Evolution of the ancestral mammalian karyotype and syntenic regions

Abstract

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Unraveling the genetic legacy of commercial whaling in bowhead whales and narwhals

“…While outliers in the PCA could represent migrants from other genetic populations, more samples would help investigate their structure in more detail. Within large geographical regions, it appears gene flow is generally high in bowhead whale groups (within the Canadian Arctic [28], East Greenland [30], and western Arctic [82]). Bowhead whales are capable of large movements [83] and separate populations have overlapped summer distributions.…”

ETV2 induces endothelial, but not hematopoietic, lineage specification in birds

“…These data suggested that ancestral amniotes had both ETV2 and FLI1B genes in a genomic locus linked to COX6B1 , RBM42 , and HAUS5 genes, with subsequent loss of ETV2 and FLI1B in birds ( Fig 1D ), of FLIB in mammals ( Fig 1D ), and of ETV2 in turtles (UCSC genome browser gateway; data not shown). Linkage of ETV2 gene to RBM42 and HAUS5 genes was seen in amphibia (Tibetan frog, X. levis , and X. tropicalis ) and to RBM42 gene in teleost fish (zebrafish, medaka, and tetraodon) (UCSC genome browser gateway), suggesting that syntenic organization of ETV2 and its neighboring genes in ancestral amniotes was the result of rearrangements of homologous syntenic blocks during tetrapod evolution ( Sacerdot et al, 2018 ; Damas et al, 2021 , 2022 ).…”

Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 21 species

“…This result also further rationalizes the chromosome number variation in this genus. Chromosome polymorphisms within species in natural populations of vertebrates are far less common and are believed to be temporary transitions during chromosomal evolution (Damas et al 2021, 2022). Likewise, the Zanthoxylum may be experiencing chromosomal evolution.…”