Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

Abstract

Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family

“…Most studies of speciation and biogeography in temperate‐zone birds have focused on describing the historical population structure of single species, or of a few closely related species (e.g., Drovetski, Raković, Semenov, Fadeev, & Red'kin, ; Drovetski et al., ; Haring, Gamauf, & Kryukov, ; Irwin, Bensch, & Price, ; Li et al., ; Milá, McCormack, Castaneda, Wayne, & Smith, ; Ödeen & Björklund, ; Pavlova, Rohwer, Drovetski, & Zink, ; Pavlova, Zink, & Rohwer, ; Pavlova, Zink, Rohwer, Koblik, et al., ; Qvarnström, Rice, & Ellegren, ; Saitoh et al., ; Song et al., ; Zhao et al., ; Zink, Pavlova, Drovetski, & Rohwer, ; Zink et al., ). In order to find general patterns, there is a need to build complete species level phylogenies for larger taxonomic groups, with species in different stages of the speciation process.…”

Evolutionary history of passerine birds (Aves: Passeriformes) from the Qinghai–Tibetan plateau: from a pre-Quarternary perspective to an integrative biodiversity assessment

“…But going back in time and evolutionary history, diversification and speciation processes among eight species of snowfinches and among four Holarctic lineages of the Horned Lark were suggested to date back to even late Pliocene times (in fact with quite similar split ages estimates; Table 1; compare Lei et al 2014;Alström et al 2013a). Possible evolutionary scenarios and taxonomic consequences are still under lively debate particularly for Horned Larks because of a low signal of nuclear markers and fundamental differences among split age estimates inferred from independent studies (Alström et al 2013a;Drovetski et al 2014). To date, a centre of origin and diversification has not been hypothesised for either of these two groups, but at least for snowfinches a QTP 'cradle of evolution' is a quite likely hypothetical scenario that can be put to test in future studies (see below).…”

Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass

“…A comprehensive study on lark phylogeny resolving the complex relationships among larks (Alaudidae) indicated dramatic morphological divergence in some lineages as well as multiple examples of parallel morphological evolution 17 . Within larks, the systematics and evolution of the genus Eremophila were until recently poorly understood, with many subspecies described (owing in part to the variation and divergence in plumage 18,19 ). However, a recent study from Ghorbani et al 20 based on ND2 and cytb genes identified four distinct Eremophila lineages that diverged in the late Pliocene to early Pleistocene.…”