Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene
- Jilin University, China
- Northwest A&F University, China
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, China
- Shaanxi Provincial Institute of Archaeology, China
- Ningxia Institute of Cultural Relics and Archaeology, China
- Lanzhou University, China
- Université Paul Sabatier, CNRS UMR 5288, France
Abstract
The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth-of-coverage. Radiocarbon dating demonstrates that this lineage survived until ~3,500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree, and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 Million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species' chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
Data availability
Sequencing data have been deposited in the European Nucleotide Archive under the accession number PRJEB44527.
-
This study aims at improving the genome reference of the domestic donkey using the Chicago/HiRiSe technologyEuropean Nucleotide Archive, PRJEB24845.
-
Speciation with gene flow in equids despite extensive chromosomal plasticityEuropean Nucleotide Archive, PRJEB7446.
-
Sample from Equus caballusNCBI, SAMN02953672.
Article and author information
Author details
Funding
Major Program of National Fund of Philosophy and Social Science of China (17ZDA221)
- Dawei Cai
H2020 European Research Council (681605)
- Ludovic Orlando
National Natural Science Foundation of China (31822052)
- Yu Jiang
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- George H Perry, Pennsylvania State University, United States
Publication history
- Received: August 25, 2021
- Accepted: May 11, 2022
- Accepted Manuscript published: May 11, 2022 (version 1)
Copyright
© 2022, Cai et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 438
- Page views
-
- 101
- Downloads
-
- 0
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Further reading
-
- Ecology
- Evolutionary Biology
Many animals rely on complex signals that target multiple senses to attract mates and repel rivals. These multimodal displays can however also attract unintended receivers, which can be an important driver of signal complexity. Despite being taxonomically widespread, we often lack insight into how multimodal signals evolve from unimodal signals and in particular what roles unintended eavesdroppers play. Here, we assess whether the physical movements of parasite defense behavior increase the complexity and attractiveness of an acoustic sexual signal in the little torrent frog (Amolops torrentis). Calling males of this species often display limb movements in order to defend against blood-sucking parasites such as frog-biting midges that eavesdrop on their acoustic signal. Through mate choice tests we show that some of these midge-evoked movements influence female preference for acoustic signals. Our data suggest that midge-induced movements may be incorporated into a sexual display, targeting both hearing and vision in the intended receiver. Females may play an important role in incorporating these multiple components because they prefer signals which combine multiple modalities. Our results thus help to understand the relationship between natural and sexual selection pressure operating on signalers and how in turn this may influence multimodal signal evolution.
-
- Computational and Systems Biology
- Evolutionary Biology
Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.
