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Earthworm distributions are not driven by measurable soil properties. Do they really indicate soil quality?
No full textAbundance and distribution of earthworms in agricultural fields is frequently proposed as a measure of soil quality assuming that observed patterns of abundance are in response to improved or degraded environmental conditions. However, it is not clear that earthworm abundances can be directly related to their edaphic environment, as noted in Darwin’s final publication, perhaps limiting or restricting their value as indicators of ecological quality in any given field. We present results from a spatially explicit intensive survey of pastures within United Kingdom farms, looking for the main drivers of earthworm density at a range of scales. When describing spatial variability of both total and ecotype-specific earthworm abundance within any given field, the best predictor was earthworm abundance itself within 20–30 m of the sampling point; there were no consistent environmental correlates with earthworm numbers, suggesting that biological factors (e.g. colonisation rate, competition, predation, parasitism) drive or at least significantly modify earthworm distributions at this spatial level. However, at the national scale, earthworm abundance is well predicted by soil nitrate levels, density, temperature and moisture content, albeit not in a simple linear fashion. This suggests that although land can be managed at the farm scale to promote earthworm abundance and the resulting soil processes that deliver ecosystem services, within a field, earthworm distributions will remain patchy. The use of earthworms as soil quality indicators must therefore be carried out with care, ensuring that sufficient samples are taken within field to take account of variability in earthworm populations that is unrelated to soil chemical and physical properties.Copyright: © 2021 Hodson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The linked file is the published version of the article.NHM Repositor
The genome sequence of the click beetle, Ampedus sanguinolentus sanguinolentus (Schrank, 1776)
Get PDFWe present a genome assembly from a female specimen of Ampedus sanguinolentus sanguinolentus (click beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The assembly contains two haplotypes with total lengths of 1,574.76 megabases and 1,572.87 megabases. Most of haplotype 1 (97.13%) is scaffolded into 10 chromosomal pseudomolecules, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 15.99 kilobases in length.Copyright: © 2025 Sivell D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the accepted version of the article - you are advised to refer to the published version if you wish to cite from it.NHM Repositor
Using joint species distribution modelling to identify climatic and non‐climatic drivers of Afrotropical ungulate distributions
No full textThe relative importance of the different processes that determine the distribution of species and the assembly of communities is a key question in ecology. The distribution of any individual species is affected by a wide range of environmental variables as well as through interactions with other species; the resulting distributions determine the pool of species available to form local communities at fine spatial scales. A challenge in community ecology is that these interactions (e.g. competition, facilitation, etc.) often are not directly measurable. Here, we used hierarchical modelling of species communities (HMSC), a recently developed framework for joint species distribution modelling, to estimate the role of biotic effects alongside environmental factors using latent variables. We investigate the role of these factors determining species distributions in communities of Artiodactyla, Perissodactyla and Proboscidea in the Afrotropics, an area of peak species richness for hoofed mammals. We also calculate pairwise trait dissimilarity between these species, from a mixture of morphological and behavioural traits, and investigate the relationship between dissimilarity and estimated residual co‐occurrence in the model. We find that while ungulate distributions appear to be predominantly determined (~ 70%) by climatic variables, such as precipitation, a substantial proportion of the variance in ungulate species distributions (~ 30%) can also be attributed to modelled latent variables that likely represent a combination of dispersal barriers and biotic factors. Although we find only a weak relationship between residual co‐occurrence and trait dissimilarity, we suggest that our results may show evidence that biotic factors, likely influenced by historical barriers to species dispersal, are important in determining species communities over a continental area. The HMSC framework can be used to provide insight into factors affecting community assembly at broad scales, and to make more powerful predictions about future species distributions as we enter an era of increasing impacts from anthropogenic change.Copyright © 2024 The Author(s). Ecography published by John Wiley & Sons Ltd on behalf of Nordic Society Oikos. The linked file is the published version of the article.NHM Repositor
Harnessing large language models for coding, teaching and inclusion to empower research in ecology and evolution
No full textAbstract - 1.) Large language models (LLMs) are a type of artificial intelligence (AI) that can perform various natural language processing tasks. The adoption of LLMs has become increasingly prominent in scientific writing and analyses because of the availability of free applications such as ChatGPT. This increased use of LLMs not only raises concerns about academic integrity but also presents opportunities for the research community. Here we focus on the opportunities for using LLMs for coding in ecology and evolution. We discuss how LLMs can be used to generate, explain, comment, translate, debug, optimise and test code. We also highlight the importance of writing effective prompts and carefully evaluating the outputs of LLMs. In addition, we draft a possible road map for using such models inclusively and with integrity.
2.) LLMs can accelerate the coding process, especially for unfamiliar tasks, and free up time for higher level tasks and creative thinking while increasing efficiency and creative output. LLMs also enhance inclusion by accommodating individuals without coding skills, with limited access to education in coding, or for whom English is not their primary written or spoken language. However, code generated by LLMs is of variable quality and has issues related to mathematics, logic, non‐reproducibility and intellectual property; it can also include mistakes and approximations, especially in novel methods.
3.) We highlight the benefits of using LLMs to teach and learn coding, and advocate for guiding students in the appropriate use of AI tools for coding. Despite the ability to assign many coding tasks to LLMs, we also reaffirm the continued importance of teaching coding skills for interpreting LLM‐generated code and to develop critical thinking skills.
4.) As editors of MEE, we support—to a limited extent—the transparent, accountable and acknowledged use of LLMs and other AI tools in publications. If LLMs or comparable AI tools (excluding commonly used aids like spell‐checkers, Grammarly and Writefull) are used to produce the work described in a manuscript, there must be a clear statement to that effect in its Methods section, and the corresponding or senior author must take responsibility for any code (or text) generated by the AI platform.Copyright © 2024 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society. The linked file is the published version of the article.NHM Repositor
The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772)
Get PDFWe present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.Copyright: © 2024 Boyes D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article.NHM Repositor
Clarification on the name-bearing type designation of several cyclophorid species (Mollusca, Gastropoda) by H. H. Godwin-Austen (1915)
Get PDFThe type series boundary and the name-bearing type designation of each cyclophorid taxon originally described by Godwin-Austen are clarified based on an interpretation that complies with the ICZN. Previous statuses of type specimens designated by previous authors are reconsidered. Lectotypes of Spiraculum oakesi Godwin-Austen, 1915, Spiraculum kempi Godwin-Austen, 1915, Pterocyclos aborensis Godwin-Austen, 1915, Pterocyclos miriensis Godwin-Austen, 1915, Pterocyclos brahmakundensis Godwin-Austen, 1915, Spiraculum luyorensis Godwin-Austen, 1915, Spiraculum putaoensis Godwin-Austen, 1915, and Theobaldius oakesi Godwin-Austen, 1915 are here designated to stabilize the existing nomenclature. In addition, the type specimens of Pterocyclos miriensis and Theobaldius oakesi are photographed and figured for the first time.Copyright Parin Jirapatrasilp et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
Confusing female Taiwanese Tarsiger bush robins and designation of a lectotype for Ianthia johnstoniae Ogilvie-Grant, 1906
Get PDFRecent research reveals that the original series, a male and female, used to describe Ianthia johnstoniae Ogilvie-Grant, 1906 (= Collared Bush Robin Tarsiger johnstoniae), held in the Natural History Museum, Tring, is mixed. The male is a Collared Bush Robin, but the female is an example of the morphologically very similar White-browed Bush Robin T. indicus formosanus. Because the syntypes represent two different species and in order to fix the identity on the universally
understood taxonomic concept associated with T. johnstoniae, we select as its lectotype the unambiguously identified male specimen (NHMUK 1907.12.12.39).Copyright © 2024 The Authors; This is an open‐access article distributed under the terms of the Creative Commons Attribution-NonCommercial Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article.NHM Repositor
Tracing the earliest stages of hydrothermal alteration on the CM chondrite parent body
Get PDFAbstract The CM carbonaceous chondrites are an important resource in our efforts to understand the role of volatiles in the formation of planetary systems. We report the bulk mineralogy, water abundance, and infrared (IR) reflectance spectra of the CM chondrites LaPaz Icefield (LAP) 04514, LAP 04796, LAP 04565, and LAP 02333. They contain abundant Fe‐ and Mg‐rich serpentines (~70–80 vol%), and based on their phyllosilicate fractions, we classify LAP 04514, LAP 04796, and LAP 04565 as petrologic subtype 1.6 and LAP 02333 as 1.4. This is consistent with estimated water abundances of 9.9 (±1.1) wt% for LAP 04796, 10.4 (±0.1) wt% for LAP 04565, and 11.5 (±0.5) wt% for LAP 02333. However, LAP 04514 contains less water (8.8 ± 0.3 wt%), has a shallower 3 µm band depth, and lacks tochilinite having experienced posthydration temperatures of ~300–400 °C. We conclude that LAP 04514, LAP 04796, and LAP 04565 are among the least altered CM chondrites, which retain primitive features from the initial building blocks of the CM parent body. Finally, we use the IR spectral features of LAP 04514, LAP 04796, and LAP 04565 to identify C‐complex asteroid surfaces that record mild levels of hydration.Copyright © 2021 The Meteoritical Society (MET). The attached file is the published version of article.NHM Repositor
A primordial 15N-depleted organic component detected within the carbonaceous chondrite Maribo
Get PDFAbstract We report on the detection of primordial organic matter within the carbonaceous chondrite Maribo that is distinct from the majority of organics found in extraterrestrial samples. We have applied high-spatial resolution techniques to obtain C-N isotopic compositions, chemical, and structural information of this material. The organic matter is depleted in 15N relative to the terrestrial value at around δ15N ~ -200‰, close to compositions in the local interstellar medium. Morphological investigations by electron microscopy revealed that the material consists of µm- to sub-µm-sized diffuse particles dispersed within the meteorite matrix. Electron energy loss and synchrotron X-ray absorption near-edge structure spectroscopies show that the carbon functional chemistry is dominated by aromatic and C=O bonding environments similar to primordial organics from other carbonaceous chondrites. The nitrogen functional chemistry is characterized by C-N double and triple bonding environments distinct from what is usually found in 15N-enriched organics from aqueously altered carbonaceous chondrites. Our investigations demonstrate that Maribo represents one of the least altered CM chondrite breccias found to date and contains primordial organic matter, probably originating in the interstellar medium.Copyright © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The attached file is the published version of the article.NHM Repositor
New species and a key to members of the Geminata clade (Solanum L.; Solanaceae) in Colombia
Get PDFAs part of ongoing studies of Solanum in South America, three new species of the Geminata clade are described for Colombia. Solanum caquetense J.D.Tovar sp. nov., from the Department of Caquetá, is a riverside shrub found in lowland rainforests, with willow-like leaves characteristic of rheophyte plants. Solanum pinguiculum J.D. Tovar sp. nov. is confined to the understory of cloud forests on the eastern Andean slopes in the Departments of Cauca, Huila, and Putumayo, and is a tiny subshrub with somewhat watery stems and minute flowers. Solanum sabu J.D. Tovar sp. nov. is a rare plant, represented by a single collection from the eastern Andean slopes of the Cordillera Central in the Department of Tolima; it is a shrub with loose dendritic trichomes on abaxial leaf surface, and is described here to encourage further investigation in the field and herbaria. Differences between these new taxa and morphologically similar species are discussed, and photos, preliminary conservation status, and distribution maps are provided for all newly described species. To facilitate the identification of these morphologically very similar plants, a dichotomous key for all members of the Geminata clade occurring in Colombia is provided together with a synopsis of their distribution by Department.This is an open-access article distributed under the terms of the Creative Commons Attribution License.NHM Repositor