Molecular Phylogeny Reveals High Diversity, Geographic Structure and Limited Ranges in Neotenic Net-Winged Beetles <i>Platerodrilus</i> (Coleoptera: Lycidae)

<div><p>The neotenic <i>Platerodrilus</i> net-winged beetles have strongly modified development where females do not pupate and retain larval morphology when sexually mature. As a result, dispersal propensity of females is extremely low and the lineage can be used for reconstruction of ancient dispersal and vicariance patterns and identification of centres of diversity. We identified three deep lineages in <i>Platerodrilus</i> occurring predominantly in (1) Borneo and the Philippines, (2) continental Asia, and (3) Sumatra, the Malay Peninsula and Java. We document limited ranges of all species of <i>Platerodrilus</i> and complete species level turnover between the Sunda Islands and even between individual mountain regions in Sumatra. Few dispersal events were recovered among the major geographical regions despite long evolutionary history of occurrence; all of them were dated at the early phase of <i>Platerodrilus</i> diversification up to the end of Miocene and no exchange of island faunas was identified during the Pliocene and Pleistocene despite the frequently exposed Sunda Shelf as sea levels fluctuated with each glacial cycle. We observed high diversity in the regions with persisting humid tropical forests during cool periods. The origins of multiple species were inferred in Sumatra soon after the island emerged and the mountain range uplifted 15 million years ago with the speciation rate lower since then. We suppose that the extremely low dispersal propensity makes <i>Platerodrilus</i> a valuable indicator of uninterrupted persistence of rainforests over a long time span. Additionally, if the diversity of these neotenic lineages is to be protected, a high dense system of protected areas would be necessary.</p></div

Timing of the <i>Platerodrilus</i> radiation.

<p>Estimated ages of nodes are based on Bayesian analysis of all fragments and Muscle alignment. The bars depict 95% confidence intervals.</p

The length of DNA fragments and the numbers of informative characters in datasets (gaps considered as the 5^th character).

<p>The length of DNA fragments and the numbers of informative characters in datasets (gaps considered as the 5^th character).</p

Reconstruction of ancestral ranges using statistical parsimony.

<p>Reconstruction of ancestral ranges using statistical parsimony.</p

Distribution of <i>Platerodrilus</i>.

<p>The taxa were assigned to clades by the phylogenetic analysis and/or morphological similarity. <i>P</i>. <i>testaceicollis</i> Pic, 1921 is known in a damaged holotype and no diagnostic characters are available to evaluate its relationships.</p

Female larvae, late instars.

<p>A-C <i>Platerodrilus</i>, Bornean clade; A—from Borneo, Sabah, Mt. Kinabalu, B—Borneo, Sabah, Poring, C—Mindanao, New Bataan; D—<i>Macrolibnetis</i>, Malaysia, Pahang, Cameron Highlands.</p

A—Relative age of nodes estimated using penalized likelihood.

<p>The age of <i>Platerodrilus</i> was arbitrarily set to 100. The lower axes show ageestimation in mya derived from the age of <i>Platerodrilus</i> inferred at 47 mya by Bocak <i>et al</i>. (2008). B—Lineage-through-time pot for <i>Platerodrilus</i>, the time axis is calibrated as in Fig 5A.</p

Phylogenetic hypothesis for <i>Platerodrilus</i> Pic, 1921 based on a maximum likelihood analysis of the Muscle alignment.

<p>Numbers at the branches are maximum likelihood bootstrap values and Bayesian posterior probabilities.</p

Additional file 1: of Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

Text the morphology-based classifications of Rhinorhipidae. Table S1. The list of taxa included in the LSU rRNA, SSU rRNA, rrnL, and cox1 mitochondrial DNA dataset with GenBank accession and voucher ID numbers. Table S2. The list of taxa included in the mitogenomic analysis with GenBank accession numbers. Table S3. The list of taxa included in the LSU rRNA, SSU rRNA, and six nuclear protein coding genes. Table S4. The list of taxa included in the 65-gene dataset. Table S5. The list of markers in the 95-gene dataset with information on multi-copy genes. Table S6. The list of taxa included in the phylotranscriptomic dataset and the number of sequences available for each taxon. Table S7. Overview of official gene sets of six reference species used for transcript ortholog assessment, including the source, version and number of genes. Table S8. Gene descriptions for the 4220 ortholog groups (OGs) as present in. OrthoDB 9.1. Each OG contains one gene of each of the 6 reference species. Table S9. Success of transcript assignment to ortholog groups (OGs) of Rhinorhipus, published beetles transcriptomes and genomes. Table S10. The models and partition selections recovered with ModelFinder for the maximum likelihood analysis of the LSU rRNA, SSU rRNA, rrnL mtDNA, and cox1 mtDNA dataset. Table S11. Identification of the best partition scheme and models for the mitochondrial DNA dataset. Table S12. The LSU rRNA, SSU rRNA, and six nuclear protein coding genes dataset: characteristics, partition scheme and models of DNA evolution. Table S13. The transcriptomic supermatrix 3: partition scheme and models of DNA evolution (amino acid dataset, 4220 orthologs). Table S14. The transcriptomic supermatrix 4: partition scheme and models of DNA evolution (amino acid dataset, 943 orthologs). Figure S1. Maximum likelihood tree for Rhinorhipus, 517 Elateriformia and 46 outgroups recovered from the LSU rRNA, SSU rRNA, rrnL mtDNA and cox1 mtDNA dataset. Figure S2. Maximum likelihood tree for 83 species of beetles recovered from 15 mitochondrial genes. Figure S3. Maximum likelihood tree for 139 species of beetles recovered from the. LSU rRNA, SSU rRNA and six nuclear protein coding genes. Figure S4. Bayesian tree for 139 species of beetles recovered from the LSU rRNA, SSU rRNA and six nuclear protein coding genes. Figure S5. Maximum likelihood (RaxML) tree for 372 species of beetles and for outgroups recovered from the 66-gene amino acid dataset. Figure S6. Maximum likelihood (iQ) tree for 372 species of beetles and for outgroups recovered from the 66-gene amino acid dataset. Figure S7. Maximum likelihood (iQ) tree for 372 species of beetles and for outgroups recovered from the 66-gene nucleotide dataset. Figure S8. Tree network obtained from the separate maximum likelihood analyses of 968 orthologs 590. Figure S9. Dated phylogenetic tree of beetle relationships inferred from the Bayesian analysis of mitogenomic dataset using maximum likelihood topology. Figure S10. Dated phylogenetic tree of beetle relationships inferred from the Bayesian analysis of mitogenomic dataset using Bayesian topology. Figure S11. Dated phylogenetic tree of beetle relationships inferred from the Bayesian analysis of eight-gene dataset using constrained Bayesian topology and two calibration points (A, B) and verified by mapping of nineteen fossil records reported by Toussaint et al. (2016). The bottom diagram shows accumulation of the number of extant beetle families (red dots on the tree). Time line relates the tree to extinction events and geologic periods. Red bars designate the origin of Rhinorhipidae. (PDF 30160 kb