Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds

Organ, Chris L.; Rasmussen, Matthew D.; Baldwin, Maude W.; Kellis, M; Edwards, Scott V.

doi:10.1002/9780470619902.ch14

Cited by 6 publications

(5 citation statements)

References 81 publications

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“…Lineage-specific duplications and losses of olfactory receptor genes is characteristic of the evolution of the OR gene family in vertebrates and have resulted in a large range of OR gene repertoire size across lineages 5,[10][11][12]20 . The co-occurrence of γ-c intact, partial and pseudogenes in the shearwater OR repertoire, sometimes in the same contig, agrees with the extreme dynamic nature of the evolutionary models proposed to govern the genes encoding OR and other vertebrate multi-gene families 14,44,45 . In the context of the olfactory receptor evolution, the presence of many paralogs facilitates the evolution of novel gene functions that allow the recognition of new odors, under a scenario of neo-functionalization, but may also result in large number of pseudogenes due to functional redundancy and consequent relaxation of selective constraints [45][46][47] .…”

Section: Discussionsupporting

confidence: 77%

Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabirds

Silva

Chibucos

Munro

et al. 2020

Sci Rep

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olfactory receptors (oRs), encoded by the largest vertebrate multigene family, enable the detection of thousands of unique odorants in the environment and consequently play a critical role in species survival. Here, we advance our knowledge of oR gene evolution in procellariiform seabirds, an avian group which relies on the sense of olfaction for critical ecological functions. We built a cosmid library of cory's Shearwater (Calonectris borealis) genomic DnA, a model species for the study of olfactionbased navigation, and sequence oR gene-positive cosmid clones with a combination of sequencing technologies. We identified 220 OR open reading frames, 20 of which are full length, intact OR genes, and found a large ratio of partial and pseudogenes to intact OR genes (2:1), suggestive of a dynamic mode of evolution. phylogenetic analyses revealed that while a few genes cluster with those of other sauropsid species in a γ (gamma) clade that predates the divergence of different avian lineages, most genes belong to an avian-specific γ-c clade, within which sequences cluster by species, suggesting frequent duplication and/or gene conversion events. We identified evidence of positive selection on full length γ-c clade genes. these patterns are consistent with a key role of adaptation in the functional diversification of olfactory receptor genes in a bird lineage that relies extensively on olfaction.

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Section: Discussionsupporting

confidence: 77%

Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabirds

Silva

Chibucos

Munro

et al. 2020

Sci Rep

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“…Most genes belong to gene families, and the size of the average gene family in the chicken is smaller than in mammals (Hillier et al, 2004;Organ et al, 2010). In addition, the vast majority of gene duplicates in Gallus appear to have arisen recently, producing an exponentially distributed pattern of gene family ages (Organ et al, 2010), a pattern consistent within other Eukaryotes (Lynch & Conery, 2000).…”

Section: Short Genes Multigene Families and Isochoresmentioning

confidence: 82%

“…In addition, the vast majority of gene duplicates in Gallus appear to have arisen recently, producing an exponentially distributed pattern of gene family ages (Organ et al, 2010), a pattern consistent within other Eukaryotes (Lynch & Conery, 2000). This pattern implies that most genes are pseudogenized through the accumulation of deleterious mutations soon after duplicating (assuming a relatively constant rate of gene duplication) and are ultimately eliminated from the genome.…”

Section: Short Genes Multigene Families and Isochoresmentioning

confidence: 95%

Major Events in Avian Genome Evolution

Organ

Edwards

2011

Living Dinosaurs

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“…Gene trees play a fundamental role in understanding gene family evolution ( Thornton, 2004 ; Yang, 2007 ), and are used for inferring evolutionary events such as gene duplication and horizontal gene transfer ( Choi et al. , 2012 ; Organ et al. , 2010 ; Zhaxybayeva, 2009 ), inferring orthologs, paralogs and xenologs ( Koonin, 2005 ; Sennblad and Lagergren, 2009 ; Storm and Sonnhammer, 2002 ; Vilella et al.…”

Section: Introductionmentioning

confidence: 99%

Improved gene tree error correction in the presence of horizontal gene transfer

Bansal

Alm

et al. 2015

Bioinformatics

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Motivation: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem of accurate gene tree inference has received considerable attention, most existing methods are only applicable to gene families unaffected by horizontal gene transfer. As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem.Results: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer. Our method efficiently models horizontal gene transfers, gene duplications and losses, and uses a statistical hypothesis testing framework [Shimodaira–Hasegawa (SH) test] to balance sequence likelihood with topological information from a known species tree. Using a thorough simulation study, we show that existing phylogenetic methods yield inaccurate gene trees when applied to horizontally transferred gene families and that our method dramatically improves gene tree accuracy. We apply our method to a dataset of 11 cyanobacterial species and demonstrate the large impact of gene tree accuracy on downstream evolutionary analyses.Availability and implementation: An implementation of our method is available at http://compbio.mit.edu/treefix-dtl/Contact: mukul@engr.uconn.edu or manoli@mit.eduSupplementary information: Supplementary data are available at Bioinformatics online.

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Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds

Cited by 6 publications

References 81 publications

Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabirds

Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabirds

Major Events in Avian Genome Evolution

Improved gene tree error correction in the presence of horizontal gene transfer

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