Tracking population genetic signatures of local extinction with herbarium specimens

Looking back to look ahead: the temporal dimension of conservation seed bank collections

A wealth of plant material and data is stored globally in conservation seed banks. This material represents not only a repository of plant genetic resources but also an asset for nature-based solutions (NbS), such as ecological restoration and reforestation, and research in plant science. Here, we explore the temporal and spatial dimensions of seed collections and the challenges limiting their use in NbS and research, while highlighting how they could be a source of material for adaptation and evolution studies. However, existing seed lots originally collected for conservation purposes will not be sufficient to support NbS and research on their own. We propose a long-term experimental approach that, together with new targeted collecting programmes, can leverage the temporal dimension of seed collections by carrying out repeated sampling from the same population. At the same time, we stress how these approaches will benefit from new dedicated collections holding seeds from each maternal line separately. By moving towards a bidimensional (space and time) collecting approach, conservation seed banks can go beyond long-term conservation per se and transform their collections into dynamic repositories capable of addressing pressing ecological, evolutionary, and conservation questions and help to understand and shape plant communities of the future.

Museomics of an extinct European flat oyster population

Understanding the factors that predispose species and populations to decline and extinction is a major challenge of biodiversity research. In the present study, we investigated the historical population genomics of an extinct population of the European oyster (Ostrea edulis L.) from the Wadden Sea collected between 1868 and 1888, and compared it to French and English populations sampled at the same time. Our museomic results indicate that the now-extinct population was genetically isolated from the French and English populations and showed signs of local adaptation in the form of Fst outlier loci between the Wadden Sea and the other two populations. Thus the Wadden Sea oysters may have been predisposed for extinction because they were not naturally replenished from other populations. A comparison of population-wide genomic diversity may hint towards a sudden population contraction of the Wadden Sea population, possibly being the result of stronger - or earlier - population decline in this population than in the others. In summary, our historical population genomic exploration hints at some potential causes of population decline in flat oysters from the Wadden Sea, which might have led to their extinction.

Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant-animal interactions

Premise

The importance of natural history collections in modern ecological and genetic research cannot be overstated. Herbarium specimens provide historical information that can be used to investigate community ecology, phenology, and population genetics. In this study, environmental DNA (eDNA) metabarcoding and next-generation sequencing were used to test the efficacy of detecting historical plant-animal interactions from herbarium specimen flowers.

Methods

A modified eDNA isolation method and standard Illumina sequencing protocols were used. Animal eDNA was amplified using both cytochrome c oxidase subunit I (COI) and 16S primers to increase detection probability. The relationship between specimen age (0-69 years) and target taxa read depth was also investigated.

Results

We generated and identified over 1.5 million sequences of animal taxa belonging to 29 clades (families or orders). These methods enabled the detection of taxa including birds, mammals, hymenopterans, lepidopterans, coleopterans, and taxa belonging to "intrafloral" communities. While herbarium specimens overall yielded less identifiable eDNA compared to fresh material, the age of the herbarium specimen negligibly affected the amount of target and/or non-target eDNA detected in flowers.

Discussion

With careful consideration of the types of data that may be obtained through sampling eDNA from herbarium specimens, these methods could prove valuable to future research on plant-animal interactions.

Guidelines for the effective and ethical sampling of herbaria

The use of herbaria for science and conservation is enabling greatly enhanced scopes and scales of discovery, exploration and protection of biodiversity. The availability of digital, open-access herbarium data is, perhaps counter-intuitively, expanding the use of physical collections by researchers who use digital collections to find specimens and then sample physical collections for multiomics investigations, including genomics, transcriptomics, metabolomics, proteomics and microbiomics. These investigations are leading to new scientific insights and supporting the development of conservation actions, but they come with a substantial cost: the partial or complete destruction of often irreplaceable specimens, which constitute a global heritage that should be permanently safeguarded for future reference. Here we provide a set of recommended best practices for the sustainable, equitable and ethical sampling of herbarium specimens. Our recommendations are intended for two complementary and partially overlapping audiences-users and stewards-who together build, use and protect herbarium collections.

Habitat fragmentation increases the risk of local extinction of small reptiles: A case study on Phrynocephalus przewalskii

Habitat fragmentation represents a multifaceted global conservation threat, exerting both direct and indirect effects on individual animals and communities. Reptiles, particularly smaller species with limited migratory abilities, are especially vulnerable to these changes. This study examines how small reptiles adapt their life history strategies in fragmented habitats and determines whether their responses are primarily due to phenotypic plasticity or genetic adaptation. We focused on Phrynocephalus przewalskii, analyzing body size, reproductive strategies, genetic structure, and diversity across three habitats with varying degrees of fragmentation. This study investigated the response of P. przewalskii to varying degrees of habitat fragmentation in Wuhai City, Inner Mongolia. The study compared morphological characteristics, reproductive investment, genetic diversity, and fluctuating asymmetry of P. przewalskii individuals from the sampling areas. Results showed that individuals in highly fragmented areas exhibited smaller body size, higher reproductive investment, and lower genetic diversity. Genomic analyses revealed significantly fewer SNPs, INDELs, and SVs in the highly fragmented area compared to others, with the slowest linkage disequilibrium decay rate, indicating strong environmental pressure. Furthermore, individuals in the highly fragmented area had significantly higher fluctuating asymmetry, serve as an important ecological and biological indicator reflecting habitat fragmentation. These findings demonstrated that habitat fragmentation negatively impacts the survival and reproduction of P. przewalskii, reducing its genetic diversity and adaptive potential, and increasing the risk of local extinction. This study provides crucial data for understanding the mechanisms of animal adaptation to fragmented habitats and aids in assessing species extinction risks and developing conservation strategies.

Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe

Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.

Utilising bryophyte herbarium material as a source of fungal novelty: a case study presenting new records of Bryobroma gymnomitrii (Döbbeler) Döbbeler on Gymnomitrion Corda in Britain and North America

Introduction

Bryophyte herbarium material often contains inadvertently collected bryophilous fungi preserved with their host plant tissues, providing snapshots of the biotic aspects of bryophyte ecology in space and time. During an ongoing project to study bryophilous fungi on leafy liverworts in the genus Gymnomitrion, new records of the bryophilous ascomycete Bryobroma gymnomitrii (≡ Bryomyces gymnomitrii) were discovered in herbarium material from areas in which the fungus was previously unknown. While many host vouchers were screened, the fungus was observed in only five collections. Using B. gymnomitrii as a case study, some of the advantages and limitations associated with the utility of bryophyte collections for bryo-mycological analyses are considered.

Methods

More than 400 herbarium specimens from across Europe and North America were screened for the presence of fungi by different researchers at the following four herbaria: ALA, BBSUK, NMW and OSC.

Key results and conclusions

Bryobroma gymnomitrii appears to be specific to Gymnomitrion concinnatum and G. corallioides, forming gregarious, black perithecioid fruitbodies on the lower parts of host shoots. The study expands the known distribution of the fungus from a stronghold in northern and northeastern Europe to include the Aleutian Islands in Alaska. One of the host bryophytes, G. corallioides, is threatened by deterioration of its high-altitude Arctic-montane habitats, especially along the southern parts of its range, including Britain and Ireland. Our work supports the concept that research utilising herbarium material may provide valuable, unexpected outcomes, with bryophytes as important sources of fungi that have been inadvertently collected in the past.

Genetic diversity assessment of Helichrysum arenarium (Asteraceae) for the genetic restoration of declining populations

Helichrysum arenarium (L.) Moench (Asteraceae) is a self-compatible, insect-pollinated herb occurring in sand grasslands, and is declining and endangered in many parts of its European distribution range. A recovery plan of H. arenarium has been conducted in southern Belgium, involving plant translocations. We developed multiplex genotyping protocol for nine microsatellite markers previously published for Helichrysum italicum and two newly developed microsatellite markers for H. arenarium. Eleven polymorphic loci were associated (pooled) in two multiplex panels, to assess the genetic status of the only small remaining population in Belgium and of three large German populations used as seed source for propagating transplants. The small Belgian population was characterized by high clonality, with only two, however heterozygous, genets detected. The three large German populations showed high genetic diversity (H e ranging from 0.635 to 0.670) and no significant inbreeding coefficient values, despite expectations of geitonogamous selfing. Management practices (grazing livestock) increasing seed dispersal distances, inbreeding depression at early stages of development, and mechanisms preventing or delaying selfing might be hypothesized to explain the observed patterns. The two Belgian genotypes remained within genetic variation range of German populations so that the high genetic differentiation between Belgian and German populations (F ST values ranging from 0.186 to 0.206) likely resulted from genetic drift effects and small sample size. Transplants obtained from seeds sampled from the three large source populations from Germany constitute a highly diverse, noninbred gene pool, and are thus of high genetic quality for plant translocations.

Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies

Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.

Population size affected by environmental variability impacts genetics, traits, and plant performance in Trifolium montanum L

Population size, genetic diversity, and performance have fundamental importance for ecology, evolution, and nature conservation of plant species. Despite well-studied relationships among environmental, genetic, and intraspecific trait variation (ITV), the influence of population size on these aspects is less understood. To assess the sources of population size variation, but also its impact on genetic, functional trait, and performance aspects, we conducted detailed population size estimations, assessed 23 abiotic and biotic environmental habitat factors, performed population genetic analyses using nine microsatellite markers, and recorded nine functional traits based on 260 Trifolium montanum individuals from 13 semi-dry grassland locations of Central Europe. Modern statistical analyses based on a multivariate framework (path analysis) with preselected linear regression models revealed that the variation of abiotic factors (in contrast to factors per se) almost completely, significantly explained fluctuations in population size (R 2 = .93). In general, abiotic habitat variation (heterogeneity) was not affected by habitat area. Population size significantly explained genetic diversity (N A: R 2 = .42, H o: R 2 = .67, H e: R 2 = .43, and I: R 2 = .59), inbreeding (F IS: R 2 = .35), and differentiation (G ST: R 2 = .20). We also found that iFDCV (ITV) was significantly explained by abiotic habitat heterogeneity, and to a lesser extent by genetic diversity H e (R 2 = .81). Nevertheless, habitat heterogeneity did not statistically affect genetic diversity. This may be due to the use of selectively neutral microsatellite markers, and possibly by insufficient abiotic selective pressures on habitats examined. Small T. montanum populations in nonoptimal habitats were characterized by reduced genetic and functional trait diversity, and elevated genetic inbreeding and differentiation. This indicates reduced adaptability to current and future environmental changes. The long-term survival of small populations with reduced genetic diversity and beginning inbreeding will be highly dependent on habitat protection and adequate land-use actions.

A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming

Premise

The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library.

Methods

Plants collected for the Hawaiian Plant DNA Library were simultaneously accessioned as herbarium specimens at the time of collection, from 1994-2019. Paired samples were sequenced using short-read sequencing and assessed for chloroplast assembly and nuclear gene recovery.

Results

Herbarium specimen-derived DNA was statistically more fragmented than freezer-stored DNA derived from fresh tissue, leading to poorer chloroplast assembly and overall lower coverage. The number of nuclear targets recovered varied mostly by total sequencing reads per library and age of specimen, but not by storage method (herbarium or long-term freezer). Although there was evidence of DNA damage in the samples, there was no evidence that it was related to the length of time in storage, whether frozen or as herbarium specimens.

Discussion

DNA extracted from herbarium tissues will continue to be invaluable, despite being highly fragmented and degraded. Rare floras would benefit from both traditional herbarium storage methods and extracted DNA freezer banks.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.