Evidence for a single loss of mineralized teeth in the common avian ancestor

Meredith, Robert W.; Zhang, Guojie; Gilbert, M. Thomas P.; Jarvis, Erich D.; Springer, Mark S.

doi:10.1126/science.1254390

Cited by 103 publications

(110 citation statements)

References 95 publications

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“…Our analyses have revealed that, similar to observations in other lineages (Wang et al 2006;Meredith et al 2014), gene loss through pseudogenization has had a significant impact on the evolution and diversification of pangolin genomes and their biology. We detected and validated pseudogenes in pathways related to multiple morphological or physiological functions including dentition, vision, and immunity.…”

Section: Discussionsupporting

confidence: 54%

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Pangolin genomes and the evolution of mammalian scales and immunity

et al. 2016

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Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.

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Section: Discussionsupporting

confidence: 54%

“…S7.1,S7.2). Loss of function of these genes through pseudogenization has also been reported in other edentulous vertebrates such as toothless baleen whales, birds, and turtles (Meredith et al 2014).…”

Section: Pangolin-specific Phenotypesmentioning

confidence: 99%

Pangolin genomes and the evolution of mammalian scales and immunity

et al. 2016

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“…In fact, there are strong hints that large deletions caused a substantial level of gene loss in birds (274 protein-coding genes) with potentially profound phenotypic consequences (46,81,82). The foreseeable improvement of genome assembly via third-generation sequencing (e.g., long-read sequencing and gap filling; see ref.…”

Section: Dna Gain and Loss Analysis Reveals The Elasticity Of Avian Amentioning

confidence: 99%

Dynamics of genome size evolution in birds and mammals

Kapusta

Suh

Feschotte

2017

Proc. Natl. Acad. Sci. U.S.A.

357

358

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Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.genome size evolution | DNA loss | transposable elements | amniotes | flight T he nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate (1-7). Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) (3). Additionally, the fixation probability of slightly deleterious deletions or insertions would be higher in species with smaller effective population sizes, where natural selection acts less efficiently (3,8). On the other hand, a number of correlative associations between genome size and phenotypic traits, such as cell size (9, 10) and metabolic rate associated with powered flight (11, 12), suggest that natural selection and adaptive processes also shape genome size evolution. Teasing apart the relative importance of these two forces (drift and selection) requires a better understanding of the mode and processes by which DNA is gained and lost over long evolutionary periods in different taxa. Thus, establishing an integrated view of the contribution of gain and loss of DNA to genome size variation (or lack thereof) remains an important goal in genome biology (e.g., refs. 1, 2, 13, and 14).Most studies of genome size evolution have focused on taxa with extensive variation in genome sizes, such as flowering plants (15)(16)(17)(18)(19)(20), conifers (21), insects (22-...

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“…Using the phylogenomic backbone and the information about all genes that are present in a genome assembly and annotation, Meredith et al (2014) found that mineralised teeth were lost only a single time in the common avian ancestor. In all of the 48 bird taxa of the genome project, the genes that are responsible for the formation of dentin and enamel were inactivated by mutations, whereas these genes are still active in crocodiles.…”

Section: A First Phylogenomic Avian Tree Of Lifementioning

confidence: 99%

Avian genomics: fledging into the wild!

Kraus

Wink

2015

J Ornithol

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Next generation sequencing (NGS) technologies provide great resources to study bird evolution and avian functional genomics. They also allow for the identification of suitable high-resolution markers for detailed analyses of the phylogeography of a species or the connectivity of migrating birds between breeding and wintering populations. This review discusses the application of DNA markers for the study of systematics and phylogeny, but also population genetics and phylogeography. Emphasis in this review is on the new methodology of NGS and its use to study avian genomics. The recent publication of the first phylogenomic tree of birds based on genome data of 48 bird taxa from 34 orders is presented in more detail.

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Evidence for a single loss of mineralized teeth in the common avian ancestor

Cited by 103 publications

References 95 publications

Pangolin genomes and the evolution of mammalian scales and immunity

Pangolin genomes and the evolution of mammalian scales and immunity

Dynamics of genome size evolution in birds and mammals

Avian genomics: fledging into the wild!

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