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BMC Ecology and Evolution May 2024Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials...
BACKGROUND
Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials can take decades, hence any approach that supports focussing on a likely set of candidates may save time and money. We use a non-stationary statistical analysis with spatially varying coefficients to identify ecotypes that indicate first regions of similarly adapted varieties of Douglas-fir (Pseudotsuga menziesii (Mirbel) Franco) in North America. For over 70,000 plot-level presence-absences, spatial differences in the survival response to climatic conditions are identified.
RESULTS
The spatially-variable coefficient model fits the data substantially better than a stationary, i.e. constant-effect analysis (as measured by AIC to account for differences in model complexity). Also, clustering the model terms identifies several potential ecotypes that could not be derived from clustering climatic conditions itself. Comparing these six identified ecotypes to known genetically diverging regions shows some congruence, as well as some mismatches. However, comparing ecotypes among each other, we find clear differences in their climate niches.
CONCLUSION
While our approach is data-demanding and computationally expensive, with the increasing availability of data on species distributions this may be a useful first screening step during the search for climate-change adapted varieties. With our unsupervised learning approach being explorative, finely resolved genotypic data would be helpful to improve its quantitative validation.
Topics: Climate Change; Pseudotsuga; Ecotype; Adaptation, Physiological; Models, Biological; North America
PubMed: 38807083
DOI: 10.1186/s12862-024-02260-z -
Scientific Reports May 2024Stress drop is an earthquake property indicative for the characteristic relation of slip to fault dimension. It is furthermore affected by fault strength, fault...
Stress drop is an earthquake property indicative for the characteristic relation of slip to fault dimension. It is furthermore affected by fault strength, fault topography, the presence of fluids, rupture size, slip, and velocity. In this article, the stress drop image of an entire subduction zone, namely for the seismically highly active northernmost part of Chile, is combined with mapped b-values and their corresponding magnitude distribution in order to better constrain the conditions under which earthquakes of different provenances may nucleate. The underlying recent earthquake catalog contains over 180,000 events, covering 15 years of seismicity, from which more than 50,000 stress drop estimates were computed. Their spatial average segments the subduction zone into different parts, i.e., average stress drop between seismotectonic areas is different, although this difference is small compared to the natural scatter of stress drop values. By considering stress drop variations, b-value map, magnitude distribution, and thermal models, candidate earthquake nucleation mechanisms are identified which can explain the observed distributions. This is done for two exemplary regions: (1) The plate interface, where principally lower stress drop events are found, while at the same time a high spatial heterogeneity of stress drop values is observed. This indicates relatively smooth or lubricated rupture surfaces, and locally it suggests the existence of alternating regions controlled by strong asperities, weaker material, or creep. (2) The highly active intermediate depth (ID) seismicity region, where the variation of stress drop and b-value point to a gradual change of nucleation mechanism from dehydration embrittlement at the top of the ID cloud, over dehydration driven stress transfer in its central part, to thermal runaway shear mechanisms at its bottom. In both cases, the combination of stress drop and b-value distribution helps to better understand the origin and the differences of the observed seismicity.
PubMed: 38806618
DOI: 10.1038/s41598-024-63015-w -
BMJ (Clinical Research Ed.) May 2024
PubMed: 38806186
DOI: 10.1136/bmj.q1149 -
BMJ (Clinical Research Ed.) May 2024
Topics: Humans; Social Media; Smartphone; Adolescent; Mental Health; Mental Disorders; Adolescent Health
PubMed: 38806185
DOI: 10.1136/bmj-2024-079828 -
PloS One 2024Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and...
Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.
Topics: Plasmids; Genetic Engineering; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Mutation; Base Sequence; Sequence Analysis, DNA
PubMed: 38805426
DOI: 10.1371/journal.pone.0304164 -
Astrobiology Jun 2024Geological evidence and atmospheric and climate models suggest habitable conditions occurred on early Mars, including in a lake in Gale crater. Instruments aboard the...
Geological evidence and atmospheric and climate models suggest habitable conditions occurred on early Mars, including in a lake in Gale crater. Instruments aboard the Curiosity rover measured organic compounds of unknown provenance in sedimentary mudstones at Gale crater. Additionally, Curiosity measured nitrates in Gale crater sediments, which suggests that nitrate-dependent Fe oxidation (NDFO) may have been a viable metabolism for putative martian life. Here, we perform the first quantitative assessment of an NDFO community that could have existed in an ancient Gale crater lake and quantify the long-term preservation of biological necromass in lakebed mudstones. We find that an NDFO community would have the capacity to produce cell concentrations of up to 10 cells mL, which is comparable to microbes in Earth's oceans. However, only a concentration of <10 cells mL, due to organisms that inefficiently consume less than 10% of precipitating nitrate, would be consistent with the abundance of organics found at Gale. We also find that meteoritic sources of organics would likely be insufficient as a sole source for the Gale crater organics, which would require a separate source, such as abiotic hydrothermal or atmospheric production or possibly biological production from a slowly turning over chemotrophic community.
Topics: Mars; Nitrates; Oxidation-Reduction; Iron; Extraterrestrial Environment; Geologic Sediments; Exobiology; Organic Chemicals; Lakes
PubMed: 38805190
DOI: 10.1089/ast.2023.0109 -
Plants (Basel, Switzerland) May 2024The Asian chestnut gall wasp (ACGW) (Hymenoptera Yasumatsu) is a severe pest of sweet chestnut ( Mill.) with a strong impact on growth and nut production. A comparative...
The Asian chestnut gall wasp (ACGW) (Hymenoptera Yasumatsu) is a severe pest of sweet chestnut ( Mill.) with a strong impact on growth and nut production. A comparative field trial in Central Italy, including provenances from Spain, Italy, and Greece, was screened for ACGW infestation over consecutive years. The Greek provenance Hortiatis expressed a high proportion of immune plants and was used to perform a genome-wide association study based on DNA pool sequencing (Pool-GWAS) by comparing two DNA pools from 25 susceptible and 25 resistant plants. DNA pools were sequenced with 50X coverage depth. Sequence reads were aligned to a reference genome and the pools were compared to identify SNPs associated with resistance. Twenty-one significant SNPs were identified and highlighted a small genomic region on pseudochromosome 3 (Chr 3), containing 12 candidate genes of three gene families: , , and . Functional analyses revealed a putative metabolic gene cluster related to saccharide biosynthesis in the genomic regions associated with resistance that could be involved in the production of a toxic metabolite against parasites. The comparison with previous genetic studies confirmed the involvement of Chr 3 in the control of resistance to ACGW.
PubMed: 38794426
DOI: 10.3390/plants13101355 -
PloS One 2024The exchange of information and social interactions on broad spatial scales between human groups in the past can be studied through the provenance of key indicators of...
Middle through late Holocene long-distance transport of exotic shell personal adornments in Central West Patagonia (southern South America). The archaeomalacological assemblage of Baño Nuevo 1.
The exchange of information and social interactions on broad spatial scales between human groups in the past can be studied through the provenance of key indicators of distant origin recorded at archaeological sites. The remains of shells of mollusk species, especially when crafted as elements of personal ornaments, express aspects of the behaviors and valuations for the populations that selected, transformed, and exchanged such items. In the southern cone of South America, past hunter-gatherer groups traveled long distances and interacted with communities distributed throughout the territory to acquire goods for technological use, visual display or considered highly valued materials. When recorded at distant locations, these goods of extra local origin are very informative regarding the differences between commonly used home ranges and the occasional access to remote spaces. We present the results of the analysis of the archaeomalacological assemblage of the Baño Nuevo 1 site, a cave with exceptional preservation conditions in Central West Patagonia. This site has yielded a diverse group of artifacts made of shells with origins from multiple distances, as well as evidence of the use of marine, freshwater, and terrestrial species. Its deposits, which extend over the last 11,000 years, reveal an antiquity of at least the middle Holocene for the acquisition, manufacture, use and transport of goods as personal ornaments from shells in the macroregion.
Topics: Archaeology; Humans; Animals; History, Ancient; Animal Shells; South America; Caves; Fossils; Argentina
PubMed: 38787897
DOI: 10.1371/journal.pone.0304454 -
Journal of Human Evolution Jun 2024The Kocabaş specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of...
The Kocabaş specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of the right and left parietal and left and right parts of the frontal bone. The fossil was assumed to belong to the Homo erectus s.l. hypodigm by some authors, whereas others see similarities with Middle Pleistocene fossils (Broken Hill 1/Kabwe, Bodo, or Ceprano). Here, we present the first attempt to make a complete reconstruction of the missing medial portion of the frontal bone and a comprehensive geometric morphometric analysis of this bone. We restored the calotte by aligning and mirroring the three preserved fragments. Afterward, we restored the missing portion by applying the thin-plate spline interpolation algorithm of target fossils onto the reconstructed Kocabaş specimen. For the geometric morphometric analyses, we collected 80 landmarks on the frontal bone (11 osteometric points, 14 bilateral curve semilandmarks, and 41 surface semilandmarks). The comparative sample includes 21 fossils from different chronological periods and geographical areas and 30 adult modern humans from different populations. Shape analyses highlighted the presence in Kocabaş of features usually related to Middle Pleistocene Homo, such as a developed supraorbital torus associated with a relatively short frontal squama and reduced post-toral sulcus. Cluster analysis and linear discriminant analysis classification procedure suggest Kocabaş being part of the same taxonomic unit of Eurasian and African Middle Pleistocene Homo. In light of our results, we consider that attributing the Kocabaş hominin to H. erectus s.l. may be unwarranted. Results of our analyses are compatible with different evolutionary scenarios, but a more precise chronological framework is needed for a thorough discussion of the evolutionary significance of this specimen. Future work should clarify its geological age, given uncertainties regarding its stratigraphic provenance.
Topics: Fossils; Hominidae; Animals; Turkey; Biological Evolution; Frontal Bone
PubMed: 38781712
DOI: 10.1016/j.jhevol.2024.103517 -
ENeuro Jun 2024Scientific research demands reproducibility and transparency, particularly in data-intensive fields like electrophysiology. Electrophysiology data are typically analyzed...
Scientific research demands reproducibility and transparency, particularly in data-intensive fields like electrophysiology. Electrophysiology data are typically analyzed using scripts that generate output files, including figures. Handling these results poses several challenges due to the complexity and iterative nature of the analysis process. These stem from the difficulty to discern the analysis steps, parameters, and data flow from the results, making knowledge transfer and findability challenging in collaborative settings. Provenance information tracks data lineage and processes applied to it, and provenance capture during the execution of an analysis script can address those challenges. We present Alpaca (Automated Lightweight Provenance Capture), a tool that captures fine-grained provenance information with minimal user intervention when running data analysis pipelines implemented in Python scripts. Alpaca records inputs, outputs, and function parameters and structures information according to the W3C PROV standard. We demonstrate the tool using a realistic use case involving multichannel local field potential recordings of a neurophysiological experiment, highlighting how the tool makes result details known in a standardized manner in order to address the challenges of the analysis process. Ultimately, using Alpaca will help to represent results according to the FAIR principles, which will improve research reproducibility and facilitate sharing the results of data analyses.
Topics: Animals; Electrophysiology; Electrophysiological Phenomena; Information Dissemination; Software; Humans; Data Analysis
PubMed: 38777610
DOI: 10.1523/ENEURO.0476-23.2024