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

Wintersparv Stervander, Martin LU ; Alström, Per; Olsson, Urban; Ottosson, Ulf; Hansson, Bengt LU and Bensch, Staffan LU (2016) In Molecular Phylogenetics and Evolution 102. p.233-245
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.... (More)

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.

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organization
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Contribution to journal
publication status
published
subject
keywords
Cryptic taxa, Museum specimens, Phylogeny, RAD, SNAPP
in
Molecular Phylogenetics and Evolution
volume
102
pages
13 pages
publisher
Elsevier
external identifiers
  • scopus:84976274864
  • wos:000380622600021
ISSN
1055-7903
DOI
10.1016/j.ympev.2016.05.032
language
English
LU publication?
yes
id
8dc08042-a39a-425a-8957-c9b32093ff0a
date added to LUP
2016-11-28 16:01:29
date last changed
2017-04-30 17:47:28
@article{8dc08042-a39a-425a-8957-c9b32093ff0a,
  abstract     = {<p>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.</p>},
  author       = {Wintersparv Stervander, Martin and Alström, Per and Olsson, Urban and Ottosson, Ulf and Hansson, Bengt and Bensch, Staffan},
  issn         = {1055-7903},
  keyword      = {Cryptic taxa,Museum specimens,Phylogeny,RAD,SNAPP},
  language     = {eng},
  month        = {09},
  pages        = {233--245},
  publisher    = {Elsevier},
  series       = {Molecular Phylogenetics and Evolution},
  title        = {Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves : Alaudidae)},
  url          = {http://dx.doi.org/10.1016/j.ympev.2016.05.032},
  volume       = {102},
  year         = {2016},
}