Here, we combine hybridization-based targeted capture and high-throughput sequencing to generate 54 complete mammoth mitochondrial genomes, including 22 from temperate localities across Eurasia.
Here, we combine hybridization-based targeted capture and high-throughput sequencing to generate 54 complete mammoth mitochondrial genomes, including 22 from temperate localities across Eurasia.Tags: Science Fiction Novel Research PaperCommunication Deficiencies A Case Study In Project ManagementOnline Cover Letter SubmissionCritical Thinking StrategyTurabian Citation Book Of EssaysResearch Proposal GuidelinesPennsylvania Colleges Creative Writing MajorsPhd Thesis On Suicide12 Month Business PlanNational Homeworkers Association
To both of these, we added 17 previously published mitochondrial genomes and nine sequences obtained using a multiplex PCR and pyrosequencing approach (Supplementary Materials), for a total of 143 mitochondrial genome sequences in the relaxed alignment and 96 in the strict alignment.
The molecular clock was informed using the root-and-tip-dating method.
Gradual improvements in methodology and instrumentation have enabled recovery of a DNA from more challenging remains, such as from mammoth bones preserved in temperate regions of Eurasia.
These data can be used to resolve persisting questions regarding mammoth diversity and population structure. According to the current model based on morphology, a population of southern mammoths gave rise to the steppe mammoth around ~1.7 million years ago (Ma) in Asia.
For each sample, de-multiplexing, mapping and duplicate removal resulted in between 367 and 211,184 unique mitochondrial reads, which is equivalent to 1-fold to 819-fold coverage of the mitochondrial genome (Table S1).
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To evaluate potential error associated with missing and low-coverage data and to include the largest number of individuals possible, we adopted two strategies for consensus calling and filtering (see Methods) that resulted in two data sets: a relaxed alignment of 117 mammoth mitochondrial genomes and a strict alignment of 70 mitochondrial genomes.Eurasian mammoths have received far less attention thus far.Previous population-level genetic analyses beyond the permafrost regions of Western Beringia were restricted to a small fragment of the mitochondrial genome.Our understanding of the evolutionary history of Mammuthus has been developed largely from morphological study of their fossils, especially the most resilient and therefore most abundant elements: molar teeth. Later, perhaps as early as 0.7 Ma, a second transition occurred in Asia as a steppe mammoth population gave rise to the woolly mammoth.According to the fossil evidence, mammoths evolved in Africa during the late Miocene and later dispersed into Asia and Europe, and eventually North America via Beringia, during the Middle Pliocene to Early Pleistocene. Subsequently, these species dispersed out of Asia into Europe and North America.Posterior probability for each clade is provided either as black numbers along branch leading to major clades, or indicated as 95% by the presence of a black dot.The timescale is offset by 4651 years, which is the age of the youngest sample in the data set. Figure 1 shows the maximum clade credibility (MCC) mammoth mitochondrial genealogy resulting from a Bayesian phylogenetic analysis of the relaxed data set, using a strict molecular clock and the root-and-tip calibration approach; the results from the strict data set are provided in Figure S2.The three main mammoth mitochondrial clades shared a most recent common ancestor (MRCA) ~2.0–1.0 Ma (Fig. Clade 3 (haplogroup B) shows the deepest divergence of the three lineages, with a MRCA ~1.4–0.7 Ma.This lineage has been referred to in the past as the European clade.Morphology-based taxonomic identifications are provided as rectangular bars to the right of sample names.Nodes leading to major clades are labeled and highlighted as magenta dots, with the inferred t MRCA (95% highest posterior density of node ages, magenta numbers below the branch leading to the clade).