Shall we chat? Evolutionary relationships in the genus Cercomela (Muscicapidae) and its relation to Oenanthe reveals extensive polyphyly among chats distributed in Africa, India and the Palearctic

Climate cycling did not affect haplotype distribution in an abundant Southern African avian habitat generalist species, the familiar chat (Oenanthe familiaris)

Avian species diversity in Southern Africa is remarkably high, yet the mechanisms responsible for that diversity are poorly understood. While this is particularly true with respect to species endemic to the subregion, it is unclear as to how more broadly distributed African species may have colonized southern Africa. One process that may in part account for the high bird species diversity in southern Africa is a "species pump" model, wherein the region was repeatedly colonized by lineages from areas further north: a pattern related to climate cycling and the eastern African arid corridor. Once occupying southern Africa, with its many varied biomes, it is possible that climate cycling further affected lineages by generating genetic diversity in multiple refugia, a pattern recently shown for several southern African bird species. Here, we used mtDNA to address these questions in a widespread, sedentary habitat generalist bird species, the familiar chat (Oenanthe familiaris). The phylogenetic structure suggests a north-to-south colonization pattern, supporting the "species pump" model. Haplotype diversity was partitioned into two distinct clusters: southern Africa and Malawi (East Africa). Southern African haplotypes were not geographically partitioned, and we hypothesize that this pattern has arisen because this species is a habitat generalist, and as such resilient to habitat-altering climate perturbations. Based on our phylogenetic results, we discuss the validity of currently recognized subspecies.

A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.

A near-complete and time-calibrated phylogeny of the Old World flycatchers, robins and chats (Aves, Muscicapidae)

The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts over the past two decades, there is still no comprehensive and well-resolved species-level phylogeny for Muscicapidae. Here we present a supermatrix phylogeny that includes all 50 currently recognized genera and ca. 92% of all the species, built using data from up to 15 mitochondrial and 13 nuclear loci. In addition to assembling nucleotide sequences available in public databases, we also extracted sequences from the genome assemblies and raw sequencing reads from GenBank and included a few unpublished sequences. Our analyses resolved the phylogenetic position for several previously unsampled taxa, for example, the Grand Comoro Flycatcher Humblotia flavirostris, the Collared Palm Thrush Cichladusa arquata, and the Taiwan Whistling-Thrush Myophonus insularis, etc. We also provide taxonomic recommendations for genera that exhibit paraphyly or polyphyly. Our results suggest that Muscicapidae diverged from Turdidae (thrushes and allies) in the early Miocene, and the most recent common ancestors for the four subfamilies (Muscicapinae, Niltavinae, Cossyphinae and Saxicolinae) all arose around the middle Miocene.

Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds?

The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm’s Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.

Complete mitochondrial genome of the isabelline wheatear Oenanthe isabellina (Passeriformes, Muscicapidae)

The isabelline wheatear Oenanthe isabellina was widespread in Northern Hemisphere, but the information of this species is poorly known. In this study, the complete sequence of O. isabellina mitochondrial genome was obtained by L-PCR and conserved primer-walking approaches. The results showed that the entire mitochondrial genome of O. isabellina was 16,812 bp in length with 52.7% A + T content; the genome harbored the same gene order as that of other birds, including 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop). All protein-coding genes of O. isabellina mitochondrial genome started with an ATG codon, except for COI with GTG. For terminate codon usage, most of the genes use TAA or TAG. The control region of O. isabellina was located between tRNA-Glu and tRNA-Phe with 1244 bp length, no repetitive sequence. The mitochondrial data are potentially important for understanding this poorly known species.

Morphological shifts of the external flight apparatus across the range of a passerine (Northern Wheatear) with diverging migratory behaviour

We studied morphological differentiation in the flight apparatus of the four currently recognised sub-species of Northern Wheatears, Oenanthe oenanthe. Considering all measured birds without assigning them a priori to any sub-species we found a clinal morphological shift. Relative wing length, wing pointedness, and the degree of tail forking were positively correlated with migratory distance, whereas tail length (relative to wing length) was negatively correlated. The large-sized, long-distance migrant "Greenland" Wheatear, O. o. leucorhoa, is characterized by relatively longer, broader and more pointed wings and more forked tails, similar to the smaller-sized nominate Northern Wheatear, O. o. oenanthe, from North Europe, Siberia and Russia. In contrast, the short distance migrant "Seebohm's" Wheatear, O. o. seebohmi, from northwest Africa, possesses much rounder wings, and the tail is relatively longer and less forked. Sub-species with intermediate migratory habits (different populations of nominate Northern Wheatear, O. o. oenanthe, and "Mediterranean" Northern Wheatear, O. o. libanotica) show, as expected, intermediate features according to their intermediate migratory behaviour. Our results are congruent with other inter- and intraspecific studies finding similar adaptations for energy-effective flight in relation to migration distance (morphological migratory syndrome).

Phylogeny of the mourning wheatear Oenanthe lugens complex

The phylogenetic relationship of many species and subspecies within the genus Oenanthe (wheatears) is still debated. Only recently molecular approaches have been used to clarify their basal taxonomy. One of the main unsolved groups is summarized under the name mourning wheatear O. lugens, which comprises depending on the underlying species concept 3-8 different taxa. These include the wheatears of the subspecies group lugens (halophila, lugens, persica), the subspecies group lugubris (lugubris, schalowi, vauriei), and the subspecies group lugentoides (lugentoides, boscaweni). In order to shed light on this unsolved issue we studied the taxonomy of the mourning wheatear complex by means of molecular markers and comparative morphometry. We found reasonable evidence to follow a narrow species concept treating all the three subspecies groups of the mourning wheatear in future as three independent taxonomic entities (super-species O. lugens, O. lugentoides, O. lugubris). Further within the subspecies group O. lugens we suggest treating halophila and lugens as members of the polytypic species O. lugens, while the Persian mourning wheatear O. persica merits the status of an independent monotypic species, endemic to the Iranian Plateau. Genetic and morphometric characters support a long separation of this form (a half to one Million years). For the black form "basalti" from Syria and Jordan our molecular data indicates a close relationship to lugens and this form is therefore probably best treated as a colour morph of lugens, adapted to the local habitat conditions. However, future behavioural studies have to show if there exist prezygotic barriers between both forms.