ArticleGenome biology and evolution2011
Genome-wide detection of gene extinction in early mammalian evolution.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
- Article
- Enigmatic Nodal and Lefty gene repertoire discrepancy: Latent evolutionary history revealed by vertebrate-wide phylogeny.Developmental dynamics : an official publication of the American Association of Anatomists · 2025Review
- Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication.Communications biology · 2020Article
- Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks.Scientific reports · 2020Article
- Nodal paralogues underlie distinct mechanisms for visceral left-right asymmetry in reptiles and mammals.Nature ecology & evolution · 2020Article
- Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.Genome research · 2019Article
- Evolutionary Origin and Nomenclature of VertebrateZebrafish · 2019Article
- TGF-β Family Signaling in Early Vertebrate Development.Cold Spring Harbor perspectives in biology · 2018Review
- Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes.BMC biology · 2018Article
- Evolution of mammalian Opn5 as a specialized UV-absorbing pigment by a single amino acid mutation.The Journal of biological chemistry · 2014Article
- Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history.Proceedings. Biological sciences · 2014Article
- Unexpected multiplicity of QRFP receptors in early vertebrate evolution.Frontiers in neuroscience · 2014Article
- Diversity and history of the long-chain acyl-CoA synthetase (Acsl) gene family in vertebrates.BMC evolutionary biology · 2013Article
- Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.PloS one · 2013Article
- GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes.PloS one · 2012Article
- A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.PloS one · 2012Article
- The evolution of pepsinogen C genes in vertebrates: duplication, loss and functional diversification.PloS one · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Detecting gene losses is a novel aspect of evolutionary genomics that has been made feasible by whole-genome sequencing. However, research to date has concentrated on elucidating evolutionary patterns of genomic components shared between species, rather than identifying disparities between genomes. In this study, we searched for gene losses in the lineage leading to eutherian mammals. First, as a pilot analysis, we selected five gene families (Wnt, Fgf, Tbx, TGFβ, and Frizzled) for molecular phylogenetic analyses, and identified mammalian lineage-specific losses of Wnt11b, Tbx6L/VegT/tbx16, Nodal-related, ADMP1, ADMP2, Sizzled, and Crescent. Second, automated genome-wide phylogenetic screening was implemented based on this pilot analysis. As a result, we detected 147 chicken genes without eutherian orthologs, which resulted from 141 gene loss events. Our inventory contained a group of regulatory genes governing early embryonic axis formation, such as Noggins, and multiple members of the opsin and prolactin-releasing hormone receptor ("PRLHR") gene families. Our findings highlight the potential of genome-wide gene phylogeny ("phylome") analysis in detecting possible rearrangement of gene networks and the importance of identifying losses of ancestral genomic components in analyzing the molecular basis underlying phenotypic evolution.
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