**6. Phylogeography**

Another area of interest is the distribution and evolution of a species over time and space. This is the realm of phylogeography [15]. In order to use DNA for such analyses, we require highly informative DNA and methods with a high degree of resolution. Although variable mtDNA is useful in many instances, a better resolution can be obtained from the analysis of microsatellite markers. Increasingly, partial (RADSeq) and complete genome analyses from High-throughput sequencing are also used to study phylogeography because we can obtain information of millions of single nucleotide polymorphisms (SNPs). In case of human evolution, such data could trace human migrations over time and ancient hybridizations with Neanderthals and Denisovans in fascinating details [3]. It will take some time, until we will have similar data for any species of birds. But, as the costs for NGS come down, it is probably only a matter of time, until we will get there.

We have analyzed the phylogeography of several birds and reptile species on oceanic islands (Macaronesia), in the Amazon region and in Eurasia. The pattern, which we discovered, differed substantially between regions. Although the Macaronesian islands (including Canary Islands, and Madeira and Azores) are sometime not far from each other, the local bird populations are resident and do not exchange between islands [29, 30]. All these oceanic islands are of volcanic origin and between 20 to 1 million years old. They are known for their richness of endemic fauna and flora.

When we studied the variation of mitochondrial DNA sequences of birds from different Macaronesian islands, we discovered, that many of them had specific and unique island haplotypes, suggesting that gene flow between islands is very low or not existing [29, 30]. As a consequence, some of the islands species obtained species rank, such as *Phyllocopus canariensis*. In *Fringilla coelebs, Cyanistes caeruleus, Erythacus rubecula, Regulus regulus, Sylvia melanocephala*, and others we could define new island specific subspecies (see references in [29, 30]). A similar diversification can be seen on the Island archipelago of the Wallace zone in Australasia [31]. However, if we look at bird population on the Aegean Islands in Greece or Turkey (except for Cyprus), little or no differentiation can be seen [32]. The Aegean islands have been connected with each other during the last few million years, which allowed gene flow among island taxa.

We also studied some bird taxa in the Amazon region and to our surprise found a strong degree of phylogeographic patterning, which correlated with the large river systems in the area. As a result, a number of morphologically similar species could be split into new taxa mostly on account of DNA data, sometimes also because of differences in vocalization [33–37].

To our surprise, we found some genetic variation in Eurasian bird species, but could often not discover a robust phylogeographic pattern. Examples are: *Lanius collurio, Merops apiaster, Upupa epops, Dendrocopus major, Tyto alba, Athene noctua, Falco peregrinus* or *Acrocephalus palustris* [38–43]. The apparent reason for this

**17**

*DNA Analyses Have Revolutionized Studies on the Taxonomy and Evolution in Birds*

phenomenon concerns the climate in the last two million years, which saw a continuous cycle of warm and cold periods. During cold periods (ice ages) large parts of the northern hemisphere was covered by ice and bird populations, which settled these areas during warm periods, had to escape further south to climatically more favorable refugia, which existed on the Iberian peninsula, in North Africa and the Near East. In refugia, bird lineages met, mixed and then spread north again when the next warm period came. This has happened more than 10–20 times during the last 2 million years when most species of extant birds evolved. This has led to a complex mixing of genetic lineages in most Eurasian bird species (review in 44]). The last ice age ended about 12000 years ago and gradually, woodland and wetland habitats in Central, North and Eastern Europe developed, which were then colonized from birds out of their southern refugia. When humans cleared forest and created agricultural landscapes, species of open land also settled in Europe. As a consequence, even if local bird populations are philopatric by now, the time period was too short to develop new haplotypes in different parts of Eurasia. Thus, Eurasian birds offers a great challenge for the phylogeographic analysis. However, if we would use similar markers for birds (SNPs) as used for humans, we might solve these problems.

The analysis of bird migration is still a challenge. The use of bird ringing and tracking system (geolocators, GPS sensors, satellite transmitters) have brought substantial progress. Since each individual bird carries a unique DNA profile, it should also be possible to connect a bird on migration or in the wintering grounds to its place of birth [44]. As discussed before, we need DNA markers of extremely resolution to solve this problem. MtDNA and microsatellite analyses are not informative enough in most cases [38, 45]. Genome-wide SNP analyses should help, as

As a consequence of new DNA analyses and the use of cladistics, the number of extent bird species is growing from year to year. We presently recognize well over10,806 bird species; some estimates assume even more than 18,000 bird taxa if subspecies will attain species level [28]. Even if we see very good progress over recent years, it will certainly take some time until the final "Avian Tree of Life" will be published, in which the phylogenetic position and history for each of the avian species is reconstructed. A Tree of Life, will enable a better understanding of avian evolution in general, of systematics but also of the evolution of traits and

I would like to thank my students and collaborators over 30 years for their continuous support. Our work was funded by grants of German Science Foundation (DFG), German Academic Exchange Service (DAAD), COST, Chinese Scholarship Council (CSC), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), National Council of Science and Technology (CONACYT), Science and Technology Development Fund (STDF) and German Ornithologist Society (DO-G.

*DOI: http://dx.doi.org/10.5772/intechopen.97013*

they did with human migrations.

**7. Outlook**

adaptations.

**Acknowledgements**

**Conflict of interest**

The author declares no conflict of interest.

#### *DNA Analyses Have Revolutionized Studies on the Taxonomy and Evolution in Birds DOI: http://dx.doi.org/10.5772/intechopen.97013*

phenomenon concerns the climate in the last two million years, which saw a continuous cycle of warm and cold periods. During cold periods (ice ages) large parts of the northern hemisphere was covered by ice and bird populations, which settled these areas during warm periods, had to escape further south to climatically more favorable refugia, which existed on the Iberian peninsula, in North Africa and the Near East. In refugia, bird lineages met, mixed and then spread north again when the next warm period came. This has happened more than 10–20 times during the last 2 million years when most species of extant birds evolved. This has led to a complex mixing of genetic lineages in most Eurasian bird species (review in 44]).

The last ice age ended about 12000 years ago and gradually, woodland and wetland habitats in Central, North and Eastern Europe developed, which were then colonized from birds out of their southern refugia. When humans cleared forest and created agricultural landscapes, species of open land also settled in Europe. As a consequence, even if local bird populations are philopatric by now, the time period was too short to develop new haplotypes in different parts of Eurasia. Thus, Eurasian birds offers a great challenge for the phylogeographic analysis. However, if we would use similar markers for birds (SNPs) as used for humans, we might solve these problems.

The analysis of bird migration is still a challenge. The use of bird ringing and tracking system (geolocators, GPS sensors, satellite transmitters) have brought substantial progress. Since each individual bird carries a unique DNA profile, it should also be possible to connect a bird on migration or in the wintering grounds to its place of birth [44]. As discussed before, we need DNA markers of extremely resolution to solve this problem. MtDNA and microsatellite analyses are not informative enough in most cases [38, 45]. Genome-wide SNP analyses should help, as they did with human migrations.
