Research ArticleEVOLUTIONARY BIOLOGY

Chitinase genes (CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals

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Science Advances  16 May 2018:
Vol. 4, no. 5, eaar6478
DOI: 10.1126/sciadv.aar6478
  • Fig. 1 Placental mammal CHIA gene tree, simplified from fig. S3.

    Closed circles indicate functional CHIAs, and open circles indicate pseudogenic CHIAs and/or CHIAs lacking a chitinolytic and/or chitin-binding domain. Colored branches correspond to a subset of placental mammal clades: green, Cetartiodactyla; orange, Carnivora; pink, Perissodactyla; red, Xenarthra; purple, Afrotheria; brown, Scandentia; cyan, Strepsirrhini; blue, Anthropoidea; yellow, Dermoptera. Silhouettes and licenses here and throughout are from phylopic.org.

  • Fig. 2 PGLS regression of the number of functional contig-derived CHIAs versus the percent of the diet consisting of invertebrates.

    See text for discussion of highlighted species.

  • Fig. 3 Examples of CHIA shared inactivating mutations.

    Each alignment has a Tarsius syrichta ortholog to provide a functional outgroup comparison. See Fig. 4 for gene inactivations shown in (A) to (M) mapped onto the placental mammal phylogeny.

  • Fig. 4 Patterns of CHIA loss through time.

    (A) The cumulative number of CHIA losses in placental mammals relative to the origin of eutherians, placental mammals, and the K/Pg boundary. Red symbols indicate mean estimates of gene inactivation dates based on four model assumptions, and purple symbols indicate minimum pseudogenization dates based on shared inactivating mutations. Solid bars indicate the range of estimates (table S7), and dashed bars indicate potential range of dates based on branch lengths. (B) The phylogenetic positioning of the CHIA inactivation estimates shown in (A). Letters correspond to gene losses shown in Fig. 3. (C) Timetree (24) indicating lineages sampled for CHIA analyses (red branches). The dashed box indicates zoomed-in portion of phylogeny shown in (B).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/5/eaar6478/DC1

    fig. S1. Vertebrate RAxML CHIA gene tree based on CHIA gene models.

    fig. S2. Placental mammal RAxML CHIA gene tree based on genomic contig–derived and mRNA sequences.

    fig. S3. Placental mammal RAxML CHIA gene tree based on genomic contig–derived and mRNA sequences, after removing chiropteran CHIA4 and CHIA5 sequences.

    fig. S4. Diagram demonstrating synteny of CHIA paralogs and nearby genes on their respective genomic scaffolds/contigs.

    fig. S5. T. syrichta CHIA1, CHIA2, CHIA3, CHIA4, and CHIA5 gene models showing conserved chitinolytic domain (DXXDXDXE).

    fig. S6. T. syrichta CHIA1, CHIA2, CHIA3, CHIA4, and CHIA5 gene models showing chitin-binding domain with six conserved cysteine residues.

    fig. S7. Cladogram showing relationships of species in WGS data set and mapped gene losses.

    table S1. CHIA summary.

    table S2. Synteny of CHIA paralogs.

    table S3. CHIA gene expression analyses.

    table S4. Distribution of genetic lesions and missing data across CHIA exons.

    table S5. Discussion of CHIA number, timing of loss, diets of extant taxa, and the fossil record.

    table S6. dN/dS ratio models used for gene inactivation estimates.

    table S7. CHIA inactivation date estimates calculated from dN/dS ratio models in table S6 and assuming divergence dates from the study of Emerling et al. (24).

    table S8. Scaffold/contig coordinates of OVGP1, PIFO, and DENND2D for species in fig. S4.

    table S9. Evidence of gene conversion between CHIA4 and CHIA5.

    data set S1. Alignments used for analyses.

    data set S2. Alignments used for constructing CHIA genes from scaffolds/contigs.

    References (5179)

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Vertebrate RAxML CHIA gene tree based on CHIA gene models.
    • fig. S2. Placental mammal RAxML CHIA gene tree based on genomic contig–derived and mRNA sequences.
    • fig. S3. Placental mammal RAxML CHIA gene tree based on genomic contig–derived and mRNA sequences, after removing chiropteran CHIA4 and CHIA5 sequences.
    • fig. S4. Diagram demonstrating synteny of CHIA paralogs and nearby genes on their respective genomic scaffolds/contigs.
    • fig. S5. T. syrichta CHIA1, CHIA2, CHIA3, CHIA4, and CHIA5 gene models showing conserved chitinolytic domain (DXXDXDXE).
    • fig. S6. T. syrichta CHIA1, CHIA2, CHIA3, CHIA4, and CHIA5 gene models showing chitin-binding domain with six conserved cysteine residues.
    • fig. S7. Cladogram showing relationships of species in WGS data set and mapped gene losses.
    • Legends for data sets S1 and S2
    • References (51–79)

    Download PDF

    Other Supplementary Material for this manuscript includes the following:

    • table S1 (Microsoft Excel format). CHIA summary.
    • table S2 (Microsoft Excel format). Synteny of CHIA paralogs.
    • table S3 (Microsoft Excel format). CHIA gene expression analyses.
    • table S4 (Microsoft Excel format). Distribution of genetic lesions and missing data across CHIA exons.
    • table S5 (Microsoft Excel format). Discussion of CHIA number, timing of loss, diets of extant taxa and the fossil record.
    • table S6 (Microsoft Excel format). dN/dS ratio models used for gene inactivation estimates.
    • table S7 (Microsoft Excel format). CHIA inactivation date estimates calculated from dN/dS ratio models in table S6 and assuming divergence dates from the study of Emerling et al. (24).
    • table S8 (Microsoft Excel format). Scaffold/contig coordinates of OVGP1, PIFO and DENND2D for species in fig. S4.
    • table S9 (Microsoft Excel format). Evidence of gene conversion between CHIA4 and CHIA5.
    • data set S1 (.Chitinase datasets format). Alignments used for analyses.
    • data set S2 (.txt format). Alignments used for constructing CHIA genes from scaffolds/contigs.

    Download Tables S1 to S9

    Download Data sets S1 and S2

     

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