Ancient DNA reveals twenty million years of aquatic life in beavers

Xenikoudakis, Georgios; Ahmed, Mayeesha; Harris, Jacob; Wadleigh, Rachel; Paijmans, Johanna L. A.; Hartmann, Stefanie; Barlow, Axel; Lerner, Heather R. L.; Hofreiter, Michael

doi:10.1016/j.cub.2019.12.041

Cited by 4 publications

(10 citation statements)

References 10 publications

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“…S. eseri shows evidence of living in family groups and swimming specializations 91 . This, in combination with aDNA evidence 12 , suggests Castorinae and Castoroidinae are derived from a semiaquatic ancestor in the early Miocene.…”

Section: Discussionmentioning

confidence: 73%

“…woodcutting performance was poorer than that of modern Castor 11 . The appearance of woodcutting in Dipoides sp., a distant relative of Castor , implies that this behaviour originated 20 to 24 Ma ago, in a group of semiaquatic beavers that includes both extant species (C astor canadensis and Castor fiber ), the small Holarctic genus Dipoides , and the North American Ice Age giant beaver Castoroides 7 , 9 , 12 . And yet recent research shows that the diet of Ice Age Castoroides , a close relative of Dipoides , was dominated by submerged plants, not trees and shrubs 13 .…”

Section: Introductionmentioning

confidence: 99%

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Evolution of woodcutting behaviour in Early Pliocene beaver driven by consumption of woody plants

Plint

Longstaffe

Ballantyne

et al. 2020

Sci Rep

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Here, we present stable carbon and nitrogen isotope data for Pliocene-age (i) plant macrofossils and (ii) bone collagen from High Arctic Dipoides sp. subfossil remains. The specimens originate from a peat deposit at the Beaver Pond fossil site, located on Ellesmere Island (locally known as Umingmak Nuna, meaning "land of muskoxen"), situated within the Canadian Arctic Archipelago (78° 33′ N, 82° 25′ W) (Fig. 1). We reconstruct High Arctic Dipoides sp. palaeodiet within the context of coeval terrestrial and freshwater plant macrofossil remains excavated from the same ~ 4 Ma old peat layer. The Beaver Pond site provides a very rare opportunity for such a palaeodiet reconstruction using coeval herbivore and plant remains.

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Section: Discussionmentioning

confidence: 73%

Section: Introductionmentioning

confidence: 99%

Evolution of woodcutting behaviour in Early Pliocene beaver driven by consumption of woody plants

Plint

Longstaffe

Ballantyne

et al. 2020

Sci Rep

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“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted December 17, 2021. ; https://doi.org/10.1101/2021.12.16.472923 doi: bioRxiv preprint An accurate reconstructed assembly is crucial for the reliability of downstream analyses; the incorrect incorporation of nucleotides may bias evolutionary inferences. A single mitogenome from an extinct species is commonly used to estimate when the species diverged from its closest living relative (Mitchell et al, 2014;Westbury et al, 2017;Xenikoudakis et al, 2020). However, the inclusion of errors would artificially inflate (in the case of random insertions/substitutions) or deflate (in the case of mapping biases towards the bait reference allele) divergence estimates, leading to erroneous inferences of the driving forces of divergence events, e.g.…”

Section: Discussionmentioning

confidence: 99%

“…We investigated BWA and MITObim, as they are most commonly used to generate mitogenomes from extinct species (Anmarkrud & Lifjeld, 2017;Delsuc et al, 2016;Kehlmaier et al, 2017;Westbury et al, 2017;Xenikoudakis et al, 2020). However, other .…”

Section: Discussionmentioning

confidence: 99%

“…Even with ample data, mitogenome assembly can be challenging in the absence of a close relative with which to align. Iterative mapping has become a popular approach to overcome the lack of a close reference sequence (Hahn et al, 2013), and has been used to generate mitogenomes from an array of extinct vertebrate species (Mitchell et al, 2014;Paijmans et al, 2017;Westbury et al, 2017;Xenikoudakis et al, 2020). In short, iterative mapping works by (i) mapping short-read data to a bait reference genome, (ii) generating a new consensus sequence from the mapped reads, and (iii) using the latter as a new mapping reference.…”

Section: Introductionmentioning

confidence: 99%

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Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

Westbury

Lorenzen

2021

Preprint

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Within evolutionary biology, mitochondrial genomes (mitogenomes) provide useful insights at both population and species level. Several approaches are available to assemble mitogenomes. However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA.Iterative mapping can overcome the lack of a close reference sequence, and has been applied to an array of extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies are yet to be comprehensively assessed. Here, we investigated the influence of mapping software (BWA or MITObim), parameters, and bait reference phylogenetic distance on the accuracy of the reconstructed assembly using two simulated datasets: (i) spotted hyena and various mammalian bait references, and (ii) southern cassowary and various avian bait references. Specifically, we assessed the accuracy of results through pairwise distance (PWD) to the reference conspecific mitogenome, number of incorrectly inserted base pairs (bp), and total length of the reconstructed assembly.We found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters, and bait references. PWD to the reference conspecific mitogenome, which reflected the level of incorrect base calls, was consistently higher with BWA than MITObim. The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower. Overall, the most accurate results were obtained with MITObim using mismatch values of 3 or 5, and the phylogenetically closest bait reference sequence. Accuracy could be further improved by combining results from multiple bait references.We present the first comprehensive investigation of how mapping software, parameters, and bait reference influence mitogenome reconstruction from ancient DNA through iterative mapping. Our study provides information on how mitogenomes are best reconstructed from divergent, short-read data. By obtaining the most accurate reconstruction possible, one can be more confident as to the reliability of downstream analyses, and the evolutionary inferences made from them.

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The oldest semi-aquatic beaver in the world and a new hypothesis for the evolution of locomotion in Castoridae

Calede

2022

R. Soc. open sci.

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The North American rodent fossil record includes hundreds of species representing both an incredible taxonomic diversity and great ecological disparity. Although it is during the Oligocene that taxonomic diversity first peaks, it is not until the Miocene, almost 10 Myr later, that many ecologies, particularly locomotory ecologies, are recorded. Here, I present a new Oligocene-aged species of beaver from Montana, Microtheriomys articulaquaticus sp. nov., which represents the oldest semi-aquatic rodent in North America and the oldest amphibious beaver in the world, pushing the advent of semi-aquatic ecology in beavers by 7 Myr. I also provide morphological data supporting a terrestrial ecology for the sister taxon to Castoridae. Together with existing data, these findings lead to a new hypothesis for the evolutionary ecology of castorids whereby swimming was exapted from burrowing during the Oligocene. This evolution of semi-aquatic locomotion may have taken place in North America instead of Eurasia. It started in small beavers with gigantism achieved only much later. Indeed, body size evolution in castoroids follows a directional drift. Beavers obey Cope's rule, a selection for larger size over time that appears associated with semi-aquatic ecology and may well explain their low modern diversity.

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Ancient DNA reveals twenty million years of aquatic life in beavers

Cited by 4 publications

References 10 publications

Evolution of woodcutting behaviour in Early Pliocene beaver driven by consumption of woody plants

Evolution of woodcutting behaviour in Early Pliocene beaver driven by consumption of woody plants

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

The oldest semi-aquatic beaver in the world and a new hypothesis for the evolution of locomotion in Castoridae

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