**4. Towards a new "Avian Tree of Life"**

Genome studies of birds started later than in other animal groups [13, 14]. Following the genome of *Gallus gallus*, the next in line were *Taeniopygia guttata*, *Meleagris gallopavo*, *Ficedula hypoleuca*, *F. albicollis*, *Falco peregrinus, Falco cherrug*, and *Anas platyrhynchos*) [13, 14, 17]. Today, several hundred genomes have been sequenced and the information is available in open databases, such as NCBI and GenBank. The initial genome data were instrumental for avian phylogenomics as the sequences could be used to assemble and align the millions of sequence snippets obtained via NGS.

The Avian Phylogenetic Consortium [18] published in 2014 a first phylogenomic Tree of life (**Figure 5**). 2015 saw a more detailed DNA analysis [19] based on target sequencing of 259 nuclear genes and a total of 394,000 nucleotides, covering 198 species in 122 families and 40 orders (**Figure 6**). The study of Prum et al. [19] can be discussed as a follow-up of Hackett et al. [14] who had sequenced 19 nuclear genes of each of the major bird families using traditional Sanger sequencing.

Simplified phylogenies [18, 19] are illustrated in **Figures 5** and **6**. Main findings include a common ancestry of swifts and nightjars, the sister-pair relationship of grebes and flamingos, the separation of falcons from diurnal raptors, inclusion of New World vultures in the raptor clade and a new clade combining falcons, parrots and passerine birds [1, 13, 14, 18, 19].

A new phylogenomic analysis covering 363 taxa from 92% of all bird families was published by Feng et al. [20]. This phylogeny contains for the first time information for many of the families within Passeriformes. The new data are combined with putative data from over 10100 bird taxa to generate a phylogeny hypothesis as

**11**

**Figure 5.**

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

shown in **Figure 7**. This analysis is preliminary and phylogenetic trees shown were reconstructed based on transposable elements. For non-passerine orders, the new phylogeny is very similar to the tree of Jarvis et al. [18] (**Figure 5**), maybe because the same taxa and genome sequences were used. For Passeriformes, the phylogeny is

More than 60% of all birds (6204 species) belong to the Order Passeriformes. Its systematics has seen great advantages recently. In "The Largest Avian Radiation" Jon Fjeldså, Les Christidis and Per Ericson [21] have put all evidence together to reconstruct its complex phylogeny. Passerines (also parrot and falcons) apparently evolved about 55 to 50 million years ago, just after the Cretaceous/Tertiary boundary in Australasia and then immigrated all over the world. The main radiation

similar to that of Fjeldså et al. (**Figure 8**) [21].

*The first phylogenomic avian phylogeny (modified from [18]).*

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

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

#### **Figure 5.**

*Birds - Challenges and Opportunities for Business, Conservation and Research*

by the new High-Throughput Sequencers [13, 14].

tant to reconstruct phylogenies [14].

**4. Towards a new "Avian Tree of Life"**

and passerine birds [1, 13, 14, 18, 19].

a few years (see Chapter 4).

obtained via NGS.

After 2000, next generation sequencing (NGS) became available in which whole genomes are analyzed by parallel sequencing [13]. Hundreds of millions of short DNA sequences can be generated in a single NGS run. These sequences are then assembled into longer DNA segments by bioinformaticians and assigned to known genes ("annotation"). Homologous DNA sequences are aligned and, as with marker genes, evaluated using phylogeny programs. A larger and more comprehensive collection of genes or even complete genomes and transcriptomes can be sequenced

The pyrosequencer 454 from Roche represented the first generation of NGS sequencers. Several companies developed new NGS strategies and sequencers, such as Illumina, SOLiD, IonTorrent, and PacBio [1, 13, 14]. The Illumina technology is a market leader at present; these sequencers generate of up to 250 million short sequences (50 to 200 nucleotides) in a single lane. The short sequences introduce a number of problems for bioinformatics, thus new developer look sequencers that generate longer reads. 3rd generation sequencers from PacBio or Nanopore Sequencing are beginning to reach the laboratory. The longer sequences allow a localization of the sequence on a chromosome and to reconstruct complete gene assemblies including repetitive elements. Longer and high quality reads are impor-

Several thousand genome sequences are now available, mainly from prokaryotes. The number of genome sequences from animals is comparably small. But already many genome sequences are available to reconstruct the large-scale phylogenomics of animal groups, such as birds: It is foreseeable that the phylogeny of most evolutionary lineages can be reliably reconstructed via genome sequencing in

Genome studies of birds started later than in other animal groups [13, 14]. Following the genome of *Gallus gallus*, the next in line were *Taeniopygia guttata*, *Meleagris gallopavo*, *Ficedula hypoleuca*, *F. albicollis*, *Falco peregrinus, Falco cherrug*, and *Anas platyrhynchos*) [13, 14, 17]. Today, several hundred genomes have been sequenced and the information is available in open databases, such as NCBI and GenBank. The initial genome data were instrumental for avian phylogenomics as the sequences could be used to assemble and align the millions of sequence snippets

The Avian Phylogenetic Consortium [18] published in 2014 a first phylogenomic Tree of life (**Figure 5**). 2015 saw a more detailed DNA analysis [19] based on target sequencing of 259 nuclear genes and a total of 394,000 nucleotides, covering 198 species in 122 families and 40 orders (**Figure 6**). The study of Prum et al. [19] can be discussed as a follow-up of Hackett et al. [14] who had sequenced 19 nuclear genes of each of the major bird families using traditional Sanger sequencing.

Simplified phylogenies [18, 19] are illustrated in **Figures 5** and **6**. Main findings include a common ancestry of swifts and nightjars, the sister-pair relationship of grebes and flamingos, the separation of falcons from diurnal raptors, inclusion of New World vultures in the raptor clade and a new clade combining falcons, parrots

A new phylogenomic analysis covering 363 taxa from 92% of all bird families was published by Feng et al. [20]. This phylogeny contains for the first time information for many of the families within Passeriformes. The new data are combined with putative data from over 10100 bird taxa to generate a phylogeny hypothesis as

**10**

*The first phylogenomic avian phylogeny (modified from [18]).*

shown in **Figure 7**. This analysis is preliminary and phylogenetic trees shown were reconstructed based on transposable elements. For non-passerine orders, the new phylogeny is very similar to the tree of Jarvis et al. [18] (**Figure 5**), maybe because the same taxa and genome sequences were used. For Passeriformes, the phylogeny is similar to that of Fjeldså et al. (**Figure 8**) [21].

More than 60% of all birds (6204 species) belong to the Order Passeriformes. Its systematics has seen great advantages recently. In "The Largest Avian Radiation" Jon Fjeldså, Les Christidis and Per Ericson [21] have put all evidence together to reconstruct its complex phylogeny. Passerines (also parrot and falcons) apparently evolved about 55 to 50 million years ago, just after the Cretaceous/Tertiary boundary in Australasia and then immigrated all over the world. The main radiation

*A simplified phylogeny of birds according to Prum et al. [19] based on nucleotide sequences of 259 nuclear genes.*

#### **Figure 7.**

*A comprehensive avian tree of life [20]. (the article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format).*

**13**

**Figure 8.**

*and infraorders (right of the red brackets).*

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

of passerine families occurred later between 20 and 35 million years ago. The

history of bird systematics and outlines many of the open questions.

timing and spacing of migration events [23, 24].

Passeriformes (**Figure 8**) are divided into three Suborders: Acanthisitti, Tyranni and Passeri. They are divided into several Infraorders and Parvorders. **Figure 8** shows a phylogeny reconstruction of the majority of families with an indication of Suborders and Infraorders. Species numbers are uneven in these groups: The Acanthisitti comprise 4 species, the Tyranni about 1290 taxa and the Passeri 4910 species. In Passeri, the largest Infraorder Corvides comprises 775 species, whereas the Passerides contain the majority of 3800 species. The book of Fjeldså et al. [21] provides phylogenies of most families of passerine birds, if available. The book is a milestone in the

*A time-calibrated phylogeny of families within the Passeriformes (after [21]). Names of suborders (blue line)* 

High-throughput sequencing can also be used to study the transcriptome of birds. This information is important to understand the phenotype of an individual or adaptations to ecological or biological challenges (review in [22]). Examples are studies of the migratory phenotype of birds and the question which genes influence

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

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

**Figure 8.**

*Birds - Challenges and Opportunities for Business, Conservation and Research*

*A simplified phylogeny of birds according to Prum et al. [19] based on nucleotide sequences of 259 nuclear genes.*

*A comprehensive avian tree of life [20]. (the article is licensed under a creative commons attribution 4.0 international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or* 

**12**

**Figure 7.**

*format).*

**Figure 6.**

*A time-calibrated phylogeny of families within the Passeriformes (after [21]). Names of suborders (blue line) and infraorders (right of the red brackets).*

of passerine families occurred later between 20 and 35 million years ago. The Passeriformes (**Figure 8**) are divided into three Suborders: Acanthisitti, Tyranni and Passeri. They are divided into several Infraorders and Parvorders. **Figure 8** shows a phylogeny reconstruction of the majority of families with an indication of Suborders and Infraorders. Species numbers are uneven in these groups: The Acanthisitti comprise 4 species, the Tyranni about 1290 taxa and the Passeri 4910 species. In Passeri, the largest Infraorder Corvides comprises 775 species, whereas the Passerides contain the majority of 3800 species. The book of Fjeldså et al. [21] provides phylogenies of most families of passerine birds, if available. The book is a milestone in the history of bird systematics and outlines many of the open questions.

High-throughput sequencing can also be used to study the transcriptome of birds. This information is important to understand the phenotype of an individual or adaptations to ecological or biological challenges (review in [22]). Examples are studies of the migratory phenotype of birds and the question which genes influence timing and spacing of migration events [23, 24].
