Species In Britain Research Articles

Population status and ecology of the globally threatened liverwort Marsupella profunda Lindb. in Britain

ABSTRACT Introduction Marsupella profunda Lindb. is known from Britain, Portugal and Macaronesia. Its population status and ecology in Britain were investigated. Methods An inventory of records of Marsupella profunda was prepared, and surveys were conducted at a subset of sites. Population size was measured by counts of ‘individual-equivalents’, defined as occupied 1 m grid cells. Habitat and community composition were recorded by relevés. Key results and conclusions Marsupella profunda is confined to habitat created by china clay quarrying, and mostly occurs on kaolinised granite. It is one of the earliest colonists of this substrate. The longevity of habitat patches is limited mainly by competitive exclusion by other bryophytes and excessive shade from scrub development. It has been recorded from six sites in West Cornwall but presently survives at only one of these, where it will likely become extinct within the next 20 years due to vegetation succession. In East Cornwall, an enormous complex of active and disused quarries within the St Austell China Clay Region supports a large population (10,000–20,000 individual-equivalents), but this is declining because china clay production has decreased greatly over the past 30 years. Attempts to conserve the species by the special protection of areas of land have failed because the quarrying process that originally supplied fresh suitable substrate no longer operates in these areas, habitat management measures have been insufficient, and scrub development has progressed. The future of the species in Britain depends on the uncertain future of commercial quarrying in areas of kaolinised granite in Cornwall.

A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project.

Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.

COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

The microclimate occupied by the hyperoceanic liverwort Leptoscyphus cuneifolius (Hook.) Mitt. within a temperate rain forest in Wales

ABSTRACT Introduction Because climate change risks serious negative impacts on drought-sensitive species in Britain, in the short as well as the long term, the microclimate occupied by the hyperoceanic liverwort Leptoscyphus cuneifolius within a temperate rain forest in Wales was investigated. Methods At Coed y Rhygen, Gwynedd, Wales, 10 trees occupied by the liverwort were randomly selected, and its abundance was measured on the southerly and northerly aspect of each trunk. Data loggers were installed to measure temperature, relative humidity and illuminance on both aspects, from 1 January 2020 to 31 December 2022. Temperature and relative humidity values were used to calculate vapour pressure deficit (VPD). Bootstrap paired t-tests were used to test for significant differences in the mean number of locations of Leptoscythus cuneifolius on the southerly versus northerly aspects of trunks, and in the monthly mean values of temperature, VPD and illuminance on the southerly versus northerly aspects. Results and conclusions Leptoscyphus cuneifolius is significantly more abundant on the northerly aspect of trunks, and the microclimate that it occupies is dynamic, both spatially and temporally. In early spring, a sharp peak occurs in solar radiation and VPD, especially on the southerly aspect, caused by the altitude of the sun rising from its winter low and the subsequent emergence of the deciduous forest leaf canopy. Further study is required to understand the effects of the macroclimate on the microclimate occupied by hyperoceanic bryophytes in temperate rain forest, and to what extent this habitat may provide a refuge from climate change.

Multiple introductions and human-aided dispersal of the UK’s most widespread non-native amphibian

The alpine newt Ichthyosaura alpestris has achieved a widespread distribution as a non-native (alien) species in Britain since its initial introduction over a century ago, but the patterns of its release and subsequent dispersal have never yet been collectively analysed. We employed a multi-disciplinary combination of methods, using geographic profiling to estimate the likely number and locations of introductions, and mitochondrial DNA polymorphisms to investigate the likely geographic source of primary introductions, including the potential role of the pet trade. In parallel we used population genetic analysis and coalescence-based modelling to infer the demographics and directionality of dispersal from founding populations. Our results show that alpine newts have been released at multiple sites. We found a close resemblance between patterns of mtDNA haplotypes in the pet trade and those of established alpine newt populations, suggesting a relationship between trade, releases, and dispersal. Results from demographic modelling using Approximate Bayesian Computation are also consistent with multiple independent introductions with limited local dispersal, and additionally suggest that releases may occur from intermediate sources, such as captive populations. Our results support the hypothesis that deliberate human activity is largely responsible for both introductions of alpine newts into the UK and their wider dispersal post-introduction. The likely involvement of the international pet trade highlights the risk that ongoing releases of I. alpestris may expose native species to pathogens, whether pre-existing or novel.

COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project.

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

High mountain trees: altitudinal records recently broken for eleven different tree species in Britain

In 2022 a project was initiated utilising citizen science to document observations of trees growing in Britain above 900 m. This focused recording effort contributed to eleven new altitudinal records for tree species in this country, including Sorbus aucuparia at 1150 m and Picea sitchensis at 1125 m (both East Inverness-shire, v.c.96). Some of these observations involved increases of at least 200 m above previous known altitudinal limits. The new records were a mix of small, stunted plants not expected to reach maturity in these extreme environments, as well as arctic-alpine Salix shrubs adapted to low temperatures and exposed conditions. Although these findings are currently too restricted to draw broad conclusions on the impacts of climate warming and land management on tree colonisation in mountain environments, long-term data collection may allow an analysis of drivers of change in the future. Out of a total of 72 tree records above 900 m collated by the author in 2022, 56% were Picea sitchensis, highlighting the ability of this neophyte to spread into high elevation habitats. The project has been useful for generating public interest in biological recording at and above the altitudinal treeline, and the continuation of such work will assist with mountain woodland restoration projects for a variety of ecologically important taxa and plant communities.

The identification and distribution of Sphagnum balticum (Russow) C.E.O.Jensen in Britain

ABSTRACT Introduction The aims of this study were to help clarify the identification of Sphagnum balticum in Britain, to review its distribution, and to investigate the possible presence of hybrids between it and either S. cuspidatum or S. fallax. Methods All sites at which Sphagnum balticum has been recorded recently in Britain were visited in 2020, and a search made for it and other species with which it could be confused, together with possible hybrids. Samples were collected when suitable material was found. DNA was extracted from 31 shoots, each representing one field sample. Fifteen microsatellites that have been developed for Sphagnum species were amplified and genotyped. The genetic structure of the data was investigated using principal coordinate analysis and cluster analysis. Results The results of the genetic analysis support the recognition of four taxa, which corresponded to four morphologically identified taxa: Sphagnum angustifolium, S. balticum, S. cuspidatum and S. fallax. There was no evidence of hybrids. Over-recording of S. balticum has occurred in Britain due to confusion with some forms of S. cuspidatum and S. fallax, which can exhibit some morphological characters usually used to identify S. balticum. An illustrated identification key is provided to help solve this problem. Conclusions Sphagnum balticum is a very rare species in Britain that has undergone a decline due to habitat destruction and alteration. It is presently known to survive at only three sites, of which two are within protected areas.

A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.

Genetic diversity and differentiation of isolated rear‐edge populations of a cold adapted butterfly, Erebia aethiops, in Britain

Abstract Rear‐edge populations of cold‐adapted species are highly vulnerable to climate change, their adaptations maybe critical for the persistence of the species as a whole. Using AFLP, we investigated population genetic diversity and differentiation of Scotch argus (Erebia aethiops), a cold‐adapted butterfly, comparing isolated rear‐edge and core populations in Britain, a relict part of the species range. We also examined genetic differences among sub‐populations and dispersal distances conducting a mark‐release‐recapture (MRR) study at the rear‐edge. Genetic diversity was higher in the isolated rear‐edge populations than populations at the core of the range and declined with latitude, supporting the idea that current differences in genetic diversity levels across Britain are likely the result of historical range changes after the last glaciation. Populations were genetically differentiated among regions, meaning that losing the isolated rear‐edge populations may prove detrimental for the survival of the species in Britain, as these populations are likely to be better adapted to warmer climates. We found that the largest population at the rear‐edge is genetically robust, with gene flow among patches, likely maintained by males as indicated by the higher dispersal distances recorded for males in the MRR, but colonisation of empty patches is constrained by females' low mobility. Our results highlight that isolated populations at the rear‐edge of cold‐adapted species should be considered of high conservation priority, as they hold higher levels of genetic diversity and differentiation which may prove to be key for the survival of these species under global warming.

Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Sequencing our seas

The Darwin Tree of Life (DToL) project has been established to collect all eukaryote species in Britain and Ireland for genomic sequencing. New tech developments have enabled high-quality genomic data to be a feasible outcome for some of Earth’s smallest inhabitants. This project will create a new resource of data open to all, which will contain the blueprint of thousands of organisms, holding the key to the evolutionary histories of understudied single-cell protists alongside more well-understood animals like the grey seal. This ambitious project is a collaboration of experts from different geographic and intellectual areas. It will provide the templates for new ways of working and uncover new scientific ground. In a world struggling under the threat of ecological collapse, this project will provide new bio-tech and engineering information to aid our understanding and management of natural ecosystems and the creatures which create them. The Marine Biological Association UK, based in Plymouth, is currently in the process of collecting marine organisms for the project. The marine environment has not been as well studied as terrestrial environments, and this offers a huge opportunity to expand our understanding of this underexplored realm and the creatures that live there, as well as providing context and detail to marine science which will provide new insights to marine research.

Book Review

Book Review

Differential outcomes of novel plant-herbivore associations between an invading planthopper and native and invasive Spartina cordgrass species

Non-native plants may benefit, briefly or permanently, from natural enemy release in their invaded range, or may form novel interactions with native enemy species. Likewise, newly arrived herbivores may develop novel associations with native plants or, where their hosts have arrived ahead of them, re-establish interactions that existed previously in their ancestral ranges. Predicting outcomes from this diversity of novel and re-established interactions between plants and their herbivores presents a major challenge for invasion biology. We report on interactions between the recently arrived invasive planthopper Prokelisia marginata, and the multi-ploidy Spartina complex of four native and introduced species in Britain, each representing a different level of shared evolutionary history with the herbivore. As predicted, S. alterniflora, the ancestral host, was least impacted by planthopper herbivory, with the previously unexposed native S. maritima, a nationally threatened species, suffering the greatest impacts on leaf length gain, new leaf growth and relative water content. Contrary to expectations, glasshouse trials showed P. marginata to preferentially oviposit on the invasive allododecaploid S. anglica, on which it achieved earlier egg hatch, faster nymphal development, larger female body size and greatest final population size. We suggest P. marginata is in the process of rapid adaptation to maximise its performance on what is now the most abundant and widespread host in Britain. The diversity of novel and re-established interactions of the herbivore with this multi-ploidy complex makes this a highly valuable system for the study of the evolutionary ecology of plant–insect interactions and their influence on invasion dynamics.

DNA barcodes for UK freshwater arthropod species: coverage, quality and implications

DNA-based identification methods have been shown to have high detection capability and reduced costs compared to traditional methods and can also enable the detection of species that might be missed using traditional methods (e.g. rare species, cryptic species, larval stages). The success of DNA-based identification is dependent on the ‘DNA barcodes’ of target species being present in a barcode reference database. In order to use DNA-based identification methods to assess and monitor UK freshwater arthropods for biodiversity and ecological quality assessments, it is vital that comprehensive reference databases are available. Incomplete reference databases result in many sequences derived from metabarcoding not being assigned to species. Two current projects aim to create collections of high-quality sequences from expertly identified specimens of UK species. The Darwin Tree of Life project aims to sequence the genomes of all the eukaryotic species in Britain and Ireland and FreshBase aims to create a genomic reference collection for UK freshwater invertebrates. The Barcode of Life Data System (BOLD) is one of the main reference databases for animal barcodes. Prioritising the sequencing of UK freshwater arthropod species that are not yet represented in BOLD, would enable more complete identification of UK freshwater biodiversity using metabarcoding and would enable the development of primers to target specific arthropod groups or species. We analysed the coverage of UK freshwater arthropod species in BOLD. Our analyses show that coverage varies between taxonomic groups and large proportions of sequences in some orders are only represented by privately stored sequences in BOLD. Analyses of intra- and inter-specific variation in sequences stored in BOLD show that misidentifications or errors can reduce the barcode gap in some species which could cause difficulties in accurately identifying sequences derived from metabarcoding. Representation in BOLD by specimens from the UK is extremely low and analyses show that high geographic variation in sequences in some species could be important for accurate DNA-based identification of UK species. Our results have implications for prioritising the sequencing of UK freshwater arthropods and for the quality control of stored sequences in order to reduce the occurrence of misidentifications and errors that could impact the accuracy of DNA-based identification.

Brexit and invasive species: a case study of the cognitive and affective encoding of ‘abject nature’ in contemporary nationalist ideology

ABSTRACT The article addresses the issue of invasive non-native species in Britain and its proximate cultural and political implications. Notably, it charts the co-option of this issue by sections of the nationalist press since the escalation of the European migrant crisis in 2015 and their strategic metaphorical alignment of human and extra-human migration, particularly in the period surrounding the Brexit referendum. These reports serve as the basis for a wider conjunctural analysis; assessing contemporary figurations of nature in nationalist ideology, the ideological importance of such metaphor framing techniques, and the common speculation that climate anxieties are being displaced onto new forms of anti-immigrant racism. Contextualizing the reports against a broader history of deploying metaphors of ‘abject nature’ in xenophobic and racist discourse, the article traces the outline of an emergent politics of abjection shaped by historically specific constructions of both race and nature.

Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia

BackgroundThe earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period.ResultsFrom these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N = 6) and D (N = 2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D.ConclusionsThe presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.

An evidence‐based assessment of the past distribution of Golden and White‐tailed Eagles across Wales

AbstractTwo species of eagles (Golden and White‐tailed) bred in Wales during prehistoric and historic times and became regionally extinct as breeding species in the mid‐1800s. They are iconic and charismatic, and discussions about reintroducing them back into the Welsh landscape have been ongoing for years. Reintroductions, however, can be risky, costly and/or contentious. To address these concerns, and to judge whether it is appropriate to reintroduce a regionally extinct species; the “International Union for Conservation of Nature (IUCN)” have produced criteria by which a proposed reintroduction can be assessed. A key criterion is that the potential reintroduction location lies within the former range of the species. In this study, we addressed this criterion by assessing the past distributions of Golden and White‐tailed Eagles within Wales. Using historic observational data, fossil/archaeological records and evidence from place‐names in the Welsh language, we demonstrated strong evidence for the presence of both of these eagle species in Wales in pre‐historic and historic times. We used kernel density functions to model the likely core distributions of each species within Wales. The resulting core distributions encompassed much of central and west‐north Wales for both species, with the White‐tailed Eagle exhibiting a wider core distribution extending into south Wales. Our results fill knowledge gaps regarding the historic ranges of both species in Britain, and support the future restoration of either or both species to Wales.

Invasion, isolation and evolution shape population genetic structure in Campanula rotundifolia.

The distribution and genetic structure of most plant species in Britain and Ireland bear the imprint of the last ice age. These patterns were largely shaped by random processes during recolonization but, in angiosperms, whole-genome duplication may also have been important. We investigate the distribution of cytotypes of Campanula rotundifolia, considering DNA variation, postglacial colonization, environmental partitioning and reproductive barriers. Cytotypes and genome size variation from across the species’ range were determined by flow cytometry and genetic variation was assessed using cpDNA markers. A common garden study examined growth and flowering phenology of tetraploid, pentaploid and hexaploid cytotypes and simulated a contact zone for investigation of reproductive barriers. Irish populations were entirely hexaploid. In Britain, hexaploids occurred mostly in western coastal populations which were allopatric with tetraploids, and in occasional sympatric inland populations. Chloroplast markers resolved distinct genetic groups, related to cytotype and geographically segregated; allopatric hexaploids were distinct from tetraploids, whereas sympatric hexaploids were not. Genome downsizing occurred between cytotypes. Progeny of open-pollinated clones from the contact zone showed that maternal tetraploids rarely produced progeny of other cytotypes, whereas the progeny of maternal hexaploids varied, with frequent pentaploids and aneuploids. The presence of distinctive hexaploid chloroplast types in Ireland, Scottish islands and western mainland Britain indicates that its establishment preceded separation of these land masses by sea-level rise c. 16 000 years BP. This group did not originate from British tetraploids and probably diverged before postglacial invasion from mainland Europe. The combination of cytotype, molecular, contact zone and common garden data shows an overall pattern reflecting postglacial colonization events, now maintained by geographic separation, together with more recent occasional local in situ polyploidisation. Reproductive barriers favour the persistence of the tetraploid to the detriment of the hexaploid.

Evidence of ecological niche shift in Rhododendron ponticum (L.) in Britain: Hybridization as a possible cause of rapid niche expansion.

Biological invasions threaten global biodiversity and natural resources. Anticipating future invasions is central to strategies for combating the spread of invasive species. Ecological niche models are thus increasingly used to predict potential distribution of invasive species. In this study, we compare ecological niches of Rhododendron ponticum in its native (Iberian Peninsula) and invasive (Britain) ranges. Here, we test the conservation of ecological niche between invasive and native populations of R. ponticum using principal component analysis, niche dynamics analysis, and MaxEnt‐based reciprocal niche modeling. We show that niche overlap between native and invasive populations is very low, leading us to the conclusion that the two niches are not equivalent and are dissimilar. We conclude that R. ponticum occupies novel environmental conditions in Britain. However, the evidence of niche shift presented in this study should be treated with caution because of nonanalogue climatic conditions between native and invasive ranges and a small population size in the native range. We then frame our results in the context of contradicting genetic evidence on possible hybridization of this invasive species in Britain. We argue that the existing contradictory studies on whether hybridization caused niche shift in R. ponticum are not sufficient to prove or disprove this hypothesis. However, we present a series of theoretical arguments which indicate that hybridization is a likely cause of the observed niche expansion of R. ponticum in Britain.