scholarly journals Elevated substitution rates estimated from ancient DNA sequences

2007 ◽  
Vol 3 (6) ◽  
pp. 702-705 ◽  
Author(s):  
Simon Y.W Ho ◽  
Sergios-Orestis Kolokotronis ◽  
Robin G Allaby
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Recent Criticism ◽  
Large Collection ◽  
Substitution Rates ◽  
Independent Calibration ◽  
Phylogenetic Method

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate size, it produces accurate estimates of rates, while appearing robust to assumptions about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.

Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA

2013 ◽  
Vol 16 (2) ◽  
pp. 265-273 ◽  
Author(s):  
J. Zeyland ◽  
Ł. Wolko ◽  
J. Bocianowski ◽  
M. Szalata ◽  
R. Słomski ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Gradual Process ◽  
Mtdna Sequence ◽  
History Of

Abstract Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon- dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

scholarly journals Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

2015 ◽  
Vol 97 (2) ◽  
pp. 394-404 ◽  
Author(s):  
Juan F. Díaz-Nieto ◽  
Sharon A. Jansa ◽  
Robert S. Voss
Keyword(s):  
Soft Tissue ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Morphological Character ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Taxon ◽  
Evolutionary Relationships ◽  
Fresh Material

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

scholarly journals Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages

2012 ◽  
Vol 30 (2) ◽  
pp. 253-262 ◽  
Author(s):  
Martyna Molak ◽  
Eline D. Lorenzen ◽  
Beth Shapiro ◽  
Simon Y.W. Ho
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Estimation Error ◽  
Phylogenetic Analyses ◽  
Published Data ◽  
Molecular Clocks ◽  
Data Sets ◽  
Data Set ◽  
Temporal Sampling ◽  
The Impact

Abstract In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.

scholarly journals The identity of the Depuch Island rock-wallaby revealed through ancient DNA

2013 ◽  
Vol 35 (1) ◽  
pp. 101 ◽  
Author(s):  
D. Haouchar ◽  
J. Haile ◽  
P. B. S. Spencer ◽  
M. Bunce
Keyword(s):  
Cytochrome B ◽  
Control Region ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Potential Candidate ◽  
Red Foxes ◽  
North West ◽  
The North ◽  
Unidentified Species

Ancient DNA is becoming increasingly recognised as a tool in conservation biology to audit past biodiversity. The widespread loss of Australian biodiversity, especially endemic mammal populations, is of critical concern. An extreme example occurred on Depuch Island, situated off the north-west coast of Western Australia, where an unidentified species of rock-wallaby (Petrogale sp.) became extinct as a result of predation by red foxes. Two potential candidate species, Petrogale lateralis and P. rothschildi, both have ranges adjacent to Depuch Island, making identification based on geography difficult. A museum bone (one of the only surviving Depuch Island specimens) was subjected to standard ancient DNA analyses and procedures. Mitochondrial DNA cytochrome b and hypervariable control region were targeted for species identification. Ancient DNA was successfully recovered from the bone: 200 base pairs (bp) of control region and 975 bp of the cytochrome b gene. Bayesian phylogenetic analyses were employed to model the Depuch Island rock-wallaby DNA sequences together with sequences of other rock-wallaby taxa from GenBank. Evidence suggests that of the two Petrogale lateralis subspecies proposed to have inhabited Depuch Island, Petrogale lateralis lateralis was identified as the most likely. The identification of the Depuch Island rock-wallaby population may assist in the reintroduction of an insurance population of Petrogale lateralis lateralis, which is becoming increasingly threatened on mainland Australia.

scholarly journals Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content

2011 ◽  
Vol 60 (3) ◽  
pp. 366-375 ◽  
Author(s):  
Simon Y. W. Ho ◽  
Robert Lanfear ◽  
Matthew J. Phillips ◽  
Ian Barnes ◽  
Jessica A. Thomas ◽  
...  
Keyword(s):  
Bayesian Estimation ◽  
Information Content ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Substitution Rates

scholarly journals Placing ancient DNA sequences into reference phylogenies

2020 ◽  
Author(s):  
Rui Martiniano ◽  
Bianca De Sanctis ◽  
Pille Hallast ◽  
Richard Durbin
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Current Standard ◽  
Phylogenetic Placement ◽  
Target Capture ◽  
Y Chromosomes ◽  
Sequencing Studies ◽  
Low Coverage

AbstractDuring the last decade, large volumes of ancient DNA (aDNA) data have been generated as part of whole-genome shotgun and target capture sequencing studies. This includes sequences from non-recombining loci such as the mitochondrial or Y chromosomes. However, given the highly degraded nature of aDNA data, post-mortem deamination and often low genomic coverage, combining ancient and modern samples for phylogenetic analyses remains difficult. Without care, these factors can lead to incorrect placement.For the Y chromosomes, current standard methods focus on curated markers, but these contain only a subset of the total variation. Examining all polymorphic markers is particularly important for low coverage aDNA data because it substantially increases the number of overlapping sites between present-day and ancient individuals which may lead to higher resolution phylogenetic placement. We provide an automated workflow for jointly analysing ancient and present-day sequence data in a phylogenetic context. For each ancient sample, we effectively evaluate the number of ancestral and derived alleles present on each branch and use this information to place ancient lineages to their most likely position in the phylogeny. We provide both a parsimony approach and a highly optimised likelihood-based approach that assigns a posterior probability to each branch.To illustrate the application of this method, we have compiled and make available the largest public Y-chromosomal dataset to date (2,014 samples) which we used as a reference for phylogenetic placement. We process publicly available African ancient DNA Y-chromosome sequences and examine how patterns of Y-chromosomal diversity change across time and the relationship between ancient and present-day lineages. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 901-910 ◽  
Author(s):  
Joel P. Olfelt ◽  
William A. Freyman
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Phylogenetic Analyses ◽  
Black Hills ◽  
Trnl Intron ◽  
The North ◽  
Alpine Habitats ◽  
Rare And Endangered ◽  
Chloroplast Dna Sequences ◽  
Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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