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Abstract Background Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir’s genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates. Results Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas. Conclusions Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.

Abstract Microbiota plays an essential role in fish growth and health and may be influenced by the changing environmental conditions. Here, we explored the microbiota of wild common sole, one of the most important fishery resources in the Mediterranean Sea, collected from different areas in the North Adriatic Sea. Our results show that the sole microbiota differs from that of the surrounding environment and among the different body sites (gill, skin and gut). Gut microbiota composition showed to be strongly related to fish age, rather than maturity, sex or sampling site. Age-related shifts in gut microbial communities were identified, with increased abundances of Bacteroidia and Desulfobacteria, unveiling potential microbial proxies for age estimation crucial for fisheries management. Our results expand the limited knowledge of the wild common sole microbiota, also in the light of the potential usefulness of the fish microbiota as a tool for future stock identification and connectivity studies.

Abstract Background While most game theoretical models assume that individuals randomly interact with all other group members, strong evidence indicates that individuals tend to preferentially interact with some of them. The position of an individual in a network affects, among other factors related to survival, its predation risk and competitive success. Here I then modified the Hawk-Dove game to explore the effect of social network structure on competitive strategy of individuals that differ in their fighting ability and may adjust their use of the Hawk, Dove and Assessor tactics to maximize their foraging success when they meet opponents they are connected with. Results From randomly generated networks, I demonstrate that phenotypic assortment by fighting ability reduces individuals’ aggressiveness and, as such, favours cooperative interactions. Furthermore, the success of individuals with the weakest fighting ability is usually highest within networks where they most frequently meet opponents with the same fighting ability as their own, suggesting they might benefit from breaking connections with strong contestants. This might be the case when strong contestants systematically rely on the aggressive Hawk tactic or the risk of being predated is low and independent of the number of neighbours. Thus, I extended the model and built a dynamic model to allow individuals not only to adjust their behaviour to local conditions but also to modify the structure of the social network. The number of connections and degree of phenotypic assortment are then affected by ecological factors (e.g. resources value and predation risk), but above all by whether individuals can reliably assess the competitive ability of their opponents and adjust their behaviour accordingly. Conclusions These findings provide strong evidence that behaviour can play a key role in shaping network structure and highlight the importance of considering the coevolution of network and behaviour to apprehend its consequences on population dynamics.

Abstract Background Rivea ornata, a rare species from the morning glory family, exhibits uncommon characteristics compared to other typical morning glories, including nocturnal flowers that fit the classic moth pollination syndrome. However, the accuracy of its predicted pollination syndrome and its mating system have never been assessed. Additionally, R. ornata flowers attract not only pollinators but also florivores, potentially reducing plant reproductive success. Therefore, this study examined two populations of R. ornata in Thailand and assessed traits related to pollinator attraction and reward, determined its mating system, identified floral visitors and effective pollinators, and investigated the effect of florivory on reproductive success. Results Rivea ornata is highly fertile but self-incompatible and an obligate outcrosser, rendering it highly dependent on pollinators. Lepidopterans, particularly nocturnal hawk moths, were found to account for a significant proportion of all visits and were the sole effective pollinators of this plant species, in correspondence with its predicted pollination syndrome. Surprisingly, florivory did not significantly reduce reproductive success. This phenomenon may be explained by the strategies employed by R. ornata, which align with the optimal defense hypothesis and functional trade-offs. Specifically, R. ornata appears to invest resources in defending key floral structures while, simultaneously, guard ants are conspicuously absent from flowers, resulting in some florivore damage to non-vital floral organs but ensuring that pollinators are not deterred by ants and thus maintaining high pollinator visitation rates. Conclusions Our findings indicate that reproduction-related traits in R. ornata, including those involved in pollinator attraction and reward and florivore defense, are highly effective and work in concert to maximize plant reproductive success. Therefore, a main risk that R. ornata faces is the decline or disappearance of hawk moths and other lepidopterans given its extreme specialization and high dependence on pollinators, and conservation efforts should include habitat protection for both R. ornata and its pollinators.

The Mediterranean, a global hotspot for rare ant species, hosts a significant representation of the global diversity of the mainly Holarctic ant genus Temnothorax. However, several groups still require significant taxonomic efforts. The taxonomy of the T. luteus complex species was revised in 2014 when morphometrics allowed distinguishing two valid species and two synonyms out of four taxa that had been originally described from France. The two species recognized since then are T. luteus, distributed from Iberia to the Alps, and the largely sympatric but much more xerothermophilic T. racovitzai. In Italy, only a few records of the complex were ever published, and the identity of the Italian population was never thoroughly assessed. We combined morphometrics with phylogenomic data to assess the identity of the T. luteus populations that spanned from Sicily to the Italian Alps and discovered that all Italian samples belong to a new cryptic species, which we describe as T. apenninicus sp. nov. whose glacial refugium was probably in the southern Apennines.

Research voyages on board RV ‘Investigator’ between 2015 and 2022 sampled benthic communities of Australia’s Eastern and Southern continental margins from the slope down to abyssal depths (463–5000 m) as well as the seamounts off the Indian Ocean Australian Territories (IOT) that include Christmas Island and Cocos (Keeling) Islands. Over 500 specimens of the annelid family Aphroditidae were collected during the voyages. Some of the most common aphroditids collected during these voyages belonged to the large-bodied members of the genus Laetmonice. We used fragments of COI and 16S genes to investigate the diversity of the genus. Phylogenetic studies revealed the presence of at least nine distinct mitochondrial genetic lineages within Laetmonice, four of which have been described here as Laetmonice hutchingsae sp. nov., L. murrayae sp. nov., L. mensahaedorum sp. nov. and L. paxtonae sp. nov. The new taxa are clearly structured by their bathymetric distributions. These results argue against eurybathic distribution within the genus Laetmonice and demonstrate the existence of genetically divergent taxa isolated by bathymetric environmental gradients.

Research voyages onboard RV ‘Investigator’ in 2021 (IN2021_V08) and 2022 (IN2022_V04) sampled benthic communities of seamounts off Christmas Island and Cocos (Keeling) Islands, also known as Indian Ocean Australian Territories (IOT). Over 150 specimens of the family Serpulidae collected during the voyages were deposited in the Australian Museum. The animals belonged to the filogranin genera Apomatus, Bathyvermilia, Bathyvermiloides gen. nov., Filogranula, and Protis, as well as to serpulin genera Hyalopomatus, Placostegus and Vitreotubus. In total, 12 species were identified, including three named, but very poorly known serpulids Bathyvermilia challengeri, Filogranula stellata, and Vitreotubus digeromimoi. Nine species Apomatus nishii n. sp., Bathyvermilia rolandobastidai n. sp., Bathyvermiloides juliebrockae n. sp., Protis melmackenzieae n. sp., Protis perneti n. sp., Hyalopomatus nogueirai n. sp., Hyalopomatus rossanae n. sp., Hyalopomatus suelindsayae n. sp., and Placostegus leslieharrisae n. sp. were described. All species descriptions are accompanied by DNA sequence data and their phylogenetic positions in the family Serpulidae have been assessed.

The Australian Museum has a large palaeontological collection of Triassic specimens from the Sydney Basin, including many type specimens. This study reviewed every presently described Sydney Basin Hawkesbury Sandstone plant and animal taxon that has representative specimens held in the Australian Museum. Fifty-two taxa are included from numerous sites. These include three amphibians, twenty-eight fishes, eleven insects, one horseshoe “crab”, one scorpion, three crustaceans, two molluscs and three plants. Basic taxonomic history is noted, together with specimen registration numbers and their position in the collection. Also included are references to relevant specimens held in the Geological Survey of New South Wales and the Natural History Museum, London collections. Images of every taxon are included. To place the collection in context, particularly for educators working with students, brief descriptions of the geology that forms the Hawkesbury Sandstone, and the inferred ecosystems that existed during the Middle Triassic, are included. The results of this study will help to facilitate further researchers by providing important details of the fossil collections held at the Australian Museum.

Abstract Background Anthropogenic threats are causing alteration of coastal areas worldwide. Most of the coastal biodiversity is endangered, taking a particular toll on island ecosystems, like the Azores. To better understand the biotic and abiotic factors constraining the distribution and conservation status of two endemic plants, Azorina vidalii (Campanulaceae) and Lotus azoricus (Fabaceae), we performed a global survey of coastal plant communities in the archipelago, also covering environmental descriptors, natural and anthropogenic threats. Moreover, we revised their IUCN conservation status and estimated the population fractions within protected areas. Results Non-indigenous plants were commonly found in plots with or without the target endemics, contributing to the absence of well-defined coastal plant communities. Nonetheless, indigenous taxa commonly occurred at the plots with L. azoricus. With a larger area of occurrence, A. vidalii ecological niche differed from that of L. azoricus, the latter being restricted to dry and rocky sea cliffs, mostly in Santa Maria Island. Besides the presence of invasive plants, signs of habitat destruction, trampling and grazing, and of natural threats, such as coastal erosion, were commonly observed. Conclusions Occurrence data indicated an endangered status for both species, although this would change to critically endangered for L. azoricus when using smaller-sized occurrence cells. Both species are threatened since their habitat is restricted to a very narrow vegetation belt, strongly limited by sea influence and human pressure, and with the frequent presence of invasive plants. While focusing on two endemic plants, our study allowed a broader view of the impact of anthropogenic disturbance on Azorean coastal plant communities.

Abstract Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., “macro-haplogroups”) vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers' understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This “clutter” leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as “macro-haplogroups”, “meso-haplogroups”, and “micro-haplogroups”. Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster, and then implemented into haplogroup callers such as HaploGrep3. This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies.

Abstract Artificial linear landscape elements, including roads, pipelines, and drainage channels, are main sources of global habitat fragmentation. Restoration of natural habitats on unused linear landscape elements can increase habitat quality and connectivity without interfering with agricultural or industrial development. Despite that topsoil removal and transfer are widely applied methods in restoration projects, up to our knowledge these were previously not compared in the same study system. To address this knowledge gap, we compared spontaneous vegetation recovery after the elimination of positive (embankments) and negative landscape scars (drainage channels) in lowland alkaline landscapes in South Hungary. The novelty of our study is that we compared the fine-scale and landscape-scale results of both methods. At the fine scale, we monitored the spontaneous vegetation development on the created open surfaces in the first, second and fourth year after restoration in 160 permanent plots per year. For characterizing the habitat changes on the landscape scale, we prepared habitat maps and assigned naturalness scores to each patch before and after the restoration activities. Both restoration methods resulted in a rapid vegetation recovery at the fine scale, progressing toward the reference state. In the topsoil removal treatment, a large part of the soil seed bank was removed; therefore, the colonization of the bare surface was a slower process. Seeds of halophytes, including the endemic and protected Suaeda pannonica, were probably present in the deeper soil layers, and these species became established in the restored surfaces, despite being absent in the surrounding vegetation. For restoring vegetation cover, topsoil transfer was a more rapid option; however, vegetation closure and competition by generalist species and weeds hampered the establishment of target species. The removal of the landscape scars by both methods made the sites accessible for grazing. At the landscape scale, the two methods had different effects: there was a slight increase in the habitat naturalness in the topsoil removal site, and a slight decrease in the topsoil transfer site because of weed encroachment. Spreading an upper layer of nutrient-poor soil with low amounts of weed seeds, direct propagule transfer, and targeted grazing regimes could enhance restoration success.

Abstract Background The fossil record provides the unique opportunity to observe evolution over millions of years, but is known to be incomplete. While incompleteness varies spatially and is hard to estimate for empirical sections, computer simulations of geological processes can be used to examine the effects of the incompleteness in silico. We combine simulations of different modes of evolution (stasis, (un)biased random walks) with deposition of carbonate platforms strata to examine how well the mode of evolution can be recovered from fossil time series, and how test results vary between different positions in the carbonate platform and multiple stratigraphic architectures generated by different sea level curves. Results Stratigraphic architecture and position along an onshore-offshore gradient has only a small influence on the mode of evolution recovered by statistical tests. For simulations of random walks, support for the correct mode decreases with time series length. Visual examination of trait evolution in lineages shows that rather than stratigraphic incompleteness, maximum hiatus duration determines how much fossil time series differ from the original evolutionary process. Gradual directional evolution is more susceptible to stratigraphic effects, turning it into punctuated evolution. In contrast, stasis remains unaffected. Conclusions • Fossil time series favor the recognition of both stasis and complex, punctuated modes of evolution. • Not stratigraphic incompleteness, but the presence of rare, prolonged gaps has the largest effect on trait evolution. This suggests that incomplete sections with regular hiatus frequency and durations can potentially preserve evolutionary history without major biases. Understanding external controls on stratigraphic architectures such as sea level fluctuations is crucial for distinguishing between stratigraphic effects and genuine evolutionary process.

Abstract The songs of birds are complex signals that may have several functions and vary widely among species. Different ecological, behavioural and morphological factors, as well as phylogeny, have been associated as predictors of the evolution of song structure. However, the importance of differences in development, despite their relevance, has seldom been considered. Here, we analysed the evolution of song in two families of songbirds that differ in song development, manakins (suboscines) and cardinals (oscines), with their phylogeny, morphology, and ecology. Our results show that song characteristics had higher phylogenetic signal in cardinals than in manakins, suggesting higher evolutionary lability in the suboscines. Body mass was the main predictor of song parameters in manakins, and together with habitat type, had a major effect on cardinals’ song structure. Precipitation and altitude were also associated with some song characteristics in cardinals. Our results bring unexpected insights into birdsong evolution, in which non-learners (manakins) revealed greater evolutionary lability than song learners (cardinals).

Abstract Background Shellfish reef restoration is relatively new in Australia, particularly to intertidal estuarine environments. In late 2019/early 2020 the first large-scale shellfish reef restoration project of the Sydney rock oyster, Saccostrea glomerata was undertaken in the Myall and Karuah Rivers, Port Stephens, on the mid north coast of New South Wales (NSW), Australia. The present study aimed to determine whether locally sourced clean conspecific oyster shells, and/or locally quarried rocks were better for natural recruitment of natural S. glomerata for large-scale oyster reef restoration, and subsequent recruitment of fishes and invertebrates. Over two years, recruitment of S. glomerata spat, and associated fishes and invertebrates were assessed on reefs made of: (1) rock, and (2) rock and shell. Results The mean (± SE) density of oyster spat on rock reefs (Myall River: 1790 ± 48, Karuah River: 1928 ± 68) was significantly greater (Myall River: ANOVA Si: MS 2, 18 = 31080167, F = 96.05, P

Abstract Background Some of the most consistent factors associated with college students’ evolution acceptance are how much they know about evolution (understanding), and the extent to which they identify as religious (religiosity). However, few studies explore how the relationship between understanding and acceptance can be impacted by student religiosity levels. Further, students show different levels of acceptance of evolution depending on the scale of evolution and context of evolution, but few studies explore how evolution understanding is related to acceptance at different scales and in different contexts. In this study, we analyzed survey responses from 11,409 college biology students sampled from across the United States. Using linear mixed models, we explored the relationship between students’ understanding and acceptance of evolution and how their religiosity impacted that relationship. We also explored how these relationships changed based on scale and context of evolution. Results We found evidence of six different scales or contexts of evolution ranging from acceptance of microevolution to accepting that all life on Earth shares a common ancestor. We found that students were most likely to accept microevolution while they were the least likely to accept the common ancestry of life. Interactions between student religiosity and understanding of evolution were significant predictors of their acceptance of macroevolution, human evolution within the species, human common ancestry with other apes, and the common ancestry of life. Notably, among highly religious students, how much they understood about evolution was not related to how much they accepted the common ancestry of life. Conclusions This study provides evidence for six different scales or contexts of evolution for which college students have different levels of acceptance. Students accepted the common ancestry of life the least indicating that this might be important to expand upon in future research. Further, we provide evidence that the relationship between evolution acceptance and understanding depends on scale and context of evolution as well as student religiosity levels. These results indicate that acceptance of evolution among college students is more multifaceted than previously thought and that highly religious students may find it particularly difficult to translate their understanding of evolution to their acceptance.

Abstract Background Understanding evolution is an important part of undergraduate biology education. Despite its importance, however, students often struggle to understand evolution, often holding preconceived notions of what evolution is. Here, we investigate how students in both majors and non-majors introductory biology define and conceive of evolution at the start of the semester for a two-year college and a four-year university near each other. We analyze open-ended responses to an in-class activity on the first day of the semester that asked students to define evolution, generating insight into how students are thinking of evolution prior to any formal instruction on evolution in college. Results Our analysis of over 300 student responses reveals that students hold diverse conceptions about evolution, with some students perceiving evolution in the context of evolutionary processes while other students define evolution by referring to perceived evolutionary consequences. In addition, we identify multiple non-normative conceptions about evolution, including students viewing evolution and natural selection as synonymous and not recognizing other evolutionary forces, and find that very few students likely have developed mental models linking evolution and genetics. In addition, we find few differences between how students at the two- and four-year institutions perceive evolution, and similarly few differences between students in a majors and non-majors introductory biology, suggesting that these conceptions of evolution are widespread at the beginning of introductory biology, regardless of major or institution. Conclusions We situate our results in the existing literature examining student conceptions of evolution, with our results extending past work that has primarily relied on more closed-ended questions or focused on specific evolutionary concepts (e.g., natural selection). Our results largely align with past work on student thinking of evolution but provide a broader, more holistic perspective at the ideas and framework that students are drawing upon when introductory biology instructors first introduce the term ‘evolution’. We conclude our paper by discussing implications for the biology education research community as well as instructors.

Abstract Biogeographic barriers to gene flow are central to studies of plant phylogeography. There are many physical and geographic barriers in China, but few studies have used molecular ecological evidence to investigate the natural geographic isolation barrier of the Qinling Mountains-Huaihe River Line (QHL). Allium macrostemon is a precious Chinese perennial herb belonging to the Amaryllidaceae family. It is used as a food and medicine, with a variety of health and healing properties. Five SSR markers, three chloroplast DNA (cpDNA) markers (psbA-trnH, rps16 and trnL-F), one nuclear ribosomal DNA (nrDNA) marker (ITS), and simplified genome GBS sequencing were used to analyse the genetic diversity and structure of A. macrostemon. Combining SSR, cpDNA, nrDNA ITS data and GBS analysis results, we divided A. macrostemon populations into northern and southern groups, with the southern group further divided into southwestern and central-southeastern groups. Niche simulation results reveal that the distribution area of A. macrostemon will reach its maximum in the future. These data indicate that the regional separation of A. macrostemon has been maintained by the combined influence of a geographical barrier and Quaternary climate, and that the back-and-forth fluctuations of QHL and Quaternary climate have played an important role in this process. QHL acts as a north-south dividing line in phylogeography and population genetic structure, promoting physical geographic isolation. This study provides a theoretical basis for the conservation, development, and utilization of A. macrostemon resources. It further provides a reference for understanding the systematic geographical pattern of the large-scale spatial distribution of plants in China and enriches our understanding of Quaternary plant evolution in areas with complex terrain.

Abstract It has been widely demonstrated that air and sand temperatures influence the anatomy of sea turtle hatchlings. We examined the impact of precipitation during the nesting season on the hatchling body size of loggerhead and green turtles from 37 beaches worldwide. Longitudinal data collected between 2012 and 2018 from Florida (US) and from a sample on Bõa Vista Island (Cabo Verde) carried out in 2019 showed that loggerhead body size at hatching was negatively correlated with precipitation, while precipitation was not correlated with hatchling body size in green turtles. A meta-analysis revealed that precipitation is positively correlated with hatchling mass in loggerhead turtles, while it is positively correlated with straight carapace length and width in green turtle hatchlings. The strongest influence of precipitation was found in the middle of the incubation period of loggerhead turtles in Cabo Verde, and we posit that this is due to an increase in the uptake of water for embryonic growth. These findings highlight the great importance of understanding the correlated effects of regional environmental variables, such as precipitation, on the development of sea turtle hatchlings and will have an impact on the evaluation of ongoing conservation and climate change discussions.

Abstract In 2024, researchers from around the world entered the joint BMC Ecology and Evolution and BMC Zoology image competition. The photos, a celebration of the wonders and mysteries of the natural world, emphasise the importance of protecting life on our planet. This editorial announces the winning images chosen by the Editors and senior members of the journal’s editorial boards.

Abstract Background Understanding how endangered species respond to climatic changes is fundamental for their conservation. Due to its restricted geographic range, its sensitivity to the ongoing global warming and its continuing decline, the Southwestern-Alpine endemic wolf spider Vesubia jugorum is currently classified as Endangered in the IUCN Red List. Here, we combined species distribution modelling (SDM) and phylogeographic inference to describe the present, the past and the future of this species in light of the mtDNA genetic structure of extant populations. Results Phylogenetic and network analyses show a high level of genetic differentiation and a strong genetic structure of the populations, likely explicable by a long history of isolation and survival in separate refugia. The SDM projection into past climatic conditions supports these results by showing a smaller distribution range compared to present, mostly restricted to the Maritime and Ligurian Alps, which possibly served as main refugium. Future forecast shows a significant shift in the bioclimatic range towards higher altitudes and latitudes, with a drastic decrease of habitat suitability in the central and south-eastern parts of the range, with consequent general loss of haplotype diversity. Conclusion SDM and phylogeographic inference support the hypothesis that the current distribution and the genetic structure of the extant populations mirror the survival in situ of Vesubia jugorum across repeated glacial and interglacial phases, in line with the ‘long-term stability hypothesis’. Future predictions show a significant shift in the bioclimatic range that V. jugorum will be likely unable to track, with profound impact on its long-term survival and its genetic diversity. Our considerations have implication for conservation genetics, highlighting the pivotal role of the transboundary protected areas of the SW-Alps in promoting conservation efforts for this species.

Abstract Thyroid hormones are crucial regulators of metamorphosis and development in bilaterians, particularly in chordate deuterostomes. Recent evidence suggests a role for thyroid hormone signaling, principally via 3,5,3′,5′-Tetraiodo-L-thyronine (T4), in the regulation of metamorphosis, programmed cell death and skeletogenesis in echinoids (sea urchins and sand dollars) and sea stars. Here, we test whether TH signaling in skeletogenesis is a shared trait of Echinozoa (Echinoida and Holothouroida) and Asterozoa (Ophiourida and Asteroida). We demonstrate dramatic acceleration of skeletogenesis after TH treatment in three classes of echinoderms: sea urchins, sea stars, and brittle stars (echinoids, asteroids, and ophiuroids). Fluorescently labeled thyroid hormone analogues reveal thyroid hormone binding to cells proximal to regions of skeletogenesis in the gut and juvenile rudiment. We also identify, for the first time, a potential source of thyroxine during gastrulation in sea urchin embryos. Thyroxine-positive cells are present in tip of the archenteron. In addition, we detect thyroid hormone binding to the cell membrane and nucleus during metamorphic development in echinoderms. Immunohistochemistry of phosphorylated MAPK in the presence and absence of TH-binding inhibitors suggests that THs may act via phosphorylation of MAPK (ERK1/2) to accelerate initiation of skeletogenesis in the three echinoderm groups. Together, these results indicate that TH regulation of mesenchyme cell activity via integrin-mediated MAPK signaling may be a conserved mechanism for the regulation of skeletogenesis in echinoderm development. In addition, TH action via a nuclear thyroid hormone receptor may regulate metamorphic development. Our findings shed light on potentially ancient pathways of thyroid hormone activity in echinoids, ophiuroids, and asteroids, or on a signaling system that has been repeatedly co-opted to coordinate metamorphic development in bilaterians.

Abstract In recent years, demographers have parsed variation in survivorship into two distinct components: the shape and the pace of ageing. The pace of ageing is defined by measures of longevity such as mean life expectancy or maximum longevity, whereas measures of the shape of ageing attempt to classify different shapes of the survivorship curve. We recently published a paper pointing out that a commonly used discretization of a shape measure, Keyfitz' entropy, does not correctly classify survivorship curves into negatively and positively senescing curves (de Vries et al., 2023). In that paper, we also suggested an alternative, accurate discrete‐time version of Keyfitz' entropy. de Vries et al. (2023) ended with two open questions, both of which have been answered by Giaimo (2024) now: (1) Can a discrete‐time entropy measure of survivorship be generalized beyond age‐based population models? Giaimo (2024) introduce a new formula that achieves this. (2) Will a discretization of Keyfitz' derivation of his measure as the elasticity of lifespan to a uniform change in mortality lead to the same formula as a discretization of Keyfitz' result? Giaimo (2024) answers: no. Here, we briefly discuss the implications of the results obtained by Giaimo (2024), and the implementation of his new formula into the Rpackage Rage, which is widely used for comparative demographic studies. We showcase the strength of the new method by reanalysing a comparison of Keyfitz' entropy to another shape measure. We find that the comparison is significantly altered by using Giaimo's new Keyfitz' formula. This example strengthens Giaimo's (2004) words of warning in approaching discretizations with attentiveness.

Abstract A major impediment to wildlife conservation and management, from a quantitative perspective, is dealing with high degrees of uncertainty associated with population estimates. Integrated population models (IPMs) can help alleviate that challenge, but they are often limited to narrow spatial or temporal windows owing to the financial and logistical burdens of acquiring requisite datasets. To expand the spatiotemporal scope of practical IPM implementation, we developed a novel method that expresses demographic relatedness among sampled and unsampled locations using geographic principles of spatial autocorrelation. We interpolated demographic parameters at unsampled locations using parameter estimates from data‐informed locations. Errors attributable to the interpolative process were corrected using a joint likelihood and locally recorded count data (‘cheaper’ and broadly distributed). We evaluated the spatially interpolated IPM (SIIPM) for precision and accuracy under variable levels of spatial autocorrelation using simulated data and a Leave‐One‐Out Cross‐Validation (LOOCV) technique. Conventional IPMs and state‐space models (SSM) were fit to the same simulated datasets to provide a comparative assessment of the novel method. In a final, empirical demonstration we fit the SIIPM to data collected from Greater Sage‐Grouse (Centrocercus urophasianus; sage‐grouse) populations located in Nevada, U.S.A. during 2013–2021. SIIPMs outperformed conventional IPMs when fit to data possessing moderate‐to‐high levels of spatial autocorrelation. Under moderate levels of autocorrelation, the average improvement in parameter estimation was 13.6% for survival, 65.3% for recruitment and 23.7% for rate of population change (λ). When spatial autocorrelation was low, the SIIPM still outperformed contemporary approaches in areas that were geographically close (

Abstract Knowledge of variation in population processes (e.g. population growth) across broad spatiotemporal scales is fundamental to population ecology and critical for conservation decision‐making. Count data from rigorous surveys (e.g. surveys with probabilistic sampling design and distance sampling information) can inform population processes but are often limited in space and time. Participatory science data cover broader spatiotemporal extents but are prone to bias due to limited to no sampling design and lack of distance sampling information, hindering their capability of informing population processes. Here, we developed an integrated dynamic N‐mixture model that jointly analyses rigorous survey and participatory science data to inform population growth at broad spatiotemporal extents. The model contains a flexible scaling parameter that allows fixed and random effects to account for biases and errors in participatory science data. We conducted simulations to evaluate the inference performance of this model across a broad range of spatial and temporal overlap between rigorous survey and participatory science data. We also conducted a case study of Baird's Sparrow (Centronyx bairdii), a species of conservation concern, to illustrate the application of the integrated model with rigorous survey data from the Integrated Monitoring in Bird Conservation Regions programme and participatory science North American Breeding Bird Survey and eBird data. Simulations showed that the integrated model improved precision without biasing parameter estimates, in comparison with a model informed by rigorous survey data alone. The case study further demonstrated the utility of the integrated model for quantifying range‐wide, long‐term population processes and environmental drivers despite limited spatiotemporal extent of rigorous survey data. In particular, we found that population growth rate peaked under medium temperature, which were only apparent in the integrated model. The integrated model developed in this study is useful for understanding wildlife population processes at broad spatiotemporal scales with count data. The flexible structure of this model, in particular the scaling parameter, makes it highly adaptable to a broad range of ecological systems and survey procedures. These properties make this modelling approach highly relevant for both population ecology and conservation practice.

Abstract Understanding temporal dynamics in ecological networks is crucial to predict their capability to cope with global changes. Despite this, proper quantification of network dynamics still remains a challenge. Temporal dynamics are typically studied using data of interaction networks over time, through the evaluation of interaction turnover and its two components: changes related to species turnover (species gains and losses) or rewiring (switching partners among the set of species shared over time). However, with this approach based exclusively on network data, dynamics are computed similarly for species that are truly missing from the community at a given temporal period, and for species occurring in the community but that do not interact with any other. This might lead to an underestimation of the real extent of rewiring, while overestimating the species turnover component of interaction turnover. We used data on 20 plant–pollinator communities to calculate interaction turnover components accounting also for the species that occurred in the communities at different temporal periods but did not appear in some of the temporal interaction networks (non‐interacting species) and then compared these estimates with conventional ones. Besides, we used empirical data and simulations to evaluate the extent to which dynamics estimates were affected by sampling effort when including and excluding non‐interacting species. As expected, disregarding the non‐interacting species that occurred in the communities at different temporal periods led to the underestimation of rewiring and the overestimation of species turnover as components of interaction turnover. Effect size was moderate when independent pollinator data were included, and large when including plants or both trophic levels. Simulations indicated that, in general, considering the non‐interacting species reduced biases at the time of identifying changes due to the different interaction turnover components. Accounting for non‐interacting species was particularly important to reduce bias when sampling effort was low and when dynamics were calculated seasonally. Despite sampling effort effects, phenology was the main determinant of species' rewiring frequencies. Our approach contributes to reducing biases and improving the estimates of interaction flexibility in networks, which are necessary to comprehend the response of communities in the face of global change.

Abstract Step selection functions (SSFs) are used to jointly describe animal movement patterns and habitat preferences. Recent work has extended this framework to model inter‐individual differences, account for unexplained structure in animals' space use and capture temporally varying patterns of movement and habitat selection. In this paper, we formulate SSFs with penalised smooths (similar to generalised additive models) to unify new and existing extensions, and conveniently implement the models in the popular, open‐source mgcv R package. We explore non‐linear patterns of movement and habitat selection, and use the equivalence between penalised smoothing splines and random effects to implement individual‐level and spatial random effects. This framework can also be used to fit varying‐coefficient models to account for temporally or spatially heterogeneous patterns of selection (e.g. resulting from behavioural variation), or any other non‐linear interactions between drivers of the animal's movement decisions. We provide the necessary technical details to understand several key special cases of smooths and their implementation in mgcv, showcase the ecological relevance using two illustrative examples and provide R code to facilitate the adoption of these methods. This paper offers a broad overview of how smooth effects can be applied to increase the flexibility and biological realism of SSFs.

Abstract We recently published a study discussing the pitfalls of non‐probability sampling when selecting monitoring sites. We demonstrated that selecting sites based on abundance can often lead to biased inference, and we suggested that researchers use probability sampling. We also called for nuance when interpreting results of monitoring programs that use non‐probability sampling. We suggested that inference from sites of great abundance might still be useful for inference into population dynamics of long‐lived species such as raptors. Perret et al. seem to misinterpret our call for nuance as advocating for non‐probability sampling. They state that we concluded the general recommendation of using probability sampling should be revised. We did not conclude this. In fact, we agree with their recommendation. Perret et al. implemented simulations that are unrealistic within the context of our study. We use empirical data for 12 raptor species to demonstrate that our previous results are valid and that simulations implemented by Perret et al. do not reflect the biology of long‐lived raptors. The time series simulated by Perret et al. fluctuated greatly in abundance with populations often more than doubling within a year. This is extremely unlikely for populations of long‐lived species having high site fidelity. Many historical programs monitor sites of great abundance and thus risk biased results. We demonstrate that this risk is minimal under some important conditions and our results likely apply to other long‐lived species. Acknowledging this nuance could rescue many long‐term monitoring programs and their data thereby preserving efforts of costly conservation programs. Consistent with our original study, these exceptions do not invalidate the general recommendation to avoid non‐probability sampling; however, they do support our call for nuance when interpreting results of studies that monitored animals at sites of great abundance.

Abstract Understanding the complex interactions between external and internal factors that influence pollinator foraging behaviour is essential to understand ecosystem functioning, design agricultural practices or develop effective conservation strategies. However, it remains challenging to collect large and reliable data sets with reasonable personnel and workload. In this study, we present a wireless and cost‐effective robotic flower equipped with internet of things (IoT) technology that automatically offers nectar to visiting insects while monitoring visitation time and duration. The robotic flower is easy to manipulate and settings such as nectar refill rates can be remotely altered, making it ideal for field settings. The system transmits data completely wirelessly and autonomously, is mobile and easy to clean. The prototype settings allow for approximately 2 weeks of uninterrupted data collection for each battery charge. As a proof‐of‐concept application, a foraging preference dual choice experiment with bumblebees was performed. On average, more than 7000 flower visits per colony were registered daily with a set‐up consisting of 16 robotic flowers. The data show a gradual preference shift away from the pre‐trained low concentration, confirming the hypothesis of favouring sugar water with higher concentration. The robotic flower provides accurate and reliable data on insect behaviour, significantly reducing the price and/or labour costs. Although primarily designed for (bumble)bees, the system could be easily adapted for other flower‐visiting insects. The robotic flower is user‐friendly and can be easily adapted to address a wide range of research questions in pollination ecology, conservation biology, biocontrol and ecotoxicology, and allows for detailed studies on how nectar traits, flower colour and shape or pollutants affect foraging behaviour.

Abstract Phenological shifts across plant species is a powerful indicator to quantify the effects of climate change. Today, mobile applications with automated species identification open new possibilities for phenological monitoring across space and time. Here, we introduce an innovative spatio‐temporal machine learning methodology that harnesses such crowd‐sourced data to quantify phenological dynamics across taxa, space and time. Our algorithm links individual phenological responses across thousands of species and geographical locations, using a similarity measure. The analysis draws on nearly ten million plant observations collected through the AI‐based plant identification app Flora Incognita in Germany from 2018 to 2021. Our method quantifies changes in synchronisation across the annual cycle. During the growing season, synchronised behaviour can be encoded by a few characteristic macrophenological patterns. Nonlinear spatio‐temporal changes of these patterns can be efficiently quantified using a data compressibility measure. Outside the growing season, the phenological synchronisation diminishes introducing noise into the patterns. Despite biases and uncertainties associated with crowd‐sourced data, for example due to human data collection behaviour, our study demonstrates the feasibility of deriving meaningful indicators for monitoring plant macrophenology from individual plant observations. As crowd‐sourced databases continue to expand, our approach holds promise to study climate‐induced phenological shifts and feedback loops.

Abstract Ecosystems contain numerous species interacting with each other and the environment. However, data on all relevant state variables is rarely available, hampering inference and prediction. Empirical dynamic modelling (EDM) is a valuable tool for prediction, inference and control in such partially observed systems. However, EDM typically assumes that the available time series are observed without error. Failing to account for observation noise strongly biases estimates of Lyapunov exponents and reduces forecast accuracy. To address this limitation, we propose incorporating EDM into a hidden Markov framework and using an iterative scheme based on the expectation maximization (EM) algorithm to obtain filtered state and parameter estimates. We evaluate the performance of this approach on several simulated dynamical systems with a range of additive noise levels, as well as on insect population time series. Accounting for observation noise improved accuracy of population forecasts and estimates of Lyapunov exponents (LE) over a wide range of noise levels relevant to ecological time series.

Abstract Global change drives multiple facets of biodiversity including interaction diversity, which is fundamental for ecosystem functioning. However, studying trophic interactions is challenging in meta‐ecosystems, that is ecosystems connected by spatial flows of energy, materials and organisms across ecosystem boundaries. While analytical methods based on abundances of polyunsaturated fatty acids (PUFAs) and stable isotopes of amino acids (AAs) are being increasingly used, it has never been explored if both approaches could be: (i) combined in mixing models to enhance precision in dietary inference (ii) compared to disentangle transfers of various PUFAs and proteins in food webs in the wild. We explore the utility of analytical approaches based on PUFA abundances and AA isotopes to resolve resource transfers in a natural riparian food web. We focus on spiders and their potential prey from blue, green and brown sources to address three important and persisting methodological issues in food‐web ecology, namely whether (i) essential AA carbon isotopes can resolve protein origin from blue, green and brown resources, (ii) PUFA relative abundance and AA isotopes can be combined in a mixing model to provide higher precision estimates (i.e. narrower intervals) and (iii) combining the two approaches can unveil the coupling of protein and PUFA transfers in food webs. Our research demonstrates the power of AA isotopes and PUFAs to distinguish blue, green, and brown sources and their transfer up to consumers. We show that combining PUFA relative abundance and AA isotopes in a mixing model provides overall estimates similar to the individual estimates but significantly increases precision. In addition, we showcase how combining approaches unveil the coupling of protein and PUFA transfers. For instance, we show that most PUFAs are less concentrated from prey to predators, relative to proteins, highlighting uncoupling of PUFAs and protein transfer along food chains. We show for the first time the effectiveness of combining AA isotopes and PUFA abundances, particularly relevant for complex trophic interactions in a meta‐ecosystem context. Our study illustrates the trophic uncoupling of proteins and PUFAs, highlighting the necessity in combining both approaches.

Abstract Effective visualization of infectious disease risks is crucial for the development of efficient prevention and control strategies. However, the efficacy of mainstream models is hindered by a scarcity of reliable data in target areas, a situation that is particularly acute when dealing with emerging or re‐emerging infectious diseases. Additionally, these models typically fail to integrate local disease‐related risk factors in line with the ‘One Health’ concept, resulting in inaccurate predictions. Consequently, accurately assessing infectious disease risks without reliable data is challenging. This study introduces SpatMCDA, an innovative R package designed to assess infectious disease risk areas through spatial multi‐criteria decision analysis (MCDA). SpatMCDA is structured around six core modelling steps: standardizing risk factors, determining factor weights, constructing risk maps, performing One‐at‐a‐Time sensitivity analysis, calculating the Mean of Absolute Change Rates and conducting an uncertainty analysis. By examining the case of West Nile virus (WNV) in China, this study illustrates how SpatMCDA can be useful in identifying disease transmission risks in the absence of reliable outbreak data. The assessment identified areas at risk for WNV in northwestern, eastern and southern China. By integrating spatial and epidemiological data, SpatMCDA enhances infectious diseases risk assessment in situations where data are limited. Its efficiency in using available data for accurate risk mapping and adaptability in weighting various risk factors enables tailored analyses. This tool enhances public health strategies, contributing to global health security.

Abstract Keyfitz's entropy originally is a shape measure of senescence for continuous‐time models. But a later formula of Keyfitz's entropy for discrete time also exists. de Vries et al. (2023) showed that this discrete‐time formula is not a genuine shape measure of senescence and proposed a new discrete‐time formula for entropy that qualifies as a shape measure. However, these authors obtained their new formula by discretizing an alternative version of Keyfitz' continuous‐time formula and not by following his original derivation, that is not by computing the elasticity of life expectancy to an age‐uniform mortality change. Hence, they regarded as a loose end of their work whether discretizing Keyfitz' original derivation would also lead to their new formula. These authors also deemed lack of direct applicability to stage‐classified models a major downside of the new formula they proposed. Here we do two separate things: we discretize Keyfitz' original derivation of entropy and we generalize the new discrete‐time formula for this quantity proposed by de Vries et al. (2023). We show that the discrete‐time formula for entropy that de Vries et al. (2023) propose to supersede, while potentially problematic for studying senescence, is, as Keyfitz' original formula, an elasticity. Generalizing the work of de Vries et al. (2023) leads to a formula for entropy that can be directly applied as a shape measure of senescence to models with any demographic classification. We also prove convergence properties that validate the application of this general formula to models classified by stage. We thus support and generalize the successful approach by de Vries et al. (2023) of obtaining new discrete‐time formulas for Keyfitz' entropy from a shape perspective: merits of shape measures of senescence, which capture the overall age‐pattern of mortality, should be based on their desirable properties and not necessarily on their means of derivation. Moreover, our work gives one more example of how in ecological and evolutionary modelling the passage from continuous to discrete time may be non‐obvious.

Abstract Population monitoring programmes typically rely on sampling because it is impossible to survey all the sites within the study area. In such a situation, the general recommendation to obtain unbiased estimates of population trends is to select monitoring sites using probability sampling. However, site selection not based on probability sampling, such as selecting sites with the largest abundance of individuals at the beginning of the monitoring programme, is common in practice. Nevertheless, these methods carry the risk of obtaining biased trend estimates. Using simulations, McClure & Rolek (2023) investigated whether three non‐probability sampling site selection methods can yield unbiased trend estimates under some specific conditions. For two of these methods, that is selecting high quality sites and selecting sites known to be occupied, the authors conclude that there is a major risk of obtaining biased trend estimates. For the third method, that is selecting sites with the largest initial abundance, they found conditions in which unbiased estimates can be obtained. They conclude that the general recommendation to use probability sampling should be revised. Here, we show that the authors' results, although perfectly correct, do not invalidate this recommendation. First, we point out that the authors made strong assumptions about the populations' functioning in their simulations, especially that inter‐annual variance in abundance is similar for all sites, which is unlikely in most real populations. We show through simple simulations that even slightly relaxing this assumption invalidates the authors' results. We also point out that for most of the hypotheses made by the authors, it is generally not known at the beginning of a study whether they will be respected. Furthermore, the authors did not provide evidence that selecting sites based on high initial abundance leads to more precise trend estimates than probability sampling methods. Therefore, neither the benefits nor the risks of this method are known. We conclude that until evidence is provided that abundance‐based site selection improves estimate precision and the situations in which it provides unbiased estimates are clearly identified, using probability sampling should remain the rule.

Abstract Global climate‐driven ocean warming has decreased dissolved oxygen (DO) levels (ocean deoxygenation) leading to expansions of hypoxic zones, which will affect the movements, behaviour, physiology and distributions of marine animals. However, the precise responses of animals to low DO remains poorly understood because movements and activity levels are seldom recorded alongside instantaneous DO in situ. We describe a new animal‐attached (dissolved oxygen measuring, DOME) archival tag with an optical oxygen sensor for recording DO, in addition to sensors for temperature and depth, a triaxial accelerometer for fine‐scale movements and activity, and a GPS for tag recovery. All sensors were integrated on a single electronic board. Calibration tests demonstrated small mean difference between DOME tag and factory‐calibrated DO sensors (mean relative error of 5%). No temporal drift occurred over a test period three times longer than the maximum deployment time. Deployments on four blue sharks (Prionace glauca) in the central North Atlantic Ocean showed regular vertical oscillations from the surface to a maximum of 404 m. Profiles from diving sharks recorded DO concentrations ranging from 217 to 272 μmol L−1, temperatures between 13°C and 23°C, and identified an oxygen maximum at ~45 m depth, all of which were consistent with ship‐based measurements. Interestingly, the percentage of time sharks spent burst swimming was greater in the top 85 m compared to deeper depths, potentially because of higher prey availability in the surface layer. The DOME tag described blue shark fine‐scale movements and activity levels in relation to accurately measured in situ DO and temperature, with the potential to offer new insights of animal performance in low oxygen environments. Development of a tag with physico‐chemical and movement sensors on a single electronic board is a first step towards satellite relay of these data over broader spatiotemporal scales (months over thousands of kilometres) to determine direct and indirect responses of marine animals to heatwave and deoxygenation events.

Abstract The availability and appropriateness of nesting sites significantly influence the reproductive success and overall welfare of wild bees. Human‐induced factors contribute to the destruction of natural nesting habitats. To address these limitations, innovative solutions such as the development of artificial nests, offer alternative nest sites to support wild bee populations. We designed the Osmia3DNest, a 3D printed standardized nest tube for solitary cavity‐nesting bees, aiming to provide a safe for the environment, long‐life, time‐saving and biodegradable product that anyone can print. We proudly present the two Osmia3DNest models for mason bees—closed and open—using polylactic acid filament. We demonstrate the effectiveness of Osmia3DNest on mason bee reproduction parameters compared with traditional reed nests. Osmia3DNest can be an alternative to the other artificial nests, which people can customize for their necessity depending on their place of living (rural or urban area), and they can also be washed and reused several times and then decomposed. Osmia3DNest holds potential for wildlife biologists, management of pollinators, and educational outreach, offering adaptability for different bee species and experimental needs.

Abstract Environmental DNA (eDNA) monitoring of species distribution has become a critical tool in ecology, conservation biology and fisheries for identifying the presence and distribution of diverse organisms, including important, threatened and invasive species. However, eDNA detection still has room for improvement in sensitivity, requiring time‐consuming real‐time polymerase chain reaction (qPCR) steps and costly machines. In this study, we report a CRISPR‐Cas13‐based method for rapid, easy, sensitive, low‐cost and on‐site detection of eDNA. The assay for the detection of common carp (Cyprinus carpio) and medaka (Oryzias latipes) nucleic acid employs a two‐step process, starting with recombinase polymerase amplification (RPA) and followed by cleavage using Cas13 nuclease, to effectively identify mitochondrial DNA or RNA. Our results showed that the Cas13‐based method has a higher sensitivity than the qPCR‐based method in detecting tiny amounts of eDNA. When combined with reverse transcription of environmental RNA (eRNA), our method increased detection sensitivity by approximately one order of magnitude. Cas13‐based detection could achieve on‐site detection of eDNA using a quick nucleic acid extraction solution and lateral flow strips. Cas13‐based detection of eDNA and eRNA requires minimal training efforts and can be performed in 1 h, without the need for centrifugation and qPCR machines. The portability of the Cas13‐based method, along with its accuracy and relative ease in designing primers and CRISPR RNA (crRNA), underscores its potential to broaden the application of eDNA and eRNA in various fields, including biodiversity conservation.

Abstract Background Understanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either ‘natural’ or ‘disturbed’ landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion. Results A phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3–0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE. Conclusions Bee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.

Abstract Even though the high plateaus of Qinghai-Tibet and Iran share many faunal elements, the historical biogeography of the species present in this area are not very well understood. We present a complete COI barcode library for Aporia Hübner and a first comprehensive phylogeny for the genus including all known species and majority of subspecies using ten available genes (COI-COII, ND1, ND5, Cytb, EF-1a, Wg, 16S, 28S-D2/D3 and 28S-D8). We then focus on A. leucodice (Eversmann, 1843) and related taxa in order to resolve some long-standing taxonomic issues in this species-group. Based on DNA sequence data as well as morphology, we raise Aporia illumina (Grum-Grshimailo 1890) stat. nov. (= pseudoillumina Tshikolovets 2021 syn. nov.) as a distinct species and designate a lectotype; synonymize Aporia leucodice leucodice Eversmann, 1843 (= A. l. morosevitshae Sheljuzhko, 1908 syn. nov.); and describe a new species, Aporia ahura sp. nov., from the Central Alborz Mountains in northern Iran.

Abstract Background Tongoloa is a genus comprising approximately 20 species, primarily distributed in the mountainous regions of southwest China. The insufficiency of specimen materials and morphological similarities among species render it a taxonomically challenging genus within the Apiaceae family. To elucidate the phylogenetic relationships and taxonomy of Chinese Tongoloa, this study utilized a total of 115 nrITS sequences, including 47 recently obtained sequences, for phylogenetic reconstruction. Results Phylogenetic relationships reconstructed from ITS sequences indicate that the East Asia Clade and the Komarovia Clade are sister groups, and Tongoloa belongs to the East Asia Clade. Species of Tongoloa are subdivided into 3 distinct groups, all sharing similar fruit morphologies and are clearly differentiated from related taxa. Several Tongoloa-like members classified under other genera are interpreted to be closely related to Tongoloa. Morphological and molecular data indicate that Tongoloa, Sinolimprichtia subclade and Chinese Trachydium subclade are separate yet genetically contiguous taxa. It is confirmed that Tongoloa zhongdianensis belongs to the Hymenidium Clade, while Sinocarum is classified within the Acronema Clade. Two new taxa are found in the Hengduan Mountains. Conclusion Tongoloa is a genus within the East Asia Clade of Apiaceae, and the phylogeny reconstructed based on ITS sequences divides it into 3 main groups. By integrating fruit morphology and molecular phylogenetic analyses, we preliminary clarified the intricate taxonomic relationships among Tongoloa and related taxa. These results provide valuable opportunities for a deeper understanding of the phylogeny of Tongoloa.

Abstract Epidemic of Cashew Fusarium wilt disease (CFWD) has been a continuous focal challenge in the cashew farming, in Tanzania. Limited to edaphic conditions as a major factor in its epidemic, the current study aimed to assess the habitat-disease relationship. Purposive surveys involving assessment of disease prevalence and habitat compositions were conducted across four landscapes of southeastern zone from 2019 to 2023. Findings revealed a widespread of CFWD across diversified landscapes possessing varying habitat characteristics, mainly cultivated land with mature cashew, brownish sand loamy soils, grassland or shrub vegetation, seasonal river streamlines and natural water wells. The highest disease incidence and severity were noted at Nachingwea/Masasi plain (99.28:88.34%) followed by Liwale inland plain (98.64:89.3%), Coastal zone (72.72:59.83%) and Tunduru dissected plain (62.13:54.54%). The habitat characteristics were strongly similar within the landscape (0.86-Jaccard index) except between villages of the coastal zone (0.71-Jaccard index). Across landscapes, Nachingwea/Masasi plains and the Coastal zone were strongly similar to Tunduru dissected plain (0.63—1.0-Jaccard index), but strongly dissimilar with the Liwale inland plain (0.67—0.70- Jaccard distance). Furthermore, the presence of greater than 0.5 suitability indices across landscapes were revealed, with Liwale inland plain having strongest suitability index of 0.743 followed by Coastal zone (0.681), Tunduru dissected plain (0.617) and Nachingwea/Masasi plain. Significantly, the habitats had an increase of 0.1 suitability index, and positively correlated with disease prevalence by triggering disease incidence of 13.9% and severity of 31.4%. The study for the first time revealed the presence of an association between disease prevalence and landscape habitat characteristics of southeastern, Tanzania; paving the way to inclusive thinking of habitat as one of the drivers in the prevalence of fusarium wilt disease of cashews. Further research on the genetic coevolution of Fusarium oxysporum across landscapes to strengthen disease risk management in the cashew industry is recommended.

Abstract Evolutionary theory is based on the conflict that arises when certain heritable variants out-compete others. Given this foundational conflict, a central question for evolutionary biologists concerns the presence of cooperation found throughout all levels of biological organization; from biochemical pathways to complex animal societies. Human behavior is often distinguished from other animal behavior by the presence of acts of cooperative behavior called altruism. Altruism is a cooperative act that penalizes the actor for actions that benefit the recipient. Any other form of cooperation, one that does not penalize the actor, is formally not considered altruistic. How can costly altruistic behavior evolve? This question was the basis for development of a web application tool incorporating a game theory model to investigate conditions affecting cooperative behavior. The game theory model described as Prisoner’s Dilemma incorporates acts of cooperation and non-cooperation (defection). Computer simulations of Prisoner’s Dilemma were developed and online applications were administered for five semesters at Georgia Gwinnett College, using two simulation environments referred to as Random and Non-random. Data collected from simulation runs were used to evaluate the effect of environment on student cooperative behavior and actively engage students in concepts associated with the evolution of cooperation and game theory. Results from student game play suggest group simulation environment played a significant role in the likelihood of observing cooperative behavior. Educational content and attitudinal surveys suggested that PD game play in the undergraduate evolution class at Georgia Gwinnett College improved student knowledge and self-confidence.

Four species of the genus Panaspis – P. cabindae, P. wahlbergii, P. maculicollis and P. mocamedensis – are currently known from Angola. The analysis of recently collected specimens from Serra da Neve Inselberg, an isolated mountain located in northern Namibe Province, revealed unexpected taxonomic diversity in the group. Using an integrative taxonomy approach based on morphological and DNA sequence data, with both mitochondrial (16S) and nuclear (RAG-1) genes, we were able to distinguish two distinct populations, described here as two new species, Panaspis ericae sp. nov. and P. mundavambo sp. nov. Both species are assumed to be endemic to the inselberg. This reinforces our notion of southwestern Angola as a hotspot of skink diversity, and highlights the urgent need for the conservation of Serra da Neve.

Abstract Background Inbreeding and relationship coefficients are essential for conservation and breeding programs. Whether dealing with a small conserved population or a large commercial population, monitoring the inbreeding rate and designing mating plans that minimize the inbreeding rate and maximize the effective population size is important. Free, open-source, and efficient software may greatly contribute to conservation and breeding programs and help students and researchers. Efficient methods exist for calculating inbreeding coefficients. Therefore, an efficient way of calculating the numerator relationship coefficients is via the inbreeding coefficients. i.e., the relationship coefficient between parents is twice the inbreeding coefficient of their progeny. A dummy progeny is introduced where no progeny exists for a pair of individuals. Calculating inbreeding coefficients is very fast, and finding whether a pair of individuals has a progeny and picking one from multiple progenies is computationally more demanding. Therefore, the R package introduces a dummy progeny for any pair of individuals whose relationship coefficient is of interest, whether they have a progeny or not. Results Runtime and peak memory usage were benchmarked for calculating relationship coefficients between two sets of 250 and 800 animals (200,000 dummy progenies) from a pedigree of 2,721,252 animals. The program performed efficiently (200,000 relationship coefficients, which involved calculating 2,721,252 + 200,000 inbreeding coefficients) within 3:45 (mm:ss). Providing the inbreeding coefficients (for real animals), the runtime was reduced to 1:08. Furthermore, providing the diagonal elements of D in $$\textbf{A} = \textbf{TDT}^{\prime }$$ A = TDT ′ (d), the runtime was reduced to 54s. All the analyses were performed on a machine with a total memory size of 1 GB. Conclusions The R package FnR is free and open-source software with implications in conservation and breeding programs. It proved to be time and memory efficient for large populations and many dummy progenies. Calculation of inbreeding coefficients can be resumed for new animals in the pedigree. Thus, saving the latest inbreeding coefficient estimates is recommended. Calculation of d coefficients (from scratch) was very fast, and there was limited value in storing those for future use.

Abstract Marine ecosystems are facing a dramatic loss of biodiversity worldwide, together with a widespread collapse of habitats and their functionality. In this context, Marine Citizen Science (MCS) can be a powerful tool to monitor these changes over time. The flowering of very well-structured international projects is strengthening the scientific credibility of MCS data, especially when data are collected after specifically designed training programs and shared in public user-friendly repositories. Here we present a new perspective on the use of MCS in the Mediterranean area, along with the main benefits for the stakeholders (i.e., diving centers, trainers, and policymakers) and the users (i.e., divers), resumed in three pillars: Pillar I – MCS as a tool for the site valorization; Pillar II – MCS as a new career opportunity for graduated students; Pillar III – MCS as a business opportunity for diving centers. In the frame of the Quintuple Helix Approach, for which there is a strong need of a socioecological transition of the society and economy, we show how MCS can be a win-win-win solution for all the actors involved, providing the vision for new and highly qualified job and business opportunities for the diving sector.

Abstract Background The acquisition of air-breathing organs is one of the key innovations for terrestrialization in animals. Terrestrial isopods, a crustacean lineage, can be interesting models to study the evolution of respiratory organs, as they exhibit varieties of air-breathing structures according to their habitats. However, the evolutionary processes and origins of these structures are unclear, due to the lack of information about their developmental processes. To understand the developmental mechanisms, we compared the developmental processes forming different respiratory structures in three isopod species, i.e., ‘uncovered lungs’ in Nagurus okinawaensis (Trachelipodidae), ‘dorsal respiratory fields’ in Alloniscus balssi (Alloniscidae), and pleopods without respiratory structures in Armadilloniscus cf. ellipticus (Detonidae). Results In N. okinawaensis with uncovered lungs, epithelium and cuticle around the proximal hemolymph sinus developed into respiratory structures at post-manca juvenile stages. On the other hand, in Al. balssi with dorsal respiratory fields, the region for the future respiratory structure was already present at manca 1 stage, immediately after hatching, where the lateral protrusion of ventral epithelium occurred, forming the respiratory structure. Furthermore, on pleopods in Ar. cf. ellipticus, only thickened dorsal cuticle and the proximal hemolymph sinus developed during postembryonic development without special morphogenesis. Conclusions This study shows that the respiratory structures in terrestrial isopods develop primarily by postembryonic epithelial modifications, but the epithelial positions developing into respiratory structures differ between uncovered lungs and dorsal respiratory fields. This suggests that these two types of respiratory structures do not result from simple differences in the degree of development. Future analysis of molecular developmental mechanisms will help determine whether these are the result of heterotopic changes or have different evolutionary origins. Overall, this study provides fundamental information for evolutionary developmental studies of isopod respiratory organs.

Abstract Background Adaptation to a stressor can lead to costs on other traits. These costs play an unavoidable role on fitness and influence the evolutionary trajectory of a population. Host defense seems highly subject to these costs, possibly because its maintenance is energetically costly but essential to the survival. When assessing the ecological risk related to pollution, it is therefore relevant to consider these costs to evaluate the evolutionary consequences of stressors on populations. However, to the best of our knowledge, the effects of evolution in irradiate environment on host defense have never been studied. Using an experimental evolution approach, we analyzed fitness across 20 transfers (about 20 generations) in Caenorhabditis elegans populations exposed to 0, 1.4, and 50.0 mGy.h− 1 of 137Cs gamma radiation. Then, populations from transfer 17 were placed in the same environmental conditions without irradiation (i.e., common garden) for about 10 generations before being exposed to the bacterial parasite Serratia marcescens and their survival was estimated to study host defense. Finally, we studied the presence of an evolutionary trade-off between fitness of irradiated populations and host defense. Results We found a lower fitness in both irradiated treatments compared to the control ones, but fitness increased over time in the 50.0 mGy.h− 1, suggesting a local adaptation of the populations. Then, the survival rate of C. elegans to S. marcescens was lower for common garden populations that had previously evolved under both irradiation treatments, indicating that evolution in gamma-irradiated environment had a cost on host defense of C. elegans. Furthermore, we showed a trade-off between standardized fitness at the end of the multigenerational experiment and survival of C. elegans to S. marcescens in the control treatment, but a positive correlation between the two traits for the two irradiated treatments. These results indicate that among irradiated populations, those most sensitive to ionizing radiation are also the most susceptible to the pathogen. On the other hand, other irradiated populations appear to have evolved cross-resistance to both stress factors. Conclusions Our study shows that adaptation to an environmental stressor can be associated with an evolutionary cost when a new stressor appears, even several generations after the end of the first stressor. Among irradiated populations, we observed an evolution of resistance to ionizing radiation, which also appeared to provide an advantage against the pathogen. On the other hand, some of the irradiated populations seemed to accumulate sensitivities to stressors. This work provides a new argument to show the importance of considering evolutionary changes in ecotoxicology and for ecological risk assessment.

Abstract The Portezuelo Formation preserves an outstanding record of the upper Turonian – lower Coniacian. Despite the discovery of a significant quantity of sauropod fossil material from the formation, only two species have been formally described to date: Malarguesaurus florenciae and Futalognkosaurus dukei. Here we present new sauropod material mostly composed of non-articulated caudal vertebrae (MCF-PVPH 916 and 917) that belong to two titanosauriforms on the basis of the following features: anterior caudal vertebrae with procoelous-opisthoplatyan articulations, transverse processes that reach the posterior articular face of the centrum and neural spines with a transverse width of around 50% of their anteroposterior length; anterior and middle caudal vertebrae with the neural arch restricted to the anterior half of the centrum; middle caudal centra with circular cross-section. Phylogenetic analysis recovers the new material in close relation to Malarguesaurus within a monophyletic clade at the base of Somphospondyli. This clade shares large pedicel height with a vertical anterior border on the middle caudal vertebrae, a vertical orientation of the neural spines on the distalmost middle caudal vertebrae and proximalmost posterior caudal vertebrae, and subequal relative lengths of the proximal ulnar condylar processes. The specimens presented here are distinct not only from Futalognkosaurus, but also from other indeterminate titanosaurian remains from the same formation. However, there are no significant differences between the specimen MCF-PVPH 917 and Malarguesaurus, but there are differences between the posterior caudal vertebrae of MCF-PVPH 916 and Malarguesaurus, so they could be considered different species. Whilst we err on the side of caution in not naming new taxa here, the two specimens significantly expand what we know about sauropods in the Turonian–Coniacian ecosystems of Patagonia, which will continue to do so as more material is discovered.

Abstract Background The light organs of the splitfin flashlight fish Anomalops katoptron are necessary for schooling behavior, to determine nearest neighbor distance, and to feed on zooplankton under dim light conditions. Each behavior is coupled to context-dependent blink frequencies and can be regulated via mechanical occlusion of light organs. During shoaling in the laboratory individuals show moderate blink frequencies around 100 blinks per minute. In this study, we correlated bioluminescent blinks with the spatio-temporal dynamics of swimming profiles in three dimensions, using a stereoscopic, infrared camera system. Results Groups of flashlight fish showed intermediate levels of polarization and distances to the group centroid. Individuals showed higher swimming speeds and curved swimming profiles during light organ occlusion. The largest changes in swimming direction occurred when darkening the light organs. Before A. katoptron exposed light organs again, they adapted a nearly straight movement direction. Conclusions We conclude that a change in movement direction coupled to light organ occlusion in A. katoptron is an important behavioral trait in shoaling of flashlight fish.

Abstract Fruit traits mediate animal-plant interactions and have to a large degree evolved to match the sensory capacities and morphology of their respective dispersers. At the same time, fruit traits are affected by local environmental factors, which may affect frugivore-plant trait match. Temperature has been identified as a major factor with a strong effect on the development of fruits, which is of serious concern because of the rising threat of global warming. Nonetheless, this primarily originates from studies on domesticated cultivars in often controlled environments. Little is known on the effect of rising temperatures on fruit traits of wild species and the implications this could have to seed dispersal networks, including downstream consequences to biodiversity and ecosystem functioning. In a case study of five plant species from eastern Madagascar, we addressed this using the elevation-for-temperature approach and examined whether a temperature gradient is systematically associated with variation in fruit traits relevant for animal foraging and fruit selection. We sampled across a gradient representing a temperature gradient of 1.5–2.6 °C, corresponding to IPCC projections. The results showed that in most cases there was no significant effect of temperature on the traits evaluated, although some species showed different effects, particularly fruit chemical profiles. This suggests that in these species warming within this range alone is not likely to drive substantial changes in dispersal networks. While no systemic effects were found, the results also indicate that the effect of temperature on fruit traits differs across species and may lead to mismatches in specific animal-plant interactions.