Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographical patterns in insular systems, but largely focused on volcanic oceanic systems. Through this study we aim to extend this work by investigating the role of late Quaternary sea-level fluctuations in shaping species richness patterns in continental shelf island systems. Focusing on the Aegean archipelago, we first reconstructed the area’s geography using published data, under three sea-level stands: 1) current; 2) median over the last nine Glacial-Interglacial cycles; 3) Late Glacial Maximum (LGM). We compiled taxon-island occupancy for angiosperms (70 islands) and centipedes (56 islands). We investigated the impact of present-day and past geographical settings on chorological groups by analysing Island Species-Area Relationships (ISARs) and using Generalized Linear Mixed Models selection based on multiple metrics of goodness-of-fit. Our results confirm that the Aegean’s geography has changed dramatically since the LGM, while the median sea-level scenario only modestly differs from the present configuration. Paleogeographical changes largely shaped Aegean plant diversity patterns, and to a lesser degree centipede species richness patterns. The LGM geographic configuration affected both native and endemic species diversity through establishing connections between land-bridge islands and the mainland. Particularly on land-bridge islands we detected supersaturation of native species and stronger underrepresentation of endemics on those same islands. Unlike oceanic islands, where the longer lasting median configuration has ample effect on the current species diversity, the shorter lasting LGM configurations promoted increased connectivity with the mainland counteracting processes promoting endemism. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems, highlighting the importance of distinguishing between them while studying biota from the perspective of historical biogeography.

Understanding the scaling between leaf size and leafing intensity is crucial for comprehending theories about light interception and leaf carbon uptake and adjustments in life history strategies. To test whether have the broad scope predictions between leaf size variation and leafing intensity on first year stem in evergreens and deciduous. A comprehensive data set of minimum (Mmin) and maximum (Mmax) leaf mass and total leaf number in twig was compiled, as well as data for the stem volume and mass. The datasets provide measurements of 123 woody species in subtropical mountain forests. Standardized major axis (SMA) analysis was used to determine the effects of the variation in leaf size (i.e., Mmin to Mmax) and the effects of different functional groups on the trade-off between leaf size and leafing intensity, i.e., the leafing intensity based on stem volume (LIV) and stem mass (LIM). Leaf size plasticity variation did not differ between evergreen and deciduous functional groups, but Mmin scaled as the 1.19 power of Mmax. Across the 123 species, the scaling exponents of the pooled data ranged between -1.14 to -0.96 for Mmin and Mmax vs. the leafing intensity based on stem volume (LIV) and from -1.24 to -1.04 for Mmin and Mmax vs. the leafing intensity based on stem mass (LIM). Across the subtropical woody species examined in this study, the results show the scaling relationship between leaf mass and leafing intensity is constrained to be ≤ -1.0. More importantly, the scopes in twig leaf size and the leafing intensity correlate with the biomass allocation to minimum and maximum leaf mass, and not sensitive to plant functional groups in subtropical mountain forests.

Ancient DNA research has developed rapidly over the past few decades due to the improvement in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from the raw sequencing data. This is often difficult due to the degradation of ancient DNA and high levels of contamination, especially homologous contamination. In this study, we collected whole genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from the homologous contaminations, we attempted to recover reads based on the ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing the homologous contaminations to a very low proportion. Overall, these recommendations for ancient DNA mapping and separation of endogenous DNA in this study could facilitate future studies of ancient DNA.

1. Trees are characterised by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance? 2. We have studied these questions with the Neotropical Symphonia syngameon. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set-up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances. 3. Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalised when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it’s a specialist of a high-risk high-gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments. 4. Synthesis: The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different ecotypes in the Symphonia syngameon living in intimate sympatry despite occasional gene flow.

1. The role of interspecific interactions in structuring low-diversity helminth communities is a controversial topic in parasite ecology research. Most parasitic communities of fish are species poor; thus, interspecific interactions are believed to be unimportant in structuring these communities. 2. We explored the factors that might contribute to the richness and coexistence of helminth parasites of a poecilid fish in a neotropical river. 3. Repeatability of community structure was examined in parasitic communities among 11 populations of Pseudoxiphophorus bimaculatus in the La Antigua River Basin, Veracruz, Mexico. We examined the species saturation of parasitic communities and explored the patterns of species co-occurrence. We also quantified the associations between parasitic species pairs and analysed the correlations between helminth species abundance to look for repeated patterns among the study populations. 4. Our results suggested that interspecific competition could occur in species-poor communities, aggregation played a role in determining local richness, and intraspecific aggregation allowed the coexistence of species by reducing the overall intensity of interspecific competition.

Aim Kelp forests worldwide are important marine ecosystems that foster high primary to secondary productivity and multiple ecosystem services. These ecosystems are increasingly under threat from extreme storms, changing ocean temperatures, harvesting, and greater herbivore pressure at regional and global scales, necessitating urgent documentation of their historical to present day distributions. Species range shifts to higher latitudes have already been documented in some species that dominate subtidal habitats within Europe. Very little is known about kelp forest ecosystems in Ireland, where rocky coastlines are dominated by Laminaria hyperborea. In order to rectify this substantial knowledge gap, we compiled historical records from an array of sources to present historical distribution, kelp and kelp forest recording effort over time, and present rational for the monitoring of kelp habitats to better understand ecosystem resilience. Location Ireland (Northern Ireland and Éire). Methods Herbaria, literature from the Linnaean society dating back to late 1700s, journal articles, government reports, and online databases were scoured for information on L. hyperborea. Information about kelp ecosystems was solicited from dive clubs and citizen science groups that are active along Ireland’s coastlines. Results Data were used to create distribution maps, analyse methodology and technology used to record L. hyperborea presence and kelp ecosystems within Ireland. We discuss the recent surge in studies on Irish kelp ecosystems and fauna associated with kelp ecosystems that may be used as indicators of ecosystem health and suggest methodologies for continued monitoring. Main Conclusions While there has been a steady increase in recording effort of the dominant subtidal kelp forest species, L. hyperborea, only recently have studies begun to address other important eco-evolutionary processes at work in kelp forests including connectivity among kelp populations in Ireland. Further monitoring, using suggested methodologies, is required to better understand the resilience of kelp ecosystems in Ireland.

Birds have been observed to have dietary preferences for unsaturated fatty acids (FAs) during migration. Polyunsaturated fatty acids (PUFAs) increase the exercise performance of migrant birds; however, PUFAs are also peroxidation prone and might therefore incur increased costs in terms of enhanced oxidative stress in migratory individuals. To shed light on this potential constraint, we analysed plasma FA composition and estimated the susceptibility to peroxidation of migrants and residents of the partially migratory common blackbird (Turdus merula) at a stop-over site during autumn migration. As predicted, migrant birds had higher relative and absolute levels of PUFAs compared to resident birds. This included the strictly dietary ω-3 PUFA α-linoleic acid, suggesting a dietary preference for these fatty acids in migrants. Interestingly, the FA unsaturation index, which is an index of lipid peroxidation susceptibility, did not differ between migrants and residents. These findings suggest a mechanism where birds alter their levels of metabolic substrate to increase exercise performance without simultaneously increasing the risk of lipid peroxidation and oxidative stress. In summary, our results are in line with the hypothesis of increased exercise performance being constrained by oxidative stress during migration, which is manifested in changes in the composition of key FAs to retain the unsaturation index constant despite the increased levels of peroxidizable PUFAs.

Leaf soluble sugars and starch are important components of nonstructural carbohydrates (NSCs), which are crucial for plant growth, development, and reproduction. Although there is a large body of research focusing on the regulation of plant NSC (soluble sugars and starch) concentrations, the response of foliar NSC concentrations to continuous nitrogen (N) and phosphorus (P) addition is still unclear, especially in tropical forests. Here, we used a long-term manipulative field experiment to investigate the response of leaf NSC concentrations to continuous N and P addition (3-, 5-, and 8-year fertilization) in a tropical forest in southern China. We found significant species-specific variation in leaf NSC concentrations in this tropical forest. Phosphorus addition dramatically decreased both leaf soluble sugar and starch concentrations, while N addition had no significant effects on leaf soluble sugar and starch concentrations. These results suggest that, in plants growing in P-limiting tropical soil, leaf NSC concentrations are regulated by soil P availability rather than N availability. Moreover, the negative relationships between NSC concentrations and leaf mass per area (LMA) revealed that NSCs could supply excess carbon (C) for leaf expansion under P addition. This was further supported by the increased structural P fraction after P fertilization in our previous study at the same site. We conclude that soil P availability strongly regulates leaf starch and soluble sugar concentrations in the tropical tree species included in this study. The response of leaf NSC concentrations to long-term N and P addition can reflect the close relationships between plant C dynamics and soil nutrient availability in tropical forests. Maintaining relatively higher leaf NSC concentrations in tropical plants can be a potential mechanism for adapting to P-deficient conditions.

1. Previous macrophysiological studies suggested that temperature-driven colour lightness and body size variations strongly influence biogeographical patterns in ectotherms, but whether these trait-environment relationships scale to local assemblages and the extent to which they can be modified by dispersal remains largely unexplored. We test whether the predictions of the thermal melanism hypothesis and the Bergmann’s rule hold for local assemblages. We also assess whether these trait-environment relationships are more important for species adapted to less stable (lentic) habitats, due to their greater dispersal propensity compared to those adapted to stable (lotic) habitats. 2. We quantified the colour lightness and body volume of 99 European dragon- and damselflies (Odonata) and combined these trait information with survey data for 518 local assemblages across Europe. Based on this continent-wide yet spatially explicit dataset, we tested for effects temperature and precipitation on the colour lightness and body volume of local assemblages and assessed differences in their relative importance and strength between lentic and lotic assemblages, while accounting for spatial and phylogenetic autocorrelation. 3. The colour lightness of assemblages of odonates increased and body size decreased with increasing temperature. Trait-environment relationships in the average and phylogenetic predicted component were equally important for assemblages of both habitat types but were stronger in lentic assemblages when accounting for phylogenetic autocorrelation. 4. Our results show that the mechanism underlying colour lightness and body size variations scale to local assemblages, indicating their general importance. These mechanisms were of equal evolutionary significance for lentic and lotic species, but higher dispersal ability seems to enable lentic species to cope better with historical climatic changes. The documented differences between lentic and lotic assemblages also highlight the importance of integrating interactions of thermal adaptations with proxies of the dispersal ability of species into trait-based models, for improving our understanding of climate-driven biological responses.

Leaf shape is a defining feature of how we recognise and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterised the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing a genome wide association studies (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we performed gene co-expression network analyses from a developmental series, which is publicly available at http://aspleaf.plantgenie.org. We additionally used gene expression measurements across the population to analyse GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.

Predator-prey interactions are critical to understand how communities function. However, we need to describe intraspecific variation in diet to accurately depict those interactions. Harbor seals (Phoca vitulina, Linnaeus 1758) are an abundant marine predator that prey on species of conservation concern. We estimated intrapopulation feeding diversity of harbor seals in the Salish Sea relative to sex, time, and location with a novel approach that combined molecular techniques, repeated cross-sectional sampling of scat, and a specialization metric (within-individual consistency in diet). Based on 1,083 scat samples collected from five haul-out sites during four non-sequential years, we quantified diet using metabarcoding techniques, and determined the sex of the scat depositor using a molecular assay. Results suggest that intrapopulation feeding diversity was pervasive. Specialization was high over short periods (24 - 48 hours,〖PS〗_i = 0.392, 95% CI = 0.013, R = 100,000) and variable in time and space. Females showed more specialization than males, particularly during summer and fall, and demersal and benthic prey species were correlated with more specialized diets. The latter finding suggests that this type of prey likely require specific foraging strategies and that there are trade-offs between pelagic and benthic foraging styles for harbor seals. This differential feeding on prey species, as well as between sexes of harbor seals, indicate that predator-prey interactions in harbor seals are complex and that each sex may have a different impact on species of conservation concern. As such, describing intraspecific variation in diet may unravel hitherto unknown complex predator-prey interactions in the community.

1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper

Secondary contact between closely related species can lead to the formation of hybrid zones, allowing for interspecific gene flow among taxa. Species replacement can take place if one of the species possesses a competitive advantage over the other, resulting in hybrid zone movement. This displacement may leave a genomic footprint across the landscape in the form of asymmetric introgression of selectively neutral alleles from the displaced to the advancing species. Hybrid zone movement has been suggested for marbled newts in the Iberian Peninsula, supported by the presence of a Triturus marmoratus stronghold surrounded by populations of the supposedly advancing T. pygmaeus in the northwest of the Lisbon Peninsula, i.e., an enclave. Moreover, a newly constructed two-species distribution model suggests that climate conditions following the Last Glacial Maximum may have favoured T. pygmaeus over T. marmoratus along the Atlantic coast. To test for the presence of a T. marmoratus genomic footprint in the area that may have witnessed species displacement, we developed and employed 54 nuclear SNPs and one mitochondrial DNA marker. We found no additional enclaves nor genetic traces of T. marmoratus in T. pygmaeus populations. Therefore, two main hypothesis arise in the absence of a genomic footprint: i) species replacement without hybridisation, either in allopatry or in sympatry under strong reproductive isolation; or ii) displacement with hybridisation where the footprint was eroded due to strong purifying selection. We predict testing for a genomic footprint north of the reported enclave could confirm that species replacement in the marbled newts occurred with hybridisation.

Small mammal abundances are frequently limited by resource availability but predators can exert strong lethal (direct mortality) and non-lethal limitations (e.g. depressed site-level activity). Artificially increasing resource availability for small mammals provides a unique opportunity to examine predator-prey interactions. We monitored the 3-year response of arboreal rodents and their predators at nest platforms (n = 598; 23 young forest sites), using annual inspections and remote cameras (n = 168). One year after adding nest platforms we found a 2.9 to 9.2-fold increase in red tree vole (Arborimus longicaudus) use at the site-level, but little use by potential predators. Predator use of nest platforms began in year two and increased in year three of the study. Most potential nest predators were positively correlated with tree vole presence at nest platforms but effect size and direction varied with temporal grain considered (e.g. hour vs day time-bin widths). Flying squirrels (Glaucomys humboldtensis) were positively correlated with disturbances caused by digging birds. Using a Cormack-Jolly-Seber model and encounter histories produced from visual re-captures of marked tree voles, we estimated apparent annual survival to be 0.099 ± 0.057 (x̄ ± 1 SE) for females and 0.005 ± 0.014 for males. Weasels (Mustela spp.), an active seeking predator, preyed upon tree voles most frequently with 10% of weasel detections resulting in mortality of a tree vole (n = 8) whereas owls, an ambush predator, did not prey upon tree voles at nest platforms even though they were detected at similar frequencies as weasels. Weasels also exerted potential non-lethal effects and we observed a >10-fold reduction in the number of tree vole detections per week after weasel detection. Our evidence indicates that predators exert direct and indirect effects on tree vole populations with active seeking predators being the most important predators at nest sites.

Anthropogenic perturbations such as harvesting often select against a large body size, and are predicted to induce rapid evolution towards smaller body sizes and earlier maturation. However, the evolvability of body size and size-correlated traits remains seldom evaluated in wild populations. Here, we use a laboratory experiment over 6 generations to measure the ability of wild-caught medaka fish (Oryzias latipes) to evolve in response to bidirectional size-dependent selection mimicking opposite harvest regimes. Specifically, we imposed selection against a small body size (Large line), against a large body size (Small line) or random selection (Control line), and measured correlated responses across multiple phenotypic, life-history and endocrine traits. As expected, the Large line evolved faster somatic growth and delayed maturation, but also evolved smaller body sizes at hatch, with no change in average levels of pituitary gene expressions of luteinizing, follicle-stimulating or growth (GH) hormones. In contrast, the Small medaka line was unable to evolve smaller body sizes or earlier maturation, but showed marginally-significant signs of increased reproductive investment, including larger egg sizes and elevated pituitary GH production. Natural selection on medaka body size was too weak to significantly hinder the effect of artificial selection, indicating that the asymmetric body-size response to size-dependent selection reflected an asymmetry in body-size evolvability. Our results show that trait evolvability may be contingent upon the direction of selection, and that a detailed knowledge of trait evolutionary potential is needed to forecast population response to anthropogenic change.

1. 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 is 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. 2. 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 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. 3. 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. 4. 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.

Recurrent sea urchin mass mortality has recently affected eastern Atlantic populations of the barren-forming sea urchin Diadema africanum. This new episode of die-off affords the opportunity to determine common meteorological and oceanographic conditions that may promote disease outbreaks. The population dynamics of this sea urchin species are well known—urchin barrens have persisted for many decades along most of the coastlines off the archipelagos of Madeira, Selvages and the Canary Islands, where they limit macroalgae biomass growth. However, this new and explosive mortality event decimated the sea urchin population by 93% on Tenerife and La Palma Islands. Two severe episodes of southwestern rough sea that lead to winter storms, in February 2010 (Xynthia) and February 2018 (Emma), preceded both mass mortality events. The autumn and winter months of those years were anomalous and characterized by swells with an average wave height above 2 m that hit the south and southwest sides of the islands. The amoeba Paramoeba brachiphila was the only pathogen isolated this time from the moribund and dead sea urchins, suggesting that the amoeba was the primary cause of the mortality. This new sea urchin die-off event supports the “killer-storm” hypothesis that has been already described for western Atlantic coasts. These anomalous southwest storms during winters generate pronounced underwater sediment movement and large-scale vertical mixing, detected in local tide gauge, which may promote paramoebiasis. This study presents valuable insights about climate-mediated changes in disease frequency and its impacts on the future of coastal marine ecosystems in the Atlantic.

Fungi are a key component of tropical biodiversity. Due to their inconspicuous and largely subterranean nature, they are however usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomies) emerges as the strongest factor in explaining fungal community composition. Naturally open areas – campinas – are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi–plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short-reads can suffice for diversity and community comparison, long-reads add taxonomic precision and have the potential to reveal population diversity.