Limits...
Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium.

Buckley M, FariƱa RA, Lawless C, Tambusso PS, Varela L, Carlini AA, Powell JE, Martinez JG - PLoS ONE (2015)

Bottom Line: However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested.The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium.These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, United Kingdom.

ABSTRACT
For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the 'native' South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual 'Malagasy aardvark' shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomics-based sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.

No MeSH data available.


MALDI-ToF mass spectra of collagen extracted from Lestodon and Megatherium digested with trypsin. *Note the clearly observable difference in deamidation as a marker for protein ageing due to the presence of a glutamine residue in this peptide.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4634953&req=5

pone.0139611.g001: MALDI-ToF mass spectra of collagen extracted from Lestodon and Megatherium digested with trypsin. *Note the clearly observable difference in deamidation as a marker for protein ageing due to the presence of a glutamine residue in this peptide.

Mentions: MALDI mass spectrometric fingerprints of the extracted Megatherium and Lestodon bone collagen (Fig 1) were evaluated primarily for qualitative purposes to confirm the extraction and subsequent enzymatic digestion of protein from the sub-fossil material, but peak differences were also studied for potential variations that could aid the subsequent in-depth proteome analysis. Close inspection of the fingerprints (Fig 1) indicate numerous potentially homologous differences (Table 1), each likely to possess one or more amino acid substitutions. The number of shared MALDI peaks was substantially greater between the two extant sloths than between any other pair of taxa (Table 1). By comparison there are more amino acid substitutions in the recovered proteomic data between the two extinct ground sloths identified from the LC-MS/MS data (Table 1; S1 File). However, it should be noted that sequence coverage can be highly variable between analyses of different species, ranging from 56% to 77% when only peptide matches above the highest scoring false positive match are used (Table 2).


Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium.

Buckley M, FariƱa RA, Lawless C, Tambusso PS, Varela L, Carlini AA, Powell JE, Martinez JG - PLoS ONE (2015)

MALDI-ToF mass spectra of collagen extracted from Lestodon and Megatherium digested with trypsin. *Note the clearly observable difference in deamidation as a marker for protein ageing due to the presence of a glutamine residue in this peptide.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4634953&req=5

pone.0139611.g001: MALDI-ToF mass spectra of collagen extracted from Lestodon and Megatherium digested with trypsin. *Note the clearly observable difference in deamidation as a marker for protein ageing due to the presence of a glutamine residue in this peptide.
Mentions: MALDI mass spectrometric fingerprints of the extracted Megatherium and Lestodon bone collagen (Fig 1) were evaluated primarily for qualitative purposes to confirm the extraction and subsequent enzymatic digestion of protein from the sub-fossil material, but peak differences were also studied for potential variations that could aid the subsequent in-depth proteome analysis. Close inspection of the fingerprints (Fig 1) indicate numerous potentially homologous differences (Table 1), each likely to possess one or more amino acid substitutions. The number of shared MALDI peaks was substantially greater between the two extant sloths than between any other pair of taxa (Table 1). By comparison there are more amino acid substitutions in the recovered proteomic data between the two extinct ground sloths identified from the LC-MS/MS data (Table 1; S1 File). However, it should be noted that sequence coverage can be highly variable between analyses of different species, ranging from 56% to 77% when only peptide matches above the highest scoring false positive match are used (Table 2).

Bottom Line: However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested.The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium.These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, United Kingdom.

ABSTRACT
For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the 'native' South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual 'Malagasy aardvark' shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomics-based sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.

No MeSH data available.