Revising the recent evolutionary history of equids using ancient DNA

Abstract

The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.DNA taxonomy ͉ equid evolution ͉ macroevolution ͉ phylogeny ͉ ancient DNA T he original sequence of horse fossils found in the 1870s by paleontologist Othaniel Charles Marsh, and popularized by Thomas Huxley (1), has been enriched by a large fossil record over the years and has now become one of the most widely known examples of macroevolutionary change (2). The original linear model of gradual modification of fox-sized animals (Hyracothere horses) to the modern forms has been replaced by a more complex tree, showing periods of explosive diversification and branch extinctions over 55 MY (3). The end of the Early Miocene (15-20 MYA) marks a particularly important transition, separating an initial phase of small leafy browsers from a second phase of more diverse animals, exhibiting tremendous body-size plasticity and modifications in tooth morphology (4). This explosive diversification has been accompanied by several stages of geographic extension from North America to the rest of the New and Old Worlds, so that by the end of the Miocene (5 MYA) more than a dozen distinct genera are represented in the fossil record (4) (Astrohippus,

Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art

“…It is therefore not entirely surprising that not all wild horses shared the bay-dun or black-dun phenotypes. Moreover, previous studies suggested that morphological-and genetic-variability was much larger in Pleistocene animal populations compared with their modern counterparts (30)(31)(32), and it is likely that this increased variability extended to color phenotypes as well. However, the overall picture still supports the notion that artificial selection was the driving force behind the rapid increase of coat-color variation in domestic animals and resulting in their remarkable modern variability.…”

First evidence of Equus asinus L. in the Chalcolithic disputes the Phoenicians as the first to introduce donkeys into the Iberian Peninsula

“…We drilled and extracted the tooth sample which we named P2_Leceia (415 mg) and for comparison a second tooth P1_Porto (a left M/2 collected from Porto das Carretas, a Chalcolithic site in the south of Portugal, near the Guadiana river, and dated to around the same time as the Leceia sample, the second half of the third millennium BC) 185e332 mg were obtained from three extractions by a silica-based extraction protocol as in Orlando et al (2009) with appropriate extraction controls in an ancient DNA laboratory at the Centre for GeoGenetics, Copenhagen, Denmark. We then built the DNA extractions into indexed blunt-end libraries using the NEBNext DNA Library Prep Master Mix set for 454 (Biolabs,ref:E6070s) and amplified the libraries as in Vilstrup et al (2013).…”

“…28, 51, 225) and even for the manufacture of shields for war (Antunes, 2006), supporting venatory activities, and also to prevent the destruction of crops by this herd living animal. The correlation between E. hydruntinus and the "zebro", though attractive, has been rejected by ancient DNA analyses that assigned the remains purported to have been the last representative of this species, to donkeys (Orlando et al, 2009). Therefore, the "zebro" were most likely domestic donkeys (E. asinus) turned feral, a possibility proposed by C. Liesau, during several stages of the historic record, related to epidemic diseases, which conduced to the abandonment of the fields (pers.…”

Discovery of lost diversity of paternal horse lineages using ancient DNA

“…For the infinitely dated samples, the 95% CIs include the range 30,000-80,000 years, and the weight of the sample density is concentrated around 52,000 years. A further calibration was incorporated at the time of divergence between E. asinus, and the remaining lineages: We used a lognormal prior sampling between 1.0 and 5.5 myrs; these confidence intervals incorporate both the fossil record age estimates [57][58][59] and previous divergence estimates based on molecular data 60 . The results of the tip-dating analysis are shown in Supplementary Table S7. …”