Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Abstract

The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.

discomark: nuclear marker discovery from orthologous sequences using draft genome data

“…(). The phylogeny of the Cloeon ‐species complex presented here also is in complete agreement with species tree reconstructions based on 59 nDNA markers (Rutschmann et al ., ).…”

Elevation in tropical sky islands as the common driver in structuring genes and communities of freshwater organisms

“…The diversity indexes are estimated by an additive partitioning of species diversity (ɣ = β + α) with gamma being the total diversity, beta the among-site diversity (average amount of diversity not found in a single site), and alpha the average within-site diversity (as described in Lu et al . 71 ). Linear regressions of observed α, β and ɣ diversity against elevation revealed statistically significant relationships for two indexes, the β and ɣ diversities (β: adjusted R 2 = 0.1638, P = 0.0138; ɣ: adjusted R 2 = 0.1706, P = 0.0121); the correlation between elevation and α diversity was not significant (adjusted R 2 = 0.0061, P = 0.2856).…”

“…To account for cryptic lineages in morphospecies, or resolve recent diversification events, Rutschmann et al . 71 suggested an approach combining coalescent-based phylogeographic, species delimitation and phylogenetic reconstruction using a large number of nuclear genes. Even though no species delimitation essay was performed in the present study, the coalescent-based phylogenetic reconstruction shows that ongoing divergence between low and high elevation populations generally dates back from less than a million years ago, a scale that is compatible with the intra-specific evolutionary time scale.…”

Reports of Baetidae (Ephemeroptera) species from Tafna Basin, Algeria and biogeographic affinities revealed by DNA barcoding

“…The species delimitation within the genus Cloeon Leach, 1815 (sensu Kluge 2016b ) is also highly problematic. Most of the reports of the widely-distributed Cloeon dipterum (Linnaeus, 1761) or Cloeon cognatum Stephens, 1835 must be considered with caution as several independent lineages are hidden behind these concepts ( Rutschmann et al 2014 , Rutschmann et al 2017 ).…”