Research ArticlePALEONTOLOGY

Phylogenetic and physiological signals in metazoan fossil biomolecules

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Science Advances  10 Jul 2020:
Vol. 6, no. 28, eaba6883
DOI: 10.1126/sciadv.aba6883
  • Fig. 1 Changes in the molecular composition of animal tissues through geologic time.

    (A) ChemoSpace PCA and discriminant analysis (DA) of in situ Raman spectra of modern and fossil animal samples (n = 96) averaged by individual tissue types (band set 1). PC 1 and PC 2 define a principal component space on which a measure of functional diversity {z axis} is plotted for each modern and fossil animal tissue type (see Materials and Methods). Blue columns represent unaltered biomolecules in modern tissues (corresponding to the blue convex hull), and orange columns represent biomolecular fossilization products in fossil tissues (orange convex hull). Modern tissues remodeled in vivo are labeled. The functional diversity of structural biomolecules in modern tissues is high, whereas that in different fossil tissues is much lower. The red vector arrow indicates the general trajectory [recovered in PCA (Principal Component Analysis) and DA] in molecular composition followed by samples during fossilization and identifies the processes of glycoxidation and lipoxidation. (B to D) Structural biomolecules in modern tissues with labeled functional groups. (B) Protein, a tripeptide with the amino acids lysine, cysteine, and valine. (C) Lipid. (D) Sugar (the glycosaminoglycan chitin). The colored circles indicate extensions of the biopolymer.

  • Fig. 2 High-resolution in situ Raman spectra of fossil animal tissues and assessment of their diagenetic alteration.

    (A) Plot of Raman spectra of fossil metazoans in light blue; averaged spectra: black, all fossil metazoans (n = 76); dotted blue, vertebrates (n = 41); and dotted red, invertebrates (n = 35). Red arrows: advanced lipoxidation/glycoxidation end products ALEs/AGEs; R, variable residues. Units evident in fossil tissues are displayed at the top. (B) Bar charts, averaged for tissue type (Supplementary Data), show normalized signal intensities at 1685 cm−1: blue, trans-amide, peptide bond (Ap); and at 1701 cm−1: yellow, cis-amide, diagenetically formed (Ad). Ratios (Ap/Ad) are based on these signals. Asterisks, pristine preservation of the protein/PFP phase: Ap/Ad > 1. Yellow/blue circles, extension of the polymer. (C) Molecular mechanisms for the transformation of structural biomolecules during fossilization. Cat, catalyst; Nu, nucleophile; pRCS, primary RCS; Δ, thermal energy input. Blue circles, extension of the polymer. (D) Discriminant analysis of organic matter in fossil animal tissues (n = 76; green dots) and sediments (n = 17; gray dots) based on Raman intensities at 24 band positions (Supplementary Data). Green/gray arrows, trajectory of fossil/sediment samples. Discriminant factors are listed. a.u., arbitrary units.

  • Fig. 3 Clustering of fossil animal tissues.

    (A) Biomineralization signal for all metazoan fossils based on spectral intensities at 24 Raman band positions (n = 76) (see Materials and Methods) complemented by a discriminant analysis of the biomineralized (n = 56, blue dots) and non-biomineralized (n = 20, yellow dots) samples, based on the same Raman data. Black outlined dots, vertebrate samples (generally more ALEs, compare Table 1); red outlined, invertebrate samples (generally fewer ALEs than AGEs, compare Table 1); Δ, thermally matured samples (Cambrian Burgess Shale); blue arrow, trajectory of biomineralized tissues; yellow arrow, that of no-nbiomineralized tissues. (B) Tissue-type signal. Data on vertebrate eggshells (n = 14), bones (n = 19), and teeth excluding conodonts (n = 8) from the data set used in (A) were subjected to a discriminant analysis. Green, eggshells; dark blue, bones; and light blue, teeth.

  • Fig. 4 Assessment of the phylogenetic signal preserved in fossils.

    Hierarchical cluster analysis of metazoan fossils based on Raman intensities at 20 band positions characterizing the specific composition of N– and S–cross-links (n = 37); vertebrate fossil soft tissues are not included (see Materials and Methods). Samples in each cluster are selected by tissue type. Node colors: blue, correct; orange, incorrect solution (Supplementary Data, Specimen Data). The topology calculated from fossil tooth spectra can be found in the Supplementary Data. (A) Cross-tissue–type cluster analysis of phylogenetic signals (Materials and Methods). Orange dots, invertebrates; blue dots, vertebrates. (B) Vascularized bone (n = 19, samples as in Fig. 3B) in a PCA ChemoSpace based on the abundance of in vivo metabolic cross-links. Blue dots, metabolic rate <1 ml O2 hour−1 g−0.67; orange dots, metabolic rate >1 ml O2 hour−1 g−0.67. (C) Fossil bones: Correspondence with published consensus trees is 62%. (D) Biomineralized and non-biomineralized invertebrate tissues (clusters determined independently and combined): Correspondence is 75% and 40%, respectively; even derived nodes are accurately resolved (Crustacea in Ecdysozoa). (E) Fossil eggshells: Correspondence is 83%.

  • Fig. 5 Molecular mechanism for the preservation of phylogenetic signals in fossils (based on data in Figs. 1A, 2A, 3, and 4, A and C to E).

    The reactive amino acids lysine, arginine, histidine, cysteine, and the protein N terminus (labeled in red) form characteristic fossilization products under suitable conditions. Brown circles indicate extensions of the geopolymer. Nu, nucleophile; Δ, thermal energy input.

  • Table 1 Summary data related to fossilization.

    The six tissue types considered here are compared in terms of composition (the relative in vivo abundance of structural biomolecules listed in decreasing order). Avascular tissues that are not remodeled in vivo retain a high phylogenetic signal. Tissues retaining a weak phylogenetic signal, in contrast, suffer from in vivo tissue remodeling. The ratio of S- to N-heterocycles ([─C─S─]/[─C─N─]) in fossils is quantified for eggshells (n = 14), teeth including conodonts (n = 14), bones (n = 19), vertebrate soft tissues (n = 9), invertebrate biomineralized tissues (n = 9), and non-biomineralized tissues (n = 11). This ratio and the data shown in Fig. 2B characterize the degree to which organic matter is altered (in vivo or diagenetically) and identify glycoxidation or lipoxidation as the process responsible based on tissue-specific in vivo abundance of lipids and sugars as RCS sources. PFPs, protein fossilization products.

    Tissue typeCompositionRemodeling[CS][CN]AlterationRCS generationPhylogenetic
    signal
    EggshellProteins, sugarsNone0.52LowGlycoxidationHigh
    TeethProteins, lipids,
    sugars
    Remodeled1.40HighLipoxidation/
    glycoxidation
    Low
    BoneProteins, sugars,
    lipids
    Remodeled0.98HighLipoxidation/
    glycoxidation
    Low
    Vertebrate soft tissueProteins, sugarsNone0.22LowGlycoxidationHigh
    Invertebrate
    biomineralized tissue
    Sugars, proteins,
    lipids
    None0.42LowGlycoxidation/
    lipoxidation
    High
    Invertebrate soft
    tissue
    Sugars, proteinsNone0.11HighGlycoxidationHigh

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