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Limited Niche Change After Dispersal From Africa by Leopards (Panthera pardus) Hundreds of Thousands of Years AgoABSTRACT Aim The leopard (Panthera pardus) is a generalist species inhabiting Africa and Asia, reflecting dispersal from an ancestral African range. When dispersal events occur, they can entail ecological differentiation and local adaptation. This study compares the bioclimatic niches of African and Asian leopard subspecies, to investigate whether they retained their ancestral ecology during dispersal from Africa, or adapted to novel conditions and shifted niche. Location Africa and Eurasia. Methods We assembled a database of leopard presences from public resources and associated them with bioclimatic variables to identify which are relevant in predicting the species' distribution. We constructed a species distribution model and compared distributions predicted from models based on presences from all subspecies, versus models built only using African leopard records. Finally, we used multivariate analysis to visualise the niche occupied by each subspecies in climate space, and calculated overlaps to assess ecological differentiation. Results The species distribution model trained only on African occurrences predicted most of the Asian range, but not the extension into more extreme environments such as the colder areas inhabited by several Northern Asian subspecies, and seasonal and rugged areas inhabited by Persian leopards. Niche overlaps suggest that Asian subspecies mostly retained their ancestral niche, but in some cases started to use climatic conditions that are not found in Africa. The Persian leopard is the only subspecies for which this expansion represents most of its current niche. Main Conclusions Despite some expansion into high altitude, seasonal environments in Northern Asian populations, the results suggest generally limited adaptation to novel climates after dispersal from Africa and little ecological differentiation among Asian leopard populations. This finding complements recent genetic studies that suggest limited genetic differentiation among Asian leopards. Resolving the relationships between taxonomy and biological differentiation is important due to its relevance for the conservation of the species.
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A multi-model approach to the spatial and temporal characterization of the African Humid PeriodDuring the last c. 20,000 years, African climates experienced temperature shifts related to the last period of global deglaciation and moisture availability changes that defined what has become known as the African Humid Period (AHP) c. 14,800–5500 years ago. However, spatio-temporal variations in climate, and the mechanisms behind them, across Africa remain poorly defined and debated. Here, we first characterize climatic change across tropical Africa (15°N to 15°S) over the last c. 20,000 years based on two independent site-specific modelling approaches at nine locations, using: (i) probability-based reconstructions based on pollen data from nine previously published pollen records, and (ii) climate simulation-based reconstructions based on mechanistic models of the Earth system. Trends in past climate change per site were found to be similar between the two modelling approaches; however, estimates of precipitation were higher in the pollen-based reconstructions when compared with those from the mechanistic model. Given the overall similarity between the two modelling approaches at the sites, we then used the mechanistic model to produce maps of past climate across Africa at 1000-year time slices. Interrogation of the model supports previous suggestions that the AHP in the west was driven by increasing precipitation (c. 13,000 years ago). In the eastern and southern portions of the study region, the AHP signal is more complex, likely driven by the interplay between different climate mechanisms; with the onset of the wettest AHP conditions in eastern Africa not commencing until c. 9000 years ago.
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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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Hominin glacial-stage occupation 712,000 to 424,000 years ago at Fordwich Pit, Old Park (Canterbury, UK)Abstract Few high-latitude archaeological contexts are older than marine isotope stage (MIS) 15 and even fewer provide evidence of early human occupation during a glacial period. New discoveries at Old Park, Canterbury (UK), provide evidence of both the oldest accessible artefact-bearing sediment in northern Europe and cold-stage adaptation. Radiometric and palaeomagnetic dating places the earliest suggested occupation of this site between 773 thousand years ago (ka) and 607 ka, with hominin presence inferred during MIS 17–16. Two additional artefact-bearing stratigraphic units, dated to around 542 ka and 437 ka, strongly align with the MIS 14 and 12 cold stages, respectively. The latter unit contains convincing evidence of glacial-stage occupation by Acheulean hominins; fresh, unabraded flakes (including biface-thinning) between clearly defined glacial-aged sediments displaying mixed grassland palaeoenvironmental evidence. An historically collected assemblage of more than 330 handaxes is argued to be derived from both the MIS 17–16 and MIS 12 sediments, providing evidence of the earliest known Acheulean bifaces in northern Europe, and re-occupation by Acheulean populations 200,000 years later. Together, Old Park provides evidence for Lower Palaeolithic hominins reoccupying a location over several mid-Pleistocene MIS cycles, early human presence above 51° latitude during a glacial stage and handaxe production in northern Europe from MIS 17 to 16.
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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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Revisiting the genus Bolbosoma Porta, 1908 (Acanthocephala: Polymorphidae): host specificity, phylogeny, and species synonymizationAbstract Background: Acanthocephalans of the genus <jats:italic>Bolbosoma</jats:italic> Porta, 1908 are trophically transmitted parasites that infect marine mammals (mostly cetaceans and less frequently pinnipeds) worldwide. There are 12 species currently considered as valid; however, most records lack information on the maturity stage of the specimens. This, coupled with the scarce phylogenetic information available, hinders a correct understanding of their patterns of host specificity, evolutionary history, and taxonomy. A particularly intriguing case is that of <jats:italic>Bolbosoma vasculosum</jats:italic> (Rudolphi, 1819), which has been frequently reported in odontocetes but rarely as an adult, having been suggested to be synonymous with <jats:italic>Bolbosoma capitatum</jats:italic> (von Linstow, 1880). Methods: We used a comprehensive approach to investigate the concept of <jats:italic>Bolbosoma</jats:italic>. First, we conducted a bibliographic review of records of <jats:italic>Bolbosoma</jats:italic> spp. to clarify which are the final hosts for each species. We paid particular attention to <jats:italic>B. vasculosum</jats:italic>, using morphological and molecular analyses to compare it with <jats:italic>B. capitatum</jats:italic>. Second, we characterized the complete mitochondrial genome of <jats:italic>Bolbosoma balaenae</jats:italic> (Gmelin, 1790), <jats:italic>Bolbosoma turbinella</jats:italic> (Diesing, 1851), <jats:italic>B. capitatum</jats:italic>, and <jats:italic>B. vasculosum</jats:italic>. Then, we reconstructed the phylogenetic relationships of <jats:italic>Bolbosoma</jats:italic> spp. and related taxa using full mitochondrial genomes (or only <jats:italic>cox1</jats:italic> when full mitogenomes were unavailable) and nuclear ribosomal genes (18S and 28S). Results: Bolbosoma</jats:italic> spp. exhibit high specificity for cetaceans, with no confirmed records of adult specimens in other host groups. Within this genus, <jats:italic>B. vasculosum</jats:italic> appears to be conspecific with <jats:italic>B. capitatum</jats:italic> based on both morphological and molecular evidence. This species shows high affinity to odontocetes, while the remaining species are specific to mysticetes. Phylogenetic analyses showed strong support for the monophyly of <jats:italic>Bolbosoma</jats:italic> spp., which appeared as sister taxa to <jats:italic>Corynosoma</jats:italic> spp. and <jats:italic>Andracantha</jats:italic> spp.. The resulting topology aligns with the patterns of specificity indicated by host records, revealing two distinct clades for species specific to odontocetes and mysticetes, respectively. Conclusions: The phylogenetic relationships obtained support the hypothesis that the association of <jats:italic>Bolbosoma</jats:italic> spp. with cetaceans originated through a host-switching event from aquatic birds.
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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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Redescription of Mesoschendyla javanica (Attems, 1907) and its first records from Borneo (Chilopoda, Geophilomorpha, Schendylidae)The geophilomorph Mesoschendyla javanica (Attems, 1907) was originally described from a small number of males collected from bat guano in Tjompea (Ciampea), Java. Subsequently, no additional material was identified. The type series remained the only specimens belonging to this genus known from Asia. Mesoschendyla javanica is re-discovered 118 years after its original description amongst centipedes collected from soil cores taken during the 1977–1978 Royal Geographical Society Gunung Mulu Expedition to Sarawak (Borneo, East Malaysia) and is deposited in the collection of the Natural History Museum (London). The new material comprising 49 specimens, amongst which are the first known females, is described and illustrated, shedding light on intraspecific morphological variation. The syntypes and sole previously available specimens are redescribed and illustrated, completing the summary original description of the species. Ecological and biogeographical notes are provided for Sarawak specimens.
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Phytochemical, Antioxidant and Anticancer Properties of Ayusip (Vaccinium uliginosum L.) from Benguet Province, PhilippinesTraditional medicinal knowledge remains an important source of healthcare for many communities in the Philippines, particularly in rural and Indigenous areas where access to modern treatments is limited. In this context, Vaccinium uliginosum (locally known as Ayusip), a plant used by indigenous peoples in Tublay, Benguet Province, has drawn interest due to its reported therapeutic applications for ailments such as cough, flu, and even cancer. This study investigates the cytotoxic properties of Ayusip, aiming to provide scientific validation for its traditional use and assess its potential as a source of bioactive compounds for cancer treatment. Leaves of V. uliginosum were collected, identified, and subjected to methanol extraction, with further partitioning using n-hexane and ethyl acetate. Phytochemical analysis indicated high levels of flavonoids, saponins, steroids, and tannins. Quantification showed significant phenolic (24.58±8.11 GAE mg/g) and flavonoid (121.38±14.04 QE mg/g) content. Antioxidant testing (DPPH assay) revealed strong activity (97.86±1.33%) at 25 mg/mL. The cytotoxicity of V. uliginosum was assessed against normal embryonic lung fibroblasts (MRC-5) and cancer cell lines HCT-116 (colorectal) and A549 (lung adenocarcinoma) using the MTT assay. Results showed that only the n-hexane extract was toxic to MRC-5 cells at high concentrations, while methanol and n-hexane extracts were highly cytotoxic to HCT-116 cells. In A549 cells, only n-hexane extract exhibited cytotoxicity. These findings suggest that V. uliginosum has promising cytotoxic effects, particularly at higher concentrations, with notable activity against HCT-116 cells. Interestingly, its cytotoxicity is biphasic: high concentrations induce maximum toxicity, whereas lower concentrations may encourage cell proliferation. Overall, this study offers insights into the cytotoxic potential of V. uliginosum, a traditionally used plant among Benguet’s IPs, highlighting its potential medicinal value.
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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.
