Complete mitochondrial DNA sequence analysis of Bison bison and bison–cattle hybrids: Function and phylogeny

Douglas, Kory C.; Halbert, Natalie D.; Kolenda, Claire; Childers, Christopher P.; Hunter, David; Derr, James N.

doi:10.1016/j.mito.2010.09.005

Cited by 51 publications

(60 citation statements)

References 65 publications

(81 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This length is similar to the lengths of Bison bison mitochondrial genomes, which range from 16,318 to 16,323 bp [27]. The genome consists of 13 protein-coding genes, 22 tDNA genes, 2 rDNA genes, and the D-loop region (S3 Table).…”

Section: Resultsmentioning

confidence: 52%

“…SGE2seq shows 114 differences (listed in S4 Table) compared to the reference Bison bison mitochondrial genome, including two indels: a 1-bp insertion located in the D-loop region and a 2-bp deletion at the end of the tRNA serine gene (this shorter tRNA serine allele is also present in some Bison bison mitochondrial genomes [27]). The other differences comprise 105 transitions and 6 transversions.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave

et al. 2015

View full text Add to dashboard Cite

Despite the abundance of fossil remains for the extinct steppe bison (Bison priscus), an animal that was painted and engraved in numerous European Paleolithic caves, a complete mitochondrial genome sequence has never been obtained for this species. In the present study we collected bone samples from a sector of the Trois-Frères Paleolithic cave (Ariège, France) that formerly functioned as a pitfall and was sealed before the end of the Pleistocene. Screening the DNA content of the samples collected from the ground surface revealed their contamination by Bos DNA. However, a 19,000-year-old rib collected on a rock apart the pathway delineated for modern visitors was devoid of such contaminants and reproducibly yielded Bison priscus DNA. High-throughput shotgun sequencing combined with conventional PCR analysis of the rib DNA extract enabled to reconstruct a complete mitochondrial genome sequence of 16,318 bp for the extinct steppe bison with a 10.4-fold coverage. Phylogenetic analyses robustly established the position of the Bison priscus mitochondrial genome as basal to the clade delineated by the genomes of the modern American Bison bison. The extinct steppe bison sequence, which exhibits 93 specific polymorphisms as compared to the published Bison bison mitochondrial genomes, provides an additional resource for the study of Bovinae specimens. Moreover this study of ancient DNA delineates a new research pathway for the analysis of the Magdalenian Trois-Frères cave.

show abstract

Section: Resultsmentioning

confidence: 52%

Section: Resultsmentioning

confidence: 99%

Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave

et al. 2015

View full text Add to dashboard Cite

show abstract

“…We aligned mitochondrial genomes from the 35 ancient bison described above with previously published mitochondrial genomes from 10 present-day American bison (33,34), an ancient Siberian bison (35), and 4 yaks (Bos grunniens). We then created two datasets for phylogenetic analysis: one comprising the complete mitochondrial genome (full dataset), and another limited to only those sites in the mitochondrial genome in which we were able to call a consensus base for the Snowmass bison (reduced dataset).…”

Section: Methodsmentioning

confidence: 99%

“…We assembled complete mitochondrial genomes from an additional 6 Siberian and 26 North American bison ranging in age from ∼0.4-45 kyBP (Dataset S1). We then estimated the evolutionary relationship between these and 10 presentday American (33,34) and an ancient Siberian bison (35), using stratigraphic ages and radiocarbon dates to inform the molecular clock (Materials and Methods and SI Text).…”

Section: )mentioning

confidence: 99%

Fossil and genomic evidence constrains the timing of bison arrival in North America

Froese

Stiller

Heintzman

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

100

View full text Add to dashboard Cite

The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada’s Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus. We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195–135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45–21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.

show abstract

“…Today, in parallel with the modern developments in statistical calculations, some progress has been made in the Bootstrap method and its use in applied statistics has become widespread. The use of the Bootstrap method has increased highly especially in the areas of molecular genetics [7][8][9] , population genetics [10] , phylogenetics [11] and virology [12] .…”

Section: Introductionmentioning

confidence: 99%

Hayvancılık Alanında Bootstrap Tekniğinin Bir Uygulaması: Yumurta Sarı Rengi Örneği

Narinç¹,

Aygün²,

Küçükönder³

et al. 2015

Kafkas Univ Vet Fak Derg

View full text Add to dashboard Cite

In this study, it was aimed to introduce the Bootstrap technique and to reveal the relationship between measurements of yolk color fan grades and digital colorimeter that is used for determining the yellow color of egg by utilizing this technique. For this purpose, a total of 1350 samples of 15 color grades of Roche yolk color fan and L* (lightness), a* (redness), b* (yellowness) values in the same samples were compared. The means, standard errors and confidence intervals for each color parameters of fan grades have been demonstrated by the Bootstrap technique. The grades of Roche yolk color fan in terms of L* values have been divided into 10 groups (P<0.01), while only divided into 9 groups in terms of b* values (P<0.01). According to the means of Redness (a*), all of the Roche yolk color fan grades (15 grades) have been determined as independent from each other (P<0.01). With the Bootstrap method, the standard error values of means were decreased by 42.03%, 35.38% and 30.24%, respectively, and the confidence intervals were narrowed by the ratio of 42.03%, 35.38% and 30.24%, respectively. The results of the study were compared with the results of the study that was conducted by using Roche yolk color fan which is cheaper but less reliable and by using digital colorimeter method which is expensive but reliable. Keywords: Bootstrapping, Resampling, Egg yolk color fan, Digital colorimeter Hayvancılık Alanında Bootstrap Tekniğinin Bir Uygulaması: Yumurta Sarı Rengi Örneği ÖzetBu çalışmada Bootstrap tekniğinin tanıtılması ve bu metottan faydalanarak yumurta sarı renginin belirlenmesinde kullanılan yumurta sarı renk yelpazesi ve dijital renk ölçüm cihazı ölçümleri arasındaki ilişkinin ortaya konulması amaçlanmıştır. Bu amaçla Roche sarı renk yelpazesinin 15 renk sınıfına ait toplam 1350 örnek ile aynı örneklerde ölçülen L* (parlaklık), a* (kırmızılık), b* (sarılık) değerleri karşılaştırılmıştır. Yelpaze sınıflarının her renk parametresine ait ortalamaları, standart hataları ve güven aralıkları Bootstrap tekniğiyle ortaya konulmuştur. L* değerleri bakımından Roche sarı renk yelpazesi 10 gruba ayrılırken (P<0.01), b* değerleri bakımından sınıflar sadece 9 gruba ayrılmıştır (P<0.01). Kırmızılık (a*) ortalamalarına göre ise Roche sarı renk yelpaze sınıflarının tümü (15 sınıf ) birbirinden bağımsız olarak tanımlanabilmiştir (P<0.01). Bootstrap yöntemi ile L*, a* ve b* ortalamalarının standart hata değerleri sırasıyla 42.03%, 35.38% ve 30.24% azalmış, güven aralıkları 48.10%, 55.43%, 34.47% oranlarında daralmıştır. Araştırmadan elde edilen sonuçlar kullanılarak mevcut literatürde daha ucuz ama güvenilirliği düşük olan Roche sarı renk yelpazesi ile yapılan çalışmalar ve pahalı ama güvenilir yöntem olan dijital renk ölçüm cihazı kullanılarak gerçekleştirilen çalışma sonuçları karşılaştırılmıştır.

show abstract

Complete mitochondrial DNA sequence analysis of Bison bison and bison–cattle hybrids: Function and phylogeny

Cited by 51 publications

References 65 publications

Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave

Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave

Fossil and genomic evidence constrains the timing of bison arrival in North America

Hayvancılık Alanında Bootstrap Tekniğinin Bir Uygulaması: Yumurta Sarı Rengi Örneği

Contact Info

Product

Resources

About