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Topic:Pleistocene

The Pleistocene epoch, spanning from approximately 2.6 million to 11,700 years ago, was a period marked by significant climatic changes and the evolution and extinction of various species, including horses. During this epoch, horses underwent numerous adaptations in response to changing environments, such as shifts in climate and vegetation. Fossil records from this period provide insights into the morphological changes and distribution patterns of equine species. Research in this area explores the evolutionary history, habitat preferences, and extinction events of horses during the Pleistocene. This page compiles peer-reviewed research studies and scholarly articles that investigate the paleobiology, ecology, and evolutionary dynamics of horses throughout the Pleistocene epoch.
Decoupled ecomorphological evolution and diversification in Neogene-Quaternary horses.
Science (New York, N.Y.)    February 12, 2017   Volume 355, Issue 6325 627-630 doi: 10.1126/science.aag1772
Cantalapiedra JL, Prado JL, Hernández Fernández M, Alberdi MT.Evolutionary theory has long proposed a connection between trait evolution and diversification rates. In this work, we used phylogenetic methods to evaluate the relationship of lineage-specific speciation rates and the mode of evolution of body size and tooth morphology in the Neogene and Quaternary radiation of horses (7 living and 131 extinct species). We show that diversification pulses are a recurrent feature of equid evolution but that these pulses are not correlated with rapid bursts in phenotypic evolution. Instead, rapid cladogenesis seems repeatedly associated with extrinsic factors t...
Complete mitochondrial genome of an extinct Equus (Sussemionus) ovodovi specimen from Denisova cave (Altai, Russia).
Mitochondrial DNA. Part B, Resources    February 6, 2017   Volume 2, Issue 1 79-81 doi: 10.1080/23802359.2017.1285209
Druzhkova AS, Makunin AI, Vorobieva NV, Vasiliev SK, Ovodov ND, Shunkov MV, Trifonov VA, Graphodatsky AS. is an extinct subgenus of first characterized and delineated in 2010. The almost complete mitochondrial genome is available only for a single specimen of - a 40,000 years old from Proskuryakova cave (Khakassia, Russia). Our studies of ancient horses from Denisova cave (Altai, Russia) revealed mitochondrial DNA of this species in a 32,000 years old sample. Using alignments to multiple mitochondrial genomes of non-caballine equids, we recovered 100% complete mitochondrial genome of for the first time. Phylogenetic analysis demonstrates close relationship between this individual and the one ...
Spotted phenotypes in horses lost attractiveness in the Middle Ages.
Scientific reports    December 7, 2016   Volume 6 38548 doi: 10.1038/srep38548
Wutke S, Benecke N, Sandoval-Castellanos E, Döhle HJ, Friederich S, Gonzalez J, Hallsson JH, Hofreiter M, Lõugas L, Magnell O, Morales-Muniz A....Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became domina...
Polymorphism and preadaptation of horses (Equus) of the mountains surrounding Lake Baikal in Pleistocene.
Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections    May 20, 2016   Volume 467, Issue 1 59-62 doi: 10.1134/S0012496616020010
Kalmykov NP.The first data on polymorphism and preadaptation of the Pleistocene horses in the mountains surrounding Lake Baikal are presented. It has been shown that disregard of intraspecific polymorphism leads to unreasonable ignoring of their diversity, phylogenetically false constructions, and incorrect interpretation of natural environment.
The origin of Chinese domestic horses revealed with novel mtDNA variants.
Animal science journal = Nihon chikusan Gakkaiho    April 13, 2016   Volume 88, Issue 1 19-26 doi: 10.1111/asj.12583
Yang Y, Zhu Q, Liu S, Zhao C, Wu C.The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple-origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant ha...
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.
Proceedings of the National Academy of Sciences of the United States of America    November 23, 2015   Volume 112, Issue 50 E6889-E6897 doi: 10.1073/pnas.1513696112
Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD....Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specim...
A Geographic Assessment of the Global Scope for Rewilding with Wild-Living Horses (Equus ferus).
PloS one    July 15, 2015   Volume 10, Issue 7 e0132359 doi: 10.1371/journal.pone.0132359
Naundrup PJ, Svenning JC.Megafaunas worldwide have been decimated during the late Quaternary. Many extirpated species were keystone species, and their loss likely has had large effects on ecosystems. Therefore, it is increasingly considered how megafaunas can be restored. The horse (Equus ferus) is highly relevant in this context as it was once extremely widespread and, despite severe range contraction, survives in the form of domestic, feral, and originally wild horses. Further, it is a functionally important species, notably due to its ability to graze coarse, abrasive grasses. Here, we used species distribution mod...
Identification of the hair of a Holocene “Yukagir horse” (Equus spp.) mummy.
Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections    July 12, 2015   Volume 462 141-143 doi: 10.1134/S0012496615020076
Chernova OF, Boeskorov GG, Protopopov AV.No abstract available
A new approach for deciphering between single and multiple accumulation events using intra-tooth isotopic variations: Application to the Middle Pleistocene bone bed of Schöningen 13 II-4.
Journal of human evolution    April 23, 2015   Volume 89 114-128 doi: 10.1016/j.jhevol.2015.02.012
Julien MA, Rivals F, Serangeli J, Bocherens H, Conard NJ.It is often difficult to differentiate between archaeological bonebeds formed by one event such as a mass kill of a single herd, and those formed by multiple events that occurred over a longer period of time. The application of high temporal resolution studies such as intra-tooth isotopic profiles on archaeological mammal cohorts offers new possibilities for exploring this issue, allowing investigators to decipher between single and multiple accumulation events. We examined (18)O and (13)C isotopic variations from the enamel carbonate of 23 horse third molars from the Middle Pleistocene archae...
Ancient DNA. The thoroughly bred horse.
Science (New York, N.Y.)    December 20, 2014   Volume 346, Issue 6216 1439 doi: 10.1126/science.346.6216.1439
Gibbons A.No abstract available
Prehistoric genomes reveal the genetic foundation and cost of horse domestication.
Proceedings of the National Academy of Sciences of the United States of America    December 15, 2014   Volume 111, Issue 52 E5661-E5669 doi: 10.1073/pnas.1416991111
Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M....The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleist...
Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences    December 10, 2014   Volume 370, Issue 1660 20130386 doi: 10.1098/rstb.2013.0386
Ludwig A, Reissmann M, Benecke N, Bellone R, Sandoval-Castellanos E, Cieslak M, Fortes GG, Morales-Muñiz A, Hofreiter M, Pruvost M.Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our result...
Global evolution of Equidae and Gomphotheriidae from South America.
Integrative zoology    September 23, 2014   Volume 9, Issue 4 434-443 doi: 10.1111/1749-4877.12064
Prado JL, Alberdi MT.The contemporary South American mammalian communities were determined by the emergence of the Isthmus of Panama and by the profound climatic oscillations during the Pleistocene. Horses and gomphotheres were 2 very conspicuous groups of immigrant mammals from North America that arrived in South America during the Pleistocene. The present study compiles updated data on the phylogeny, systematics and ecology of both groups in South America. The horses in South America are represented by 2 genera, Hippidion and Equus, as are the gomphotheres, represented by Cuvieronius and Stegomastodon. Both gene...
Investigation of equid paleodiet from Schöningen 13 II-4 through dental wear and isotopic analyses: Archaeological implications.
Journal of human evolution    September 18, 2014   Volume 89 129-137 doi: 10.1016/j.jhevol.2014.04.002
Rivals F, Julien MA, Kuitems M, Van Kolfschoten T, Serangeli J, Drucker DG, Bocherens H, Conard NJ.The paleodietary traits of the equid population from Schöningen 13 II-4 were investigated through tooth mesowear and microwear analyses, as well as stable isotopic analyses. The mesowear pattern observed on the upper teeth indicates a low abrasion diet with a significant amount of browse in the diet of the horses. The tooth microwear analysis and the isotopic data confirm that the horses from Schöningen 13 II-4 were mixed feeders, like many populations from other Pleistocene localities in Northern and Eastern Europe. Microwear also provides information on seasonal changes in the diet of the ...
Preliminary analyses of the frozen mummies of mammoth (Mammuthus primigenius), bison (Bison priscus) and horse (Equus sp.) from the Yana-Indigirka Lowland, Yakutia, Russia.
Integrative zoology    October 24, 2013   Volume 9, Issue 4 471-480 doi: 10.1111/1749-4877.12079
Boeskorov GG, Potapova OR, Mashchenko EN, Protopopov AV, Kuznetsova TV, Agenbroad L, Tikhonov AN.The frozen bodies of a young woolly mammoth (Mammuthus primigenius), a wild horse (Equus sp.) and a steppe bison (Bison priscus) were recently found in the northern Yakutia (northeastern Siberia). All specimens have preserved bones, skin and soft tissues. Whereas the woolly mammoth and the Pleistocene horse were represented by partial frozen bodies, the steppe bison body was recovered in an absolutely complete state. All specimens were found frozen in the permafrost, with some of the tissues mummified. The wild horse and steppe bison are of Holocene age, and the mammoth is of Late Pleistocene ...
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Nature    June 26, 2013   Volume 499, Issue 7456 74-78 doi: 10.1038/nature12323
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M....The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that ...
Dispersal of Pleistocene Equus (Family Equidae) into South America and calibration of GABI 3 based on evidence from Tarija, Bolivia.
PloS one    March 20, 2013   Volume 8, Issue 3 e59277 doi: 10.1371/journal.pone.0059277
MacFadden BJ.The dispersal of Equus into South America during the Great American Biotic Interchange (GABI) represented a major event for Pleistocene land-mammal age chronology on that continent. It has been argued that this dispersal occurred during the late Pleistocene, ∼0.125 Ma, and it defines the base of the Lujanian South American Land Mammal Age (SALMA). In this scenario, Equus dispersed during the fourth and latest recognized phase of the interchange, i.e., GABI 4. Although Equus was widely distributed in South America during the Pleistocene, only a few localities are calibrated by independent chr...
Mitochondrial phylogenomics of modern and ancient equids.
PloS one    February 20, 2013   Volume 8, Issue 2 e55950 doi: 10.1371/journal.pone.0055950
Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM....The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further charact...
Origins of the domestic horse.
Proceedings of the National Academy of Sciences of the United States of America    October 12, 2012   Volume 109, Issue 46 E3148-E3149 doi: 10.1073/pnas.1210326109
Forster P, Hurles ME, Jansen T, Levine M, Renfrew C.No abstract available
Improving the performance of true single molecule sequencing for ancient DNA.
BMC genomics    May 10, 2012   Volume 13 177 doi: 10.1186/1471-2164-13-177
Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G, Froese D, Steinmann KE, Thompson JF, Al-Rasheid KA, Gilbert TM....Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucl...
Reconstructing the origin and spread of horse domestication in the Eurasian steppe.
Proceedings of the National Academy of Sciences of the United States of America    May 7, 2012   Volume 109, Issue 21 8202-8206 doi: 10.1073/pnas.1111122109
Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A.Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and...
Paleolithic cave rock art, animal coloration, and specific animal habitats.
Proceedings of the National Academy of Sciences of the United States of America    April 16, 2012   Volume 109, Issue 20 E1212-E1213 doi: 10.1073/pnas.1200729109
Bar-Oz G, Lev-Yadun S.No abstract available
Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.
BMC evolutionary biology    November 14, 2011   Volume 11 328 doi: 10.1186/1471-2148-11-328
Lippold S, Matzke NJ, Reissmann M, Hofreiter M.DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. Results: In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds an...
Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art.
Proceedings of the National Academy of Sciences of the United States of America    November 7, 2011   Volume 108, Issue 46 18626-18630 doi: 10.1073/pnas.1108982108
Pruvost M, Bellone R, Benecke N, Sandoval-Castellanos E, Cieslak M, Kuznetsova T, Morales-Muñiz A, O'Connor T, Reissmann M, Hofreiter M, Ludwig A.Archaeologists often argue whether Paleolithic works of art, cave paintings in particular, constitute reflections of the natural environment of humans at the time. They also debate the extent to which these paintings actually contain creative artistic expression, reflect the phenotypic variation of the surrounding environment, or focus on rare phenotypes. The famous paintings "The Dappled Horses of Pech-Merle," depicting spotted horses on the walls of a cave in Pech-Merle, France, date back ~25,000 y, but the coat pattern portrayed in these paintings is remarkably similar to a pattern known as...
Highlight: a massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski’s horses.
Genome biology and evolution    September 13, 2011   Volume 3 1094-1095 doi: 10.1093/gbe/evr091
Venton D.No abstract available
Discovery of lost diversity of paternal horse lineages using ancient DNA.
Nature communications    August 23, 2011   Volume 2 450 doi: 10.1038/ncomms1447
Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M.Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA ...
True single-molecule DNA sequencing of a pleistocene horse bone.
Genome research    July 29, 2011   Volume 21, Issue 10 1705-1719 doi: 10.1101/gr.122747.111
Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I....Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-...
Eurasian wild asses in time and space: morphological versus genetic diversity.
Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft    July 8, 2011   Volume 194, Issue 1 88-102 doi: 10.1016/j.aanat.2011.06.002
Geigl EM, Grange T.The Equidae have a long evolutionary history that has interested palaeontologists for a long time. Their morphology-based taxonomy, however, is a matter of controversy. Since most equid species are now extinct, the phylogenetic tree based on genetic data can be established only imperfectly via deduction of present day genomes and little is known about the past genetic diversity of these species. Recent studies of ancient DNA preserved in fossil bones have led to a simplification of the phylogenetic tree and the classification system. The situation is still particularly unclear for the wild ass...
Ancient feeding ecology inferred from stable isotopic evidence from fossil horses in South America over the past 3 Ma.
BMC ecology    June 14, 2011   Volume 11 15 doi: 10.1186/1472-6785-11-15
Prado JL, Sánchez B, Alberdi MT.Stable isotope ratios (13C/12C and 18O/16O) in fossil teeth and bone provide key archives for understanding the ecology of extinct horses during the Plio-Pleistocene in South America; however, what happened in areas of sympatry between Equus (Amerhippus) and Hippidion is less understood. Results: Here, we use stable carbon and oxygen isotopes preserved in 67 fossil tooth and bone samples for seven species of horses from 25 different localities to document the magnitude of the dietary shifts of horses and ancient floral change during the Plio-Pleistocene. Dietary reconstructions inferred from s...
Origin and history of mitochondrial DNA lineages in domestic horses.
PloS one    December 20, 2010   Volume 5, Issue 12 e15311 doi: 10.1371/journal.pone.0015311
Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A.Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population r...