Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set

Kawahara, Akito Y.; Breinholt, Jesse W.; Espeland, Marianne; Storer, Caroline; Plotkin, David; Dexter, Kelly M.; Toussaint, Emmanuel F. A.; Laurent, Ryan A. St; Brehm, Gunnar; Vargas, S. A.; Forero, Dimitri; Pierce, Naomi E.; Lohman, David J.

doi:10.1016/j.ympev.2018.06.002

Cited by 46 publications

(44 citation statements)

References 41 publications

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“…Maximum likelihood (ML) tree of Baorini grass skippers based on anchored phylogenomics. Best‐scoring ML phylogenetic tree inferred in iq‐tree based on the concatenated dataset of 13 loci comprised in the butterfly 2.0 kit (Kawahara et al , ). The five main Baorini clades are labelled I–V.…”

Section: Resultsmentioning

confidence: 99%

“…We used the butterfly 2.0 probe set (Kawahara et al , ) to capture the following 13 loci: acetyl‐CoA (ACOA, 1020 bp), carbamoyl‐phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD, 1854 bp), catalase (CAT, 1290 bp), cytochrome oxidase c subunit 1 (CO1, 1341 bp), dopa decarboxylase (DDC, 702 bp), elongation factor 1 alpha (EF1A, 1059 bp), glyceraldhyde‐3‐phosphate dehydrogenase (GAPDH, 606 bp), hairy cell leukaemia protein 1 (HCL, 633 bp), isocitrate dehydrogenase (IDH, 708 bp), malate dehydrogenase (MDH, 681 bp), ribosomal protein S2 (RPS2, 471 bp), ribosomal protein S5 (RPS5, 555) and wingless (WGL, 240 bp).…”

Section: Methodsmentioning

confidence: 99%

“…v.0.4.0 (http://www.bioinformatics.babraham.ac.uk), allowing a minimum read size of 30 bp, and we removed bases with a Phred score < 20. The 13 loci that were sequenced using the butterfly 2.0 kit (Kawahara et al , ) were assembled with iterative baited assembly (Breinholt et al , ), in which only reads with both forward and reverse reads that passed filtering were included. Assembled reads from the probe region were blasted against the Danaus plexippus Linnaeus (Nymphalidae) reference genome and blast results were used for single hit and orthology filtering.…”

Section: Methodsmentioning

confidence: 99%

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Out of the Orient: Post‐Tethyan transoceanic and trans‐Arabian routes fostered the spread of Baorini skippers in the Afrotropics

Toussaint

Vila

Yago

et al. 2019

Systematic Entomology

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The origin of taxa presenting a disjunct distribution between Africa and Asia has puzzled biogeographers for more than a century. This biogeographic pattern has been hypothesized to be the result of transoceanic long‐distance dispersal, Oligocene dispersal through forested corridors, Miocene dispersal through the Arabian Peninsula or passive dispersal on the rifting Indian plate. However, it has often been difficult to pinpoint the mechanisms at play. We investigate biotic exchange between the Afrotropics and the Oriental region during the Cenozoic, a period in which geological changes altered landmass connectivity. We use Baorini skippers (Lepidoptera, Hesperiidae) as a model, a widespread clade of butterflies in the Old World tropics with a disjunct distribution between the Afrotropics and the Oriental region. We use anchored phylogenomics to infer a robust evolutionary tree for Baorini skippers and estimate divergence times and ancestral ranges to test biogeographic hypotheses. Our phylogenomic tree recovers strongly supported relationships for Baorini skippers and clarifies the systematics of the tribe. Dating analyses suggest that these butterflies originated in the Oriental region, Greater Sunda Islands, and the Philippines in the early Miocene c. 23 Ma. Baorini skippers dispersed from the Oriental region towards Africa at least five times in the past 20 Ma. These butterflies colonized the Afrotropics primarily through trans‐Arabian geodispersal after the closure of the Tethyan seaway in the mid‐Miocene. Range expansion from the Oriental region towards the African continent probably occurred via the Gomphotherium land bridge through the Arabian Peninsula. Alternative scenarios invoking long‐distance dispersal and vicariance are not supported. The Miocene climate change and biome shift from forested areas to grasslands possibly facilitated geodispersal in this clade of butterflies.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Out of the Orient: Post‐Tethyan transoceanic and trans‐Arabian routes fostered the spread of Baorini skippers in the Afrotropics

Toussaint

Vila

Yago

et al. 2019

Systematic Entomology

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“…However, this method could be used at least for PCR-based analysis, such as sanger sequencing and microsatellite analysis. This method could also be used in high-throughput genotyping or sequencing techniques, which do not require high-quality DNA, such as genotyping using sequencing multiplexed ISSR (MIG-seq;Suyama & Matsuki, 2015), target capture (Kawahara et al, 2018) and mitogenome resequencing (Mikheyev et al, 2017). Although this study did not determine the preservation of arthropod samples in 95% ethanol or acetone in a freezer (at −20°C to −80°C), this method is recommended for analyses requiring very high-quality DNA (Quicke et al, 1999;Vink et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Methods for retaining well-preserved DNA with dried specimens of insects

Nakahama¹,

Isagi²,

Itô³

2019

Eur. J. Entomol.

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To prevent degradation, DNA samples are generally preserved in 95-99.5% ethanol or acetone, or in a freezer, or a combination of these (preserved in 95-99.5% ethanol or acetone and stored in a freezer at −20°C to −80°C) because this prevents DNA degradation (Reiss et al., 1995;Quicke et al., 1999;Vink et al., 2005;Nasu et al., 2016). However, the maintenance and space costs associated with immersed or frozen specimens are greater than those associated with dried specimens. The preservation of frozen specimens requires large freezers, which are expensive and may have limited space for specimen preservation and immersed specimens must be regularly checked to ensure that the stock solution has not evaporated. In addition, morphological observations and dissections of 99% ethanol-immersed specimens are diffi cult due to dehydration (Naem et al., 2010). To overcome these problems, we tested whether DNA in the legs of dried specimens of insects can be preserved for a long time. To this end we suspended insects on a pin in 0.2-ml tubes with only the legs immersed in the preservation solution. We also considered the methods used for killing insects, because apart from dragonfl ies Abstract. Dried specimens of insects are increasingly seen as genetic resources. However, genetic analysis of dried specimens of insects is hampered by the deterioration of the DNA. In this study, we developed methods for preparing dried specimens of insects with well-preserved DNA, mainly for PCR-based genetic analysis. First, we compared the effects of either exposure to ethyl acetate vapour for from 10 min to 6 h or by freezing on the fragmentation of DNA in order to determine optimal length of time needed for killing insects using the above methods. Second, we compared the fragmentation of DNA after preservation by drying or immersion of legs in 99.5% ethanol or 99% propylene glycol in 0.2-ml tubes. We assessed degrees of fragmentation of DNA by determining polymerase chain reaction (PCR) success rates with primers for 313-, 710-and 1555-bp fragments using DNA that was collected immediately, and at one, six and 12 months after preparing the specimens. Differing times taken to kill insects did not affect the fragmentation of DNA. In dried specimens, DNA was seriously fragmented after one month, whereas that in legs prepared by immersion in 99.5% ethanol or 99% propylene glycol contained long fragments of DNA (1555 bp~) after 12 months. Propylene glycol was more suitable for preservation than ethanol, because the latter evaporates. Thus, to preserve insect DNA we suggest inserting the pin on which an insect is impaled into the hinged lid of a 0.2-ml tube containing 99% propylene glycol so that when the lid is closed the legs of the insect are preserved in the solution.

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“…In this study, we first developed a universal marker set of 94 nuclear protein-coding genes for Lepidoptera, which greatly increases the number of PCR-based markers for Lepidoptera phylogenetics. In addition to newly developed markers, this marker set includes the most commonly used genes in studies of butterfly phylogenetics, allowing data integration with results from previous studies (Heikkilä, Kaila, Mutanen, Peña, & Wahlberg, 2012;Kawahara et al, 2018;Kozak et al, 2015;Mitter et al, 2010;Simonsen et al, 2011). The focus of this study is to explore the feasibility of using DNA pools from different clade representatives to produce PCR-generated baits to effectively capture a moderate number of orthologous loci in a superdiverse group of organisms.…”

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confidence: 99%

Sequence capture across large phylogenetic scales by using pooled PCR‐generated baits: A case study of Lepidoptera

Yuan

Deng

Liang

et al. 2019

Molecular Ecology Resources

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Sequence capture across large phylogenetic scales is not easy because hybridization capture is only effective when the genetic distance between the bait and target is small. Here, we propose a simple but effective strategy to tackle this issue: pooling DNA from a number of selected representative species of different clades to prepare PCR‐generated baits to minimize the genetic distance between the bait and target. To demonstrate the utility of this strategy, we newly developed a set of universal nuclear markers (including 94 nuclear protein‐coding genes) for Lepidoptera, a superdiverse insect group. We used a DNA pool from six lepidopteran species (representing six superfamilies) to prepare PCR baits for the 94 markers. These homemade PCR baits were used to capture sequence data from 43 species of 17 lepidopteran families, and 94% of the target loci were recovered. We constructed two data sets from the obtained data (one containing ~90 kb target coding sequences and the other containing ~120 kb target + flanking coding sequences). Both data sets yielded highly similar and well‐resolved trees with 90% of nodes having >95% bootstrap support. Our capture experiment indicated that using DNA mixtures pooled from different clade‐representative species of Lepidoptera to prepare PCR baits can reliably capture a large number of targeted nuclear markers across different Lepidoptera lineages. We hope that this newly developed nuclear marker set will serve as a new phylogenetic tool for Lepidoptera phylogenetics, and the PCR bait preparation strategy can facilitate the application of sequence capture techniques by researchers to accelerate data collection.

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Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set

Cited by 46 publications

References 41 publications

Out of the Orient: Post‐Tethyan transoceanic and trans‐Arabian routes fostered the spread of Baorini skippers in the Afrotropics

Out of the Orient: Post‐Tethyan transoceanic and trans‐Arabian routes fostered the spread of Baorini skippers in the Afrotropics

Methods for retaining well-preserved DNA with dried specimens of insects

Sequence capture across large phylogenetic scales by using pooled PCR‐generated baits: A case study of Lepidoptera

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