Envisaging a global infrastructure to exploit the potential of digitised collections.

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.

More than a Bit of Fun: The Multiple Outcomes of a Bioblitz.

Bioblitzes are a popular approach to engage people and collect biodiversity data. Despite this, few studies have actually evaluated the multiple outcomes of bioblitz activities. We used a systematic review, an analysis of data from more than 1000 bioblitzes, and a detailed analysis of one specific bioblitz to inform our inquiry. We evaluated five possible bioblitz outcomes, which were creating a species inventory, engaging people in biological recording, enhancing learning about nature, discovering a species new to an area, and promoting an organization. We conclude that bioblitzes are diverse but overall effective at their aims and have advantages over unstructured biodiversity recording. We demonstrate for the first time that bioblitzes increase the recording activity of the participants for several months after the event. In addition, we provide evidence that bioblitzes are effective at bringing people and organizations together to build communities of professionals and amateurs, critical for conserving and protecting biodiversity.

Promoting scientific literacy in evolution through citizen science.

Evolutionary understanding is central to biology. It is also an essential prerequisite to understanding and making informed decisions about societal issues such as climate change. Yet, evolution is generally poorly understood by civil society and many misconceptions exist. Citizen science, which has been increasing in popularity as a means to gather new data and promote scientific literacy, is one strategy through which people could learn about evolution. However, despite the potential for citizen science to promote evolution learning opportunities, very few projects implement them. In this paper, we make the case for incorporating evolution education into citizen science, define key learning goals, and suggest opportunities for designing and evaluating projects in order to promote scientific literacy in evolution.

Hybridization of Oxalis corniculata and O. dillenii in their non-native range.

Many species have been introduced beyond their native ranges and many have become global weeds. Human mediated dispersal has removed the geographic isolation of these species, reversing millions of years of independent evolution. Examples are the Oxalis species in section Corniculatae where several species have become invasive. Here we characterize and formally describe a hybrid between O. dillenii and O. corniculata, which occurs spontaneously in Belgium and Japan. Oxalis corniculata is probably native to Japan, but both species are alien to Belgium and O. dillenii is native to North America. We formally name this hybrid as Oxalis × vanaelstii. Although this hybrid is sterile, it is nevertheless vigorous and perennial. Both parent species grow as weeds in gardens; therefore, it is likely to be more common than currently appreciated in countries where these species co-occur.

Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers.

Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers (Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.

From leaf to label: A robust automated workflow for stomata detection.

Plant leaf stomata are the gatekeepers of the atmosphere-plant interface and are essential building blocks of land surface models as they control transpiration and photosynthesis. Although more stomatal trait data are needed to significantly reduce the error in these model predictions, recording these traits is time-consuming, and no standardized protocol is currently available. Some attempts were made to automate stomatal detection from photomicrographs; however, these approaches have the disadvantage of using classic image processing or targeting a narrow taxonomic entity which makes these technologies less robust and generalizable to other plant species. We propose an easy-to-use and adaptable workflow from leaf to label. A methodology for automatic stomata detection was developed using deep neural networks according to the state of the art and its applicability demonstrated across the phylogeny of the angiosperms.We used a patch-based approach for training/tuning three different deep learning architectures. For training, we used 431 micrographs taken from leaf prints made according to the nail polish method from herbarium specimens of 19 species. The best-performing architecture was tested on 595 images of 16 additional species spread across the angiosperm phylogeny.The nail polish method was successfully applied in 78% of the species sampled here. The VGG19 architecture slightly outperformed the basic shallow and deep architectures, with a confidence threshold equal to 0.7 resulting in an optimal trade-off between precision and recall. Applying this threshold, the VGG19 architecture obtained an average F-score of 0.87, 0.89, and 0.67 on the training, validation, and unseen test set, respectively. The average accuracy was very high (94%) for computed stomatal counts on unseen images of species used for training.The leaf-to-label pipeline is an easy-to-use workflow for researchers of different areas of expertise interested in detecting stomata more efficiently. The described methodology was based on multiple species and well-established methods so that it can serve as a reference for future work.

Century-long apparent decrease in intrinsic water-use efficiency with no evidence of progressive nutrient limitation in African tropical forests.

Forests exhibit leaf- and ecosystem-level responses to environmental changes. Specifically, rising carbon dioxide (CO2 ) levels over the past century are expected to have increased the intrinsic water-use efficiency (iWUE) of tropical trees while the ecosystem is gradually pushed into progressive nutrient limitation. Due to the long-term character of these changes, however, observational datasets to validate both paradigms are limited in space and time. In this study, we used a unique herbarium record to go back nearly a century and show that despite the rise in CO2 concentrations, iWUE has decreased in central African tropical trees in the Congo Basin. Although we find evidence that points to leaf-level adaptation to increasing CO2 -that is, increasing photosynthesis-related nutrients and decreasing maximum stomatal conductance, a decrease in leaf δ13 C clearly indicates a decreasing iWUE over time. Additionally, the stoichiometric carbon to nitrogen and nitrogen to phosphorus ratios in the leaves show no sign of progressive nutrient limitation as they have remained constant since 1938, which suggests that nutrients have not increasingly limited productivity in this biome. Altogether, the data suggest that other environmental factors, such as increasing temperature, might have negatively affected net photosynthesis and consequently downregulated the iWUE. Results from this study reveal that the second largest tropical forest on Earth has responded differently to recent environmental changes than expected, highlighting the need for further on-ground monitoring in the Congo Basin.

Evolutionary trends in the distylous genus Pulmonaria (Boraginaceae): Evidence of ancient hybridization and current interspecific gene flow.

The distylous genus Pulmonaria contains approximately 18 species that are widely distributed across Eurasia. Previous studies have shown that species delimitation in the genus is problematic, but have not yet explored the evolutionary history of the genus. Premating reproductive barriers between European species appear to be weak, as several species have strongly overlapping distribution areas, flower at the same time and share the same pollinators, suggesting that hybridization may have contributed to the evolutionary history of Pulmonaria. To test this hypothesis, phylogenetic analyses of nuclear ITS and plastid data (rps16, trnH-psbA, rpl16) from 48 allopatric and four sympatric populations were performed to (1) provide a molecular phylogeny for nine of the most common Pulmonaria species in Europe, (2) detect current and ancient hybridization events, and (3) assess the contribution of hybridization versus incomplete lineage sorting to the inferred phylogenetic patterns. Our results showed that gene trees displayed widespread, strongly supported incongruence associated with the conflicting position of hybrid samples rather than incomplete lineage sorting. Evidence was found of different degrees of hybridization, ranging from current interspecific gene flow at secondary contact zones to introgression at the population level and at least one event of hybrid speciation. Overall, these results suggest that hybridization and introgression were - and could still be - important processes affecting speciation in the genus Pulmonaria.

Differences in fine-scale spatial genetic structure across the distribution range of the distylous forest herb Pulmonaria officinalis (Boraginaceae).

BACKGROUND: Geographical ranges of plants and their pollinators do not always entirely overlap and it has been suggested that the absence of specialized pollinators at range margins may induce changes in mating systems. Because a species' mating system is known to have a considerable effect on within-population pollen movement, the extent of fine-scale spatial genetic structure (SGS) can be expected to differ between populations located at different parts of their geographical range. To test this prediction, we compared the fine-scale SGS between two core and two disjunct populations of the distylous forest herb Pulmonaria officinalis. Because in disjunct populations of this species the heteromorphic self-incompatibility system showed relaxation in the long-styled morph, but not in the short-styled morph, we also hypothesized that the extent of fine-scale SGS and clustering differed between morphs. RESULTS: Spatial autocorrelation analyses showed a significant decrease in genetic relatedness with spatial distance for both core and disjunct populations with the weakest SGS found in one of the core populations (Sp = 0.0014). No evidence of stronger SGS in the long-styled morph was found in the center of the range whereas one disjunct population showed a significantly (P = 0.029) higher SGS in the long-styled morph (SpL = 0.0070) than in the short-styled morph (SpS = 0.0044). CONCLUSIONS: Consistent with previous analyses on distylous plant species, we found weak, but significant spatial genetic structure. However, the extent of SGS varied substantially between populations within regions, suggesting that population characteristics other than mating system (e.g. local pollinator assemblages, population history) may be as important in determining variation in SGS.

Strong differences in genetic structure across disjunct, edge, and core populations of the distylous forest herb Pulmonaria officinalis (Boraginaceae).

PREMISE OF THE STUDY: Populations at the edge of a species' distribution area are often small and have low levels of gene flow resulting in lower genetic variation and higher differentiation compared to core populations. This study examined genetic variation among populations of the distylous temperate forest herb Pulmonaria officinalis located in the core, the edge, and outside the species' main distribution range. METHODS: We compared patterns of genetic variation for eight microsatellite loci between disjunct (Belgium), edge (western Germany), and core (eastern Germany) populations of P. officinalis. KEY RESULTS: Disjunct populations contained only a subset of alleles found in edge and core populations and had significantly lower within-population genetic variation. No significant differences, however, in within-population genetic variation were found between edge and core populations, except for allelic and genotypic richness. Genetic differentiation was highest among disjunct (F(ST) = 0.11) and lowest among core populations (F(ST) = 0.03). Significant (P < 0.01) isolation by distance was found for disjunct and edge populations (r(M) = 0.29 and 0.50, respectively), but not for core populations (r(M) = 0.18). CONCLUSIONS: The results are best interpreted from a "dynamic range" point of view in which the observed low levels of genetic diversity and high genetic differentiation in disjunct populations are best explained through historical processes, most likely the introduction of the species in medieval times. Lower levels of gene flow caused by the pronounced fragmentation of forests in Belgium may further have contributed to the genetic structure of P. officinalis in these disjunct populations.

Biased morph ratios and skewed mating success contribute to loss of genetic diversity in the distylous Pulmonaria officinalis.

BACKGROUND AND AIMS: In heterostylous plant species, skewed morph ratios are not uncommon and may arise from a range of factors. Despite the recognized importance of skewed morph ratios on overall reproductive success within populations, little is known about the impact of skewed morph ratios on population genetic diversity and differentiation in heterostylous species. This study specifically aimed to clarify the effect of population size and morph bias on population genetic diversity and differentiation in the temperate forest herb Pulmonaria officinalis. This species is characterized by a distylous breeding system and shows morph-specific differences in reproductive success. METHODS: Genetic diversity was determined for 27 P. officinalis populations in northern Belgium by using eight recently developed microsatellite markers. Multiple regressions were used to assess the relationship between genetic diversity, morph bias and population size, and F(ST)-values were calculated for short- and long-styled morphs separately to study genetic differentiation as a function of morph type. KEY RESULTS: For all genetic measures used, morph bias was more important in explaining patterns of genetic diversity than population size, and in all cases patterns of population genetic diversity followed a quadratic function, which showed a symmetrical decrease in genetic diversity with increasing morph bias. However, probably due to the reproductive advantage of L-morphs relative to S-morphs, maximum genetic diversity was found in populations showing an excess of L-morphs (60·7 % L-morph). On the other hand, no significant difference in pairwise genetic distances between populations was observed between L- (0·107) and S-morphs (0·106). CONCLUSIONS: Our results indicate that significant deviations from equal morph ratios not only affect plant reproductive success but also population genetic diversity of heterostylous plant species. Hence, when defining conservation measures for populations of heterostylous plant species, morph ratios should be considered as an important trait affecting their long-term population viability.