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

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.

Species identification and decay assessment of Late Pleistocene fragmentary vertebrate remains from Pin Hole Cave (Creswell Crags, UK) using collagen fingerprinting

“…Using this information, previously published sequence information as well as fingerprints, these markers were identified for all taxa in this study with novel ones confirmed through tandem sequencing where possible. Tandem mass spectra were acquired through the use of an LCOrbitrap Elite mass spectrometer following Wadsworth & Buckley (2014) and searches using Mascot with a local database (Buckley et al 2015) improved with select additional sequences obtained from a protein BLAST search (Table S1), particularly for red fox, beaver and walrus (the latter for improved understanding of peptide marker labels). Error tolerant searches (5 ppm and 0.5 Da error tolerances on precursor and tandem spectra, respectively) were used to confirm proposed peptide markers as homologous (e.g.…”

Identifying remains of extinct kangaroos in Late Pleistocene deposits using collagen fingerprinting

“…Peptide homology was assisted through Error Tolerant searches using Mascot (e.g. Figs S2-S7) against the SwissProt database (Buckley et al, 2015).…”

Análisis filogenético de xenartros (Mammalia) basados en elementos óseos del aparato hioides: aspectos sobre la monofilia de gliptodóntidos

“…La condición de grupo natural de los Xenarthra está claramente sustentada, en tanto que los caracteres tradicionalmente utilizados para definir las sinapomorfías clásicas de este grupo son morfológicos, basados principalmente en elementos esqueletarios y dentarios (Engelmann, 1985;Gaudin, 1995Gaudin, , 1999Gaudin, , 2004Gaudin et al, 1996, McDonald, 2003Rose et al, 2005;Gaudin & McDonald, 2008). Asimismo los estudios filogenéticos con base en datos moleculares también sostienen que este es un grupo monofilético (de Jong et al, 1985;Sarich, 1985;Delsuc et al, 2001Delsuc et al, , 2002Delsuc et al, , 2003Madsen et al, 2001;Murphy et al, 2001); en años recientes se publicaron análisis que incluyen algunos de los taxones aquí analizados (tardígrados fósiles y gliptodóntidos), basados en ADN antiguo (ADNa) y colágeno (Buckley et al, 2015;Delsuc et al, 2016;Slater et al, 2016).…”