title: Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).
abstract: The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision.
authors.affiliation: Molecular Ecology and Evolution Lab, Dept of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden; AP Leventis Ornithological Research Institute, Laminga, Jos East, Jos, Plateau, Nigeria. Electronic address: martin.stervander@biol.lu.se.
authors.forename: Martin
authors.initials: M
authors.lastname: Stervander
authors.affiliation: Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: per.alstrom@ebc.uu.se.
authors.forename: Per
authors.initials: P
authors.lastname: Alström
authors.affiliation: Department of Biological and Environmental Sciences, University of Göteborg, Box 463, SE-405 30 Göteborg, Sweden.
authors.forename: Urban
authors.initials: U
authors.lastname: Olsson
authors.affiliation: AP Leventis Ornithological Research Institute, Laminga, Jos East, Jos, Plateau, Nigeria.
authors.forename: Ulf
authors.initials: U
authors.lastname: Ottosson
authors.affiliation: Molecular Ecology and Evolution Lab, Dept of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden.
authors.forename: Bengt
authors.initials: B
authors.lastname: Hansson
authors.affiliation: Molecular Ecology and Evolution Lab, Dept of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden.
authors.forename: Staffan
authors.initials: S
authors.lastname: Bensch
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics*; D045303:Cytochromes b / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D014644:Genetic Variation; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism; D046109:Passeriformes / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D004247:DNA; D045303:Cytochromes b
keywords: Cryptic taxa; Museum specimens; Phylogeny; RAD; SNAPP