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Phylogenomic relationships of bioluminescent elateroids define the

'lampyroid' clade with clicking Sinopyrophoridae as its earliest member

Article in Systematic Entomology · July 2020

DOI: 10.1111/syen.12451

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Systematic Entomology (2020), DOI: 10.1111/syen.12451

Phylogenomic relationships of bioluminescent

elateroids define the ‘lampyroid’ clade with clicking
Sinopyrophoridae as its earliest member
D O M I N I K K U S Y 1* , J I N-W U H E 2* , S E T H M . B Y B E E 3 ,
M I C H A L M O T Y K A 1 , W E N-X U A N B I 2 , L A R S P O D S I A D L O W S K I 4 ,
X U E-Y A N L I 2 and L A D I S L A V B O C A K 1
1
Laboratory of Biodiversity and Molecular Evolution, Palacky University, Olomouc, Czech Republic, 2 State Key Laboratory of
Genetic Resources and Evolution, Kunming Institute of Zoology CAS, Kunming, China, 3 Department of Biology, Monte L. Bean
Museum, Brigham Young University, Provo, UT, U.S.A. and 4 Zoological Research Museum Alexander Koenig, Centre of Molecular
Biodiversity Research, Bonn, Germany

Abstract. Bioluminescence has been hypothesized as aposematic signalling, inter-

sexual communication and a predatory strategy, but origins and relationships among
bioluminescent beetles have been contentious. We reconstruct the phylogeny of the
bioluminescent elateroid beetles (i.e. Elateridae, Lampyridae, Phengodidae and
Rhagophthalmidae), analysing genomic data of Sinopyrophorus Bi & Li, and in light
of our phylogenetic results, we erect Sinopyrophoridae Bi & Li, stat.n. as a clicking
elaterid-like sister group of the soft-bodied bioluminescent elateroid beetles, that is,
Lampyridae, Phengodidae and Rhagophthalmidae. We suggest a single origin of bio-
luminescence for these four families, designated as the ‘lampyroid clade’, and examine
the origins of bioluminescence in the terminal lineages of click beetles (Elateridae).
The soft-bodied bioluminescent lineages originated from the fully sclerotized elateroids
as a derived clade with clicking Sinopyrophorus and Elateridae as their serial sister
groups. This relationship indicates that the bioluminescent soft-bodied elateroids are
modified click beetles. We assume that bioluminescence was not present in the most
recent common ancestor of Elateridae and the lampyroid clade and it evolved among
this group with some delay, at the latest in the mid-Cretaceous period, presumably
in eastern Laurasia. The delimitation and internal structure of the elaterid-lampyroid
clade provides a phylogenetic framework for further studies on the genomic variation
underlying the evolution of bioluminescence.

Introduction sporadically in insects (Watkins et al., 2018; Martin et al., 2019);

nevertheless, beetle bioluminescence is well known to both
Bioluminescence has been intensively studied by numerous researchers and the general public. Most luminous beetles
researchers (Costa, 1975; Branham & Wenzel, 2003; Nakatsu belong to Elateroidea and we know of ∼2000 firefly species
et al., 2006; Fallon et al., 2018). The production of light occurs (Lampyridae, Fig. 1F–J), ∼300 glow-worms or railroad-worm
beetles (Phengodidae, Rhagophthalmidae), as well as >100 bio-
Correspondence: Ladislav Bocak, Laboratory of Biodiversity and luminescent click beetle species (Elateridae; Fig. 1A–D), espe-
Molecular Evolution, Palacky University, Olomouc, Czech Republic,
E-mail: ladislav.bocak@upol.cz; and Xueyan Li, State Key Laboratory
cially in the Neotropical region (Costa, 1975, 1984). With the
of Genetic Resources and Evolution, Kunming Institute of Zoology, recent discovery of the first Palearctic bioluminescent click-
Chinese Academy of Sciences, Kunming, Yunnan, 650223, China, ing beetle, the number of bioluminescent beetle lineages has
E-mail: lixy@mail.kiz.ac.cn. increased (He et al., 2019; Bi et al., 2019; Fig. 1D–E).
The phylogenetics of Elateroidea have been studied with
∗These authors contributed equally to the study. morphology since the late 1980s, where the bioluminescent

© 2020 The Royal Entomological Society 1

2 D. Kusy et al.

Fig 1. Morphological diversity of the elaterid-lampyroid clade. Elateridae: (A) Denticollis sp.; (B) Agrypnus murinus (L.); (C) click beetle larva;
(D) Ampedus sp. The lampyroid clade. Sinopyrophoridae: (D, E) Sinopyrophorus schimmeli Bi & Li; Lampyridae: (F) Asymmetricata circumdata
(Motschulsky); (G) Lampyris noctiluca (L.), larva; (H) ditto, in copula; (I, J) Lamprohiza splendidula (L.), female. Photographs by M. Motyka (B, D,
G–J), L. Bocak (A,C) and Z.-W. Dong (F); (D, E) from Bi et al., 2019. [Colour figure can be viewed at wileyonlinelibrary.com].

soft-bodied ‘cantharoids’ and fully sclerotized click beetles were et al. (2018a) used 99 nuclear markers and Kusy et al. (2018a)
merged in a single superfamily, Elateroidea (Lawrence, 1988; analysed ∼4000 orthologous genes. Both studies provided
Branham & Wenzel, 2003; Lawrence et al., 2011). Later evidence for a clade that included five elateroid families with
studies using DNA data supported showed that the soft-bodied at least some bioluminescent taxa. However, these two studies
elateroids were polyphyletic (Bocakova et al., 2007). Some either used a low number of orthologs or restricted taxon sam-
relationships among these groups remained inconclusive pling. A phylogenomic analysis for all of Coleoptera provided
when topologies were inferred from a few widely used a timeframe for the evolution of the order based on multi-
molecular markers and the controversies persisted even ple calibration points, confirming the elateroid backbone but
when protein-coding nuclear fragments were employed contained only six elateroid terminals (McKenna et al., 2019)
(McKenna et al., 2015), or when taxon sampling was sub- (Fig S1D,E).
stantially increased (Kundrata et al., 2014; Bocak et al., 2016; Recently, the subfamily Sinopyrophorinae Bi & Li was pro-
Linard et al., 2018) (Fig S1A–C). A clade of bioluminescent posed in Elateridae for the bioluminescent Sinopyrophorus
elateroids, that is, Elateridae, Lampyridae, Phengodidae and schimmeli Bi & Li. Bi et al. (2019) included homologous
Rhagophthalmidae, was first identified by the analyses of 13 fragments of S. schimmeli in a phylogenetic reconstruction
mitochondrial genes (Timmermans et al., 2010) and confirmed from earlier published click beetle rRNA and mtDNA genes
by further analyses of these mitogenomes but with more exten- (Bocakova et al., 2007; Timmermans et al., 2010, 2016; Kun-
sive taxon sampling (Amaral et al., 2016; Bocak et al., 2016). drata et al., 2014; Amaral et al., 2016) and used glow-worms
Nevertheless, the analyses were relatively limited by the volume as outgroups. They recovered Sinopyrophorus with the elaterid
of data and resulted in ambiguous support for critical clades and subfamilies Hemiopinae and Oestodinae, but with limited statis-
contradictory results (Kundrata et al., 2014; Linard et al., 2018). tical support for many relationships among elaterid subfamilies.
Recent progress has been made possible by high throughput Herein, several thousand orthologs of S. schimmeli are used
sequencing, transcriptomes and whole-genome analyses. Zhang to investigate the evolution of the clade of bioluminescent

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

 Phylogenomics of luminescent elateroids 3

elateroid families. Large genomic datasets are proving empiri- to identify ambiguous and randomly similar aligned sections.
cally necessary if the relationships among old lineages can be Aliscore was invoked with a custom –r 1027 option, with a
recovered with some level of confidence (Misof et al., 2014; scoring approach for gap-filled amino acid sites (option -e).
Kusy et al., 2018a; McKenna et al., 2019). Based on these After that, we used Alinuc.pl (Misof et al., 2014) to create a
results, we discuss (i) the origins of bioluminescence in list of corresponding codons to be removed from nucleotide
Elateroidea, (ii) loss of the clicking mechanism, and (iii) alignments. Identified random or ambiguous similarities were
loss of a fully sclerotized body in most bioluminescent masked using ALICUT v.2.3 (Kück et al., 2010). In each gene
elateroids. This phylogeny will enable further evaluation of alignment, the short randomly aligned fragments were replaced
the similarity of the luciferase genes and track their evolution with gaps and sequences with ≥80% missing data were removed
(Fallon et al., 2018). using Python scripts (Zhang et al., 2020). We used MARE
v.0.1.2-rc (Misof et al., 2013) to calculate the information con-
tent of each gene partition. Partitions with zero information con-
Methods tent were removed.
For the remaining 4199 genes, we used AMAS
Genomic data (Borowiec, 2016) to calculate statistics (alignment length,
GC content, number of missing taxa, number of parsimony
The genomic DNA of a single male adult of S. schimmeli from informative sites) and individual gene alignments were retained
Yunnan Province (Collecting data: Husa village, 1770 m a.s.l., for coalescent analyses. The concatenated datasets were gen-
Longchuan County, 15–25 Jun 2017, coll. Wenxuan Bi) was erated using FasConCat-G v.1.4 (Kück & Longo, 2014).
shotgun-sequenced on the Illumina HiSeq4000 by Novogene From the 4199 genes, we generated the datasets A-4199-AA
Co., Ltd. (Tianjing, China) for 150 bp paired-end reads and ∼30 and B-4199-NT (designation: name-number of taxa-amino
Gbp of total data (Bi et al., 2019). Raw paired-end reads were acid or nucleotide level, Table S4). To reduce the effect
filtered using fastp v.0.20.0 (Chen et al., 2018) and low-quality of saturation (Breinholt & Kawahara, 2013), we created
reads were removed. The draft genome was assembled using dataset C-4199-NT12, with third-codon positions excluded. To
SPAdes v.3.13.1 (Bankevich et al., 2012), with k-mer sizes of 21, increase the data decisiveness, we constructed additional super-
33, 55, 77 and 99. Contigs were used to train ‘Augustus’ (Stanke matrices using only partitions with all 43 species present:
& Waack, 2003) for species-specific gene models with BUSCO datasets D-968-AA and E-968-NT. The degree of missing
v.3 (Waterhouse et al., 2018). Predicted models were used for ab data and overall completeness scores across all datasets was
initio gene predictions and protein-coding sequences were used
inspected using AliStat v.1.7 (https://github.com/thomaskf/
for analyses. Basic statistics of genome assembly were evaluated
AliStat).
with QUAST v.5 (Mikheenko et al., 2018). We performed k-mer
counts on the filtered data in Jellyfish 2.2.10 using 17 and 21-mer
sizes (Marcais & Kingsford, 2011). Based on the distribution
of k-mer occurrences, we estimated the genome size using Compositional heterogeneity tests
GenomeScope (Vurture et al., 2017).
We compiled the phylogenomic dataset using Sinopyrophorus To explore the effect of compositional heterogeneity, we
and 42 publicly available transcriptomes or genomes (Poelchau inspected the dataset A-4199-AA with BaCoCa v.1.105 (Kück
et al., 2014; Sanders & Hall, 2015; Amaral et al., 2017, & Struck, 2014). We considered compositional heterogeneity
2019; Wang et al., 2017; Fallon et al., 2018; Ye et al., 2018; among species in a given partition to be high when the overall
Kusy et al., 2018b, 2019; McKenna et al., 2019) (Table S1). RCFV value was ≥0.1 (Fernandez et al., 2016; Vasilikopoulos
The single-copy ortholog set was collated by searching the et al., 2019). Heterogeneous partitions were excluded from
OrthoDB v.9.1 database (Zdobnov et al., 2016) (Tables S2, the dataset A-4199-AA to generate dataset F-2195-AA. We
S3). We carried out Orthograph v.0.6.3 searches (Petersen used Maximum Symmetry Test (Naser-Khdour et al., 2019)
et al., 2017) on assembled transcriptomes and protein-coding to exclude the deviating genes from the dataset B-4199-NT
gene sets. Terminal stop codons were removed and internal (P-value cutoff <0.05) and the dataset G-958-NT contains only
stop codons at the translational and nucleotide levels were partitions that passed the test. The software SymTest v.2.0.49
masked using the Perl script summarize_orthograph_results.pl (https://github.com/ottmi/symtest) was used to calculate the
(Petersen et al., 2017). The amino acid sequences were aligned deviation from stationarity, reversibility and homogeneity
using Mafft v.7.407 with the L-INS-i algorithm (Katoh & (Jermiin et al., 2008) (SRH). Heatmaps were generated
Standley, 2013). Resulting alignments from each ortholog for all datasets to visualize the pairwise deviations from
group were checked for the presence of outliers using the SRH conditions. To eliminate synonymous signal (Kawa-
script checker_complete.1.3.1.2.pl and earlier reported meth- hara et al., 2011), we used Degen v.1.4 (Zwick et al., 2012)
ods (Misof et al., 2014; Peters et al., 2017). Outlier sequences (http://www.phylotools.com/ptdegendocumentation.htm). All
were removed from alignments. Then, the non-elateriform taxa sites with synonymous substitutions were replaced by the
were removed. The multiple sequence alignments of nucleotides corresponding ambiguity codes. The synonymous signal was
were generated using Pal2Nal (Suyama et al., 2006) and Alis- removed from dataset B-4199-NT and H-4199-DEGEN-NT
core v.2.2 (Misof & Misof, 2009; Kück et al., 2010) was used was generated.

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

4 D. Kusy et al.

Phylogenetic analyses Analyses of alternative relationships

Phylogenetic reconstructions were performed using maxi- We used Four-cluster Likelihood mapping (Strimmer &
mum likelihood (ML) criterion with IQ-TREE v.2.0-rc2 (Minh von Haeseler, 1997; Misof et al., 2013) (FcLM) analysis to
et al., 2020). Model selection for each gene was performed investigate alternative topologies in the datasets A-4199-AA,
with ModelFinder (Chernomor et al., 2016; Kalyaanamoorthy B-4199-NT and C-4199-NT12. The analysis determines if
et al., 2017) using the -MFP option. For amino acid superma- incongruent or confounding signals are present, which may be
trices, the substitution models LG, DCMUT, JTT, JTTDCMUT, obscured in a multispecies phylogenetic tree. The tree-likeness
DAYHOFF, WAG, and free rate models LG4X and LG4M were graph for the three possible quartet topologies shows the support
tested and all combinations of rate heterogeneity among sites for each topology. Additionally, we tested positions of Elaterinae
were allowed (options: -mrate E,I,G,I+G,R -gmedian -merit as (i) a sister to clade of Sinopyrophorus, Lampyridae, Phen-
AICc). We used the edge-linked partitioned model for tree godidae, Rhagophthalmidae (paraphyletic Elateridae) and (ii)
reconstructions (-spp option) allowing each gene to have its a sister to other Elateridae (monophyletic Elateridae) by eval-
own rate. The optimized partition schemes and best-fitting uating which gene partitions of the datasets A-4199-AA and
model were inferred for the datasets A-4199-AA, B-4199-NT, B-4199-NT favour the alternatives. We calculated log-likelihood
D-968-AA, and E-968-NT using -m MFP+MERGE − merit scores and differences of each pL score for each gene partition
AICc -gmedian options and considering the same substitu- using option -wpl in IQ-TREE (Minh et al., 2020).
tion models as above. The fast-relaxed clustering algorithm
was used (Lanfear et al., 2017). The top 10% of partitions
schemes –rclusterf 10 and maximum 10 000 partitions pairs 66-gene dataset
–rcluster-max 10 000 were considered for all datasets except for
D-968-AA and E-968-NT, where –rclusterf 10 –rcluster-max We assembled a dataset from earlier published data (Kusy
5000 were used. Ultrafast bootstrap (Hoang et al., 2018) and et al., 2018a,b, 2019; Zhang et al., 2018a) and newly produced
homologs (Table S5). Sequences of 84 elateroids and outgroups
SH-like approximate likelihood ratio test (SH-aLRT) were cal-
were used as an input to Orthograph, 66 beetle orthologs were
culated using options -bb 3000 and -alrt 10 000.
extracted, and aligned at an amino acid level using mafft v.7.394
To account for variation among gene trees owing to incom-
with the L-INS-i algorithm (Katoh & Standley, 2013). Multi-
plete lineage sorting and to account for potential gene tree
ple sequence alignments of nucleotides were generated using
heterogeneity and discordance (Degnan & Rosenberg, 2006;
Pal2Nal (Suyama et al., 2006) to produce datasets J-66-NT and
Edwards, 2009; Mirarab et al., 2016), the datasets A-4199-AA,
K-66-AA. We then manually checked all alignments for the
B-4199-NT and C-4199-NT12 were analysed using the
presence of outliers and alignment errors. The matrices for both
coalescent-based species-tree method. For every single-gene
amino acid and corresponding nucleotide alignments were gen-
partition, we calculated an ML gene tree, with 1000 ultra-
erated using FasConCat-G v.1 (Kück & Longo, 2014). The soft-
fast bootstrap replicates (-bb option) and using the same
ware SymTest v.2.0.49 (https://github.com/ottmi/symtest) was
substitution models as earlier. For coalescent species tree
used to calculate the overall SRH deviation. The fully parti-
estimation, the Accurate Species Tree Algorithm was used
tioned reconstructions were performed using the ML criterion
[ASTRAL-III v.5.6.3 (Zhang et al., 2018b)]. ASTRAL accu- with IQ-TREE. Full methods and the complete list of analyses
racy is reduced when poorly resolved gene trees are included are provided in File S1.
(Barrow et al., 2018). Therefore, we calculated average ultrafast
bootstrap and branch length for every gene tree using an R script
(https://github.com/marekborowiec/good_genes/tree_props.R)
Results
and reduced gene trees datasets were created. To account for
very poorly resolved branches on gene trees, branches with Newly generated shotgun DNA reads of S. schimmeli produced
ultra-fast bootstrap ≤10 were collapsed using Newick utilities a genome assembly with ∼190x read coverage (Fig S34A).
v.1.6 (Junier & Zdobnov, 2010) in every ASTRAL analysis. Despite fragmentation, the assembly contained a sufficient
Local posterior probabilities (Erfan & Mirarab, 2016) and amount of information for ortholog extraction and downstream
quartet frequencies of the internal branches in every species phylogenomic analyses (Table S3). The genome completeness
tree were calculated using the parameter ‘-t = 2’. Furthermore, and assembly statistics are summarized in Figs S33A, B, S34A.
we used DiscoVista v.1.0 (Erfan et al., 2018) to visualise The genome size of S. schimmeli was estimated to 171.8 and
gene-tree quartet frequencies of three topologies around 190.7 million base pairs (Mbp) (Fig S34B, C) using k-mer sizes
focal internal branches of the inferred ASTRAL nucleotide 17 and 21, respectively.
species tree in the datasets A-4199-AA, B-4199-NT, and
C-4199-NT12. Here, the following regularly recovered mono-
phyletic groups were considered: nine elateriformian outgroups, Definition and relationships of lineages
Throscidae, Lycidae, Cantharidae, Elateridae (except Elateri-
nae), Elaterinae, Sinopyrophorus, Lampyridae, Phengodidae, Two sets of topologies were produced which differ in the
Rhagophthalmidae. density of sampling and the number of orthologs. The first

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

 Phylogenomics of luminescent elateroids 5

Fig 2. Phylogenetic relationships. The topology recovered by the ASTRAL coalescent phylogenetic method applied to the full set of single-gene trees
inferred at nucleotide level from the dataset B-4199-NT; only the elaterid-lampyroid clade shown, see the full trees in Figs S17, S18. [Colour figure can
be viewed at wileyonlinelibrary.com].

set was based on 4199 orthologs and 43 taxa, nine of them In contrast to the relatively well-supported lampyroid clade,
as outgroups; the topologies were inferred under the ML cri- we found confounding signal for some relationships among ela-
terion and the coalescent method by the analyses of amino terid lineages (Figs 2, 3, 5B, D). Most analyses of genomic
acids and nucleotides (Fig. 2). The second set was based on datasets suggested the paraphyly of Elateridae with Elaterinae
the 66-orthologs, 83 elateroids and the topologies were inferred rooted as a sister to the lampyroid clade and other elaterids
by ML analyses (Figs 3A, B, S2–S22). All analyses recovered as a sister to both of them (Figs S2–33). Such a result was
a clade containing exclusively the families with at least some inferred from all ML analyses and the coalescent analysis of the
taxa that produce light, that is, Elateridae (∼2% of taxa biolumi- amino acid data, but not by the coalescent method applied to
nescent, in three subfamilies), Sinopyrophoridae (Sinopyropho- the nucleotide dataset (Fig. 2). The distribution of the signal for
rus, 1 sp., bioluminescent in an adult stage, larvae unknown), alternative topologies prefers the monophyly of Elateridae. The
Phengodidae, Rhagophthalmidae and Lampyridae (all biolumi- FcLM analysis of the nucleotide dataset B-4199-NT returned
nescent at least in the larval stage, except Phengodidae: Cydis- 58.7% for the monophyly of Elateridae versus 39.6% for their
tinae for which larvae and females are unknown and males are paraphyly (Figs 5B, S25). Similarly, the DiscoVista relative fre-
non-luminescent). Hereafter, these widely accepted families and quency analysis of the B-4199-NT dataset (node 9; Fig. 5D)
Sinopyrophorus are designated as the ‘elaterid-lampyroid clade’ preferred the monophyly of Elateridae, but paraphyly is sup-
(Figs 2–4). ported by the datasets A-4199-AA and C-4199-NT12 (Figs S23,
Sinopyrophorus was found outside of Elateridae and as a sister 24). The 66-gene amino acid dataset suggests Elateridae without
to Lampyridae, Phengodidae and Rhagophthalmidae. The topol- Sinopyrophorus as a serial paraphylum of three elaterid groups
ogy was stable regardless of the dataset and inference method to the lampyroid clade (Fig. 3A), but the same dataset produced
employed (Figs 2–3, S2–S22). Its position was also supported a monophyletic Elateridae at the nucleotide level (Fig. 3B).
by the FcLM analysis (Figs 5A, B, S25, Table S6) and alter- With regard to the positions of the clicking and non-clicking
native topologies were rejected by an approximately unbiased forms in the elaterid-lampyroid clade, our analyses always
test (AU test, Table S7). All phylogenomic analyses indicate recovered the clicking forms as the earliest splits. Biolu-
that phenotypically elaterid-like Sinopyrophorus (originally Ela- minescent taxa are always recovered in a derived position
teridae: Sinopyrophorinae, Fig. 6) and the here redefined Ela- within the elaterid-lampyroid clade, regardless of monophyly
teridae do not share a common exclusive ancestor and form a or paraphyly of click beetles inferred from various analyses
serial paraphylum towards the branch of Lampyridae, Rhagoph- (Figs 2–3), that is, the most recent common ancestor of the
thalmidae and Phengodidae. The clade of Sinopyrophorus and elaterid-lampyroid clade was clicking and non-bioluminescent.
the soft-bodied bioluminescent families is here designated as the All topologies and additional information on data are shown
‘lampyroid clade’. in Figs S2–S34.

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

6 D. Kusy et al.

Fig 3. (A) The topology recovered by the maximum likelihood analysis of the 66-gene dataset J-66-AA at the amino acid level. (B) The topology
recovered by the maximum likelihood analysis of the 66-gene dataset J-66-NT at the nucleotide level. The dark blue branches are significantly supported
(both SH-aLRT >80% and UFboot >95%). [Colour figure can be viewed at wileyonlinelibrary.com].

Taxonomy low information content in the Sanger data have produced con-
tradicting phylogenies (Bocakova et al., 2007; Sagegami-Oba
Sinopyrophoridae Bi & Li, 2019, new status et al., 2007; Lawrence et al., 2011; Kundrata et al., 2014;
Sinopyrophorinae Bi & Li, 2019 in Bi et al., 2019: 83. McKenna et al., 2015). Here, we present analyses based on more
Type genus: Sinopyrophorus Bi & Li, 2019 in Bi et al., than 4000 orthologs that support three principal relationships
2019: 89. that have not been well supported in earlier studies:
= Sinopyrophorus He et al., 2019: 565, unavailable name
due to the absence of a description in the study where the
1 The monophyly of the elaterid-lampyroid clade (Figs 2–4;
name was proposed (International Committee for Zoological
Timmermans et al., 2010; Amaral et al., 2016; Bocak
Nomenclature, 1999).
et al., 2016; Kusy et al., 2018b; McKenna et al., 2019) is
Based on the recovered relationships, Sinopyrophorus (earlier
preferred over alternative hypotheses (Bocakova et al., 2007;
Elateridae: Sinopyrophorinae) cannot be a member of Elateri-
Sagegami-Oba et al., 2007; Kundrata et al., 2014; McKenna
dae. Despite its morphological similarity and a shared clicking
et al., 2015; Zhang et al., 2018a).
mechanism, its phylogenetic position requires it to be classi-
2 We prefer the monophyly of redefined click beetles, that
fied as a separate taxon of the same rank as true click beetles,
is, including Elaterinae and Lissominae without Sinopy-
that is, family. The proposed rank fulfils the requirement of the
rophorus, as suggested by the B-4199-NT dataset and the
reciprocal monophyly of all taxa and, simultaneously, keeps tra-
coalescent method, the J-66-NT dataset and ML methods,
ditionally recognized families valid.
and as additionally supported by the FcLM analyses, Disco-
Vista analyses and AU test (Figs 2, 3B, 5B, D, S20, S22B,
S23–S26; Table S7) over a paraphyletic Elateridae obtained
Discussion from all ML analyses of the genomic datasets, from the
coalescent method analyses of C-4199-NT12/A-4199-AA
Phylogenomic relationships datasets, and the ML analysis of the I-66-AA dataset
(Figs 3A, S2–S19, S21, S22A). The paraphyletic or poly-
The uncertain homology of characters in phenotypically dis- phyletic Elateridae were recovered in earlier estimates where
parate elateroids, ambiguities in length variable alignments and datasets representing all Coleoptera were analysed (McKenna

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

 Phylogenomics of luminescent elateroids 7

Fig 4. The summary cladogram of Elateroidea with bars showing the distribution of estimated origin of Elateroidea, the earliest split within the
bioluminescent clade, and the splits within the [Lampyridae (Rhagophthalmidae, Phengodidae)] clade. The origin of Sinopyrophoridae is supposed
after the origin of the bioluminescent clade and before the earliest split between Lampyridae and Rhagophthalmidae + Phengodidae. [Colour figure can
be viewed at wileyonlinelibrary.com].

et al., 2015, 2019; Zhang et al., 2018a). In this case, only rigorous testing with a dense sampling of taxa and a higher
a slight majority of genes recover the monophyly of click number of orthologs specifically designed for this question.
beetles over their paraphyly (Figs 5B, S26). Generally, the 3 Sinopyrophoridae is decisively placed as a sister to Lampyri-
amino acid and nucleotide first + second codon position dae, Phengodidae and Rhagophthalmidae (Figs 2, 3A,
sequences are highly conservative when the set of orthologs S2–S25), or as a sister to Lampyridae (Fig. 3B) rather than
for whole Coleoptera is assembled and possibly, due to a member of the click beetles (Bi et al., 2019). Therefore,
incomplete lineage sorting, the analyses of these datasets we propose to accept Sinopyrophorus as a member of
do not support the monophyly of click beetles is analysed the ‘lampyroid clade’, that is, the ancient lineage closely
using the maximum likelihood approach (Figs 3A, S2–16). related to fireflies and glow-worms (Figs 2, 3, S2–S26).
The ASTRAL coalescent phylogenetic method applied to the The elaterid-like morphology of Sinopyrophorus supports
full set of gene trees inferred the monophyly of Elateridae the idea that the characteristic well-sclerotized body form
from the dataset B-4199-NT at the nucleotide level (Fig. 2). and clicking escape mechanism were abandoned multiple
Additionally, the FcLM and DiscoVista relative frequency times during the evolution of Elateroidea. Here, a single
analyses of the dataset B-4199-NT support, albeit weakly, shift to incomplete sclerotization in the common ancestor of
the monophyly of Elateridae (Figs 5B, D, S24, 25). Similarly, soft-bodied fireflies and glow-worms was recovered by all
the 66-gene dataset is based on highly conservative genes and analyses (Figs 2, 3). Such a process was earlier inferred for
Elateridae are split into three serial groups of the lampyroid drilids and omalisids now included in Elateridae (Kundrata
clade if amino acids are analysed (Figs 3A, S17), but the et al., 2014; Kusy et al., 2018a). The clicking mechanism is
family is monophyletic when the tree is inferred with the unique, relatively complex and we can assume that it evolved
maximum likelihood analysis at the nucleotide level (Figs 3B, once if the probabilities of the origin and the loss of the
S18). The earlier 99-gene (among them the here employed clicking mechanism are substantially different (Trueman
66 orthologs) analysis of the whole Coleoptera by Zhang et al., 2004).
et al. (2018a) suggested the polyphyly of click beetles when
Lissominae was the sister to net-winged beetles and the rest
of Elateridae formed two serial sister groups to the lampyroid Formal classification
families. We are aware that further analyses of a much larger
dataset will be needed to test the monophyly of Elateridae The elevation of Sinopyrophoridae as a separate family is our
but, based on the current results, we prefer to accept the preferred, but not a single possible solution of the formal clas-
monophyly of Elateridae. Although the genome-scale data sification. Our decision is conservative in the sense that it keeps
offer a powerful tool for phylogenetics, the relationships the family rank for all earlier designated reciprocally mono-
of elaterid subfamilies remain poorly supported and need phyletic lineages, that is, click beetles, fireflies, glow-worms and

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

8 D. Kusy et al.

Fig 5. Four cluster Likelihood Mapping tests of the selected phylogenetic hypothesis applied at the nucleotide level of the dataset B-4199-NT. (A) The
test of the position of Sinopyrophorus. (B) The test of the monophyly of Elateridae. (C) Evaluated topology. (D) DiscoVista relative frequency analyses
of the dataset B-4199-NT. [Colour figure can be viewed at wileyonlinelibrary.com].

railroad-worm beetles. There are several alternative solutions. assemblage of biologically and morphologically disparate forms
We could merge Sinopyrophoridae, Phengodidae, Rhagoph- would not be practical.
thalmidae and Lampyridae under a single family, that is, the here
recovered lampyroid clade will be called Lampyridae Latreille,
and contain five subfamilies. Lampyridae in a new wide sense Origins of the bioluminescence
would contain several morphologically distinct lineages with
differing natural history and the whole internal classification Our analyses indicate a unique origin of bioluminescence
of fireflies would be down-ranked. The formal requirement for in the common ancestor of the clade Sinopyrophoridae,
the monophyly of all named taxa would also be fulfilled by the Rhagophthalmidae, Phengodidae and Lampyridae clade and
redefinition of Elateridae sensu lato that would contain eight further independent origin of bioluminescence within click
traditional families Elateridae, Drilidae, Omalisidae, Plastoceri- beetles as defined here, that is, without Sinopyrophorus. The
dae, Lampyridae, Phengodidae, Rhagophthalmidae and Sinopy- relatively distant position of bioluminescent taxa in the formal
rophorinae. (Kusy et al., 2018a,b; Bi et al., 2019). Considering classification was confirmed by the earliest molecular phyloge-
also the logical extreme, we could accept whole Elateroidea nies (Bocakova et al., 2007; Sagegami-Oba et al., 2007) and has
as a single family (sans the artemotopodid clade) as recently been inferred due to the genetic structure around the luciferase
mentioned by Muona & Taräväinen (2020). The clade would genes from the genomes of Photinus, Aquatica and Ignelater
be defined by the clicking mechanism that was secondarily lost (Fallon et al., 2018). The position of photic organs is variable
in half of its members. Nevertheless, for convenience, we pre- in adult click beetles: prothoracic spots are reported in Balgus,
fer to keep the family status for all traditional, widely accepted Campyloxenus, and Pyrophorini: Nyctophyxina, the prothoracic
families whenever possible. Click beetles and fireflies are known and abdominal organs in Pyrophorini: Hapsodrilina and most
to non-specialists and they are intuitively distinguished also by Pyrophorina, and only the abdominal photic organs in the
the general public, for example, naturalist involved in the Fire- pyrophorine genus Hifo (Costa, 1975, 1984). Unlike these, only
fly Citizen Science Project by the Natural History Museum of abdominal photic organs are shared by all adult bioluminescent
Utah among others. Therefore, the family rank is appropriate for forms in the lampyroid clade (Branham & Wenzel, 2003; Bi
their separation and the expansion of fireflies to a heterogeneous et al., 2019).

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

 Phylogenomics of luminescent elateroids 9

Fig 6. The summary of Elateroidea relationships with the distribution of clicking, soft-bodied, and bioluminescent forms. Photographs J. Klváček and
authors. [Colour figure can be viewed at wileyonlinelibrary.com].

About 2300 species of the lampyroid clade inherited bio- Bioluminescence is scattered among some terminal lineages
luminescence from their most recent common ancestor and of click beetles, each of them being fully sclerotized and with
we must suppose that if this ancestor was a fully sclerotized a clicking mechanism. Further investigation of the origins of
elaterid-like beetle, the origin of bioluminescence preceded bioluminescent elaterids will need denser sampling of all biolu-
the shift to being soft-bodied (Fig. 6). Among bioluminescent minescent genera, including as many species as possible. Nev-
groups, only lampyrids are species-rich today (∼2000 spp.) ertheless, we support the earlier proposed hypothesis that ela-
and the second largest bioluminescent clade are glow-worms terid photic organs evolved several times (Bocakova et al., 2007;
(>200 spp.). Both are common in the Neotropical region along Sagegami-Oba et al., 2007; Fallon et al., 2018). The known
with bioluminescent elaterids (>100 spp.) (Costa, 1975, 1984). examples of elaterid bioluminescence are placed in three dif-
The effectiveness of bioluminescence as an aposematic signal ferent subfamilies (Costa, 1975, 1984), and a non-luminescent
depends on the number of taxa and individuals sharing the sig- most recent common ancestor and sister taxa have already
nal. As flashing can serve as an isolating mechanism (Branham been recovered for Balgus (Thylacosterninae) and Pyrophorini
(Agrypninae) (Bocakova et al., 2007; Kundrata et al., 2014).
& Wenzel, 2003), the intensive interactions among biolumines-
cent elateroids might have played a role in the high diversity of
extant fireflies, glow-worms and luminous click beetles in the
How old is elateroid bioluminescence?
Neotropical region (Ellis & Oakley, 2016).
Since South America is a major epicentre for bioluminescent
We do not attempt a formal dating analysis as our data
species, the region has been hypothesized as the ancestral region partly overlap with the datasets used earlier for the analyses
for the diversification of fireflies (Amaral et al., 2016). The sister of all beetles with multiple fossil calibration points (McKenna
group position of the elaterid-like East Asian Sinopyrophori- et al., 2015, 2019; Bocak et al., 2016; Toussaint et al., 2017;
dae (Figs 2, 3), the predominantly Laurasian distribution of two Kusy et al., 2018a; Zhang et al., 2018a). Most calibration points
of the deepest subfamilies of fireflies, Ototretinae and Lucioli- would not be available if we attempt an analysis restricted
nae (Kundrata et al., 2014; Martin et al., 2017, 2019; Zhang only to elateroids. Previous studies and the elateroid fossil
et al., 2018a) (Fig. 3), Southeast Asian Rhagophthalmidae, and records already serve as a guide to estimating of the origins
the presence of Phengodidae in Burmese amber (unpublished of both bioluminescence and Sinopyrophoridae. The recov-
data) suggest as an alternative hypothesis that the early diver- ered topologies place Sinopyrophorus between the first split
sification of the bioluminescent lineages took place in eastern of the elaterid-lampyroid clade and the deepest split between
Laurasia and was followed by subsequent intensive radiations soft-bodied bioluminescent fireflies, railroad and glow-worms
of fireflies in the Neotropical region. (Figs 2, 3). Most published analyses dated the earliest split

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

10 D. Kusy et al.

within the elaterid-lampyroid clade to the lower Cretaceous peri- radiation and signal diversification in the lineages which already
ods, ∼135 Ma (Toussaint et al., 2017; Zhang et al., 2018a; used some form of luminescence.
McKenna et al., 2019) (Ma; Fig. 4). More shallow estimations
of 115–125 Ma (McKenna et al., 2015; Fallon et al., 2018), as
well as a deeper one at 165 Ma (Kusy et al., 2018a,b) are also Author contributions
hypothesized. The estimations for the earliest split between the
fireflies and glow-worm clade are similarly inconclusive, at ∼98 DK analysed genomic data, carried out sequence alignments
Ma (Zhang et al., 2018a), ∼122 Ma (Martin et al., 2019), and and phylogenetic analyses, XYL and JWH produced genomic
∼140 Ma (Kusy et al., 2018a,b), but the presence of a lucioline data, MM and JWH participated in analyses, all co-authors
firefly in Burman amber supports older dates (Kazantsev, 2015). contributed to the draft of the manuscript; WXB collected the
If we consider median estimations, the elaterid-lampyroid clade specimen, DK, LB, LP, and SB conceived and designed the
would have originated in the lower Cretaceous and the subse- study, XYL and LB coordinated the study, LB, DK, SB, XYL
quent split of the Lampyridae, Rhagophthalmidae and Phengo- and JWH drafted the manuscript. All authors commented the
didae clade in the mid-Cretaceous. As a result, the ancestor of drafts and gave final approval for publication.
Sinopyrophoridae had to have split from their closest relative
∼120 Ma (Fig. 4). That period must also be considered as a
moment when bioluminescence evolved in Elateroidea for the Supporting Information
first time.
Additional supporting information may be found online in
Dating analyses using different taxon sampling, analysed
the Supporting Information section at the end of the article.
markers, applied models and calibrations often come to dif-
ferent age estimates (Fig. 4). Some studies recovered the early Figure S1. Classification of Elateroidea: an overview of
origins of the bioluminescent elateroids (Bocak et al., 2016; hypothesized phylogenies.
Kusy et al., 2018a) and we suggest these should be inspected as
a possibility. The shallower estimates (McKenna et al., 2015, Figure S1. An overview of Elateroidea topologies recovered
2019; Toussaint et al., 2017; Fallon et al., 2018; Zhang et al., by earlier studies.
2018a) set the origin of the elaterid-lampyroid clade of which
Figure S2–S22. Topologies recovered by individual analy-
click beetles is a principal branch to 115–140 Ma in contrast
ses.
with the upper Jurassic 152–158 Ma old Karatau deposits
contain a rich click beetle fauna (Doludenko et al., 1990). Figure S23–S24. DiscoVista relative frequency analyses.
Additionally, Elaterophanes (Whalley, 1985) was assigned to
Elateridae, and even if it is not a true click beetle but an ances- Figure S25. Four cluster likelihood mapping (FcLM) analy-
tral non-artematopodid elateroid lineage, its age is older than ses.
some estimates of the origin of Elateroidea (Fig. 4). Similarly,
Figure S26. Calculated log-likelihood difference analyses.
false click beetles, Eucnemidae, were reported from the lower
Jurassic Xiwan deposits (Lin, 1986) and multiple species are Figure S27–S32. AliStat and SymTest analyses.
known also from the upper Jurassic–lower Cretaceous period
(Chang et al., 2011). These fossils also support quite an early Figure S33. BUSCO3 and QUAST assessment for draft
origin of the Elateroidea. Consequently, an earlier origin of genome assembly.
bioluminescence is also possible. Figure S34. K-mer coverage depth of assembled Spades
scaffolds.
Conclusion Table S1. The list of taxa, accession numbers.

The phylogenetic studies dealing with Elateroidea produce Table S2. Overview of gene sets used for ortholog assess-
conflicting results (Bocakova et al., 2007; Sagegami-Oba ment.
et al., 2007; Lawrence et al., 2011) and similarly, the placement Table S3. Descriptive statistics and results of the orthology
of Sinopyrophorus as a terminal clade within Elateridae is assignment.
ambiguous (Bi et al., 2019; He et al., 2019). Phylogenomic data
presented here provide strong evidence that Sinopyrophoridae, Table S4. Detailed information and statistics of each gener-
stat.n., is the sister group of fireflies, railroad and glow-worm ated dataset.
beetles, despite its morphological similarity to the extant click
beetles (Fig. 6). Our finding suggests that lampyrids and their Table S5. The list of taxa included in the 66-gene datasets.
closest relatives are in fact modified click beetles. The definition Table S6. Results of four-cluster likelihood mapping and
of the Sinopyrophoridae+Phengodidae+Rhagophthalmidae+ approximately unbiased test.
Lampyridae clade supports an early origin of bioluminescence
in their common clicking ancestor, likely ∼120 Ma, in the lower Table S7. Result of approximately unbiased (AU) test for the
Cretaceous, the delayed shift to being soft-bodied and further dataset A-4199-AA.

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

 Phylogenomics of luminescent elateroids 11

Acknowledgements Branham, M.A. & Wenzel, J.W. (2003) The evolution of photic
behaviour and the evolution of sexual communication in fireflies
We are obliged for the generous advice and pipeline sharing (Coleoptera: Lampyridae). Cladistics, 84, 565–586.
to all colleagues from the Museum of A. Koenig in Bonn Breinholt, J.W. & Kawahara, A.Y. (2013) Phylotranscriptomics: sat-
and R. Bilkova is cordially acknowledged for her assistance. urated third codon positions radically influence the estimation of
J. Klváček. and Z.-W. Dong generously provided their pho- trees based on next-gen data. Genome Biology and Evolution, 5,
2082–2092.
tographs. We specially thank Wen Wang and other members in
Chang, H., Kirejtshuk, A.G. & Ren, D. (2011) On taxonomy and
his laboratory for their support. We thank to the editor and two
distribution of fossil Cerophytidae (Coleoptera: Elateriformia) with
anonymous reviewers for invaluable comments on the earlier description of a new Mesozoic species of Necromera Martynov, 1926.
version of the manuscript. The study was funded by the GACR Annales Societe Entomologique de France, 47, 33–44.
and IGA projects (18-14942S; LB, DK, and MM; PrF-2020; Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) Fastp: an ultra-fast
DK), the projects of NNSF China (31472035; X-YL) and CAS all-in-one FASTQ preprocessor. Bioinformatics, 34, i884–i890.
(‘Light of West China’; X-YL), the NSF project (DEB-1655981; Chernomor, O., von Haeseler, A. & Minh, B.Q. (2016) Terrace aware
SMB). The authors declare no conflicts of interest. data structure for phylogenomic inference from supermatrices. Sys-
tematic Biology, 65, 997–1008.
Costa, C. (1975) Systematics and evolution of the tribes Pyrophorini
and Heligmini, with description of Campyloxeninae, new subfamily
Data availability statement (Coleoptera, Elateridae). Arquivos de Zoologia, 26, 49–190.
Costa, C. (1984) Note on the bioluminescence of Balgus schnusei
The data that support the findings of this study are openly (Heller, 1914) (Trixagidae, Coleoptera). Revista Brasileira de Ento-
available in GenBank, accession number PRJNA64573 and the mologia, 28, 397–398.
datasets are openly available in the Mendeley Data repository at Degnan, J.H. & Rosenberg, N.A. (2006) Discordance of species trees
https://www.doi.org/10.17632/g4xkckycph.1. with their most likely gene trees. PLoS Genetics, 2, e68.
Doludenko, M.P., Ponomarenko, A.G. & Sakulina, G.V. (1990) La
géologie du gisement unique de la faune et de la flore du jurassique
supérieur d’Aulié (Karatau, Kazakhstan du Sud). Académie des
References Sciences de l’URSS, Institut Géologique, Moscow.
Edwards, S.V. (2009) Is a new and general theory of molecular
Amaral, D.T., Mitani, Y., Ohmiya, Y. & Viviani, V.R. (2016) Organiza- systematics emerging? Evolution, 63, 1–19.
tion and comparative analysis of the mitochondrial genomes of biolu- Ellis, E.A. & Oakley, T.H. (2016) High rates of species accumulation in
minescent Elateroidea (Coleoptera: Polyphaga). Gene, 586, 254–262. animals with bioluminescent courtship displays. Current Biology, 26,
Amaral, D.T., Silva, J.R. & Viviani, V.R. (2017) Transcriptional com- 1–6.
parison of the photogenic and non-photogenic tissues of Phrixothrix Erfan, S. & Mirarab, S. (2016) Fast coalescent-based computation of
hirtus (Coleoptera: Phengodidae) and non-luminescent Chauliog- local branch support from quartet frequencies. Molecular Biology and
nathus flavipes (Coleoptera: Cantharidae) give insights on the origin Evolution, 33, 1654–1668.
of lanterns in railroad worms. Gene Reports, 7, 78–86.
Erfan, S., James, J.B., Whitfield, B. & Mirarab, S. (2018) DiscoVista:
Amaral, D.T., Silva, J.R. & Viviani, V.R. (2019) RNA-Seq analysis
interpretable visualizations of gene tree discordance. Molecular
of the bioluminescent and non-bioluminescent species of Elateridae
Phylogenetics and Evolution, 122, 110–115.
(Coleoptera): comparison to others photogenic and non-photogenic
Fallon, T.R., Lower, S.E., Chang, C.-H. et al. (2018) Firefly genomes
tissues of Elateroidea species. Comparative Biochemistry and Physi-
illuminate parallel origins of bioluminescence in beetles. eLife, 7,
ology Part D: Genomics and Proteomics, 29, 154–165.
e36495.
Bankevich, A., Nurk, S., Antipov, D. et al. (2012) SPAdes: a new
Fernandez, R., Edgecombe, G.D. & Giribet, G. (2016) Exploring phy-
genome assembly algorithm and its applications to single-cell
logenetic relationships within Myriapoda and the effects of matrix
sequencing. Journal of Computational Biology, 19, 455–477.
Barrow, L.N., Lemmon, A.R. & Lemmon, E.M. (2018) Targeted composition and occupancy on phylogenomic reconstruction. System-
sampling and target capture: assessing phylogeographic concordance atic Biology, 65, 871–889.
with genome-wide data. Systematic Biology, 67, 979–996. He, J.W., Bi, W., Dong, Z. et al. (2019) The mitochondrial genome of the
Bi, W.X., He, J.W., Chen, C.C., Kundrata, R. & Li, X.Y. (2019) Sinopy- first luminous click-beetle (Coleoptera: Elateridae) recorded in Asia.
rophorinae, a new subfamily of Elateridae (Coleoptera, Elateroidea) Mitochondrial DNA Part B, 4, 565–567.
with the first record of a luminous click beetle in Asia and evidence Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q. & Vinh, L.S.
for multiple origins of bioluminescence in Elateridae. ZooKeys, 864, (2018) UFBoot2: improving the ultrafast bootstrap approximation.
79–97. Molecular Biology and Evolution, 35, 518–522.
Bocak, L., Kundrata, R., Andújar-Fernández, C. & Vogler, A.P. (2016) International Committee for Zoological Nomenclature (1999) Interna-
The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new tional Code of Zoological Nomenclature. International Trust for Zoo-
family of beetles from Spain, with immatures detected by environ- logical Nomenclature, London.
mental DNA sequencing. Proceedings of the Royal Society B: Bio- Jermiin, L.S., Jayaswal, V., Ababneh, F. & Robinson, J. (2008) Phylo-
logical Sciences, 283, 20152350. genetic model evaluation. Bioinformatics, Data, Sequence Analysis
Bocakova, M., Bocak, L., Hunt, T., Teräväinen, M. & Vogler, A.P. (2007) and Evolution, Vol. I (ed. by J. Keith), pp. 331–363. Humana Press,
Molecular phylogenetics of Elateriformia (Coleoptera): evolution of Totowa, New Jersey.
bioluminescence and neoteny. Cladistics, 23, 477–496. Junier, T. & Zdobnov, E.M. (2010) The Newick utilities:
Borowiec, M.L. (2016) AMAS: a fast tool for alignment manipulation high-throughput phylogenetic tree processing in the UNIX shell.
and computing of summary statistics. PeerJ, 4, e1660. Bioinformatics, 26, 1669–1670.

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

12 D. Kusy et al.

Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A. & (Coleoptera: Elateroidea). Insect Systematics and Diversity, 3,
Jermiin, L.S. (2017) ModelFinder: fast model selection for accurate 11.
phylogenetic estimates. Nature Methods, 14, 587–589. McKenna, D.D., Wild, A.L., Kanda, K. et al. (2015) The beetle tree
Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence align- of life reveals that Coleoptera survived end-Permian mass extinction
ment software version 7: improvements in performance and usability. to diversify during the Cretaceous terrestrial revolution. Systematic
Molecular Biology and Evolution, 30, 772–780. Entomology, 40, 835–880.
Kawahara, A.Y., Ohshima, I., Kawakita, A. et al. (2011) Increased McKenna, D.D., Shin, S., Ahrens, D. et al. (2019) The evolu-
gene sampling strengthens support for higher-level groups within tion and genomic basis of beetle diversity. Proceedings of the
leaf-mining moths and relatives (Lepidoptera: Gracillariidae). BMC National Academy of Sciences of the United States of America, 116,
Evolutionary Biology, 11, 182. 24729–24737.
Kazantsev, S.V. (2015) Protoluciola albertalleni gen.n., sp.n., a new Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D. & Gurevich,
Luciolinae firefly (Insecta: Coleoptera: Lampyridae) from Burmite A. (2018) Versatile genome assembly evaluation with QUAST-LG.
amber. Russian Entomological Journal, 24, 281–283. Bioinformatics, 34, i142–i150.
Kück, P. & Longo, G.C. (2014) FASconCAT-G: extensive functions for Minh, B.Q., Schmidt, H.A., Chernomor, O., Schrempf, D., Woodhams,
multiple sequence alignment preparations concerning phylogenetic M.D., von Haeseler, A. & Lanfear, R. (2020) IQ-TREE 2: new models
studies. Frontiers in Zoology, 11, 81. and efficient methods for phylogenetic inference in the genomic era.
Kück, P. & Struck, T.H. (2014) BaCoCa – a heuristic software tool for Molecular Biology and Evolution, 37, 1530–1534.
the parallel assessment of sequence biases in hundreds of gene and Mirarab, S., Bayzid, M.S. & Warnow, T. (2016) Evaluating summary
taxon partitions. Molecular Phylogenetics and Evolution, 70, 94–98. methods for multilocus species tree estimation in the presence of
Kück, P., Meusemann, K., Dambach, J., Thormann, B., von incomplete lineage sorting. Systematic Biology, 65, 366–380.
Reumont, B.M., Wägele, J.W. & Misof, B. (2010) Parametric Misof, B. & Misof, K.A. (2009) A Monte Carlo approach successfully
and non-parametric masking of randomness in sequence alignments identifies randomness in multiple sequence alignments: a more
can be improved and leads to better resolved trees. Frontiers in objective means of data exclusion. Systematic Biology, 58, 21–34.
Zoology, 7, 10. Misof, B., Meyer, B., von Reumont, B.M., Kück, P., Misof, K. & Meuse-
Kundrata, R., Bocakova, M. & Bocak, L. (2014) The comprehensive mann, K. (2013) Selecting informative subsets of sparse supermatri-
phylogeny of the superfamily Elateroidea (Coleoptera: Elateriformia). ces increases the chance to find correct trees. BMC Bioinformatics,
Molecular Phylogenetics and Evolution, 76, 162–171. 14, 348.
Kusy, D., Motyka, M., Andújar, C. et al. (2018a) Genome sequencing Misof, B., Liu, S., Meusemann, K. et al. (2014) Phylogenomics resolves
of Rhinorhipus Lawrence exposes an early branch of the Coleoptera. the timing and pattern of insect evolution. Science, 346, 763–767.
Frontiers in Zoology, 15, 21. Muona, J. & Taräväinen, M. (2020) A re-evaluation of the Eucnemidae
Kusy, D., Motyka, M., Bocek, M., Vogler, A.P. & Bocak, L. (2018b) larval characters. Papeis Avulsos de Zoologia, 60. https://doi.org/10
Genome sequences identify three families of Coleoptera as mor- .11606/1807-0205/2020.60.special-issue.28
phologically derived click beetles (Elateridae). Scientific Reports, 8, Nakatsu, T., Ichiyama, S., Hiratake, J., Saldanha, A., Kobashi, N.,
17084. Sakata, K. & Kato, H. (2006) Structural basis for the spectral
Kusy, D., Motyka, M., Bocek, M., Masek, M. & Bocak, L. (2019) difference in luciferase bioluminescence. Nature, 440, 372–376.
Phylogenomic analysis resolves the relationships among net-winged Naser-Khdour, S., Minh, B.Q., Zhang, W., Stone, S.A. & Lanfear, R.
beetles (Coleoptera: Lycidae) and reveals the parallel evolution of (2019) The prevalence and impact of model violations in phylogenetic
morphological traits. Systematic Entomology, 44, 911–925. analysis. Genome Biology and Evolution, 11, 3341–3352.
Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. & Calcott, Peters, R.S., Krogmann, L., Mayer, C. et al. (2017) Evolutionary history
B. (2017) PartitionFinder 2: new methods for selecting partitioned of the Hymenoptera. Current Biology, 27, 1013–1018.
models of evolution for molecular and morphological phylogenetic Petersen, M., Meusemann, K., Donath, A. et al. (2017) Orthograph: a
analyses. Molecular Biology and Evolution, 34, 772–773. versatile tool for mapping coding nucleotide sequences to clusters of
Lawrence, J.F. (1988) Rhinorhipidae, a new beetle family from Aus- orthologous genes. BMC Bioinformatics, 18, 111.
tralia, with comments on the phylogeny of the Elateriformia. Inverte- Poelchau, M., Childers, C., Moore, G. et al. (2014) The i5k
brate Taxonomy, 2, 1–53. Workspace@NAL enabling genomic data access, visualization
Lawrence, J.F., Slipinski, A., Seago, A.E. et al. (2011) Phylogeny of the and curation of arthropod genomes. Nucleic Acids Research, 43,
Coleoptera based on morphological characters of adults and larvae. D714–D719.
Annales Zoologici, 61, 1–217. Sagegami-Oba, R., Takahashi, N. & Oba, Y. (2007) The evolutionary
Lin, Q.B. (1986) Early Mesozoic fossil insects from South China. process of bioluminescence and aposematism in cantharoid beetles
Palaeontologia Sinica, 170, 1–112. (Coleoptera: Elateroidea) inferred by the analysis of 18S ribosomal
Linard, B., Crampton-Platt, A., Moriniere, J. et al. (2018) The contribu- DNA. Gene, 400, 104–113.
tion of mitochondrial metagenomics to large-scale data mining and Sanders, S.E. & Hall, D.W. (2015) Variation in opsin genes correlates
phylogenetic analysis of Coleoptera. Molecular Phylogenetics and with signalling ecology in north American fireflies. Molecular Ecol-
Evolution, 128, 1–11. ogy, 24, 4679–4696.
Marcais, G. & Kingsford, C. (2011) A fast, lock-free approach for Stanke, M. & Waack, S. (2003) Gene prediction with a hidden Markov
efficient parallel counting of occurrences of k-mers. Bioinformatics, model and a new intron submodel. Bioinformatics, 19, 215–225.
27, 764–770. Strimmer, K. & von Haeseler, A. (1997) Likelihood-mapping: a simple
Martin, G.J., Branham, M., Whiting, M.F. & Bybee, S.M. (2017) method to visualize phylogenetic content of a sequence alignment.
Total evidence phylogeny and the evolution of adult bioluminescence Proceedings of the National Academy of Sciences of the United States
in fireflies (Coleoptera: Lampyridae). Molecular Phylogenetics and of America, 94, 6815–6819.
Evolution, 107, 564–575. Suyama, M., Torrents, D. & Bork, P. (2006) PAL2NAL: robust con-
Martin, G.J., Stanger-Hall, K.F., Branham, M.A. et al. (2019) version of protein sequence alignments into the corresponding codon
Higher-level phylogeny and reclassification of Lampyridae alignments. Nucleic Acids Research, 34, W609–W612.

© 2020 The Royal Entomological Society, Systematic Entomology, doi: 10.1111/syen.12451

 Phylogenomics of luminescent elateroids 13

Timmermans, M.J.T.N., Dodsworth, S., Culverwell, C.L. et al. (2010) Whalley, P.E.S. (1985) The systematics and palaeogeography of the
Why barcode? High-throughput multiplex sequencing of mitochon- lower Jurassic insects of Dorset, England. Bulletin of the British
drial genomes for molecular systematics. Nucleic Acids Research, 38, Museum of Natural History, 39, 107–189.
e197. Ye, B., Zhang, Y., Shu, J., Wu, H. & Wang, H. (2018) RNA-sequencing
Timmermans, M.J.T.N., Barton, C., Haran, J. et al. (2016) Family-level analysis of fungi-induced transcripts from the bamboo wireworm
sampling of mitochondrial genomes in Coleoptera: compositional Melanotus cribricollis (Coleoptera: Elateridae) larvae. PLoS One, 13,
heterogeneity and phylogenetics. Genome Biology and Evolution, 8, e019118.
161–175. Zdobnov, E.M., Tegenfeldt, F., Kuznetsov, D. et al. (2016)
Toussaint, E., Seidel, M., Arriaga-Varera, E. et al. (2017) The peril of OrthoDBv9.1: cataloging evolutionary and functional annota-
dating beetles. Systematic Entomology, 42, 1–10. tions for animal, fungal, plant, archaeal, bacterial and viral orthologs.
Trueman, J.W.H., Pfeil, B.E., Kelchners, S.A. & Yeates, D.K. (2004) Nucleic Acids Research, 45, D744–D749.
Did stick insects really regain their wings? Systematic Entomology, Zhang, S.Q., Che, L.H., Li, Y., Dan Liang, Pang, H., Ślipiński, A. &
29, 138–139. Zhang, P. (2018a) Evolutionary history of Coleoptera revealed by
Vasilikopoulos, A., Balke, M., Beutel, R.G. et al. (2019) Phylogenomics extensive sampling of genes and species. Nature Communications, 9,
of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an 205.
evaluation of phylogenetic conflict and systematic error. Molecular Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. (2018b) ASTRAL-III:
Phylogenetics and Evolution, 135, 270–285. polynomial time species tree reconstruction from partially resolved
Vurture, G.W., Sedlazeck, F.J., Nattestad, M., Underwood, C.J., gene trees. BMC Bioinformatics, 19(S6), 153.
Fang, H., Gurtowski, J. & Schatz, M.C. (2017) GenomeScope: fast Zhang, J., Lindsey, A.R.I., Peters, R.S. et al. (2020) Conflicting signal
reference-free genome profiling from short reads. Bioinformatics, 33, in transcriptomic markers leads to a poorly resolved backbone
2202–2204. phylogeny of chalcidoid wasps. Systematic Entomology. https://doi
Wang, K., Hong, W., Jiao, H. & Zhao, H. (2017) Transcriptome .org/10.1111/syen.12427.
sequencing and phylogenetic analysis of four species of luminescent Zwick, A., Regier, J.C. & Zwickl, D.J. (2012) Resolving discrepancy
beetles. Scientific Reports, 7, 1814. between nucleotides and amino acids in deep-level arthropod phy-
Waterhouse, R.M., Seppey, M., Simão, F.A. et al. (2018) BUSCO appli- logenomics: differentiating serine codons in 21-amino-acid models.
cations from quality assessments to gene prediction and phyloge- PLoS One, 7, e47450.
nomics. Molecular Biology and Evolution, 35, 543–548.
Watkins, O.C., Sharpe, M.L., Perry, N.B. & Krause, K.L. (2018) New Accepted 23 July 2020
Zealand glowworm (Arachnocampa luminosa) bioluminescence is
produced by a firefly-like luciferase but an entirely new luciferin.
Scientific Reports, 8, 3278.

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