title: 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.
authors.affiliation: Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain. Electronic address: sereina.rutschmann@gmail.com.
authors.forename: Sereina
authors.initials: S
authors.lastname: Rutschmann
authors.affiliation: Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
authors.forename: Harald
authors.initials: H
authors.lastname: Detering
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY 10024, USA; Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Simon
authors.affiliation: Stroud Water Research Center, Avondale, PA 19311, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Funk
authors.affiliation: Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Gattolliat
authors.affiliation: Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, Apartado 1013, 5001-801 Vila Real, Portugal.
authors.forename: Samantha J
authors.initials: SJ
authors.lastname: Hughes
authors.affiliation: Research Centre in Biodiversity and Genetic Resources (CIBIO)-Açores and the Biology Department, University of Azores, Rua Mãe de Deus 13A, 9501-855 Ponta Delgada, Portugal.
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Raposeiro
authors.affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY 10024, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: DeSalle
authors.affiliation: Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Michel
authors.initials: M
authors.lastname: Sartori
authors.affiliation: Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Monaghan
mesh_terms: D000818:Animals; D044822:Biodiversity; D005075:Biological Evolution; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D005060:Europe; D056426:Genetic Loci; D016678:Genome; D007313:Insecta / Q000145:classification* / Q000235:genetics; D062312:Islands; D009656:North America; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Baetidae; Island radiation; Multispecies coalescent; Phylogeny; Phylogeography