scholarly journals Untangling the Evolutionary History of European Bison (Bison bonasus)

2018 ◽  
Author(s):  
Ayla L. van Loenen ◽  
Emilia Hofman-Kamińska ◽  
Kieren J. Mitchell ◽  
Bastien Llamas ◽  
Hervé Bocherens ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Environmental Changes ◽  
Population History ◽  
Mitochondrial Genomes ◽  
European Bison ◽  
Bison Bonasus ◽  
Anthropogenic Pressures ◽  
Eurasian Continent ◽  
History Of ◽  
Rapid Environmental Change

ABSTRACTEuropean bison (Bison bonasus) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and temporal range. In particular, population expansions following periods of extensive forest reduction combined with a decrease in anthropogenic pressures suggest that European bison remain preferentially adapted to an open steppe environment through to the present day.

scholarly journals New data on the evolutionary history of the European bison ( Bison bonasus ) based on subfossil remains from Southeastern Europe

2021 ◽  
Vol 11 (6) ◽  
pp. 2842-2848
Author(s):  
Boyko Neov ◽  
Nikolai Spassov ◽  
Latinka Hristova ◽  
Peter Hristov ◽  
Georgi Radoslavov
Keyword(s):  
Evolutionary History ◽  
Bison Bison ◽  
European Bison ◽  
Southeastern Europe ◽  
Bison Bonasus ◽  
Subfossil Remains ◽  
History Of

scholarly journals Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes

2010 ◽  
Vol 28 (1) ◽  
pp. 615-623 ◽  
Author(s):  
A. Bjork ◽  
W. Liu ◽  
J. O. Wertheim ◽  
B. H. Hahn ◽  
M. Worobey
Keyword(s):  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
History Of ◽  
Complete Mitochondrial Genomes

scholarly journals Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes

2020 ◽  
Author(s):  
Dong Zhang ◽  
Hong Zou ◽  
Jin Zhang ◽  
Gui-Tang Wang ◽  
Ivan Jakovlić
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Branch Length ◽  
Mitochondrial Genomes ◽  
Close Attention ◽  
Mtdna Sequences ◽  
Mitochondrial Data ◽  
Gc Skew ◽  
History Of ◽  
Taxonomic Approach

AbstractInversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements. We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.

scholarly journals Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1236
Author(s):  
Elisabeth Hempel ◽  
Michael V. Westbury ◽  
José H. Grau ◽  
Alexandra Trinks ◽  
Johanna L. A. Paijmans ◽  
...  
Keyword(s):  
Population Size ◽  
Population History ◽  
Phylogeographic Structure ◽  
Recent Common Ancestor ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Mammal Species ◽  
Human Disturbances ◽  
Most Recent Common Ancestor ◽  
History Of

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

scholarly journals Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Erik Tihelka ◽  
Chenyang Cai ◽  
Davide Pisani ◽  
Philip C. J. Donoghue
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
History Of

Structural variation of mitochondrial genomes sheds light on evolutionary history of soybeans

2021 ◽  
Author(s):  
Hao Liu ◽  
Junping Yu ◽  
Xiaoxia Yu ◽  
Dan Zhang ◽  
Han Chang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Structural Variation ◽  
Mitochondrial Genomes ◽  
History Of

scholarly journals The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the ‘yeast mitochondrial genetic code’

DNA Research ◽  
2017 ◽  
Vol 24 (6) ◽  
pp. 571-583 ◽  
Author(s):  
Pavol Sulo ◽  
Dana Szabóová ◽  
Peter Bielik ◽  
Silvia Poláková ◽  
Katarína Šoltys ◽  
...  
Keyword(s):  
Genetic Code ◽  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
Mitochondrial Genetic Code ◽  
History Of

scholarly journals Evolutionary history of mitochondrial genomes in Discoba, including the extreme halophile Pleurostomum flabellatum (Heterolobosea)

2020 ◽  
Author(s):  
Khaoula Ettahi ◽  
Duck Hyun Lhee ◽  
Ji Yeon Sung ◽  
Alastair G B Simpson ◽  
Jong Soo Park ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Nuclear Genome ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Transport Chain ◽  
Circular Molecule ◽  
History Of ◽  
Extreme Habitats ◽  
Genome Information ◽  
Naegleria Gruberi

Abstract Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), since this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829 bp long circular molecule, including 40 CDSs (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and N. fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved-oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).

Evolutionary history of the Persian squirrel (Sciurus anomalus): It emerged on the Eurasian continent in the Miocene

2020 ◽  
Vol 287 ◽  
pp. 17-24
Author(s):  
Marzieh Asadi Aghbolaghi ◽  
Faraham Ahmadzadeh ◽  
Bahram H. Kiabi ◽  
Nusha Keyghobadi
Keyword(s):  
Evolutionary History ◽  
Eurasian Continent ◽  
History Of
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