The rich fossil record of equids ha

The rich fossil record of equids has made them a model for evolutionary
processes1. 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)2,3. 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)
anda donkey (E. asinus). Our analyses suggest that theEquus
lineage giving rise to all contemporary horses, zebras and donkeys
originated 4.0–4.5million years before present (Myr BP), twice the
conventionally accepted time to the most recent common ancestor
of the genus Equus4,5. We also find that horse population size fluctuated
multiple times over the past 2Myr, particularly during periods
of severe climatic changes. We estimate that the Przewalski’s and
domestic horse populations diverged 38–72 kyr BP, and find no evidence
of recent admixture between the domestic horse breeds and the
Przewalski’s horse investigated. This supports the contention that
Przewalski’s horses represent the last survivingwild horse population6.
We find similar levels of genetic variation among Przewalski’s and
domestic populations, indicating that the former are genetically viable
and worthy of conservation efforts.Wealso find evidence for continuous
selection on the immune system and olfaction throughout horse
evolution. Finally, we identify 29 genomic regions amonghorse breeds
that deviate from neutrality and show low levels of genetic variation
compared to the Przewalski’s horse. Such regions could correspond to
loci selected early during domestication.
In 2003, we recovered a metapodial horse fossil at the Thistle Creek
site in west-central Yukon Territory, Canada (Fig. 1a). The fossil was
from an interglacial organic unit associated with the Gold Run volcanic
ash, dated to 735688 kyr BP2,3 (Fig. 1b). Relict ice wedges below the
unit indicate persistent permafrost since deposition (Supplementary
Information, section 1.1), whereas the organic unit, hosting the fossil,
indicates a period of permafrost degradation, or a thaw unconformity7,
during a past interglacial as warm or warmer than present3, and rapid
deposition during either marine isotope stage 19, 17 or 15. This indicates
that the fossil dates to approximately 560–780 kyr BP. The metapodial
shows typical caballine morphology, consistent with Middle
rather than the smaller Late Pleistocene horse fossils from the area
(Fig. 1c and Supplementary Information, section 1.2). This age is consistent
with small mammal fossils from this unit indicating a Late
Irvingtonian, or Middle Pleistocene, age3, and infinite radiocarbon
dates8.
Theoretical9 and empirical evidence10 indicates that this age approaches
the upper limit ofDNAsurvival. So far, no genome-wide information
has been obtained from fossil remains older than 110–130 kyr BP11.
Time-of-flight secondary ion mass spectrometry (TOF-SIMS) on the
ancient horse bone revealed secondary ion signatures typical of collagen
within the bonematrix (Fig. 2a and SupplementaryTable 7.1), and highresolutiontandemmass
spectrometry sequencing12 revealed 73 proteins,
including blood-derived peptides (Supplementary Information, section
7.4). This is consistent with good biomolecular preservation, suggesting
possibleDNAsurvival. Therefore, we conducted larger-scale destructive
sampling for genome sequencing.
We used Illumina and Helicos sequencing to generate 12.2 billion
DNA reads from the Thistle Creek metapodial. Mapping against the
horse reference genome yielded ,1.123 genome coverage. We based
the size distribution of ancient DNA templates on collapsed Illumina

Hasil (Bahasa Indonesia) 1:

The rich fossil record of equids has made them a model for evolutionaryprocesses1. Here we present a 1.12-times coverage draft genomefrom a horse bone recovered from permafrost dated to approximately560–780 thousand years before present (kyr BP)2,3. Our data representthe oldest full genome sequence determined so far by almost an orderof magnitude. For comparison, we sequenced the genome of a LatePleistocene horse (43 kyr BP), and modern genomes of five domestichorse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii)anda donkey (E. asinus). Our analyses suggest that theEquuslineage giving rise to all contemporary horses, zebras and donkeysoriginated 4.0–4.5million years before present (Myr BP), twice theconventionally accepted time to the most recent common ancestorof the genus Equus4,5. We also find that horse population size fluctuatedmultiple times over the past 2Myr, particularly during periodsof severe climatic changes. We estimate that the Przewalski’s anddomestic horse populations diverged 38–72 kyr BP, and find no evidenceof recent admixture between the domestic horse breeds and thePrzewalski’s horse investigated. This supports the contention thatPrzewalski’s horses represent the last survivingwild horse population6.We find similar levels of genetic variation among Przewalski’s anddomestic populations, indicating that the former are genetically viabledan layak upaya konservasi. Kamijuga menemukan bukti untuk terus-meneruspilihan pada sistem kekebalan tubuh dan penciuman seluruh kudaevolusi. Akhirnya, kami mengidentifikasi keturunan amonghorse daerah genom yang 29yang menyimpang dari netralitas dan menunjukkan tingkat rendah variasi genetikdibandingkan dengan Przewalski kuda. Daerah tersebut bisa sesuai denganlokus dipilih awal selama domestikasi.Pada tahun 2003, kita pulih fosil kuda metapodial di Thistle Creeksitus di Barat-tengah Yukon Territory, Kanada (Fig. 1a). Fosil adalahunit organik osilasi interglacial negara yang terkait dengan emas lari vulkanikAsh, bertarikh 735688 kyr BP2, 3 (Fig. 1b). Irisan Randa es di bawah iniunit menunjukkan gigih permafrost sejak pengendapan (tambahanInformasi, section 1.1), sedangkan unit organik, hosting fosil,menunjukkan periode permafrost degradasi, atau unconformity7 mencair,selama masa lalu interglasial sebagai hangat atau lebih hangat daripada present3, dan cepatendapan selama tahap laut isotop baik 19, 17 atau 15. Ini menunjukkanbahwa fosil tanggal ke sekitar 560-780 kyr BP. Metapodialmenunjukkan morfologi caballine yang khas, konsisten dengan tengahdaripada fosil kuda akhir Pleistosen lebih kecil dari daerah(Fig. 1c dan informasi tambahan, Bagian 1.2). Usia ini konsistenfosil-fosil mamalia kecil dari unit ini menunjukkan akhirIrvingtonian, atau Pleistosen tengah, age3, dan terbatas penanggalandates8.Theoretical9 and empirical evidence10 indicates that this age approachesthe upper limit ofDNAsurvival. So far, no genome-wide informationhas been obtained from fossil remains older than 110–130 kyr BP11.Time-of-flight secondary ion mass spectrometry (TOF-SIMS) on theancient horse bone revealed secondary ion signatures typical of collagenwithin the bonematrix (Fig. 2a and SupplementaryTable 7.1), and highresolutiontandemmassspectrometry sequencing12 revealed 73 proteins,including blood-derived peptides (Supplementary Information, section7.4). This is consistent with good biomolecular preservation, suggestingpossibleDNAsurvival. Therefore, we conducted larger-scale destructivesampling for genome sequencing.We used Illumina and Helicos sequencing to generate 12.2 billionDNA reads from the Thistle Creek metapodial. Mapping against thehorse reference genome yielded ,1.123 genome coverage. We basedthe size distribution of ancient DNA templates on collapsed Illumina