scholarly journals Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

2021 ◽  
Author(s):  
Michael Vincent Westbury ◽  
Eline D Lorenzen
Keyword(s):  
Ancient Dna ◽  
Pairwise Distance ◽  
Reference Sequence ◽  
Sequence Length ◽  
Close Relative ◽  
Mitochondrial Genomes ◽  
Phylogenetic Distance ◽  
Extinct Species ◽  
Mapping Software ◽  
Dna 2

(1) Within evolutionary biology, mitochondrial genomes (mitogenomes) provide useful insights at both population and species level. Several approaches are available to assemble mitogenomes. However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA. (2) Iterative mapping can overcome the lack of a close reference sequence, and has been applied to an array of extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies are yet to be comprehensively assessed. Here, we investigated the influence of mapping software (BWA or MITObim), parameters, and bait reference phylogenetic distance on the accuracy of the reconstructed assembly using two simulated datasets: (i) spotted hyena and various mammalian bait references, and (ii) southern cassowary and various avian bait references. Specifically, we assessed the accuracy of results through pairwise distance (PWD) to the reference conspecific mitogenome, number of incorrectly inserted base pairs (bp), and total length of the reconstructed assembly. (3) We found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters, and bait references. PWD to the reference conspecific mitogenome, which reflected the level of incorrect base calls, was consistently higher with BWA than MITObim. The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower. Overall, the most accurate results were obtained with MITObim using mismatch values of 3 or 5, and the phylogenetically closest bait reference sequence. Accuracy could be further improved by combining results from multiple bait references. (4) We present the first comprehensive investigation of how mapping software, parameters, and bait reference influence mitogenome reconstruction from ancient DNA through iterative mapping. Our study provides information on how mitogenomes are best reconstructed from divergent, short-read data. By obtaining the most accurate reconstruction possible, one can be more confident as to the reliability of downstream analyses, and the evolutionary inferences made from them.

West Palearctic cobras of the genus Naja (Serpentes: Elapidae): interrelationships among extinct and extant species

1990 ◽  
Vol 11 (4) ◽  
pp. 385-400 ◽  
Author(s):  
Jean-Claude Rage ◽  
Zbigniew Szyndlar
Keyword(s):  
Monophyletic Group ◽  
Close Relative ◽  
African Species ◽  
Naja Naja ◽  
Extinct Species ◽  
Extant Species ◽  
Asiatic Species ◽  
Extinct Genus

AbstractSome basic osteological cranial features of living and fossil members of the genus Naja are described. The extinct genus Palaeonaja Hoffstetter, 1939, is synonymized with the modern Naja Laurenti, 1768, and the extinct species Palaeonaja crassa Hoffstetter, 1939, is synonymized with Naja romani (Hoffstetter, 1939). Anatomically, the genus Naja can be divided into two main complexes, composed of: (1) living African species, N. antiqua from the Moroccan Miocene, and N. iberica from the Spanish Miocene; (2) living Asiatic species and N. romani from the Miocene of France, Austria, and Ukraine. Living members of the Asiatic complex make up a monophyletic group; they belong to at least three distinct lineages: N. oxiana, N. naja s.s. ( = N. naja naja), and the remaining taxa named here informally the 'East Asiatic Naja'. The African complex is thought to be most primitive and perhaps paraphyletic; Africa is presumed to be the centre of earliest radiation of the genus. The precise relationships of Walterinnesia, a close relative of Naja occupying the area between Asiatic and African ranges of Naja, remain unclear.

scholarly journals Resurrecting phenotypes from ancient DNA sequences: promises and perspectives

2015 ◽  
Vol 93 (9) ◽  
pp. 701-710 ◽  
Author(s):  
K.L. Campbell ◽  
M. Hofreiter
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Cell Biology ◽  
Genome Engineering ◽  
Ectopic Expression ◽  
Evolutionary Transitions ◽  
Extinct Species ◽  
Evolutionary Origins ◽  
Structural And Functional Properties

Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.

scholarly journals Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Anna Janowicz ◽  
Fabrizio De Massis ◽  
Massimo Ancora ◽  
Cesare Cammà ◽  
Claudio Patavino ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Brucella Melitensis ◽  
Reference Sequence ◽  
Snp Analysis ◽  
Phylogenetic Distance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

A new extinct species of Polynesian sandpiper (Charadriiformes: Scolopacidae: Prosobonia) from Henderson Island, Pitcairn Group, and the phylogenetic relationships of Prosobonia

2020 ◽  
Author(s):  
Vanesa L De Pietri ◽  
Trevor H Worthy ◽  
R Paul Scofield ◽  
Theresa L Cole ◽  
Jamie R Wood ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Genetic Data ◽  
Mitochondrial Genomes ◽  
Previous Record ◽  
Extinct Species ◽  
Ecological Adaptations ◽  
Austral Islands ◽  
Fossil Bones ◽  
A New Species

Abstract We describe a new species of Polynesian sandpiper from Henderson Island, Prosobonia sauli sp. nov., based on multiple Holocene fossil bones collected during the Sir Peter Scott Commemorative Expedition to the Pitcairn Islands (1991–92). Prosobonia sauli is the only species of Prosobonia to be described from bone accumulations and extends the record of known extinct Polynesian sandpipers to four. It is readily differentiated from the extant Tuamotu Sandpiper P. parvirostris in several features of the legs and bill, implying ecological adaptations to different environments. The geographically nearest Prosobonia populations to Henderson Island were found on Mangareva, where it is now extinct. A previous record of a species of Prosobonia from Tubuai, Austral Islands, is here shown to belong to the Sanderling Calidris alba. Our analyses of newly sequenced genetic data, which include the mitochondrial genomes of P. parvirostris and the extinct Tahiti Sandpiper P. leucoptera, confidently resolve the position of Prosobonia as sister-taxon to turnstones and calidrine sandpipers. We present a hypothesis for the timing of divergence between species of Prosobonia and other scolopacid lineages. Our results further provide a framework to interpret the evolution of sedentary lineages within the normally highly migratory Scolopacidae.

scholarly journals MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data

BMC Genomics ◽  
2020 ◽  
Vol 21 (S6) ◽  
Author(s):  
Chi-Ming Leung ◽  
Dinghua Li ◽  
Yan Xin ◽  
Wai-Chun Law ◽  
Yifan Zhang ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
High Sensitivity ◽  
Reference Sequence ◽  
Close Relative ◽  
Read Mapping ◽  
Seeding Strategy ◽  
Multiple Species ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Unique Species

Abstract Background Next-generation sequencing (NGS) enables unbiased detection of pathogens by mapping the sequencing reads of a patient sample to the known reference sequence of bacteria and viruses. However, for a new pathogen without a reference sequence of a close relative, or with a high load of mutations compared to its predecessors, read mapping fails due to a low similarity between the pathogen and reference sequence, which in turn leads to insensitive and inaccurate pathogen detection outcomes. Results We developed MegaPath, which runs fast and provides high sensitivity in detecting new pathogens. In MegaPath, we have implemented and tested a combination of polishing techniques to remove non-informative human reads and spurious alignments. MegaPath applies a global optimization to the read alignments and reassigns the reads incorrectly aligned to multiple species to a unique species. The reassignment not only significantly increased the number of reads aligned to distant pathogens, but also significantly reduced incorrect alignments. MegaPath implements an enhanced maximum-exact-match prefix seeding strategy and a SIMD-accelerated Smith-Waterman algorithm to run fast. Conclusions In our benchmarks, MegaPath demonstrated superior sensitivity by detecting eight times more reads from a low-similarity pathogen than other tools. Meanwhile, MegaPath ran much faster than the other state-of-the-art alignment-based pathogen detection tools (and compariable with the less sensitivity profile-based pathogen detection tools). The running time of MegaPath is about 20 min on a typical 1 Gb dataset.

scholarly journals Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Matthias Meyer ◽  
Eleftheria Palkopoulou ◽  
Sina Baleka ◽  
Mathias Stiller ◽  
Kirsty E H Penkman ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Morphological Traits ◽  
Elephas Maximus ◽  
Close Relative ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Dna Analyses ◽  
Phylogenetic Reconstructions ◽  
Forest Elephants ◽  
Loxodonta Cyclotis

The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.

scholarly journals Archaeological mitogenomes illuminate the historical ecology of sea otters ( Enhydra lutris ) and the viability of reintroduction

2020 ◽  
Vol 287 (1940) ◽  
pp. 20202343
Author(s):  
Hannah P. Wellman ◽  
Rita M. Austin ◽  
Nihan D. Dagtas ◽  
Madonna L. Moss ◽  
Torben C. Rick ◽  
...  
Keyword(s):  
British Columbia ◽  
Ancient Dna ◽  
Historical Ecology ◽  
Mitochondrial Genomes ◽  
Sea Otter ◽  
Enhydra Lutris ◽  
Dental Calculus ◽  
Sea Otters ◽  
Dna Analyses ◽  
Modern Context

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter ( Enhydra lutris ) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters ( n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.

scholarly journals Assembly by Reduced Complexity (ARC): a hybrid approach for targeted assembly of homologous sequences.

2015 ◽  
Author(s):  
Samual S Hunter ◽  
Robert T Lyon ◽  
Brice A.J. Sarver ◽  
Kayla Hardwick ◽  
Larry J Forney ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Hybrid Approach ◽  
Reference Sequence ◽  
Model Organisms ◽  
Exome Capture ◽  
Mitochondrial Genomes ◽  
Homologous Sequences ◽  
Reduced Complexity

Analysis of High-throughput sequencing (HTS) data is a difficult problem, especially in the context of non-model organisms where comparison of homologous sequences may be hindered by the lack of a close reference genome. Current mapping-based methods rely on the availability of a highly similar reference sequence, whereas de novo assemblies produce anonymous (unannotated) contigs that are not easily compared across samples. Here, we present Assembly by Reduced Complexity (ARC) a hybrid mapping and assembly approach for targeted assembly of homologous sequences. ARC is an open-source project (http://ibest.github.io/ARC/) implemented in the Python language and consists of the following stages: 1) align sequence reads to reference targets, 2) use alignment results to distribute reads into target specific bins, 3) perform assemblies for each bin (target) to produce contigs, and 4) replace previous reference targets with assembled contigs and iterate. We show that ARC is able to assemble high quality, unbiased mitochondrial genomes seeded from 11 progressively divergent references, and is able to assemble full mitochondrial genomes starting from short, poor quality ancient DNA reads. We also show ARC compares favorably to de novo assembly of a large exome capture dataset for CPU and memory requirements; assembling 7,627 individual targets across 55 samples, completing over 1.3 million assemblies in less than 78 hours, while using under 32 Gb of system memory. ARC breaks the assembly problem down into many smaller problems, solving the anonymous contig and poor scaling inherent in some de novo assembly methods and reference bias inherent in traditional read mapping.

Does evolutionary relatedness predict ecological similarity?

Paleobiology ◽  
2020 ◽  
pp. 1-17
Author(s):  
Judith A. Sclafani ◽  
Curtis R. Congreve ◽  
Mark E. Patzkowsky
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Model ◽  
Branch Length ◽  
Pairwise Distance ◽  
Phylogenetic Distance ◽  
Environmental Preferences ◽  
Occurrence Data ◽  
Evolutionary Relatedness ◽  
Species Pairs ◽  
Ecological Difference

Abstract A fundamental question in paleobiology is whether ecology is correlated with evolutionary history. By combining time-calibrated phylogenetic trees with genus occurrence data through time, we can understand how environmental preferences are distributed on a tree and evaluate support for models of ecological similarity. Exploring parameters that lend support to each evolutionary model will help address questions that lie at the nexus of the evolutionary and ecological sciences. We calculated ecological difference and phylogenetic distance between species pairs for 83 taxa used in recent phylogenetic revisions of the brachiopod order Strophomenida. Ecological difference was calculated as the pairwise distance along gradients of water depth, carbonate, and latitudinal affinity. Phylogenetic distance was calculated as the pairwise branch length between tips of the tree. Our results show no relationship between ecological affinity and phylogeny. Instead results suggest an ecological burst during the initial radiation of the clade. This pattern likely reflects scaling at the largest macroevolutionary and macroecological scales preserved in the fossil record. Hierarchical scaling of ecological and evolutionary processes is complex, but phylogenetic paleoecology is an avenue for better evaluating these questions.

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