical pathway may represent a synapomorphy of the tribe, and the ability to sequester phenolics produced by multiple pathways arose later. These findings expand on our understanding of the interactions between Lepidoptera and their lichen hosts.
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Affiliation(s)
- Clare H Scott Chialvo
- Department of Biological Sciences, PO Box 870344, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Pablo Chialvo
- Department of Biology, 320 Stanley Avenue, Lander University, Greenwood, SC 29649, USA
| | - Jeffrey D Holland
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Timothy J Anderson
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China; Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Shanlin Liu
- China National GeneBank, 8/F, Beishan Industrial Zone, Yantian District, BGI-Shenzhen, People's Republic of China; BGI-Shenzhen, Beishan Industrial Zone, Yantian District, People's Republic of China
| | - Jennifer M Zaspel
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA; Milwaukee Public Museum, 800 W Wells St, Milwaukee, WI 53233, USA
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Abstract
BACKGROUND Building the evolutionary trees for massive unaligned DNA sequences is challenging and crucial. However, reconstructing evolutionary tree for ultra-large sequences is hard. Massive multiple sequence alignment is also challenging and time/space consuming. Hadoop and Spark are developed recently, which bring spring light for the classical computational biology problems. In this paper, we tried to solve the multiple sequence alignment and evolutionary reconstruction in parallel. RESULTS HPTree, which is developed in this paper, can deal with big DNA sequence files quickly. It works well on the >1GB files, and gets better performance than other evolutionary reconstruction tools. Users could use HPTree for reonstructing evolutioanry trees on the computer clusters or cloud platform (eg. Amazon Cloud). HPTree could help on population evolution research and metagenomics analysis. CONCLUSIONS In this paper, we employ the Hadoop and Spark platform and design an evolutionary tree reconstruction software tool for unaligned massive DNA sequences. Clustering and multiple sequence alignment are done in parallel. Neighbour-joining model was employed for the evolutionary tree building. We opened our software together with source codes via http://lab.malab.cn/soft/HPtree/ .
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Affiliation(s)
- Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, People's Republic of China
- Guangdong Province Key Laboratory of Popular High Performance Computers, Shenzhen University, Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shixiang Wan
- School of Computer Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Xiangxiang Zeng
- Department of Computer Science, Xiamen University, Xiamen, China.
| | - Zhanshan Sam Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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57
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Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
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58
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Abstract
Until recently, deep-level phylogeny in Lepidoptera, the largest single radiation of plant-feeding insects, was very poorly understood. Over the past two decades, building on a preceding era of morphological cladistic studies, molecular data have yielded robust initial estimates of relationships both within and among the ∼43 superfamilies, with unsolved problems now yielding to much larger data sets from high-throughput sequencing. Here we summarize progress on lepidopteran phylogeny since 1975, emphasizing the superfamily level, and discuss some resulting advances in our understanding of lepidopteran evolution.
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Affiliation(s)
- Charles Mitter
- Department of Entomology, University of Maryland, College Park, Maryland 20742;
| | - Donald R Davis
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Michael P Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742
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59
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Bura VL, Kawahara AY, Yack JE. A Comparative Analysis of Sonic Defences in Bombycoidea Caterpillars. Sci Rep 2016; 6:31469. [PMID: 27510510 PMCID: PMC4980592 DOI: 10.1038/srep31469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/20/2016] [Indexed: 11/09/2022] Open
Abstract
Caterpillars have long been used as models for studying animal defence. Their impressive armour, including flamboyant warning colours, poisonous spines, irritating sprays, and mimicry of plant parts, snakes and bird droppings, has been extensively documented. But research has mainly focused on visual and chemical displays. Here we show that some caterpillars also exhibit sonic displays. During simulated attacks, 45% of 38 genera and 33% of 61 species of silk and hawkmoth caterpillars (Bombycoidea) produced sounds. Sonic caterpillars are found in many distantly-related groups of Bombycoidea, and have evolved four distinct sound types- clicks, chirps, whistles and vocalizations. We propose that different sounds convey different messages, with some designed to warn of a chemical defence and others, to startle predators. This research underscores the importance of exploring acoustic communication in juvenile insects, and provides a model system to explore how different signals have evolved to frighten, warn or even trick predators.
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Affiliation(s)
- Veronica L. Bura
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Jayne E. Yack
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Vogler AP, Cai W. Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models. Genome Biol Evol 2016; 8:1411-26. [PMID: 27189999 PMCID: PMC4898802 DOI: 10.1093/gbe/evw086] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
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Affiliation(s)
- Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Pei Jiang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington
| | - Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington
| | - Changhai Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alfried P Vogler
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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Ballesteros JA, Hormiga G. A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology. Mol Biol Evol 2016; 33:2117-34. [PMID: 27189539 DOI: 10.1093/molbev/msw069] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO.
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Affiliation(s)
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University
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62
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Lyu MJA, Gowik U, Kelly S, Covshoff S, Mallmann J, Westhoff P, Hibberd JM, Stata M, Sage RF, Lu H, Wei X, Wong GKS, Zhu XG. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evol Biol 2015; 15:116. [PMID: 26084484 PMCID: PMC4472175 DOI: 10.1186/s12862-015-0399-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). RESULTS Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a "F. pringlei" genotype recently used in a number of labs may be a hybrid between F. pringlei (C3) and F. angustifolia (C3-C4). CONCLUSIONS We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade.
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Affiliation(s)
- Ming-Ju Amy Lyu
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Steve Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK.
| | - Sarah Covshoff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Julia Mallmann
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich-Heine-University, Dusseldorf, Germany.
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.
| | - Haorong Lu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
| | - Xin-Guang Zhu
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China.
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Eytan RI, Evans BR, Dornburg A, Lemmon AR, Lemmon EM, Wainwright PC, Near TJ. Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment. BMC Evol Biol 2015; 15:113. [PMID: 26071950 PMCID: PMC4465735 DOI: 10.1186/s12862-015-0415-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be. RESULTS After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree. CONCLUSIONS Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.
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Affiliation(s)
- Ron I Eytan
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, 77553, TX, USA.
| | - Benjamin R Evans
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| | - Alex Dornburg
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, 32306, FL, USA.
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, 32306, FL, USA.
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, One Shields Avenue, Davis, 95616, CA, USA.
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
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64
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Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation. Proc Natl Acad Sci U S A 2015; 112:6407-12. [PMID: 25941377 DOI: 10.1073/pnas.1416679112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bat-moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼ 26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18-14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.
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65
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Liu L, Xi Z, Wu S, Davis CC, Edwards SV. Estimating phylogenetic trees from genome-scale data. Ann N Y Acad Sci 2015; 1360:36-53. [DOI: 10.1111/nyas.12747] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Liang Liu
- Department of Statistics; University of Georgia; Athens Georgia
- Institute of Bioinformatics; University of Georgia; Athens Georgia
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge Massachusetts
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology & Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences; Tianjin Medical University; Tianjin China
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge Massachusetts
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge Massachusetts
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66
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A mitochondrial genome phylogeny of owlet moths (Lepidoptera: Noctuoidea), and examination of the utility of mitochondrial genomes for lepidopteran phylogenetics. Mol Phylogenet Evol 2015; 85:230-7. [DOI: 10.1016/j.ympev.2015.02.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 01/27/2015] [Accepted: 02/06/2015] [Indexed: 11/17/2022]
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67
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Barber JR, Leavell BC, Keener AL, Breinholt JW, Chadwell BA, McClure CJW, Hill GM, Kawahara AY. Moth tails divert bat attack: evolution of acoustic deflection. Proc Natl Acad Sci U S A 2015; 112:2812-6. [PMID: 25730869 PMCID: PMC4352808 DOI: 10.1073/pnas.1421926112] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptations to divert the attacks of visually guided predators have evolved repeatedly in animals. Using high-speed infrared videography, we show that luna moths (Actias luna) generate an acoustic diversion with spinning hindwing tails to deflect echolocating bat attacks away from their body and toward these nonessential appendages. We pit luna moths against big brown bats (Eptesicus fuscus) and demonstrate a survival advantage of ∼ 47% for moths with tails versus those that had their tails removed. The benefit of hindwing tails is equivalent to the advantage conferred to moths by bat-detecting ears. Moth tails lured bat attacks to these wing regions during 55% of interactions between bats and intact luna moths. We analyzed flight kinematics of moths with and without hindwing tails and suggest that tails have a minimal role in flight performance. Using a robust phylogeny, we find that long spatulate tails have independently evolved four times in saturniid moths, further supporting the selective advantage of this anti-bat strategy. Diversionary tactics are perhaps more common than appreciated in predator-prey interactions. Our finding suggests that focusing on the sensory ecologies of key predators will reveal such countermeasures in prey.
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Affiliation(s)
- Jesse R Barber
- Department of Biological Sciences, Boise State University, Boise, ID 83725;
| | - Brian C Leavell
- Department of Biological Sciences, Boise State University, Boise, ID 83725
| | - Adam L Keener
- Department of Biological Sciences, Boise State University, Boise, ID 83725
| | - Jesse W Breinholt
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611
| | - Brad A Chadwell
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272; and
| | - Christopher J W McClure
- Department of Biological Sciences, Boise State University, Boise, ID 83725; Peregrine Fund, Boise, ID 83709
| | - Geena M Hill
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611
| | - Akito Y Kawahara
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611;
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68
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Takahashi T, Nagata N, Sota T. Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol Phylogenet Evol 2014; 80:137-44. [DOI: 10.1016/j.ympev.2014.07.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022]
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69
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Cooper ED. Overly simplistic substitution models obscure green plant phylogeny. TRENDS IN PLANT SCIENCE 2014; 19:576-582. [PMID: 25023343 DOI: 10.1016/j.tplants.2014.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/25/2014] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
Phylogenetic analysis is an increasingly common and valuable component of plant science. Knowledge of the phylogenetic relationships between plant groups is a prerequisite for understanding the origin and evolution of important plant features, and phylogenetic analysis of individual genes and gene families provides fundamental insights into how those genes and their functions evolved. However, despite an active research community exploring and improving phylogenetic methods, the analytical methods commonly used, and the phylogenetic results they produce, are accorded far more confidence than they warrant. In this opinion article, I emphasise that important parts of the green plant phylogeny are inconsistently resolved and I argue that the lack of consistency arises due to inadequate modelling of changes in the substitution process.
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Affiliation(s)
- Endymion D Cooper
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA.
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70
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Kawahara AY, Breinholt JW. Phylogenomics provides strong evidence for relationships of butterflies and moths. Proc Biol Sci 2014; 281:20140970. [PMID: 24966318 PMCID: PMC4083801 DOI: 10.1098/rspb.2014.0970] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 06/04/2014] [Indexed: 11/12/2022] Open
Abstract
Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly-moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order.
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Affiliation(s)
- Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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71
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Timmermans MJTN, Lees DC, Simonsen TJ. Towards a mitogenomic phylogeny of Lepidoptera. Mol Phylogenet Evol 2014; 79:169-78. [PMID: 24910155 DOI: 10.1016/j.ympev.2014.05.031] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/11/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire mitochondrial genomes both practical and economically viable. Prior phylogenetic studies utilised just eight of 43 currently recognised lepidopteran superfamilies. Here, we add 23 full and six partial mitochondrial genomes (comprising 22 superfamilies of which 16 are newly represented) to those publically available for a total of 24 superfamilies and ask whether such a sample can resolve deeper lepidopteran phylogeny. Using recoded datasets we obtain topologies that are highly congruent with prior nuclear and/or morphological studies. Our study shows support for an expanded Obtectomera including Gelechioidea, Thyridoidea, plume moths (Alucitoidea and Pterophoroidea; possibly along with Epermenioidea), Papilionoidea, Pyraloidea, Mimallonoidea and Macroheterocera. Regarding other controversially positioned higher taxa, Doidae is supported within the new concept of Drepanoidea and Mimallonidae sister to (or part of) Macroheterocera, while among Nymphalidae butterflies, Danainae and not Libytheinae are sister to the remainder of the family. At the deepest level, we suggest that a tRNA rearrangement occurred at a node between Adeloidea and Ditrysia+Palaephatidae+Tischeriidae.
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Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
| | - David C Lees
- Department of Zoology, Cambridge University, Downing Street CB2 3EJ, United Kingdom.
| | - Thomas J Simonsen
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
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72
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Arquez M, Colgan D, Castro LR. Sequence and comparison of mitochondrial genomes in the genus Nerita (Gastropoda: Neritimorpha: Neritidae) and phylogenetic considerations among gastropods. Mar Genomics 2014; 15:45-54. [PMID: 24798873 DOI: 10.1016/j.margen.2014.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
In the present study, we determined the mitochondrial DNA (mtDNA) sequence of three Neritas, Nerita versicolor, Nerita tessellata, and Nerita fulgurans. We present an analysis of the features of their gene content and genome organization and compare these within the genus Nerita, and among the main gastropod groups. The new sequences were used in a phylogenetic analysis including all available gastropod mitochondrial genomes. Genomic lengths were quite conserved, being 15,866bp for N. versicolor, 15,741bp for N. tessellata and 15,343bp for N. fulgurans. Intergenic regions were generally short; genes are transcribed from both strands and have a nucleotide composition high in A and T. The high similarity in nucleotide content of the different sequences, gene composition, as well as an identical genomic organization among the Nerita species compared in this study, indicates a high degree of conservation within this diverse genus. Values of Ka/Ks of the 13 protein coding genes (PCGs) of Nerita species ranged from 0 to 0.18, and suggested different selection pressures in gene sequences. Bayesian phylogenetic analyses using concatenated DNA sequences of the 13 PCGs and the two rRNAs, and of amino acid sequences strongly supported Neritimorpha and Vetigastropoda as sister groups.
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Affiliation(s)
- Moises Arquez
- Grupo de Investigación en Evolución, Sistemática y Ecología Molecular, Universidad del Magdalena, Santa Marta, Colombia.
| | - Donald Colgan
- The Australian Museum, 6 College Street, Sydney 2010, Australia.
| | - Lyda R Castro
- Grupo de Investigación en Evolución, Sistemática y Ecología Molecular, Universidad del Magdalena, Santa Marta, Colombia.
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