Abstract
A great deal of diversity in chromosome number and arrangement is observed across the amniote phylogeny. Understanding how this diversity is generated is important for determining the role of chromosomal rearrangements in generating phenotypic variation and speciation. Gaining this understanding is achieved by reconstructing the ancestral genome arrangement based on comparisons of genome organization of extant species. Ancestral karyotypes for several amniote lineages have been reconstructed, mainly from cross-species chromosome painting data. The availability of anchored whole genome sequences for amniote species has increased the evolutionary depth and confidence of ancestral reconstructions from those made solely from chromosome painting data. Nonetheless, there are still several key lineages where the appropriate data required for ancestral reconstructions is lacking. This review highlights the progress that has been made towards understanding the chromosomal changes that have occurred during amniote evolution and the reconstruction of ancestral karyotypes.
Highlights
Chromosomes, the basic units into which DNA is packaged in a nucleus, have undergone changes in gene content and organization throughout evolution
Reconstruction of ancestral karyotypes at various positions along the amniote phylogenetic tree has been made possible by the large number of crossspecies chromosome painting and gene mapping studies that have been carried out over the last 20 years, and more recently from the availability of sequenced and anchored genomes
Chromosome paints generated from eutherian species fail to detect homology with marsupial or monotreme chromosomes (Graphodatsky et al 2012) and ancestral karyotype reconstructions based solely on eutherian chromosome painting data are restricted to the eutherian lineage
Summary
Chromosomes, the basic units into which DNA is packaged in a nucleus, have undergone changes in gene content and organization throughout evolution. Reconstruction of ancestral karyotypes at various positions along the amniote (reptiles, birds and mammals) phylogenetic tree has been made possible by the large number of crossspecies chromosome painting and gene mapping studies that have been carried out over the last 20 years, and more recently from the availability of sequenced and anchored genomes. Cross-species chromosome painting, typically using probes generated from chicken chromosomes 1 to 9 and often the large Z chromosome, have shown that, in many cases, whole chromosomes have remained intact (de Oliveira et al 2008; Derjusheva et al 2004; Nanda et al 2011; Nishida et al 2008) This remarkable conservation is not restricted to the avian lineage but is even observed in outgroup species such as crocodiles and turtles (Kasai et al 2012), which last shared a common ancestor with birds ∼230 MYA. It is unclear why bird genomes are more prone to intrachromosomal than interchromosomal rearrangement but Skinner and Griffin (2012) propose that there may be an advantage for birds maintaining the association of certain
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