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Figure 1 in Multiple paths to aquatic specialisation in four species of Central American Anolis lizards
Figure 1. Plots of the four principal component (PC) axes for males (A + B) and females (C + D). Species denoted as follows: Anolis aquaticus (blue squares), A. lionotus (black diamonds), A. oxylophus (yellow triangles) and A. poecilopus (red circles). (A) PC 1 (head length and width) plotted against PC 2 (body height/body width) for males. (B) PC 3 (hindlimb length) plotted against PC 4 (forelimb length) for males. (C) PC 1 (fore- and hindlimb length) plotted against PC 2 (head length) for females. (D) PC 3 (head height and inter-limb length) plotted against PC 4 (jaw lever) for females.
Data from: emergence of structure in plant-pollinator networks: low floral resource constrains network specialisation
<p>Specialisation enhances the efficiency of plant-pollinator networks through the exchange of conspecific pollen transfer for floral resources. Floral resources form the currency of plant-pollinator interactions, but the understanding of how floral resources affect the structure of plant-pollinator networks remains modest. Previous theory predicts that optimally foraging animal species will specialise to improve resource acquisition under high resource availability. Although floral resource availability depends on both the plant production and animal consumption of the resources, previous work has assumed that production and availability to be equivalent. This potentially may have led to erroneous inferences on the effect of resource availability on specialisation. We develop a mutualistic Lotka-Volterra consumer-resource model to investigate the influence of floral resource availability on plant-pollinator network structure. The model incorporates animal adaptive foraging behaviour, floral resource dynamics, and density-dependent dynamics. Specialisation, nestedness and modularity of simulated networks generated from the model under a wide range of parameters were explained using the Generalised Linear Model. We found that the distinction between floral resource dynamics and plant density dynamics was necessary for partial specialisation of plant-pollinator networks. This is because floral resource dynamics constraint animal preference due to its depletion by animal species. Floral resource abundance had a positive effect on network specialisation, but animal density had a negative effect on network specialisation. Floral resource dynamics thus play key roles on the structure of plant-pollinator network, distinctive from plant species density dynamics.</p>
Figure 2 in Middle Miocene origins for tough-browse dietary specialisations in the koala (Marsupialia, Phascolarctidae) evolutionary tree: description of a new genus and species from the Riversleigh World Heritage Area
Figure 2. Stelakoala riversleighensis gen. et sp. nov. holotype (QM F57737) from Jim's Jaw Site, Riversleigh World Heritage Area, Qld. A-A', Occlusal stereopair; B, labelled occlusal view; C, lingual view; D, buccal view. Abbreviations: co, cristid obliqua; end, entoconid; esd, entostylid; er, entostylid ridge; hyd, hypoconid; lr, lingual ribs; med, metaconid; msd, metastylid; pad, paraconid; ppsd, preprotostylid cristid; prd, protoconid; psd, protostylid.
Figure 1 in Middle Miocene origins for tough-browse dietary specialisations in the koala (Marsupialia, Phascolarctidae) evolutionary tree: description of a new genus and species from the Riversleigh World Heritage Area
Figure 1. Map and regional schematic of the Riversleigh World Heritage Area (After Arena, 2005, and Megirian, 1992). The Type locality of Stelakoala riversleighensis gen. et sp. nov., Jim's Jaw Site, is located on the northern Gag Plateau (highlighted red).
Figure 3 in Middle Miocene origins for tough-browse dietary specialisations in the koala (Marsupialia, Phascolarctidae) evolutionary tree: description of a new genus and species from the Riversleigh World Heritage Area
Figure 3. The evolution of primary M1 trigonid cuspids (metaconid, protoconid and protostylid) in phascolarctids. A, Schematic diagram of a phascolarctid right M 1 illustrating how dimensions and percentages represented in Table 1 were obtained (adapted from Black et al., 2014a); B, Graphical representation of the relative positions and distance between the primary M 1 trigonid cuspids as a percentage of trigonid width; C, phylogenetic relationships of phascolarctids (from Black et al., 2012a). Abbreviations: end, entoconid; hyd, hypoconid; med, metaconid, prd, protoconid; psd, protostylid. Data for Madakoala, Perikoala, Litokoala, Nimiokoala and Phascolarctos, is based on M. devisi, Pe. robustus, L. kutjamarpensis, N. greystanesi and P. cinereus, respectively, with mean values used for the latter two species (Table 1).
Specialised POS Tagged Syriac Corpus for State Morphology
<h1>Overview</h1> <p>A total of twelve .TXT files each representing a Syriac text that has been transcribed and tagged for part-of-speech (POS). This corpus forms part of a PhD research project on the historical syntax of Aramaic (Syriac) at The Australian National University (2020—current) in Canberra, Australia. This research project is interested in noun state morphology, among other topics, which is reflected in the POS scheme for this corpus.</p> <h2>Method</h2> <p>A detailed summary of this methodology is provided in El-Khaissi (data paper in review with the <em>Journal of Open Data Humanities</em>).</p> <ul> <li>Transcriptions are sourced from <a href="https://syriaccorpus.org/" target="_blank" rel="noopener">Digital Syriac Corpus.</a></li> <li>POS tags are based on word matches using <a href="https://sedra.bethmardutho.org/about/openapi" target="_blank" rel="noopener">SEDRA IV API (v1.0.0).</a></li> <li>Selection of Syriac texts was optimised to minimise external influence on Syriac grammar and maximise full coverage of key periods of the Syriac language from 2nd—13th century AD.</li> </ul> <h2>POS Format & Abbreviations </h2> <p>POS tags in the text files follow the following format:</p> <blockquote> <p><syntax-category>-<state>_<syriac_word></p> </blockquote> <p>Thus, an underscore '_' marks the beginning of a tag sequence while tag values are separated by hyphen(s) '-'. For example (noting text directionality constraints):</p> <blockquote> <pre>ܒܘܪܟܬܐ_EMP-N</pre> </blockquote> <p>The following abbreviation lists the definition of all POS tags, which are based on the parameters available in <a href="https://sedra.bethmardutho.org/about/openapi" target="_blank" rel="noopener">SEDRA IV API (v1.0.0).</a></p> <table> <tbody> <tr> <td>Absolute state noun (indeterminate relic)</td> <td>ABS</td> </tr> <tr> <td>Emphatic state noun (new indeterminate)</td> <td>EMP</td> </tr> <tr> <td>Construct state noun (bound noun)</td> <td>CNS</td> </tr> <tr> <td>State not applicable</td> <td>X</td> </tr> <tr> <td>particle</td> <td>PTCL</td> </tr> <tr> <td>pronoun</td> <td>PRO</td> </tr> <tr> <td>preposition</td> <td>PREP</td> </tr> <tr> <td>verb</td> <td>V</td> </tr> <tr> <td>denominative</td> <td>DEN</td> </tr> <tr> <td>noun</td> <td>N</td> </tr> <tr> <td>numeral</td> <td>NUM</td> </tr> <tr> <td>substantive</td> <td>SBV</td> </tr> <tr> <td>adjective</td> <td>ADJ</td> </tr> <tr> <td>proper noun</td> <td>PN</td> </tr> <tr> <td>adverb</td> <td>ADV</td> </tr> <tr> <td>demonym</td> <td>DNM</td> </tr> <tr> <td>participle adjective</td> <td>PTCPADJ</td> </tr> <tr> <td>adverb</td> <td>ADV</td> </tr> <tr> <td>idiom</td> <td>IDM</td> </tr> <tr> <td>See Quality Control & Limitations below</td> <td>DUP</td> </tr> </tbody> </table> <h2>Quality Control & Limitations</h2> <p>On average per manuscript, the POS-tagging process achieved a 63.13% saturation of texts. The POS tagging process was based on an exact-match process, which does not take into account syntactic or semantic context. Syriac words which exhibit homonymy are thus tagged with the value 'DUP' and should be assessed manually based on its original context. Among all 297,981 words in the corpus with an available POS tag, approximately 73,188 (24.56%) of tags reflected some kind of homonymy involving a word with various semantic and/or syntactic interpretations.</p> <p>Since this dataset was created as part of a research project investigating noun state morphology, additional tags were created targetting various state values. Grammatical elements, like number and gender, were not required as part of this investigation and therefore excluded from the POS-tagging process.</p> <h2>Contact</h2> <p>For any questions, please contact Charbel El-Khaissi <Charbel.El-Khaissi@anu.edu.au>.</p>
Data from: Agricultural specialisation increases the vulnerability of pollination services for smallholder farmers
<p>Smallholder farms make up 84% of all farms worldwide and feed two billion people. These farms are heavily reliant on ecosystem services and vulnerable to environmental change, yet under-represented in the ecological literature. The high diversity of crops in these systems makes it challenging to identify and manage the best providers of an ecosystem service, such as the best pollinators to meet the needs of multiple crops. It is also unclear whether ecosystem service requirements change as smallholders transition towards more specialised commercial farming – an increasing trend worldwide. Here, we present a new metric for predicting the species providing ecosystem services in diverse multi-crop farming systems. Working in 10 smallholder villages in rural Nepal, we use this metric to test whether key pollinators, and the management actions that support them, differ based on a farmers' agricultural priority (producing nutritious food to feed the family versus generating income from cash crops). We also test whether the resilience of pollination services changes as farmers specialise on cash crops. We show that a farmers' agricultural priority can determine the community of pollinators they rely upon. Wild insects including bumblebees, solitary bees, and flies provided the majority of the pollination service underpinning nutrient production, whilst income generation was much more dependent on a single species - the domesticated honeybee <em>Apis cerana</em>. The significantly lower diversity of pollinators supporting income generation leaves cash crop farmers more vulnerable to pollinator declines. Regardless of a farmers' agricultural priority, the same collection of wild plant species (mostly herbaceous weeds and shrubs) were important for supporting crop pollinators with floral resources. Promoting these wild plants is likely to enhance pollination services for all farmers in the region.</p> <p><em>Synthesis and applications:</em> We highlight the increased vulnerability of pollination services when smallholders transition to specialised cash crop farming and emphasise the role of crop, pollinator, and wild plant diversity in mitigating this risk. The method we present could be readily applied to other smallholder settings across the world to help characterise and manage the ecosystem services underpinning the livelihoods and nutritional health of smallholder families.</p>
Data from: Agricultural specialisation increases the vulnerability of pollination services for smallholder farmers
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Data from: Emergence of structure in plant-pollinator networks: Low floral resource constrains network specialisation
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Niche partitioning among three snail-eating snakes revealed by dentition asymmetry and prey specialisation
<p>1. The level of dentition asymmetry in snail-eating snakes may reflect their prey choice and feeding efficiency on asymmetric land snails. The three species of Pareas snakes (Squamata: Pareidae) in Taiwan, which are partially sympatric distribution on the island, provide a potential case to test the hypothesis of niche partitioning and character displacement with regard to dentition asymmetry and specialisation in feeding behaviour.</p> <p>2. In this study, behavioural experiments confirmed that P. formosensis feeds exclusively on slugs, whereas P. atayal and P. komaii consumed both. However, P. atayal more efficiently preys on land snails than P. komaii, exhibiting a shorter handling time and fewer mandibular retractions.</p> <p>3. Micro-CT and ancestral character reconstruction demonstrated the lowest asymmetry in P. formosensis (the slug specialist), the highest dentition asymmetry in P. atayal (the land snail specialist), and flexibility in P. komaii (the niche switcher): increased dentition asymmetry when sympatrically distributed with the slug eater (character displacement), and decreased asymmetry when living alone (ecological niche release).</p> <p>4. Ecological niche modelling showed that the distribution P. formosensis is associated with the presence of slugs, while that of P. atayal could be explained by the land snails.<br> Combining the results from morphology, phylogeny, behavioural experiments and ecological niche modelling, we showed that competition in the sympatric region might have facilitated character displacement among congeners, while absence of competition in allopatric region has led to ecological niche release.</p>
Data from: Specialisation reduces foraging effort and improves breeding performance in a generalist bird
While competition is generally presumed to promote intraspecific niche diversification, populations of many apparent generalist species still exhibit considerable individual variation in foraging specialisation. This suggests that different cost-benefit trade-offs may underlie individual variation in foraging specialisation. Indeed, while specialisation may improve foraging efficiency by a better knowledge of the spatio-temporal availability of resources, individuals may also become more vulnerable to fluctuations in these resources. In this study, we used multi-year GPS tracking data of 19 Herring Gulls (Larus argentatus) breeding along the Belgian coast to assess whether foraging effort and reproductive success varied among different levels of foraging specialisation. First, we quantified spatial and habitat specialisation during incubation and chick-rearing for 31 individual breeding cycles during which birds raised young until the age of 21 days. Next, we tested whether spatial and habitat specialisation were related to the daily distance covered (as a proxy for foraging effort), and to chick growth (as a proxy for reproductive success). We found that birds primarily varied in their extent of habitat specialisation. Habitat specialisation was associated with reduced daily distances covered and increased offspring growth rates, in particular the growth rate of the youngest chicks. Yet, positive effects of habitat specialisation on chick growth decreased at high levels of spatial specialisation. Our results thus demonstrate fitness benefits of foraging specialisation during our five-year study period, but also highlight the need for longer-term studies as environmental changes may cause benefits to vary throughout a lifetime.
Vellozioid roots allow for habitat specialisation among rock- and soil-dwelling Velloziaceae in campos rupestres
<p>1. Plant growth on harsh substrates (habitat specialisation) requires specific traits to cope with stressful conditions. 2. We tested whether traits related to nutrient acquisition (root colonisation by fungal symbionts, and plant morphological and physiological specialisations), and nutrient use (leaf nitrogen (N) and phosphorus (P) concentrations and N- and P-remobilisation efficiency), were related to habitat specialisation for 27 species of Velloziaceae growing either in soil or on rocks in extremely P-impoverished <i>campos rupestres</i> habitats. If habitat specialisation were to drive trait sorting, then we expect traits to differ between those substrates. 3. Both soil and rock-dwelling species presented a very low proportion of root length colonised by arbuscular mycorrhizal and dark septate fungi. However, rhizosheaths were only observed in soil-dwelling species, and vellozioid roots, a specialisation that allows for mining P and dissolving quartzite rock, were mostly found in rock-dwelling species. We did not observe differences in nutrient-use traits between rock- and soil-dwelling species. 4. Roots specialisations are strongly correlated with microhabitats, and the presence of vellozioid roots seems to mediate bare rock specialisation. There is an overall P limitation of plant productivity both on rock and in soil of <i>campos rupestres</i>, which does not drive the sorting of traits related to aboveground nutrient use and symbiotic P acquisition. Therefore, nutrient impoverishment is indeed a very strong environmental filter in <i>campos rupestres </i>as a whole, but habitat specialisation plays an important role in the spatial distribution of Velloziaceae between contrasting substrates.</p>
Aza-Claisen rearrangement as a key step in synthesis of specialised anilines used in the production of efficient ethenolysis catalysts
<p>Data confirming the structure of the new compounds obtained within the project, published in <br><i><strong>Catal. Sci. Technol.</strong></i>, 2023,<strong>13</strong>, 3682-3688, https://pubs.rsc.org/en/content/articlelanding/2023/cy/d3cy00395g</p><p>The research was supported by the National Science Centre, Poland (OPUS grant DEC-2017/27/B/ST5/02563).</p>
Data associated with: A phylogenetic perspective on ecological specialisation reveals hummingbird and insect pollinators have generalist diets
<p>Specialisation in food resource use is a crucial process that fosters species coexistence in plant-animal networks, contributing to the maintenance of biodiversity, ecological complexity, and community stability. Notably, although there is a vast literature on ecological specialisation in pollination systems, the evolutionary similarity among the plant species visited by particular pollinators has been largely ignored. Here, we apply a robust phylogenetic approach to analyse whether the evolutionary relatedness of plant species is a significant factor in mediating pollinator visits and how it relates to the morphology of interacting species. We quantified ecological and clade specialisation of hummingbird and insect species in three mutualistic networks from the Costa Rican highlands and associated these metrics with species traits. We found that hummingbirds were overall ecologically more specialised than insects (i.e. visited a less diverse set of plant species). However, when evaluating the phylogenetic relatedness among the visited plant species, all hummingbird species and most insects had overdispersed diets, which indicates they visited phylogenetically distant plant species in the community. Moreover, a great proportion of these clade generalists visited plant species with a great variation in corolla length, showing a lack of preference for this morphological trait. Altogether, our results demonstrate that by incorporating plant phylogeny to network analysis, pollinator species were generalists and that corolla length weakly influences plant-pollinator interactions in the three studied networks. A phylogenetic perspective should occupy a central role in the study of specialisation since it contributes to understanding the interplay between ecological and evolutionary processes in mutualistic networks. Future research should focus on evaluating whether the phylogenetic structure of animal diets mediates patterns of interactions in different types of mutualisms and environmental contexts, linking these patterns to other floral traits. This knowledge may be valuable for deepening our comprehension of the underlying mechanisms shaping ecological networks.</p>
Data from: Are day-flying moths more specialised in larval dietary breadth?
<p>Although diurnality is widespread across Lepidoptera and has evolved many times independently, its causes and ecological implications are yet poorly understood. The 'Salient Aroma Hypothesis' (SAH) postulates that diurnal insect herbivores are overall more specialised in dietary breadth than species active at night. It is furthermore assumed that diurnality evolved more frequently in species that live in cooler environments. Using European geometrid moths as a model group, we tested whether diurnal activity in adults is associated with an increased larval dietary breadth as predicted by the 'Salient Aroma Hypothesis.' We further investigated whether species that exclusively occur in colder regions or whose flight period is restricted to cool seasons are more likely to exhibit a diurnal flight activity. Contrary to expectation, we found no consistent differences in larval dietary breadth between diurnal and nocturnal species, and thus no support for the 'Salient Aroma Hypothesis.' Diurnal activity occurred more frequently in species restricted to cold regions, but not in species restricted to cool seasons. We conclude that diurnality could serve as an advantageous adaptation in cold environments, depending on further factors such as resource availability or predation pressure, but has no immediate consequences for larval dietary breadth.</p>
Data & codes for "Changes in abundance and distribution of European forest bird populations depend on biome, ecological specialisation and traits"
<h1>1. Selection of European forest bird species and classification of their biome preferences</h1> <p>We selected all species that are related to forest and woodland based on two data sources: Storchová & Hořák (2018) and Tobias et al. (2022), resulting in 107 bird species studied (Data S1). We defined forest bird species as those using environments ranging from closed-canopy forests to more open-canopy woodlands (A. Lehikoinen & Virkkala, 2018; Storchová & Hořák, 2018; Tobias et al., 2022). We determined their biome specialisation using breeding distribution centroids and the overall breeding distribution of each of the species, using the global map of terrestrial ecoregions from Olson et al. (2001) and range data from European Breeding Bird Atlas 1 and 2 (Hagemeijer & Blair, 1997; Keller et al., 2020). We categorised species as Mediterranean, temperate, or boreal based on their predominant biogeographic region. We considered species commonly occurring over several biomes as “generalists”. For instance, we reclassified the two typically boreal species Glaucidium passerinum Linnaeus and Strix uralensis Pallas as “generalists” due to significant range expansions into central and southern Europe in recent decades, therefore no longer restricted to the boreal region. For the complete list of species, biome specialisation, traits, and specialisation indices, refer to Data S1.</p> <h1>2. Changes in abundance and distribution of European forest bird species</h1> <p>We assessed long-term changes in European forest bird populations through two approaches: (i) changes in estimated total European-level species abundance over a 40-year timeframe; and (ii) changes in species spatial distribution over a 30-year timeframe (Fig. 1).</p> <p>We utilized the estimated trends in European-level population size (i.e., the total number of individuals) for each common native European bird species from 1980 to 2017, as reported by Burns et al. (2021). Three species out of the 107 studied forest species were missing in the original manuscript and we used data generated with the same method from 1980 to 2018 from the European assessment, Article 12 (https://nature-art12.eionet.europa.eu/article12/). These abundance trends were calculated by Burns et al. (2021) using multi-sourced annual times series. For each species, they gathered population estimates and trends from each European country as well as European Union (EU)-level population trends. They analysed these data with a Bayesian hierarchical model to reconstruct EU-level smoothed species population time series. The model outputs include an average annual rate of abundance change and an associated 95% credible interval (Burns et al., 2021). Therefore, we did not directly use the average annual rate of abundance change, as this would have led us to consider species with low uncertainty as similar to those with high uncertainty. To account for the uncertainty, we categorised species as (i) declining, i.e., annual rates below one, (ii) increasing, i.e., annual rates above one and (iii) stable, i.e., annual rate whose 95% CI overlap one, i.e., no significant change. To better acknowledge the magnitude of the abundance change, significant changes with rates below 0.98 were labelled as “strongly declining” (i.e., 6.5% of the 107 species), while those above 1.02 were labelled as “strongly increasing” (i.e., 11% of the 107 species). To evaluate the sensitivity of the decision to categorised abundance change data, we also analysed abundance trend as continuous variable (see Supporting Information Fig. S8).</p> <p>To determine changes in species distributions, we used a comparison of species distributions between two periods (i.e., 1985-1988 and 2013-2017) using the European Breeding Bird Atlas 1 and 2 (EBBA 1 & 2; Hagemeijer & Blair, 1997; Howard et al., 2023; Keller et al., 2020). Howard et al. (2023) provided calculations of observed colonisation and extinction areas at a 50 x 50 km resolution across Europe. We measured changes in range as the difference between colonisations and extinctions of each species, with negative values indicating contracting ranges and positive values indicating expanding ranges. Additionally, we calculated the shift in the centre of gravity of the distribution range between the two periods, as a distance (km) along the south-north gradient for each species (Howard et al., 2023).</p> <h1>3. Trait and specialisation data for European forest bird species</h1> <p>We extracted data for six functional traits from several sources (Table 1). (i) The species temperature index (STI)represents the long-term average temperature within the species’ breeding range (A. Lehikoinen et al., 2021). (ii) Diet data during the breeding season were obtained from Storchová & Hořák (2018), classifying species into binary variables as vertebrate carnivorous, invertebrate carnivorous, and herbivores (combining the leaf and seed eaters). Storchová & Hořák (2018) classified species into a diet category when the corresponding food resource represented at least 10% of the species diet throughout the breeding season. Therefore, one species can be in several categories (i.e., omnivores). (iii) We obtained nesting site data from Pearman et al. (2014), classifying species into binary variables as ground nesters, tree hole nesters, or elevated nesters (> 1 m in a tree or shrub). We also included data on (iv) species dependence on old-growth forests (Data S1; mostly from Fraixedas et al. (2015) and Mönkkönen et al. (2014), if present on both references, we classified them as “1” and if only in one reference as “0.5”), (v) migration distance (Howard et al., 2023), and (vi) body mass (Tobias et al., 2022).</p> <p>Finally, we extracted and developed seven species specialisation indices. (i) We used an overall specialisation index based on multiple traits (i.e., temperature, diet, foraging behaviour and substrate, habitat, and nesting site), and (ii) a nesting specialisation index, both obtained from Morelli et al. (2019). Both indices represent species specialization based on the dispersion of trait preferences for each species: e.g., nesting specialism equal 0 for species that nest in all habitat type and equal 1 for species that nest in only one habitat type). They are both calculated using the Gini index of inequality, which measures overall dispersion across, e.g., all traits for the overall specialization, based on data from Pearman et al. (2014) and Storchová & Hořák (2018). For additional information, see Morelli et al. (2019). We also used (iii) the diet specialisation index, (iv) the species distribution range during the breeding season (hereafter “breeding range area”) and (v) the climatic niche breadth from Reif et al. (2016). The diet specialisation index was calculated as the coefficient of variation for diet preferences for each species, where high values denotes specialized species (Reif et al., 2016). The breeding range area was evaluated as the number of 50-km squares in the distribution maps in Europe occupied by each species during the reproduction period, and is based on EBBA 1 (Hagemeijer & Blair, 1997). The climatic niche breadth was calculated as the difference between the 5% hottest and the 5% coldest mean temperature between April and June in which each species occurs, using EBBA 1 (Hagemeijer & Blair, 1997; Reif et al., 2016).</p> <p>Additionally, (vi) we calculated a broadleaf forest specialisation index based on binary forest habitat preferences (Storchová & Hořák, 2018), assigning values of one for species found only in broadleaf forests; zero for those in coniferous forests, and 0.5 for those found in both. Lastly, (vii) we created a forest specialisation index based on the species habitat preferences (Storchová & Hořák, 2018). The forest specialisation index was calculated as the mean of species affinity across habitats. We used increasing habitat weights along a gradient of tree dominance: open habitats as 1, shrubland as 1.5, woodland as 2 (i.e., species associated with habitats structured by trees in lower density than in forest), forest generalist (found in both coniferous and broadleaf dense forests) as 3, and forest specialist (found only either in coniferous or broadleaf dense forests) as 4. For instance, the index value for species occurring either in shrubland, woodland or both broadleaf and coniferous forests is 2.167.</p> <h1>4. Data analysis</h1> <p>Data analyses were conducted with R software version 4.4.1. (R Core Team, 2024). Given the non-independence of species due to their genetic relatedness, we accounted for interspecific phylogenetic distance in all models. We constructed the phylogenetic tree for the 107 European forest bird species using ‘rotl’ and ‘ape’ R-packages (Michonneau et al., 2022; Paradis et al., 2023). We used rotl as an interface with the "Open Tree of Life", employing tol_induced_subtree R-function to generate the phylogenetic tree and compute.brlen R-function to set branch lengths using Grafen’s computation. We generated separate phylogenetic trees for boreal (17), temperate (15), Mediterranean (16) and “generalist” (59) species to perform biome-specific analysis (see Supplementary Information, Figs. S1 & S2).</p> <p>To investigate the effects of functional traits and specialisation indices on abundance, range changes, and distribution shift, we used two regression methods. All methods were based on the relationships between a measure of change and a functional trait or specialisation index. Our sample unit is an individual forest bird species (i.e., one value for each species, either abundance or range change, or distribution shift). Abundance change was a categorical variable (i.e., strong decline – decline – stable – increase – strong increase), while range change (i.e., difference between colonisation and extinction) and distribution shift (i.e., south-north shift) were continuous variables. Therefore, to study abundance changes, we used proportional-odds linear mixed effects model using (Phylo)clmm R-function from the ‘ordinal’ R-package (Christensen, 2022). Interspecific phylogenetic relatedness was included as a random effect, reflecting the correlation between species based on phylogenetic distances (see also Hagge et al. (2021) and Seibold et al. (2015)). For distribution changes, we employed phylogenetic generalised least squares regression (PGLS) using the gls R-function from the ‘nlme’ R-package (Pinheiro et al., 2023). The phylogenetic correlation structure was integrated into PGLS using Pagel’s lambda parameter (λ; Pagel (1999)) a widely used measured of phylogenetic signal strength (see, e.g., Hagge et al., 2021; Triviño et al., 2013).</p> <p>Furthermore, we included latitude, a key driver of bird communities at broad scales (Luoto et al., 2007), as a fixed covariable (centroid latitude of the species’ breeding distribution) in all global models (i.e., species from all biomes together), except for the STI model due to strong correlation. For biome-specific analysis, we included latitude only in boreal species models for range change and distribution shift, as it significantly improved model fit (ΔAIC < -2). We did not add latitude for models specific to temperate, Mediterranean, and generalist species since it did not improve model fits (ΔAIC > -2). Additionally, we included breeding range area in range change and distribution shift models, assuming that species with larger ranges would exhibit larger shifts. We scaled predictors to a mean of 0 and standard deviation of 1 to facilitate effect size comparisons. We adjusted p-values using the Holm method (for n=3) to account for multiple testing of traits and specialisation indices on three response variables.</p>
The non-dereliction in evolution: Trophic specialisation drives convergence in the radiation of red devil spiders (Araneae: Dysderidae) in the Canary Islands
<p>Natural selection plays a key role in deterministic evolution, as clearly illustrated by adaptive radiations. Unlike most spiders, <em>Dysdera</em> species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialisation to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to (1) characterize cheliceral morphologies, (2) unravel their dietary function, (3) examine if they evolved multiple times independently (4) verify whether convergent evolution of morphotypes has occurred and (5) test if specialization could lead to evolutionary irreversibility. We show the existence of nine cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.</p>
Plant specialisation may limit climate‐induced vegetation change to within topographic and edaphic niches on a sub‐Antarctic island
<p>Extreme changes in temperature, rainfall and wind regimes have been correlated with plant species range expansion upslope on sub-Antarctic islands. Ongoing climatic changes are expected to continue driving changes in species distributions globally, but niche specialisations may limit the capacity for range shifts. We hypothesised that non-climatic characteristics of ecological niches of vascular plant species could limit climate induced range shifts. We determined the altitudinal ranges of vascular plant species (n=13) on sub-Antarctic Marion Island and measured air temperature, topographic, foliar and soil properties along transects on geologically distinct substrates. Climatic and non-climatic associations were determined using multiple linear regression and boosted regression tree (BRT) analyses. The degree of niche specialisation was determined using outlying mean index analysis (OMI) within the range of species on the island. Several species (7 of 13) exhibited niche-specialisation. Correlation analysis revealed that edaphic properties including soil depth, loss on ignition, the principal component of most soil nutrients (Mg, Cl, K, Ca, Cu, Zn, P, S), Si, Mn and clay dominated the BRT prediction of overall plant cover. Although air temperature was correlated with plant cover in linear models, model simplification dropped temperature in both BRT and linear models. As a consequence, multiple determinants, including temperature, climate, topography and soils control the distribution of vascular plant species on this sub-Antarctic island.</p>
Data from: Integrating isotopic and nutritional niches reveals multiple dimensions of individual diet specialisation in a marine apex predator
<ol> <li>Dietary specializations are important determinants of ecological structure, particularly in species with high per-capita trophic influence like marine apex predators. These species are, however, among the most challenging in which to establish spatiotemporally integrated diets.</li> <li>We introduce a novel integration of stable isotopes with a multidimensional nutritional niche framework that addresses the challenges of establishing spatiotemporally integrated nutritional niches in wild populations, and apply the framework to explore individual diet specialization in a marine apex predator, the white shark (<em>Carcharodon carcharias</em>).</li> <li>Sequential tooth files were sampled from juvenile white sharks to establish individual isotopic (δ-space; δ<sup>13</sup>C, δ<sup>15</sup>N, δ<sup>34</sup>S) niche specialization. Bayesian mixing models were then used to reveal individual-level prey (p-space) specialization, and further combined with nutritional geometry models to quantify the nutritional (N-space) dimensions of individual specialization and their relationships to prey use.</li> <li>Isotopic and mixing model analyses indicated juvenile white sharks as individual specialists within a broader, generalist, population niche. Individual sharks differed in their consumption of several important mesopredator species, which suggested among-individual variance in trophic roles in either pelagic or benthic food webs. However, variation in nutrient intakes was small and not consistently correlated with differences in prey use, suggesting white sharks as nutritional specialists and that individuals could use functionally and nutritionally different prey as complementary means to achieve a common nutritional goal.</li> <li>We identify how degrees of individual specialisation can differ between niche spaces (δ-, p- or N-space), the physiological and ecological implications of this, and argue that integrating nutrition can provide stronger, mechanistic links between diet specialisation and its intrinsic (fitness/performance) and extrinsic (ecological) outcomes. Our time-integrated framework is adaptable for examining the nutritional consequences and drivers of food use variation at the individual, population or species level.</li> </ol>
Video of surface rendering of internal head structures in Melissotarsus worker ants, specialised for chewing healthy wood.
<p>Ants of the genus<em> Melissotarsus </em>(subfamily Myrmicinae) inhabit tunnel systems excavated in the wood of living trees, where they keep large numbers of symbiotic armoured scale insects (Diaspididae). Tunnelling through healthy wood requires tremendous power. We investigated morphology of the musculoskeletal system of <em>Melissotarsus</em> using X-ray microcomputed tomography and 3D modelling (Khalife et al. 2018).</p> <p>Segmented structures inside one half of the head of a <em>Melissotarsus </em>worker: mandible (pale green; tip cut off); closer muscles of mandible (orange); closer apodeme (red); opener muscles of mandible (light blue); opener apodeme (dark blue); brain and suboesophageal ganglion (brown); tentorium and ventromedial phragma (green).</p> <p><strong>Micro-CT </strong>scans were performed at the Okinawa Institute of Science and Technology Graduate University, Japan<strong>.</strong></p> <p><strong>Segmentation </strong>of the reconstructed image stacks was performed with ITK-SNAP 3.6.0<strong> </strong></p> <p>Khalife A, Keller R, Billen J, Hita Garcia F, Economo E & Peeters C (2018) Skeletomuscular adaptations of head and legs of <em>Melissotarsus</em> ants for tunnelling through living wood. <strong>Frontiers in Zoology</strong> 15: 30. https://doi.org/10.1186/s12983-018-0277-6</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.