The Pleistocene was an epoch of extreme climatic and environmental changes. How individual species responded to the repeated cycles of warm and cold stages is a major topic of debate. For the ...European fauna and flora, an expansion–contraction model has been suggested, whereby temperate species were restricted to southern refugia during glacial times and expanded northwards during interglacials, including the present interglacial (Holocene). Here, we test this model on the red deer (Cervus elaphus) a large and highly mobile herbivore, using both modern and ancient mitochondrial DNA from the entire European range of the species over the last c. 40 000 years. Our results indicate that this species was sensitive to the effects of climate change. Prior to the Last Glacial Maximum (LGM) haplogroups restricted today to South‐East Europe and Western Asia reached as far west as the UK. During the LGM, red deer was mainly restricted to southern refugia, in Iberia, the Balkans and possibly in Italy and South‐Western Asia. At the end of the LGM, red deer expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, Scandinavia, Germany, Poland and Belarus. Ancient DNA data cannot rule out refugial survival of red deer in North‐West Europe through the LGM. Had such deer survived, though, they were replaced by deer migrating from Iberia at the end of the glacial. The Balkans served as a separate LGM refugium and were probably connected to Western Asia with genetic exchange between the two areas.
Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that ...details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species’s current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.
Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide ...a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the 'recent African origin' model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African-Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration.
Population genetic analyses of Eurasian wolves published recently in BMC Evolutionary Biology suggest that a major genetic turnover took place in Eurasian wolves after the Pleistocene. These results ...add to the growing evidence that large mammal species surviving the late Pleistocene extinctions nevertheless lost a large share of their genetic diversity.
In order to assess the environmental impact of possible candidates such as hydrofluoroolefins to replace the CFCs in the industry, it is necessary to perform kinetic and product studies of their ...degradation in the air initiated by the main tropospheric oxidants. In this sense, the relative-rate technique has been used to determine rate coefficients for the reactions of 2-fluoropropene (CH3CFCH2); 3,3,3-trifluoro-2-(trifluoromethyl)propene ((CF3)2CCH2) and (E/Z)-1,2,3,3,3-pentafluoropropene ((E/Z)-CF3CFCHF) with OH radicals and Cl atoms at (298 ± 3) K and (760 ± 10) Torr total pressure of synthetic air using different reference compounds.
The experiments were performed in an environmental chamber with “in situ” FTIR spectroscopy to monitor the concentration–time profiles of the reactants. The following room temperature rate coefficients (in cm3 molecule−1 s−1) were obtained: k1(OH + CH3CFCH2) = (1.55 ± 0.39) × 10−11, k2 (OH + (CF3)2CCH2) = (6.58 ± 2.25) × 10−13, k3 (OH + ((E/Z)-CF3CFCHF); 93% E isomer) = (2.62 ± 0.76) × 10−12, k4 (Cl + CH3CFCH2) = (1.64 ± 0.26) × 10−10, k5 (Cl + (CF3)2CCH2) = (3.50 ± 0.85) × 10−11 and k6 (Cl + ((E/Z)-CF3CFCHF); 93% E isomer) = (4.52 ± 0.98) × 10−11. To the best of our knowledge this work provides the first kinetic study for the reactions of CH3CFCH2 and (CF3)2CCH2 with OH radicals and Cl atoms.
Free-energy relationships are presented, and the effect of F atom and CF3 group substitution in the hydrofluoroolefins is discussed in terms of reactivity toward both OH radicals and Cl atoms.
On the basis of the kinetic measurements, tropospheric lifetimes of CH3CFCH2, (CF3)2CCH2 and (E/Z)-CF3CFCHF will primarily be determined by their reaction with hydroxyl radicals with estimated lifetimes of approximately 1, 18 and 4 days, respectively. For the reactions of the fluoroalkenes with chlorine atoms the corresponding values of the lifetimes are 14, 66 and 51, respectively.
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•First kinetics for OH/Cl + CH3CFCH2 and (CF3)2CCH2 reactions.•Relative rate coefficients by ”in situ” FTIR analysis at 298 K and 1 atm.•Reactivity trends and “cis effect” discussed in terms of F and CF3 substitution.•kOH vs kCl correlated for different fluorinated alkenes.•Atmospheric lifetimes (days–1 week) with low GWPs.
Insect declines are a global issue with significant ecological and economic ramifications. Yet, we have a poor understanding of the genomic impact these losses can have. Genome‐wide data from ...historical specimens have the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses is to understand how molecular preservation varies between specimens.
Here, we highlight how Next‐Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome‐wide data from a set of 113 red‐tailed bumblebee Bombus lapidarius specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research, we generated a novel assembly of the red‐tailed bumblebee genome.
Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large‐scale post‐mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9 bp per decade. The proportion of quality filtered reads mapping to our assembled reference genome was around 50%, and decreased by 1.1% per decade.
We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population‐level analyses—for example for conservation or evolutionary studies—are entirely feasible, as long as the degraded nature of DNA is accounted for.
In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base ...pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.
Gas-phase rate coefficients for the reactions of OH and O3 with camphene have been measured over the temperature range 288-311 K using the relative rate method. The experiments were carried out in an ...environmental chamber using long-path FTIR spectroscopy to monitor the reactants. Room temperature rate coefficients (in cm3 per molecule per s) of k(camphene+OH) = (5.1 plus or minus 1.1) 10-11 and k(camphene+O3) = (5.1 plus or minus 1.1) 10-19 were obtained for the OH and O3 reactions, respectively. The temperature dependence of the reactions are best fit by the Arrhenius expressions (in cm3 per molecule per s) k(camphene+OH) = (4.1 plus or minus 1.2) 10-12 exp(754 plus or minus 44)/T for the OH reaction and k(O3+camphene) = (7.6 plus or minus 1.2) 10-18 exp-(805 plus or minus 51)/T for the O3 reaction. To the best of our knowledge, this is the first report of the temperature dependencies for the reactions of OH and O3 with camphene. In addition, product studies have been performed at (298 plus or minus 2) K and 760 Torr of synthetic air for the reaction of OH + camphene in the absence and presence of NOx, and for O3 molecules + camphene at (298 plus or minus 2) K and 750 Torr of synthetic air. For the OH reaction the following molar product yields were obtained: acetone (10 plus or minus 2)% and (33 plus or minus 6)%, and formaldehyde (3.6 plus or minus 0.7)% and (10 plus or minus 2)% in the absence and presence of NOx, respectively. Formaldehyde with a molar yield of (29 plus or minus 6)% was the only product uniquely identified and quantified for the O3 reaction.
The character and chronology of Norse colonisation in Early Medieval northern Scotland (8th–10th centuries AD) is hotly debated. The presence of reindeer antler raw material in ‘native’ or ‘Pictish’ ...type combs from the Orkney Isles, northern Scotland has been put forward as evidence for a long and largely peaceful initial period of cultural contact, as opposed to a shorter, more polarised period probably in the late ninth century. Here this hypothesis is tested using a minimally-destructive collagen peptide mass fingerprinting method (ZooMS) to speciate the raw material of 20 combs. Eleven were identified as red deer, four as reindeer and one as whale. The accuracy and gentleness of this method was tested by the subsequent application of ancient DNA (aDNA) methods to fourteen of the same samples: in ten, amplification was successful and all supported the preliminary ZooMS identification. All ‘native’-type combs in the sample are identified as red deer, and all Norse types as reindeer. These results challenge previous species identifications for these combs' raw materials. The balance of evidence no longer supports the existence of a long period of cultural contact between Atlantic Scotland and Scandinavian settlers before the late 9th century. ZooMS is shown to have considerable potential for identification of worked bone and antler artefacts, with applications in archaeology and wildlife/art-history forensics.
•Non-native reindeer antler has been identified in ‘Pictish’ combs from pre-9th century Orkney.•We tested these identifications with a non-destructive proteomic method, ZooMS.•Reindeer was identified only in Scandinavian-style combs.•Results were confirmed by subsequent DNA testing on the same samples.•Early cultural contact between Atlantic Scotland and Scandinavia was not supported.
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