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Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves : Alaudidae)

Author:
  • Martin Wintersparv Stervander
  • Per Alström
  • Urban Olsson
  • Ulf Ottosson
  • Bengt Hansson
  • Staffan Bensch
Publishing year: 2016-09-01
Language: English
Pages: 233-245
Publication/Series: Molecular Phylogenetics and Evolution
Volume: 102
Document type: Journal article
Publisher: Elsevier

Abstract english

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.

Keywords

  • Biological Systematics
  • Cryptic taxa
  • Museum specimens
  • Phylogeny
  • RAD
  • SNAPP

Other

Published
  • Speciation in birds
  • Molecular Ecology and Evolution Lab
  • ISSN: 1055-7903
Staffan Bensch
E-mail: staffan [dot] bensch [at] biol [dot] lu [dot] se

Professor

MEMEG

+46 46 222 42 92

E-C213

Sölvegatan 37, Lund

50

Head of unit

MEMEG

+46 46 222 42 92

E-C213

Sölvegatan 37, Lund

50

Research group

Molecular Ecology and Evolution Lab

Projects

Doctoral students and postdocs

PhD students, main supervisor

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