Birds are of high public interest and of great value as indicators of the state of the environment. Some 11,000 species are a number relatively well to handle. From a scientific point of view, it is not easily answerable what a species is, since speciation and extinction are ongoing evolutionary processes and differentiation among species works on various traits. Contemporary systematics attempts to take into account as many criteria as possible to delimit species. The currently most influential approach is the use of genomic sequences, be it as a neutral marker or to discover the underpinnings of functional traits. The study of the outer appearance of birds nevertheless remains fundamental, since that is the interface between a bird and its biotic and abiotic environment. For the majority of bird species, acquired traits of vocal communication add to this complex. Birds can also vary the timing of important behavior such as breeding or molting. Most fascinating among circannual behavior are the long-distance movements that can quite fast evolve and have genetic bases. Despite such dispersal ability for many bird species, geographic barriers play a large role for distribution and speciation in birds. Extant, former, and potential future ranges of a species can be modeled based on the abiotic niches individuals of this species have. Within a species’ range, genetic and phenotypic traits vary and promote to process toward species splits. Beside geographic frameworks, ecological circumstances play a major role and contribute to natural selection but also trigger individual responses such as phenotypic plasticity, modification of the environment, and habitat selection. Anthropogenic global impacts such as climate and land-use changes (e.g., urbanization) force extant species to accelerated modifications or population splits or let them vanish forever. Only if humans leave more room and time to birds and other organisms can we expect to maintain such a number of diverse bird species, although they will keep modifying, splitting, and becoming extinct—but for natural reasons. D. T. Tietze (*) Natural History Museum Basel, Basel, Switzerland e-mail: thomas.tietze@bs.ch © The Author(s) 2018 D. T. Tietze (ed.), Bird Species, Fascinating Life Sciences, https://doi.org/10.1007/978-3-319-91689-7_1 1

Bird Species : How They Arise, Modify and Vanish

Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.

https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2015.2340

Matching loci surveyed to questions asked in phylogeography

Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves:Turdidae).

Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin.

Hewitt's paradigm for effects of Pleistocene glaciations on European populations assumes their isolation in peninsular refugia during glacial maxima, followed by re-colonization of broader Europe during interstadials. This paradigm is well supported by studies of poorly dispersing taxa, but highly dispersive birds have not been included. To test this paradigm, we use the dunnock (Prunella modularis), a Western Palaearctic endemic whose range includes all major European refugia. MtDNA gene tree, multilocus species tree and species delimitation analyses indicate the presence of three distinct lineages: one in the Iberian refugium, one in the Caucasus refugium, and one comprising the Italian and Balkan refugia and broader Europe. Our gene flow analysis suggests isolation of both the Iberian and Caucasus lineages but extensive exchange between Italy, the Balkans and broader Europe. Demographic stability could not be rejected for any refugial population, except the very recent expansion in the Caucasus. By contrast, northern European populations may have experienced two expansion periods. Iberia and Caucasus had much smaller historical populations than other populations. Although our results support the paradigm, in general, they also suggest that in highly dispersive taxa, isolation of neighbouring refugia was incomplete, resulting in large super-refugial populations.

https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2018.1606

A test of the European Pleistocene refugial paradigm, using a Western Palaearctic endemic bird species.

When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.

Effects of Asymmetric Nuclear Introgression, Introgressive Mitochondrial Sweep, and Purifying Selection on Phylogenetic Reconstruction and Divergence Estimates in the Pacific Clade of Locustella Warblers

Vladimir N. Sotnikov

Papers

Effects of Asymmetric Nuclear Introgression, Introgressive Mitochondrial Sweep, and Purifying Selection on Phylogenetic Reconstruction and Divergence Estimates in the Pacific Clade of Locustella Warblers

Multi-locus reassessment of a striking discord between mtDNA gene trees and taxonomy across two congeneric species complexes.