RSS 1.0Life sciences
The Museum’s vast collections of vertebrates, invertebrates, plants and microbes support our staff's unique expertise in evolutionary biology, biodiversity and systematics.
Recent Submissions
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Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysisAbstract Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress–tolerant varieties and genes that could limit future climate-changed–induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change–resilient phenotypes.
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Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in ArgyranthemumAbstract Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.
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Mastering the difficulties presented by the peculiarities of island life. A commentary on: ‘Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequence data’This article comments on: Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090
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Open letter: A global call to strengthen national soil biodiversity action through coordination and harmonizationSoil biodiversity remains one of the least systematically studied components of global biodiversity, largely invisible in policy agendas. A coordinated soil biodiversity monitoring approach is urgently needed to enable national‐level action.
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Genomics of ecological adaptation in Canary Island Descurainia (Brassicaceae) and comparisons with other BrassicaceaeAbstract Oceanic archipelagos provide striking examples of lineages that have radiated over pronounced ecological gradients. Accompanying this diversification, lineages have evolved adaptations allowing survival in extreme environments. Here, we investigate the genomic basis of ecological adaptation in Canary Island <jats:italic>Descurainia</jats:italic> (Brassicaceae), an island relative of <jats:italic>Arabidopsis</jats:italic>. The seven endemic species have diversified in situ along an elevational and ecological gradient, from low‐elevation scrub to high‐elevation sub‐alpine desert. We first generated a reference genome for <jats:italic>Descurainia millefolia,</jats:italic> phylogenetic analysis of which placed it as sister to <jats:italic>D. sophioides</jats:italic>. Ninety‐six gene families were found to be specific to <jats:italic>D. millefolia</jats:italic> and a further 1087 and 1469 gene families have expanded or contracted in size, respectively, along the <jats:italic>D. millefolia</jats:italic> branch. We then employed genome re‐sequencing to sample 14 genomes across the seven species of Canary Island <jats:italic>Descurainia</jats:italic> and an outgroup. Phylogenomic analyses were consistent with previous reconstructions of Canary Island <jats:italic>Descurainia</jats:italic> in resolving low‐ and high‐elevation clades. Using the branch‐site dN/dS method, we detected positive selection for 275 genes on the branch separating the low‐ and high‐elevation species and these positively selected genes (PSGs) were significantly enriched for functions related to reproduction and stress tolerance. Comparing PSGs to those in analyses of adaptation to elevation and/or latitude in other Brassicaceae, we found little evidence of widespread convergence and gene reuse, except for two examples, one of which was a significant overlap between <jats:italic>Descurainia</jats:italic> and <jats:italic>Draba nivalis,</jats:italic> a species restricted to high latitudes. The study of Canary Island <jats:italic>Descurainia</jats:italic> suggests that the transition to high‐elevation environments such as that found in the high mountains of the Canary Islands involves selection on genes related to reproduction and stress tolerance but that repeated evolution across different lineages that have evolved into similar habitats is limited, indicating substantially different molecular trajectories to adaptation.
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Bayesian Methods to Analyze Historical Collections in Time and Space: A Case Study Using Cabo Verde Endemic FloraBiological collections, including herbarium specimens, are unique sources of biodiversity data presenting a window on the history of the development and accumulation of knowledge of a specific geographical region. Understanding how the process of discovery impacts that knowledge is particularly important for oceanic islands which are often characterized by both high levels of endemic diversity and high proportions of threatened taxa. The archipelagos of the Macaronesian region (i.e. Azores, Canaries, Savages, Madeira, and Cabo Verde) have been the focus of attention for scientific expeditions since the end of the 17th century. However, there is no integrated study describing the historical process of collecting, discovery and description of its flora. Using as a case study the Cabo Verde endemic angiosperm flora, we review the history of collecting in the flora and apply a Bayesian approach to assess the accumulation of species discovery, through time and space across the nine islands of the archipelago. Our results highlight the central role not only of natural characteristics (e.g. area, age, maximum altitude and average value of the terrain ruggedness index) but also historical factors (i.e. the location of major harbors) for the development of knowledge of the flora. The main factors that have determined the process of species description in the archipelago and how this impact our understanding of diversity patterns across archipelagos are discussed.
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Boosting biodiversity in school grounds: a theory of changeThe National Education Nature Park aims to involve every nursery, school, and college in England in enhancing the biodiversity on their site, whilst supporting young people’s wellbeing, pro-environmental behaviours, and green skills. Young people gather environmental data using citizen science research, and then through collaboration and collective decision-making, they design and implement their own nature recovery actions. But will this participation in community and citizen science lead to behaviour change and environmental action, and how can we build participants’ sense of agency to take environmental action through our programme? Here, we present our Theory of Change for the Nature Park and the design features of the programme that connect participation in citizen science with achieving two crucial types of change - environmental change in the form of biodiversity gain, and the behaviour change that underpins it.
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Effects of land use and soil properties on taxon richness and abundance of soil assemblagesAbstract: Land‐use change and habitat degradation are among the biggest drivers of aboveground biodiversity worldwide but their effects on soil biodiversity are less well known, despite the importance of soil organisms in developing soil structure, nutrient cycling and water drainage. Combining a global compilation of biodiversity data from soil assemblages collated as part of the PREDICTS project with global data on soil characteristics, we modelled how taxon richness and total abundance of soil organisms have responded to land use. We also estimated the global Biodiversity Intactness Index (BII)—the average abundance and compositional similarity of taxa that remain in an area, compared to a minimally impacted baseline, for soil biodiversity. This is the first time the BII has been calculated for soil biodiversity. Relative to undisturbed vegetation, soil organism total abundance and taxon richness were reduced in all land uses except pasture. Soil properties mediated the response of soil biota, but not in a consistent way across land uses. The global soil BII in cropland is, on average, a third of that originally present. However, in grazed sites the decline is less severe. The BII of secondary vegetation depends on age, with sites with younger growth showing a lower BII than mature vegetation. We conclude that land‐use change has reduced local soil biodiversity worldwide, and this further supports the proposition that soil biota should be considered explicitly when using global models to estimate the state of biodiversity.
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The genome sequence of the false flower beetle, Anaspis frontalis (Linnaeus, 1758)We present a genome assembly from a specimen of <ns5:italic>Anaspis frontalis</ns5:italic> (the false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The assembly contains two haplotypes with total lengths of 808.55 megabases and 802.05 megabases. Most of haplotype 1 (95.81%) is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.
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The genome sequence of the click beetle, Ampedus sanguinolentus sanguinolentus (Schrank, 1776)We present a genome assembly from a female specimen of <ns3:italic>Ampedus sanguinolentus sanguinolentus</ns3:italic> (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.
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The genome sequence of a longhorn beetle, Rhagium mordax (Degeer, 1775)We present a genome assembly from an individual female specimen of <ns5:italic>Rhagium mordax</ns5:italic> (longhorn beetle; Arthropoda; Insecta; Coleoptera; Cerambycidae). The genome sequence has a total length of 775.60 megabases. Most of the assembly (99.53%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.68 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,937 protein-coding genes.
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The genome sequence of the false flower beetle, Anaspis regimbarti Schilsky, 1895We present a genome assembly from a specimen of <ns3:italic>Anaspis regimbarti</ns3:italic> (the false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The genome sequence has a total length of 457.61 megabases. Most of the assembly (99.89%) is scaffolded into 8 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length.
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First record of Calyptotheca alexandriensis (Cheilostomatida, Lanceoporidae) from Ras Juddi (Pasni) Makran coast, Northern Arabian SeaThe available information regarding bryozoans in coastal areas of Pakistan is limited. This research paper presents the first record of Calyptotheca alexandriensis from Ras Juddi (Pasni) along the Makran coast, and the second record globally of this species. This species was first reported in the Eastern Harbor of Alexandria, Egypt, as a distinctive deep orange erect foliaceous bryozoan and was observed abundantly on various hard substrates, such as rocks, ropes, metal pipes supporting marina piers, and ship hulls. The discovery adds a new record of the family, Lanceoporidae, and genus, Calyptotheca, to the bryozoan fauna of Pakistan, expanding its known distribution to the Northern Arabian Sea. The present specimens were collected during December 2021–October 2022 and subjected to detailed taxonomic analysis using light microscopy and scanning electron microscopy (SEM). This study contributes to the understanding of bryozoan biodiversity in the region and highlights the potential for further discoveries along the unexplored coastal areas of Pakistan.
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Pollinator-flower interactions in gardens during the COVID-19 pandemic lockdown of 2020During the main COVID-19 global pandemic lockdown period of 2020 an impromptu set of pollination ecologists came together via social media and personal contacts to carry out standardised surveys of the flower visits and plants in gardens. The surveys involved 67 rural, suburban and urban gardens, of various sizes, ranging from 61.18° North in Norway to 37.96° South in Australia, resulting in a data set of 25,174 rows, with each row being a unique interaction record for that date/site/plant species, and comprising almost 47,000 visits to flowers, as well as records of flowers that were not visited by pollinators, for over 1,000 species and varieties belonging to more than 460 genera and 96 plant families. The more than 650 species of flower visitors belong to 12 orders of invertebrates and four of vertebrates. In this first publication from the project, we present a brief description of the data and make it freely available for any researchers to use in the future, the only restriction being that they cite this paper in the first instance. The data generated from these global surveys will provide scientific evidence to help us understand the role that private gardens (in urban, rural and suburban areas) can play in conserving insect pollinators and identify management actions to enhance their potential.
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Subfossil cyclostome bryozoans from Daidokutsu submarine cave, Okinawa, JapanA sediment core (Core 19) taken in Daidokutsu cave on Ie Island, Okinawa, spans the last 7,000 years. The sampling of multiple taxa from this submarine cave has been aimed at understanding the Holocene history of biodiversity and ecological dynamics. The results have already been published for ostracods, molluscs, foraminifera and cheilostome bryozoans. The current study focuses on the cyclostome bryozoan fauna, establishing a taxonomic foundation that will contribute to an understanding of responses by the bryozoan community in this cave habitat to environmental and climate changes through the Holocene. Very little has been published on modern and Quaternary fossil cyclostomes from Japan, and nearly all publications predate the routine use of scanning electron microscopy in cyclostome taxonomy. Fifteen cyclostome species are described here from Daidokutsu. Eight of these are new species, the remaining seven were identified only to the genus level. The high proportion of new species may not only reflect the uniqueness of the Daidokutsu cyclostome fauna but also the scarcity of studies on Japanese cyclostomes and the inadequacy of descriptions and figures in older publications, which make it difficult or impossible to interpret the species they describe. Unlike cyclostome cave faunas from the Mediterranean, erect cyclostomes strongly outnumber species with encrusting colonies. In addition, the secondary homonymy of Parasmittina ligulata, used for both a new species from Daidokutsu Cave and a Western Atlantic species, is resolved by renaming the Japanese species Parasmittina vieirai nom. nov.
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Disporella guada sp. nov., an erect-ramose rectangulate cyclostome (Bryozoa, Stenolaemata) from the Carribean Sea: convergent evolution in bryozoan colony morphologyThe taxonomy of cyclostome bryozoans is founded on characters of the skeleton, but molecular sequence data have increasingly shown that established higher taxa are not monophyletic. Here we describe the skeletal morphology of a new species from Guadeloupe (French West Indies) with erect ramose colonies consisting of long, curved zooids that are typical of the suborder Cerioporina among living cyclostomes. However, molecular evidence from nuclear ribosomal RNA genes 18S and 28S places the new taxon in the suborder Rectangulata, where this colony-form has not been previously recorded. It nests firmly within the genus Disporella Gray, 1848, in a strongly supported clade that also includes Plagioecia patina (Lamarck, 1816) (Tubuliporina) and the sister taxa Doliocoitis cyanea Gordon & Taylor, 2001 (Rectangulata) and Favosipora rosea Gordon & Taylor, 2001 (Cerioporina). The short and robust branches of the new Guadeloupe cyclostome, here named Disporella guada Harmelin, Taylor & Waeschenbach sp. nov., are well adapted to life in shallow rocky sites exposed to severe wave action, which appear to be its exclusive habitat.
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Fenestella and other bryozoans in the Carboniferous rocks of the British IslesAsk a geologist to name a fossil bryozoan found in the rocks of the British Isles and the most likely answer will be Fenestella. The net-like fossils of Fenestella are especially abundant in the Carboniferous Limestone (Figs 1 and 2), although the genus, as used in its broadest sense, is also present in the Silurian, Devonian and Permian deposits of Britain.
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New species and a key to members of the Geminata clade (Solanum L.; Solanaceae) in ColombiaAs 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.
