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https://www.readbyqxmd.com/read/29045412/self-domestication-in-homo-sapiens-insights-from-comparative-genomics
#1
Constantina Theofanopoulou, Simone Gastaldon, Thomas O'Rourke, Bridget D Samuels, Angela Messner, Pedro Tiago Martins, Francesco Delogu, Saleh Alamri, Cedric Boeckx
This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest...
2017: PloS One
https://www.readbyqxmd.com/read/29036207/little-ice-age-climatic-erraticism-as-an-analogue-for-future-enhanced-hydroclimatic-variability-across-the-american-southwest
#2
Julie Loisel, Glen M MacDonald, Marcus J Thomson
The American Southwest has experienced a series of severe droughts interspersed with strong wet episodes over the past decades, prompting questions about future climate patterns and potential intensification of weather disruptions under warming conditions. Here we show that interannual hydroclimatic variability in this region has displayed a significant level of non-stationarity over the past millennium. Our tree ring-based analysis of past drought indicates that the Little Ice Age (LIA) experienced high interannual hydroclimatic variability, similar to projections for the 21st century...
2017: PloS One
https://www.readbyqxmd.com/read/29029269/an-overlooked-paleo-tetraploidization-in-cucurbitaceae
#3
Jinpeng Wang, Pengchuan Sun, Yuxian Li, Yinzhe Liu, Nanshan Yang, Jigao Yu, Xuelian Ma, Sangrong Sun, Ruiyan Xia, Xiaojian Liu, Dongcen Ge, Sainan Luo, Yinmeng Liu, Youting Kong, Xiaobo Cui, Tianyu Lei, Li Wang, Zhenyi Wang, Weina Ge, Lan Zhang, Xiaoming Song, Min Yuan, Di Guo, Dianchuan Jin, Wei Chen, Yuxin Pan, Tao Liu, Guixian Yang, Yue Xiao, Jinshuai Sun, Cong Zhang, Zhibo Li, Haiqing Xu, Xueqian Duan, Shaoqi Shen, Zhonghua Zhang, Sanwen Huang, Xiyin Wang
Cucurbitaceae plants are of considerable biological and economic importance, and genomes of cucumber, watermelon, and melon have been sequenced. However, a comparative genomics exploration of their genome structures and evolution has not been available. Here, we aimed at performing a hierarchical inference of genomic homology resulted from recursive paleo-polyploidizations. Unexpectedly, we found that, shortly after a core-eudicot-common hexaploidy (ECH), a cucurbit-common tetraploidization (CCT) occurred, overlooked by previous reports...
September 28, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28990235/application-of-10-13-ohm-faraday-cup-current-amplifiers-for-boron-isotopic-analyses-by-solution-mode-and-laser-ablation-mc-icp-ms
#4
Nicholas S Lloyd, Aleksey Yu Sadekov, Sambuddha Misra
RATIONALE: Boron isotope ratios (δ(11) B values) are used as a proxy for seawater paleo-pH, amongst several other applications. The analytical precision can be limited by the detection of low intensity ion beams from limited sample amounts. High-gain amplifiers offer improvements in signal/noise ratio and can be used to increase measurement precision and reduce sample amounts. METHODS: 10(13) ohm amplifier technology has previously been applied to several radiogenic systems, but has thus far not been applied to non-traditional stable isotopes...
October 9, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28979799/network-analysis-of-the-hominin-origin-of-herpes-simplex-virus-2-from-fossil-data
#5
Simon J Underdown, Krishna Kumar, Charlotte Houldcroft
Herpes simplex virus 2 (HSV2) is a human herpesvirus found worldwide that causes genital lesions and more rarely causes encephalitis. This pathogen is most common in Africa, and particularly in central and east Africa, an area of particular significance for the evolution of modern humans. Unlike HSV1, HSV2 has not simply co-speciated with humans from their last common ancestor with primates. HSV2 jumped the species barrier between 1.4 and 3 MYA, most likely through intermediate but unknown hominin species. In this article, we use probability-based network analysis to determine the most probable transmission path between intermediate hosts of HSV2, from the ancestors of chimpanzees to the ancestors of modern humans, using paleo-environmental data on the distribution of African tropical rainforest over the last 3 million years and data on the age and distribution of fossil species of hominin present in Africa between 1...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28961073/manifestation-drivers-and-emergence-of-open-ocean-deoxygenation
#6
Lisa A Levin
Oxygen loss in the ocean, termed deoxygenation, is a major consequence of climate change and is exacerbated by other aspects of global change. An average global loss of 2% or more has been recorded in the open ocean over the past 50-100 years, but with greater oxygen declines in intermediate waters (100-600 m) of the North Pacific, the East Pacific, tropical waters, and the Southern Ocean. Although ocean warming contributions to oxygen declines through a reduction in oxygen solubility and stratification effects on ventilation are reasonably well understood, it has been a major challenge to identify drivers and modifying factors that explain different regional patterns, especially in the tropical oceans...
September 29, 2017: Annual Review of Marine Science
https://www.readbyqxmd.com/read/28952626/aqueous-chemistry-of-ce-iv-estimations-using-actinide-analogues
#7
Rémi Marsac, Florent Réal, Nidhu Lal Banik, Mathieu Pédrot, Olivier Pourret, Valérie Vallet
The prediction of cerium (Ce) aqueous speciation is relevant in many research fields. Indeed, Ce compounds are used for many industrial applications, which may require the control of Ce aqueous chemistry for their synthesis. The aquatic geochemistry of Ce is also of interest. Due to its growing industrial use and its release into the environment, Ce is now considered as an emerging contaminant. Cerium is also used as a proxy of (paleo)redox conditions due to the Ce(iv)/Ce(iii) redox transition. Finally, Ce(iv) is often presented as a relevant analogue of tetravalent actinides (An(iv))...
October 10, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28938079/comparing-climate-sensitivity-past-and-present
#8
Eelco J Rohling, Gianluca Marino, Gavin L Foster, Philip A Goodwin, Anna S von der Heydt, Peter Köhler
Climate sensitivity represents the global mean temperature change caused by changes in the radiative balance of climate; it is studied for both present/future (actuo) and past (paleo) climate variations, with the former based on instrumental records and/or various types of model simulations. Paleo-estimates are often considered informative for assessments of actuo-climate change caused by anthropogenic greenhouse forcing, but this utility remains debated because of concerns about the impacts of uncertainties, assumptions, and incomplete knowledge about controlling mechanisms in the dynamic climate system, with its multiple interacting feedbacks and their potential dependence on the climate background state...
September 22, 2017: Annual Review of Marine Science
https://www.readbyqxmd.com/read/28924497/phylogeographic-investigation-and-ecological-niche-modelling-of-the-endemic-frog-species-nanorana-pleskei-revealed-multiple-refugia-in-the-eastern-tibetan-plateau
#9
Bin Wang, Feng Xie, Jiannan Li, Gang Wang, Cheng Li, Jianping Jiang
The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods...
2017: PeerJ
https://www.readbyqxmd.com/read/28917590/karyotype-stability-and-unbiased-fractionation-in-the-paleo-allotetraploid-cucurbita-genomes
#10
Honghe Sun, Shan Wu, Guoyu Zhang, Chen Jiao, Shaogui Guo, Yi Ren, Jie Zhang, Haiying Zhang, Guoyi Gong, Zhangcai Jia, Fan Zhang, Jiaxing Tian, William J Lucas, Jeff J Doyle, Haizhen Li, Zhangjun Fei, Yong Xu
The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C...
October 9, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28899345/phylogeographic-structure-cryptic-speciation-and-demographic-history-of-the-sharpbelly-hemiculter-leucisculus-a-freshwater-habitat-generalist-from-southern-china
#11
Weitao Chen, Zaixuan Zhong, Wei Dai, Qi Fan, Shunping He
BACKGROUND: Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS: Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C)...
September 12, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28892362/direct-precise-measurements-of-isotopologue-abundance-ratios-in-co2-using-molecular-absorption-spectroscopy-application-to-%C3%AE-17-o
#12
Tim Stoltmann, Mathieu Casado, Mathieu Daëron, Amaelle Landais, Samir Kassi
We present an ultrasensitive absorption spectrometer based on a 30 Hz/s stability, sub-kHz line width laser source coupled to a high-stability cavity-ring-down-spectroscopy setup. It provides direct and precise measurements of the isotopic ratios δ(17)O and δ(18)O in CO2. We demonstrate the first optical absorption measurements of (17)O anomalies in CO2 with a precision better than 10 ppm, matching the requirements for paleo-environmental applications. This illustrates how optical absorption methods have become a competitive alternative to state-of-the-art isotopic ratio mass spectrometry techniques...
September 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28874273/early-hominin-landscape-use-in-the-lower-omo-valley-ethiopia-insights-from-the-taphonomical-analysis-of-oldowan-occurrences-in%C3%A2-the-shungura-formation-member-f
#13
Tiphaine Maurin, Pascal Bertran, Anne Delagnes, Jean-Renaud Boisserie
The Oldowan archeological record of the Shungura Formation, Member F (Lower Omo valley, Ethiopia) comprises more than one hundred occurrences distributed within archeological complexes, where multiple small spots were found in association with one or two larger occurrences. Such spatial patterning could reflect hominin spatial behavior, repeated occupations within a single sedimentary unit, or taphonomic and/or collection biases. Here we test these hypotheses by way of a geoarcheological and taphonomical analysis using four criteria to assess the preservation of the lithic assemblages: (1) size composition, (2) artifact abrasion, (3) bone abrasion, and (4) orientations of lithic artifacts and bones (i...
October 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28861462/nonlinear-climate-sensitivity-and-its-implications-for-future-greenhouse-warming
#14
Tobias Friedrich, Axel Timmermann, Michelle Tigchelaar, Oliver Elison Timm, Andrey Ganopolski
Global mean surface temperatures are rising in response to anthropogenic greenhouse gas emissions. The magnitude of this warming at equilibrium for a given radiative forcing-referred to as specific equilibrium climate sensitivity (S)-is still subject to uncertainties. We estimate global mean temperature variations and S using a 784,000-year-long field reconstruction of sea surface temperatures and a transient paleoclimate model simulation. Our results reveal that S is strongly dependent on the climate background state, with significantly larger values attained during warm phases...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28833668/isotopic-analysis-on-nanogram-quantities-of-carbon-from-dissolved-insect-cuticle-a-method-for-paleoenvironmental-inferences
#15
Yongtao Zhao, David M Nelson, Benjamin F Clegg, Cheng-Bang An, Feng Sheng Hu
RATIONALE: Carbon isotope (δ(13) C ) data from arthropod cuticles provide invaluable information on past and present biogeochemical processes. However, such analyses typically require large sample sizes that may mask important variation in δ(13) C values within or among species. METHODS: We have evaluated a spooling-wire microcombustion (SWiM) device and isotope ratio mass spectrometry (IRMS) to measure the δ(13) C values of carbon dissolved from the cuticle of chitinous aquatic zooplankton...
November 15, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28833664/compound-specific-amino-acid-%C3%AE-15-n-values-in-archaeological-shell-assessing-diagenetic-integrity-and-potential-for-isotopic-baseline-reconstruction
#16
Nicole Misarti, Elizabeth Gier, Bruce Finney, Kelli Barnes, Matthew McCarthy
RATIONALE: Reconstructing stable isotope (SI) ratios at the base of paleo-food webs is often challenging. For coastal systems, the SI ratios of organic matter in archeological shell represent a possible solution, providing a direct record of primary consumer SI ratios in the littoral zone. However, shell is often porous, with organic compounds being susceptible to diagenetic alteration or contamination. If molecular isotopic information is well preserved, compound-specific amino acid isotope analysis (CSI-AA) has the potential to provide direct proxies for baseline SI ratios, bypass many contamination issues, and allow assessment of the diagenetic state...
August 22, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28820899/two-disjunct-pleistocene-populations-and-anisotropic-postglacial-expansion-shaped-the-current-genetic-structure-of-the-relict-plant-amborella-trichopoda
#17
Rémi Tournebize, Stéphanie Manel, Yves Vigouroux, François Munoz, Alexandre de Kochko, Valérie Poncet
Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution...
2017: PloS One
https://www.readbyqxmd.com/read/28811644/the-link-between-enso-like-forcing-and-hydroclimate-variability-of-coastal-east-asia-during-the-last-millennium
#18
Jungjae Park, Jiwoo Han, Qiuhong Jin, Junbeom Bahk, Sangheon Yi
Inconsistent reconstructions of East Asian hydroclimate for the last millennium significantly limit our understanding of the mechanisms behind climate variability during the medieval climate anomaly (MCA) and little ice age (LIA) in the region. In this study, we present new high-resolution multiproxy records (diatom, δ(13)C, C/N, TS) from the Mulyoungari swamp, Jeju Island, South Korea. Our results indicate that El Niño southern oscillation-like variations caused the dry MCA/wet LIA pattern in the study area...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811519/high-resolution-mapping-based-on-an-unmanned-aerial-vehicle-uav-to-capture-paleoseismic-offsets-along-the-altyn-tagh-fault-china
#19
Mingxing Gao, Xiwei Xu, Yann Klinger, Jerome van der Woerd, Paul Tapponnier
The recent dramatic increase in millimeter- to centimeter- resolution topographic datasets obtained via multi-view photogrammetry raises the possibility of mapping detailed offset geomorphology and constraining the spatial characteristics of active faults. Here, for the first time, we applied this new method to acquire high-resolution imagery and generate topographic data along the Altyn Tagh fault, which is located in a remote high elevation area and shows preserved ancient earthquake surface ruptures. A digital elevation model (DEM) with a resolution of 0...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28780964/the-contexts-and-early-acheulean-archaeology-of-the-ef-hr-paleo-landscape-olduvai-gorge-tanzania
#20
Ignacio de la Torre, Rosa M Albert, Richard Macphail, Lindsay J McHenry, Michael C Pante, Ágata Rodríguez-Cintas, Ian G Stanistreet, Harald Stollhofen
Renewed fieldwork at the early Acheulean site of EF-HR (Olduvai Gorge, Tanzania) has included detailed stratigraphic studies of the sequence, extended excavations in the main site, and has placed eleven additional trenches within an area of nearly 1 km(2), to sample the same stratigraphic interval as in the main trench across the broader paleo-landscape. Our new stratigraphic work suggests that EF-HR is positioned higher in the Bed II sequence than previously proposed, which has implications for the age of the site and its stratigraphic correlation to other Olduvai Middle Bed II sites...
August 3, 2017: Journal of Human Evolution
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