Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly as tropospheric ozone (O3), which contributes to the decline of urban and peri-urban forests. A notable case are fir(Abies religiosa) forests in the peripheral mountains southwest of Mexico City, which have been severely affected by O3 pollution since the 1970s. Interestingly, some young individuals exhibiting minimal O3—related damage have been observed within a zone of significant O3 exposure. Using this setting as a natural experiment, we compared asymptomatic and symptomatic individuals of similar age (≤15 years old; n = 10) using histological, metabolomic and transcriptomic approaches. Plants were sampled during days of high (170 ppb) and moderate (87 ppb) O3 concentration. Given that there have been reforestation efforts in the region, with plants from different source populations, we first confirmed that all analysed individuals clustered within the local genetic group when compared to a species-wide panel (Admixture analysis with ~1.5K SNPs). We observed thicker epidermis and more collapsed cells in the palisade parenchyma of needles from symptomatic individuals than from their asymptomatic counterparts, with differences increasing with needle age. Furthermore, symptomatic individuals exhibited lower concentrations of various terpenes (ß-pinene, ß-caryophylene oxide, α-caryophylene and ß-α-cubebene) than asymptomatic trees, as evidenced through GC-MS. Finally, transcriptomic analyses revealed differential expression for thirteen genes related to carbohydrate metabolism, plant defense, and gene regulation. Our results indicate a rapid and contrasting phenotypic response among trees, likely influenced by standing genetic variation and/or plastic mechanisms. They open the door to future evolutionary studies for understanding how O3 tolerance develops in urban environments, and how this knowledge could contribute to forest restoration.

A document by Andrew Dean. Click on the document to view its contents.

Abstract: This study explores the habitat distribution of Pterocarpus santalinus, a valuable rosewood species, across China, focusing on its response to current and future climate changes. Utilizing the MaxEnt model, we assess its suitable habitat under present conditions and future climate scenarios (SSPs126, SSPs245, and SSPs585). Our findings reveal that the current suitable habitat, spanning approximately 409,600 km², is primarily located in the central and southern parts of Guangdong, Guangxi, Fujian, Yunnan, as well as in the Hainan provinces, along with the coastal regions of Taiwan, and the Sichuan-Chongqing border. The habitat’s distribution is significantly influenced by climatic factors such as temperature seasonality (bio4), mean temperature of the wettest quarter (bio8), annual mean temperature (bio1), and annual precipitation (bio12), while terrain and soil factors play a lesser role. Under future climate scenarios, the suitable habitat for P. santalinus is projected to expand, with a northeastward shift in its distribution center. This research not only sheds light on the geoecological characteristics and geographical distribution of P. santalinus in China but also offers a scientific basis for planning its cultivation areas and enhancing cultivation efficiency under changing climate conditions.

Roegneria yenchiana sp. nov. (Triticeae) is described as a new species collected from Shangri-la of Yunnan Province in China based on morphological, cytological, and molecular data. It is morphologically characterized by one spikelet per node, rectangular glums, awns flanked by two short mucros in lemmas, which is distinguished from other species of Roegneria. The genomic in situ hybridization results indicate that R. yenchiana is an allotetraploid, and its genomic constitution is StY. Phylogenetic analyses based on multiple loci suggested that R. yenchiana is closely related to Pseudoroegneria and Roegneria, and the Pseudoroegneria served as the maternal donors during its polyploid speciation.

Global environmental changes are predicted to lead to warmer average temperatures and more extreme weather events thereby affecting wildlife population dynamics by altering demographic processes. Extreme weather events can reduce food resources and mortality, but the contribution of such events to demographic processes are poorly understood. Estimates of season-specific survival probabilities are crucial for understanding mechanisms underlying annual mortality. However, only few studies have investigated survival at sufficient temporal resolution to assess the contribution of extreme weather events. Here, we analysed biweekly survival probabilities of 307 radio-tracked juvenile little owls (Athene noctua) from fledging to their first breeding attempt in the following spring. Biweekly survival probabilities were lowest during the first weeks after fledging in summer and increased over autumn to winter. The duration of snow cover in winter had a strong negative effect on survival probability, while being well fed during the nestling stage increased survival during the first weeks after fledging and ultimately led to a larger proportion of birds surviving the first year. Overall annual survival probability over the first year varied by 34.3 % between 0.117 (95 % credible interval 0.052 – 0.223) and 0.178 (0.097 – 0.293) depending on the severity of the winter, and up to 0.233 (0.127 – 0.373) for well-fed fledglings. The season with the lowest survival was the post-fledging period (0.508; 0.428 – 0.594) in years with mild winters, and the winter in years with extensive snow cover (0.481; 0.337 – 0.626). We therefore show that extreme weather events reduced the proportion of first-year survivors. Increasingly warmer winters with less snow cover may therefore increase annual survival probability of juvenile little owls in central Europe, but environmental changes reducing food supply during the nestling period can have similarly large effects on annual juvenile survival and therefore the viability of populations.

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant’s source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

Aim: The Amazon rainforest has approximately 23% of its sampled area dedicated to bats, making it one of the least sampled and most diverse regions for bats in Brazil. The lack of sampling results in a lack of knowledge regarding the accurate geographical distribution of bat species. This lack is referred to as the Wallacean shortfall, which should be addressed with primary data obtained from in situ collections. However, the use of Species Distribution Models (SDMs) can help alleviate this gap. Location: The states of Pará and Acre are located in the Brazilian Amazon. Methods: So, our objective is to decrease the Wallacean shortfall concerning Amazonian bat species. To achieve this, we provide (i) a list of bat species sampled in the states of Pará and Acre in the last five years (2017 to 2022); (ii) the potential distribution of species considered as new occurrences for the region; and (iii) the potential distribution of species classified as Data Deficient (DD) and Near Threatened (NT) according to the IUCN classification. Results: With 96 nights of collection and 129,600 m 2h of mist netting, we obtained 75 bat species, with an estimated total of 94.78 species. Additionally, 21 species were considered as range extensions. Main conclusions: The Brazilian Amazon region has a vast geographic expanse and few established research centers, resulting in a limited sampling of bats and other biological groups. Furthermore, we draw attention to the significant number of bat species with expanded geographical distributions, with 21 out of the 75 sampled species. This should be a reminder that primary biogeographic data is still necessary for the neotropical region.

Understanding animal movement and behaviour can aid spatial planning and inform conservation management. However, it is difficult to directly observe behaviours in remote and hostile terrain such as the marine environment. Behaviours can be inferred from telemetry data using hidden Markov models (HMMs), but model predictions are not typically validated due to difficulty obtaining ‘ground truth’ behavioural information. We investigate the accuracy of HMM-inferred behaviours by considering a unique dataset provided by Joint Nature Conservation Committee. The data consist of simultaneous proxy movement tracks of the boat (defined as visual tracks as birds are followed by eye) and seabird behaviour obtained at the same time-frequency by observers on the boat. We use these data to assess whether (i) visual track is a good proxy for true bird locations in relation to HMM-inferred behaviours, and (ii) inferred behaviours from HMMs fitted to visual tracking data accurately represent true behaviours as identified by behavioural observations taken from the boat. We demonstrate that visual tracking data can be regarded as a good proxy for true movement data of birds in terms of similarity in inferred behaviours. Accuracy of HMMs ranging from 71% to 87% during chick-rearing and 54% to 70% during incubation was generally insensitive to model choice, even when AIC values varied substantially across different models. Finally, we show that for foraging, a state of primary interest for conservation purposes, identified missed foraging bouts lasted for only a few seconds. We conclude that HMMs fitted to tracking data can accurately identify important conservation-relevant behaviours, demonstrated using visual tracking data. Therefore, confidence in using HMMs for behavioural inference should increase even when validation data are unavailable. This has important implications for animal conservation, where the size and location of protected areas are often informed by behaviours identified using HMMs fitted to movement data.

We present notable distributional updates for 13 species from western Ecuador (six amphibians amphand seven reptiles). Our findings include the northernmost confirmed sighting of of Pristimantis kuri (Yánez-Muñoz et al. 2016) and the southernmost documented appearance of Imantodes inornatus (Boulenger 1896) and and Lepidoblepharis buchwaldi (Werner 1910). Additionally, we document new records and notes of distribution range of of Agalychnis spurrelli (Boulenger 1913), 1913), Hyloscirtus alytolylax (Duellman 1972), 1972), Engystomops montubio (Ron et al. 2004), 2004), Pristimantis nyctophylax (Lynch 1976), 1976), Pristimantis walkeri (Lynch 1974), 1974), Chironius flavopictus (Werner 1909), 1909), Chironius grandisquamis (Peters 1869), 1869), Dendrophidion graciliverpa (Cadle 2012), 2012), Ninia atrata (Hallowell 1845), and and Urotheca fulviceps (Cope 1886). These observations significantly contribute to filling information gaps in our understanding of these species’ distributions. The data, derived from samples collected across diverse forested areas in the western region of Ecuador (provinces of Cañar, Guayas, El Oro, and Los Rios), provide valuable insights into the ecology and conservation of these species.

1. Recognition of favourable environmental conditions for seed germination and seedling survival in different types of forest sites is crucial both for effective regeneration of introduced tree and for control of its spontaneous spread. Studies on the encroachment of North American northern red oak Quercus rubra into European Scots pine forests revealed high abundances of seedlings and saplings under shrubs, with lower abundances in open areas or in clumps of bilberry Vaccinium myrtillus. It was unclear, does burying acorns by seed-hoarders in moss or soil in different microhabitats impact survival of red oak seeds and seedlings, and does acorn size matter? 2. Results of previous (observational) studies were verified in a 3-year experimental study: a pool of 900 sown acorns was monitored in natural conditions. 3. Study revealed that ~80% of sown acorns were lost due to pilferage, lack of germination, fungal infection, and death of sprouting acorns and leafed-out seedlings. The fate of acorns and seedlings depended largely on acorn size and differed among microsite types. Viable seedlings were twice as likely to develop from large- and medium-sized, than from small acorns. Surviving seedlings grew mainly from acorns sown under moss cover within bilberry clumps or in open area, confirming a positive ‘burial effect’. Less than 10% of acorns sown under shrubs developed into viable seedlings, contradicting former conclusions on their ‘nurse effect’. 4. The occurrence of extensive bilberry clumps and small clusters of shrubs in pine forests favours Q. rubra regeneration, but severe fluctuations of the warming climate limit the viability of red oak seeds and seedlings. Prognosed range shifts of native tree species and expected dramatic loss of V. myrtillus climatic optima will impact Q. rubra distribution in European forests. Meanwhile, to prevent red oak spread (if necessary), it is recommended to remove shrubs from pine stand.

Population size is a key parameter for the conservation of animal species. Close-kin mark-recapture (CKMR) relies on the observed frequency and type of kinship among individuals sampled from the population to estimate population size. This approach requires being able to determine the age of sampled individuals. One common approach, particularly in fish studies, is to measure animal length and using an assumed age-length relationship (a ‘growth curve’). We used simulation to test the effect of misspecifying the length measurement error and the growth curve on population size estimation. Simulated populations represented two fictional shark species, one with a relatively simple life history and the other with a more complex life history based on the grey reef shark (Carcharhinus amblyrhynchos). We estimated sex-specific adult abundance, which we assumed to be constant in time. We observed small median biases in these estimates ranging from 1.35 to 2.79% when specifying the correct measurement error and growth curve, with true coefficients of variation between 21.56 and 28.50%. Introducing error via misspecified growth curves resulted in changes in the magnitude of the estimated total population, with upwards shifts negatively biasing abundance estimates. Over- and underestimating the length measurement error did not introduce a bias and had negligible effect on the variance in the estimates. Our findings show that assuming an incorrect length measurement error has little effect on estimation, but having an accurate growth curve is crucial for CKMR whenever ageing is based on length measurements. If ageing could be biased, researchers should be cautious when interpreting CKMR results and consider the potential biases arising from inaccurate age inference.

Feeding adaptation ofFrançois’ langurs (Trachypithecus francoisi) to thefragmented limestone habitats in Southwest ChinaWei Yaoa,1, Cheng-Ming Huanga,b,1, Jia-Xin Zhaob, Rong Huangb, Wen-Hua Lib,Peng-Lai Fan a,*, Qi-Hai Zhou a,*aKey Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Chinab Institute of Zoology, Chinese Academy of Sciences, Beijing, China.c Encheng National Nature Reserve, Chongzuo, China∗Corresponding authorRunning Title: Feeding adaptation of François’ langurs to the fragmented limestone habitatsCorresponding author:Prof. Qi-Hai Zhou, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, 1# Yanshan Zhong Road, Guiling, Guangxi 541006, China. E-mail:[email protected] Prof. Pen-Lai Fan, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, 1# Yanshan Zhong Road, Guiling, Guangxi 541006, China. E-mail:[email protected] Yao and Cheng-Ming Huang are co-first authorsAbstract: Limestone forests are an unusual habitat for primates, especially fragmented limestone habitats. However, limited research has been conducted on François’ langurs (Trachypithecus francois ) in these habitats, and there is a need to understand their behavioral adaptations to the fragmented limestone habitat. We collected data on the diet of François’ langurs in a fragmented limestone habitat in Encheng National Nature Reserve, southwestern Guangxi, China, and their feeding adaptations to the fragmented forest were examined. The results indicated that a total of 101 species of plants were consumed by the langurs. The langurs ate a higher number of food species throughout the year when compared with other species, maintained a high level of food diversity, and ate more vines. Moreover, they were highly selective in their use of vegetation in their home range, and fewer plants provided a high-quality food source. During the season when food resources were scarce, similar to monkey populations in other geographic populations, the consumption of fruits and young leaves decreased as their availability decreased. This led to the use of other species, such as mature leaves and seeds. Overall, François’ langurs in Encheng National Nature Reserve are generally considered to employ energy minimization strategies. The findings support that François’ langurs adjust their feeding behavior to cope with seasonal and micro-variations in their dietary requirements and to adapt to their particular environment.Key words: François’ langurs, Feeding adaptation, Limestone habitat, Fragmentation

Quantifying genetic structure and levels of genetic variation are fundamentally important to predicting the ability of populations to persist in human-altered landscapes and adapt to future environmental changes. Genetic structure reflects the dispersal of individuals over generations, which can be mediated by species-level traits or environmental factors. Dispersal distances are commonly positively associated with body size and negatively associated with the amount of degraded habitat between sites, motivating investigation of these potential drivers of dispersal concomitantly. We quantified genetic structure and genetic variability within populations of seven Euglossine bee species in the genus Euglossa across fragmented landscapes. We genotyped bees at thousands of SNP loci and tested the following predictions: (1) deforested areas restrict gene flow; (2) larger species have lower genetic structure; (3) species with greater resource specialization have higher genetic structure; and (4) sites surrounded by more intact habitat have higher genetic diversity. Contrasting with previous work on bees, we found no associations of body size and genetic structure. Genetic structure was higher for species with greater resource specialization, and the amount of intact habitat between or surrounding sites was positively associated with parameters reflecting gene flow and genetic diversity. These results challenge the dominant paradigm that individuals of larger species disperse farther. They suggest that landscape and resource requirements are important factors mediating dispersal, and they motivate further work into ecological drivers of gene flow for bees.

Birds and ants co-occur in most terrestrial ecosystems and engage in a range of interactions. Competition, mutualism and predation are prominent examples of these interactions, but there are possibly many others that remain to be identified and characterized. This study provides quantitative estimates of the frequency of toe amputations resulting from ant bites in a population of migratory red-necked nightjars (Caprimulgus ruficollis) monitored for 15 years (2009-2023) in S Spain and identifies the attacker(s) based on taxonomic analyses of ant-mandible remains found on injured toes. Less than 1% of examined adults (N = 369) missed one or more toes. The analysis of ant remains identified African army ants (Dorylus sp.) as the primary cause of toe amputations in nightjars and revealed that body parts of the attacker may remain attached to the birds even after intercontinental migration. No cases of severe damage were observed in juveniles (N = 269), apart from the mandible of a Messor barbarus –a local ant species– attached to one of the teeth of the characteristic comb of the medial toe of nightjars. The incidence of ant-bite damage may appear unimportant for nightjar populations, but this might not be true if only birds that manage to survive their injuries and potential complications (e.g. severe bleeding and sepsis from opportunistic infections) return from the tropics. More field studies, ideally in tropical areas, that incorporate routine examination of ant-induced injuries into their protocols are needed to understand the true incidence and eco-evolutionary implications of antagonistic ant-bird interactions.

Reference conditions are difficult to find in the Anthropocene but essential for effective conservation of biodiversity. Aquatic ecosystems in the Andes-Amazon transition zone of Colombia are now at high risk due to expanded human activities after peace agreements in 2016 ended armed conflict. Expanding human land use may reduce fish diversity across the altitudinal gradient but especially in premontane streams (i.e., <500 m a.s.l.) because lands are more amenable to human use than at greater altitudes. We evaluated natural fish diversity in twelve sites over eight years bracketing the end of armed conflict. Strong differences in community structure (measured as species richness, total abundance, and effective species number, and multivariate analyses) occurred as a function of altitude, as measured by. Our results provide a baseline to identify short-term and long-term changes due to impending human land use at a critical moment for the conservation of tropical fish diversity.

In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard-to-establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured growth of three woodland forb species when inoculated with live whole-soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to: 1) understand how time since onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, 2) test growth-responses of three forb species to whole-soil inoculum from restoration sites, and 3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire-sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited greater growth in soil from the young restoration. Each forb species developed unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect growth of hard-to-establish forb species. Our results also highlight that the choice of forb species can have major effects on SMCs, with long-term potential consequences for restoration success.

Olive baboons (Papio anubis) use fixed, secure and naturally-occurring sleeping sites such as tall trees and rocky cliffs, as protection from predators. Although these sleeping sites are safe, they can be limited in availability. We documented olive baboons’ use of 45m tall high-tension electrical pylons (towers) as sleeping sites in Laikipia, Kenya. These observations suggest that olive baboons may use anthropic infrastructure for sleeping sites in areas where naturally occurring cliffs and tall trees are limited.

Bitterling fishes evolve an idiosyncratic symbiosis with freshwater mussels, in which they are obligated to spawn in the gills of mussels for reproduction. In recent years, freshwater mussel populations have been drastically diminishing, due to accelerating anthropogenic impacts, which can be large threats to the risk of bitterling’s extinction cascade (i.e. ‘coextinction’). The host mussel size may be an important factor driving the adaptation and evolution of bitterling’s reproductive phenotypes. Here we examined the host size preference and morphological adaptation of female bitterling to the host size from 17 localities at the Han River in Korea. Using our developed molecular-based species identification for bitterling’s eggs/larvae inside the mussels, we further determined the spawning patterns of seven bitterling species. Mean length of spawned mussels (N=453) was significantly larger than that of unspawned mussels (N=1,814), suggesting that bitterling prefers to use larger hosts as a spawning ground. Spawning probability was clearly greater as mussel size increases. Results of our reciprocal transplant experiments do provide some evidence supporting the ‘bitterling’s larger host preference’ hypothesis. Interspecific competition appeared to be intense as two fish species often spawned eggs in the same mussel individuals simultaneously. Longer ovipositor and more elongated egg may evolve in females of Tanakia signifier in response to larger host environments. The observed bitterling’s spawning preference for large-sized mussels may evolve perhaps because of the fitness advantage in relation to the offspring survival. Our findings further inform on the development of effective conservation and management strategy for the endangered bitterling fishes.