A phylogenetic estimate for golden moles (Mammalia, Afrotheria, Chrysochloridae).

BACKGROUND: Golden moles (Chrysochloridae) are small, subterranean, afrotherian mammals from South Africa and neighboring regions. Of the 21 species now recognized, some (e.g., Chrysochloris asiatica, Amblysomus hottentotus) are relatively common, whereas others (e.g., species of Chrysospalax, Cryptochloris, Neamblysomus) are rare and endangered. Here, we use a combined analysis of partial sequences of the nuclear GHR gene and morphological characters to derive a phylogeny of species in the family Chrysochloridae. RESULTS: Although not all nodes of the combined analysis have high support values, the overall pattern of relationships obtained from different methods of phylogeny reconstruction allow us to make several recommendations regarding the current taxonomy of golden moles. We elevate Huetia to generic status to include the species leucorhinus and confirm the use of the Linnean binomial Carpitalpa arendsi, which belongs within Amblysominae along with Amblysomus and Neamblysomus. A second group, Chrysochlorinae, includes Chrysochloris, Cryptochloris, Huetia, Eremitalpa, Chrysospalax, and Calcochloris. Bayesian methods make chrysochlorines paraphyletic by placing the root within them, coinciding with root positions favored by a majority of randomly-generated outgroup taxa. Maximum Parsimony (MP) places the root either between chrysochlorines and amblysomines (with Chlorotalpa as sister taxon to amblysomines), or at Chlorotalpa, with the former two groups reconstructed as monophyletic in all optimal MP trees. CONCLUSIONS: The inclusion of additional genetic loci for this clade is important to confirm our taxonomic results and resolve the chrysochlorid root. Nevertheless, our optimal topologies support a division of chrysochlorids into amblysomines and chrysochlorines, with Chlorotalpa intermediate between the two. Furthermore, evolution of the chrysochlorid malleus exhibits homoplasy. The elongate malleus has evolved just once in the Cryptochloris-Chrysochloris group; other changes in shape have occurred at multiple nodes, regardless of how the root is resolved.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The use of different 16S rRNA gene variable regions in biogeographical studies

DATA AVAILABILITY STATEMENT : All Illumina sequences generated and analyzed in this study were deposited into the European Nucleotide Archive (accession number PRJEB55051).SUPPORTING INFORMATION 1 : FIGURE S1. Samples located in four inland areas of the Prince Charles Mountains (ME1 from Mount Rubin, ME2 and ME3 from Mawson Escarpment, MM1 and MM2 from Mount Menzies, LT1 and LT2 from Lake Terrasovoje), in the Reinbolt Hills (RH1), and in coastal sites in proximity of the Prince Charles Mountains (C1 and C2; see Table S1). Map was produced using MODIS mosaic (125 m) imagery distributed by Quantarctica (https://cmr.earthdata.nasa.gov/; https://www.npolar.no/quantarctica/). FIGURE S2. Pearson's pairwise correlations between Bray–Curtis dissimilarity matrices calculated on relative abundance taxonomic dataset (genus level; A), and between Jaccard dissimilarity matrices calculated on presence/absence taxonomic dataset (genus level; B). Correlations were calculated for all the variable region datasets (V1–V3, V3–V4, V4, V4–V5 and V8–V9), and the mixed datasets (Mix 1, Mix 2 and Mix 3) constituted by randomly picked samples from V1–V3, V3–V4, V4, V4–V5 and V8–V9 (Table S4). Pearson's correlation coefficients (r) are reported only in case of significant correlation (p < 0.05).SUPPORTING INFORMATION 2 : TABLE S1. Sample specifics. TABLE S2. Geochemical data. TABLE S3. Relative abundance (%) of the taxonomic domains Bacteria and Archaea in sample (i.e., ME1, ME2, ME3, MM1, MM2, LT1, LT2, RH1, C1 and C2) for each variable region dataset (i.e., V1–V3, V3–V4, V4, V4–V5 and V8–V9). TABLE S4. Composition of mixed communities. TABLE S5. Number of reads at each step of the 16S rRNA gene processing pipeline. *counts reported as read pairs. TABLE S6. Number and percentage of unknown amplicon sequence variants (ASVs) at genus level for each phylum. TABLE S7. Relative abundance associated to unknown amplicon sequence variants at genus-level for each phylum. TABLE S8. Pearson's correlations from pairwise comparisons of variable region datasets performed on number of genera (A), dominant genera (i.e., genera represented by a relative abundance higher than 1% in at least one sample) (B), rare genera (i.e., genera represented by a relative abundance lower than 0.1% in all samples (C), Shannon index (D) and unique genera (E).16S rRNA gene amplicon sequencing is routinely used in environmental surveys to identify microbial diversity and composition of the samples of interest. The dominant sequencing technology of the past decade (Illumina) is based on the sequencing of 16S rRNA hypervariable regions. Online sequence data repositories, which represent an invaluable resource for investigating microbial distributional patterns across spatial, environmental or temporal scales, contain amplicon datasets from diverse 16S rRNA gene variable regions. However, the utility of these sequence datasets is potentially reduced by the use of different 16S rRNA gene amplified regions. By comparing 10 Antarctic soil samples sequenced for five different 16S rRNA amplicons, we explore whether sequence data derived from diverse 16S rRNA variable regions can be validly used as a resource for biogeographical studies. Patterns of shared and unique taxa differed among samples as a result of variable taxonomic resolutions of the assessed 16S rRNA variable regions. However, our analyses also suggest that the use of multi-primer datasets for biogeographical studies of the domain Bacteria is a valid approach to explore bacterial biogeographical patterns due to the preservation of bacterial taxonomic and diversity patterns across different variable region datasets. We deem composite datasets useful for biogeographical studies.Australian Antarctic Division, Australian Research Council and NRF SANAP.http://wileyonlinelibrary.com/journal/emi4hj2023BiochemistryGeneticsMicrobiology and Plant Patholog

Flavonoid versus artemisinin anti-malarial activity in Artemisia annua whole-leaf extracts

Artemisinin, a sesquiterpene lactone produced by Artemisia annua glandular secretory trichomes, is the active ingredient in the most effective treatment for uncomplicated malaria caused by Plasmodium falciparum parasites. Other metabolites in A. annua or related species, particularly flavonoids, have been proposed to either act as antimalarials on their own or act synergistically with artemisinin to enhance antimalarial activity. We identified a mutation that disrupts the CHALCONE ISOMERASE 1 (CHI1) enzyme that is responsible for the second committed step of flavonoid biosynthesis. Detailed metabolite profiling revealed that chi1-1 lacks all major flavonoids but produces wild-type artemisinin levels, making this mutant a useful tool to test the antiplasmodial effects of flavonoids. We used whole-leaf extracts from chi1-1 and mutant lines impaired in artemisinin production in bioactivity in vitro assays against intraerythrocytic P. falciparum Dd2. We found that chi1-1 extracts did not differ from wild-type extracts in antiplasmodial efficacy nor initial rate of cytocidal action. Furthermore, extracts from the A. annua cyp71av1-1 mutant and RNAi lines impaired in amorpha-4,11-diene synthase gene expression, which are both severely compromised in artemisinin biosynthesis but unaffected in flavonoid metabolism, showed very low or no antiplasmodial activity. These results demonstrate that in vitro bioactivity against P. falciparum of flavonoids is negligible when compared to that of artemisinin

The Evolutionary and Phylogeographic History of Woolly Mammoths: A Comprehensive Mitogenomic Analysis

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ∼1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths

Environment and shipping drive environmental DNA beta-diversity among commercial ports

The spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographical patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship-borne species spread homogenizes port communities. We first collected and metabarcoded water samples from ports in Europe, Asia, Australia and the Americas. We then calculated community dissimilarities between port pairs and tested for effects of environmental dissimilarity, biogeographical region and four alternative measures of ship-borne species transport risk. We predicted that higher shipping between ports would decrease community dissimilarity, that the effect of shipping would be small compared to that of environment dissimilarity and shared biogeography, and that more complex shipping risk metrics (which account for ballast water and stepping-stone spread) would perform better. Consistent with our hypotheses, community dissimilarities increased significantly with environmental dissimilarity and, to a lesser extent, decreased with ship-borne species transport risks, particularly if the ports had similar environments and stepping-stone risks were considered. Unexpectedly, we found no clear effect of shared biogeography, and that risk metrics incorporating estimates of ballast discharge did not offer more explanatory power than simpler traffic-based risks. Overall, we found that shipping homogenizes eukaryotic communities between ports in predictable ways, which could inform improvements in invasive species policy and management. We demonstrated the usefulness of eDNA metabarcoding and dissimilarity regression for disentangling the drivers of large-scale biodiversity patterns. We conclude by outlining logistical considerations and recommendations for future studies using this approach.Fil: Andrés, Jose. Cornell University. Department Of Ecology And Evolutionary Biology;Fil: Czechowski, Paul. Cornell University. Department Of Ecology And Evolutionary Biology; . University of Otago; Nueva Zelanda. Helmholtz Institute for Metabolic, Obesity and Vascular Research; AlemaniaFil: Grey, Erin. University of Maine; Estados Unidos. Governors State University; Estados UnidosFil: Saebi, Mandana. University of Notre Dame; Estados UnidosFil: Andres, Kara. Cornell University. Department Of Ecology And Evolutionary Biology;Fil: Brown, Christopher. California State University Maritime Academy; Estados UnidosFil: Chawla, Nitesh. University of Notre Dame; Estados UnidosFil: Corbett, James J.. University of Delaware; Estados UnidosFil: Brys, Rein. Research Institute for Nature and Forest; BélgicaFil: Cassey, Phillip. University of Adelaide; AustraliaFil: Correa, Nancy. Ministerio de Defensa. Armada Argentina. Instituto Universitario Naval de la Ara. Escuela de Ciencias del Mar; Argentina. Ministerio de Defensa. Armada Argentina. Servicio de Hidrografía Naval; ArgentinaFil: Deveney, Marty R.. South Australian Research And Development Institute; AustraliaFil: Egan, Scott P.. Rice University; Estados UnidosFil: Fisher, Joshua P.. United States Fish and Wildlife Service; Estados UnidosFil: vanden Hooff, Rian. Oregon Department of Environmental Quality; Estados UnidosFil: Knapp, Charles R.. Daniel P. Haerther Center for Conservation and Research; Estados UnidosFil: Leong, Sandric Chee Yew. National University of Singapore; SingapurFil: Neilson, Brian J.. State of Hawaii Division of Aquatic Resources; Estados UnidosFil: Paolucci, Esteban Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Pfrender, Michael E.. University of Notre Dame; Estados UnidosFil: Pochardt, Meredith R.. M. Rose Consulting; Estados UnidosFil: Prowse, Thomas A. A.. University of Adelaide; AustraliaFil: Rumrill, Steven S.. Oregon Department of Fish and Wildlife; Estados UnidosFil: Scianni, Chris. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Instituto para el Estudio de la Biodiversidad de Invertebrados; Argentina. Marine Invasive Species Program; Estados UnidosFil: Sylvester, Francisco. Universidad Nacional de Salta. Facultad de Ciencias Naturales. Instituto para el Estudio de la Biodiversidad de Invertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta; ArgentinaFil: Tamburri, Mario N.. University of Maryland; Estados UnidosFil: Therriault, Thomas W.. Pacific Biological Station; CanadáFil: Yeo, Darren C. J.. National University of Singapore; SingapurFil: Lodge, David M.. Cornell University. Department Of Ecology And Evolutionary Biology

Growth Performance and Root Transcriptome Remodeling of Arabidopsis in Response to Mars-Like Levels of Magnesium Sulfate

Martian regolith (unconsolidated surface material) is a potential medium for plant growth in bioregenerative life support systems during manned missions on Mars. However, hydrated magnesium sulfate mineral levels in the regolith of Mars can reach as high as 10 wt%, and would be expected to be highly inhibitory to plant growth. at 180 min. after initiation of treatment. mutants exhibit partial tolerance to magnesium sulfate, and by elucidating a small subset (500 vs. >10,000) of candidate genes for mutation or metabolic engineering that will enhance tolerance to magnesium sulfate soils

Antarctic biodiversity surveys using high throughput sequencing: understanding landscape and communities of the Prince Charles Mountains.

Antarctic soils are home to small, inconspicuous organisms including bacteria, unicellular eukaryotes, fungi, lichen, cryptogamic plants and invertebrates. Antarctic soil communities are distinct from other soil biota as a consequence of long-term persistence under harsh environmental conditions; furthermore their long history of isolation is responsible for a high degree of endemism. Of major concern is the establishment of non-indigenous species facilitated by human-mediated climate change and increased human activity, threatening the highly specialised endemic species. A lack of baseline information on terrestrial Antarctic biodiversity currently impairs efforts to conserve the unique but still largely unknown Antarctic biota. In this thesis I apply metagenetic high throughput sequencing (MHTS) methods to address the deficiency of biological information from remote regions of continental Antarctica, and use the data generated to explore environmental constraints on Antarctic biodiversity. In Chapter 1, I introduce current issues impeding the generation of baseline Antarctic biodiversity data and evaluate the application of using MHTS techniques. This review highlights the potential of using MHTS approaches using amplicon sequencing to retrieve Eukaryotic biodiversity information from terrestrial Antarctica. In Chapter 2, the eukaryotic diversity of three biologically unsurveyed regions in the Prince Charles Mountains, East Antarctica (PCMs) is explored. Total eukaryote biodiversity in the PCMs appears to follow an altitudinal or latitudinal trend, which is less obvious for terrestrial invertebrates. In order to apply MHTS to the study of Antarctic invertebrates, the comparative taxonomic assignment fidelities of metagenetic markers and morphological approaches are explored in Chapter 3. Fidelities of taxonomic assignments to four Antarctic invertebrate phyla differed depending on metagenetic marker, and only application of non-arbitrary sequence processing parameters resulted in these findings. In Chapter 4, I use MHTS-derived biodiversity information to explore the relationship between soil properties and invertebrate biodiversity in the PCMs. Across large spatial scales distribution of phyla Tardigrada and Arachnida and classes Enoplea (Nematoda) and Bdelloidea (Rotifera) in inland areas are constrained by terrain-age-related accumulation of salts, while other Classes (Chromadorea, Nematoda and Monogonata, Bdelloidea) are better able to tolerate high salinity. In moister, nutrient-richer and more coastal areas, this effect was less pronounced and a higher invertebrate diversity was found. The methods applied and developed in this thesis are a valuable starting point to advance the collection of biodiversity information across terrestrial Antarctica and other remote habitats. The work presented here provides examples for generation and usage of MHTS information from remote Antarctic habitats, demonstrates how biodiversity information retrieved using different metagenetic markers can be combined, developed methods for assessing the quality of MHTS markers and finally demonstrated the application of MHTS data to investigate the environmental determinants of invertebrate diversity in remote ice-free habitats. Future MHTS biodiversity studies of Antarctic terrestrial habitats should incorporate large sample numbers and use combined data from multiple genetic markers.Thesis (PhD) -- University of Adelaide, School of Biological Sciences, 201

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wahipounamu / Fiordland (Aotearoa / New Zealand) with notes on the availability of reference data for environmental DNA surveys

Codeand publishable data associated with manuscript "Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wahipounamu / Fiordland (Aotearoa / New Zealand) with notes on the availability of reference data for environmental DNA surveys" and its supplemental information.Code subject to change during peer review process, different versions are present. Final data will be appended on article acceptance

macrobiotus/mouse_mating: Release for Zenodo

&lt;p&gt;Code release for Zenodo and review.&lt;/p&gt

macrobiotus/Fiordland-eDNA: submission of revision

All code for submitting 1st revision to jounal "Environmnal DNA", after circulating second round of proofs to coauthors