Ctenostomes are a group of gymnolaemate bryozoans with an uncalcified chitinous body wall having few external, skeletal characters. Hence, species identification is challenging and their systematics remain poorly understood, even more so when they exhibit an endolithic (boring) lifestyle. Currently, there are four Recent families of endolithic bryozoans that live inside in mineralized substrates like mollusk shells. In particular, Penetrantiidae Silén, 1946 has received considerable attention and its systematic affinity to either cheilostomes or ctenostomes has been debated. Species delimitation of penetrantiids remains difficult, owing to a high degree of colonial and zooidal plasticity. Consequently, an additional molecular approach is essential to unravel the systematics of penetrantiids, their phylogenetic placement and their species diversity. We therefore sequenced the mitochondrial (mt) genomes and two nuclear markers of 27 ctenostome species including nine penetrantiids. Our phylogeny supports the Penetrantiidae as a monophyletic group placed as sister taxa to the remaining ctenostomes alongside paludicellids and arachnoidids. Our results also suggest that the endolithic lifestyle evolved at least twice independently within ctenostomes, since the boring families Terebriporidae d’Orbigny, 1847 and Penetrantiidae are well separated. Ctenostome paraphyly is supported by our data, as the cheilostomes nest within them. A Multiporata clade is also well supported, including the former victorelloid genus Sundanella. Altogether, this study provides new insights into ctenostome systematics, assists with species delimitation and contributes to our understanding of the bryozoan tree of life.

Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the genomic range of the two genes (“gene-level genotyping”). The second dataset examined 300k to 600k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean (“chromosome-level genotyping”). The gene-level analysis revealed a significant effect of domestication on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions associated with domestication at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabream, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.

Understanding the diet preferences and prey selection of invasive species is crucial to better predict their impact on community structure and ecosystem functioning. Limnomysis benedeni, a Ponto-Caspian invasive mysid shrimp, is one of the most successful invaders in numerous European river and lake ecosystems. While existing studies suggest potentially strong trophic impact due to high predation pressure on invaded plankton communities, little is known of its prey selectivity between phyto- and zooplankton, under different prey concentrations. Here, we therefore investigated the feeding selectivity of L. benedeni on two commonly occurring prey organisms in freshwaters, the small rotifer zooplankton Brachionus calyciflorus together with the microphytoplankton Cryptomonas sp. present in increasing densities. Our results demonstrated a clear shift in diet selection, with L. benedeni switching from B. calyciflorus to Cryptomonas sp. already when the two prey species were provided in equal biomasses. Different functional responses were observed for each prey type, indicating somewhat different foraging mechanisms for each prey type. These findings provide experimental evidence on the feeding flexibility of invasive mysid shrimps and potential implications for trophic interactions in invaded ecosystems.

Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1,086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3,131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs), to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describes the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.

The Francois’ langur (Trachypithecus francoisi) is a rare and endangered and the indicated primate species distributed in karst area in northern Vietnam and southwestern China. However, holistic conservation management has been hampered by research limited to specific nature reserves or sites. Building a comprehensive map of potential distribution for the Francois’ langur is essential to advance conservation efforts and ensure coordinated management across regions. Here, we used 82 occurrence records of Francois’ langur surveyed in Guangxi, Guizhou, and Chongqing from 2017 to 2020, along with 12 environmental variables to build the potential habitat model under current and future climate (for the periods 2021-2040, 2041-2060, 2061-2080, 2081-2100) using maximum entropy models (MaxEnt). Our results indicated that 1) precipitation- and temperature-associated bioclimatic variables made the greatest contributions to the distribution of Francois’ langur, vegetation, water source and anthropogenic variables were also important factors affecting the distribution of Francois’ langur; 2) 144207.44 km2 potential Francois’ langur suitable habitat across the entire range in China was estimated by the current model, moderate- and high-suitability habitat accounted for only 23.76% (34265.96 km2) of the predicted suitable habitat and mainly distributed in southwest Guangxi, east of Chongqing and the border between Guizhou and Chongqing; 3) the suitable habitats of Francois’ langur will dramatically contract under future climate change and the habitat centroid will move in the southeast direction with the shifting distance about 2.84km/year from current to 2100. The habitat prediction of Francois’ langur and related drivers proposed in this work will provide essential insights for future conservation of this species, which is, not only existing distribution areas should be monitored and protected, but also conservation beyond existing habitats should be a focus of effort, especially future expansion areas, to ensure effective and timely protection under climate change and anthropogenic pressures.

1. While territoriality is one of the key mechanisms influencing carnivore space use, most studies quantify resource selection and movement in the absence of conspecific influence or territorial structure without inference on resource selection processes. 2. Our analysis incorporated intra-specific competition in a resource selection framework, via territorial data of conspecifics, to investigate mechanisms of territoriality and to better understand the role of neighboring packs on African wild dog habitat selection. We fit integrated step selection functions to 3-hour GPS data from 12 collared wild dog packs in the Okavango Delta, and estimated selection coefficients using a conditional Poisson likelihood with random effects. 3. Packs selected for the outline of their neighbors’ 30-day boundary (defined as their 90% kernel density estimate), and for the outline of their own 90-day core (defined as their 50% kernel density estimate). Neighbors’ 30-day boundary had a greater influence on resource selection than any habitat feature. Habitat selection differed when they were within versus beyond their neighbors’ 30-day boundary. 4. Pack size, pack age, pup presence, and seasonality all mediated how packs responded to neighbors, and seasonal dynamics altered the strength of residency. While newly-formed packs and packs with pups avoided their neighbors’ boundary, older packs and those without pups selected for it. Packs also selected for the boundary of larger neighboring packs more strongly than that of smaller ones. 5. Social structure within packs has implications for how they interact with conspecifics, and therefore how they are distributed across the landscape. Future research should continue to investigate how territorial processes are mediated by social dynamics and, in turn, how territorial structure mediates resource selection and movement. These results could inform the development of a human-wildlife conflict (HWC) mitigation tool by co-opting the mechanisms of conspecific interactions to manage space use of endangered carnivores.

1. Over the last four decades coral disease research has continued to provide reports of disease states, the occurrence and severity of disease outbreaks, and associated disease signs however nomenclature and protocols for microscopic disease descriptions have yet to be implemented. Histopathology using systematic protocols is a gold standard for the microscopic assessment of diseases in veterinary and medical research. Increasing disease outbreaks on coral reefs as human impacts intensify highlights the need to also establish standardised diagnostic terminology and methodology for coral disease research. 2. Here we apply a systematic approach to collating, reviewing, and evaluating histopathological methods used to study white diseases in hard coral taxa and map research effort in this field spanning study design, sample processing and analysis in the 33 publications identified between 1984 and 2022. 3. We find that studies to-date have not uniformly detailed methodologies, and terminology associated with histopathological reporting and disease description is inconsistent between studies. Combined these limitations reduce study repeatability, limiting the uptake of histopathology in coral disease research and the capacity for researchers to compare disease reports. 4. A primary outcome of this study is revision of the most widely used terminology applied to coral tissue and development of recommendations for standardised reporting procedures with the aim of increasing accessibility and uptake of histopathology in addition to allowing for ongoing comparative analysis through living systematic reviews for the coral disease field.

Adaptive radiation as a result of ecological opportunity can have profound effects on the evolutionary outcome of species. On coral reefs, parrotfishes have been considered as one of the most dramatic examples of adaptive radiation unique in their extreme dietary specialisation. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material. This unique ability to exploit a previously untapped trophic resource is thought to have led to the early diversification of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of the spotted parrotfish (Cetoscarus ocellatus). Our findings reveal significant expansion, selection, and duplication within several gene families responsible for detoxification, including the cytochrome p450 gene family and non-cyp450 carboxylesterases. We find preliminary evidence that the structural mechanism responsible for the extreme hardness and biomineralization of parrotfish teeth may be a result of poly-glutamine expansion in the enamel protein ameloblastin. We also detect expansion and selection for several genes related to pigmentation and sequential hermaphroditism. Together, these results highlight a potentially complex interplay of adaptive radiation and sexual selection operating on coral reef ecosystems.

Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co-occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between-species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia.

Crop wild relatives provide a valuable resource for improving crops. They possess desirable traits that confer resilience to various environmental stresses. To fully utilize crop wild relatives in breeding and conservation programs, it is important to understand the genetic basis of their adaptation. Landscape genomics associates environments with genomic variation and allows for examining the genetic basis of adaptation. In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hot spot of these wild relatives. Further, we explored the correlation between these variations and the bio-climatic and soil conditions at their collection sites. Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected 396 candidate SNPs associated with ten environmental factors by applying four genotype-environment association methods. Some of these SNPs signal genes involved in pathways that help with adaptation to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. These candidate SNPs will be useful for marker-assisted improvement and characterizing the germplasm of this crop for developing climate-resilient eggplant varieties. The study provides a model for how we can apply landscape genomics to the wild relatives of other crops.

Insects perform the greatest part of pollination services (Winfree et al., 2011) and insects native to a given habitat can play an irreplaceable ecological role in food webs and plant reproduction (Travis & Kohn, 2023; Pelmyr, et al., 1996; Suarez, et al.,2000). With precipitous declines in insect species over the last decades, it is urgent to document insect assemblages in native plant communities to support conservation efforts. Identifying pollinators and their pollination activity is challenging; emerging methods involve the use of camera traps (Droissart, et al., 2021). In this study, we compare the accuracy of two different methods of monitoring to produce insect assemblage of Encinitas Baccharis (Baccharis vanessae): focal observations and video recordings from camera traps. B. vanessae is a rare, endemic species found in Coastal Sage Scrub communities in San Diego County (U.S. Fish and Wildlife Service, 2021). This federally listed species is threatened by habitat loss and fragmentation, which may also be affecting the availability of its insect pollinators (U.S. Fish and Wildlife Service, 2011). Preliminary results indicate that B. vanessae supports a variety of flower-visiting insect guilds and is in turn supported by diverse pollinators. While focal observations underreported insect activity by approximately half, the proportions of common diurnal visitors were similar with both methods. Camera traps were unable to provide sufficient detail to discern visually similar guilds, but were able to record nocturnal insect activity, which was dominated by moths (Lepidoptera, 82%). While collection protocol in this study did not record the time an insect spent interacting with a flower, moths spent notably longer periods in contact with flowers than most diurnal insects. This study has implications for the effective monitoring of endangered plant species and their affiliated pollinators.

In root-nodule symbioses (RNS) between nitrogen (N) fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: 1) phylogenetic diversity of Frankia in soil vs. nodules, 2) change in Frankia assemblages in soil vs. nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and 3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages, and fell into two large clades not previously observed. Presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.

1) Clustering is indispensable in the quest for robust vegetation classification schemes which aim to partition continua to summarise and communicate pattern. However, clustering solutions are sensitive to methods and data and are therefore unstable, a feature which is usually attributed to noise. Viewed through a central-tendency lens, noise is defined as the degree of departure from type, which is problematic since vegetation types are abstractions of continua and so noise can only be quantified relative to a particular solution to hand. Graph theory models the structure of vegetation data based on the interconnectivity of samples. Through a graph-theoretic lens, the causes of instability can be quantified in absolute terms via the degree of connectivity among objects. 2) We simulated incremental increases in sampling intensity in a dataset over five iterations and assessed classification stability across successive solutions derived using algorithms implementing, respectively, models of central-tendency and interconnectivity. We used logistic regression to model the likelihood of a sample changing groups between iterations as a function of distance to centroid and degree of interconnectivity. 3) Our results show that the degree to which samples are interconnected is a more powerful predictor of instability than the degree to which they deviate from their nearest centroid. The removal of weakly interconnected samples resulted in more stable classifications, although solutions with many clusters were apparently inherently less stable than those with few clusters, and improvements in stability flowing from the removal of outliers declined as the number of clusters increased. 4) Our results reinforce the fact that clusters abstracted from continuous data are inherently unstable, and that the quest for stable, fine-scale classifications from large regional datasets is illusory. Nevertheless, our results show that using models better suited to the analysis of continuous data may yield more stable classifications of the available data.

Acoustic communication in animals can be affected by multiple biotic (intra and interspecific) and abiotic (e.g., wind and rain) natural noises. In addition, human beings produce additional novel sources of noise, which can reduce or inhibit the reception of acoustic signals by conspecifics, leading to behavioral changes. In this study, we investigated whether sound of conspecifics and road noise additively affect the acoustic parameters of the advertisement call of males of a Yellow Heart-tongued Frog (Phyllodytes luteolus). We hypothesized that males that vocalize in larger choruses (many males) and in areas close to highways (anthropic noise) will increase their temporal and spectral acoustic parameters, respectively, to avoid acoustic signal masking. We recorded the vocalizations of 38 males in environments close (N=18) to and distant (N=20) from highways in different social contexts (many or few individuals in the chorus). Contrary to our expectation, the results indicated that individuals exposed to road noise had lower dominant frequency calls than those from natural areas, and that the density of males in the chorus had no influence on the acoustic parameters. Furthermore, we found a positive relationship between body size and intensity, indicating that larger individuals can emit calls that can reach greater distances. The advertisement call of Phyllodytes luteolus has a high dominant frequency, with little overlap with the frequency of anthropic noises (roads), which may explain its presence and reproductive success of this species in bromeliads from urbanized areas.

Livebearing fishes are a standard model for studying the effect of predation on prey biology. Numerous studies have found differences in life history, sexual selection, behavior, and morphology between populations of the same species that co-occur with predators and those that do not. Alfaro cultratus is a livebearing fish with populations in different predation environments, but unlike other livebearers, this species also has an extreme body shape that is laterally compressed. Given this unusual morphology, we asked if predation environment would still predict overall body shape, as has been documented in other species. We collected specimens from both predator and no-predator sites in Costa Rica. We used a geometric morphometrics analysis to determine if body shape is affected by the predation environment while controlling for size and river gradient. Body shape does indeed differ between predation environments; however, the observed differences contrast with the patterns found in other livebearer systems. Alfaro cultratus in predation environments had deeper and shorter bodies and deeper caudal peduncles than those found in environments without dominant fish predators.

Body size shifts in ectotherms are mostly attributed to the Temperature Size Rule stating that warming speeds up initial growth rate but leads to smaller size when food availability does not limit growth. Nevertheless, climate warming can decrease food availability, which can influence growth, fecundity and survival. However, the interactive effects of temperature and food availability on life history traits have been mostly studied in small invertebrate species. In contrast, we have limited information on how temperature and food availability jointly influence life history traits in vertebrate predators and how changes in different life history traits combines to influence population demography. We investigated the independent and interactive effects of temperature and food availability on traits of the medaka fish Oryzias latipes. We used our empirical estimates of vital rates as input parameters of an Integral Projection model to predict how modifications in vital rates translate into population demography. Our results confirm that warming leads to a higher initial growth rate and lower size leading to crossed growth curves between the two temperatures. Food-restricted fish were smaller than ad libitum fed fish throughout the experiment. Fish reared at 30 °C matured younger, had smaller size at maturity, had a higher fecundity but had a shorter life span than fish reared at 20 °C. Food restriction increased survival under both temperature conditions. Warming reduces generation time and increases mean fitness in comparison to the cold treatments. Food restriction increased generation time and fitness in the cold treatment but had no effect in the warm treatment. Our results highlight the importance of accounting for the interaction between temperature and food availability to understand how body size shifts can affects vital rates and population demography. This is of importance in the context of global warming as resources are predicted to change with increasing temperatures.

Many symbionts are sexually transmitted and impact their host’s development, ecology, and evolution. While the significance of symbionts that cause sexually transmitted diseases (STDs) is relatively well understood, the prevalence and potential significance of the sexual transmission of beneficial symbionts remain elusive. Here, we study the effects of sexually transmitted mutualist nematodes on their dung beetle hosts. Symbiotic Diplogastrellus monhysteroides nematodes are present on the genitalia of male and female Onthophagus beetles and are horizontally transmitted during mating and vertically passed on to offspring during oviposition. A previous study indicates that the presence of nematodes benefits larval development and life history in a single host species, Onthophagus taurus. However, Diplogastrellus nematodes can be found in association with a variety of beetle species. Here, we replicate these previous experiments, assess whether the beneficial effects extend to other host species, and test whether nematode-mediated effects differ between male and female hosts. Rearing three distantly related dung beetle species with and without nematodes, we find that the presence of nematodes benefits body size, but not development time or survival across all three species. Likewise, we found no difference in the benefit of nematodes to male compared to female beetles. These findings highlight the role of sexually transmitted mutualists in the evolution and ecology of dung beetles. Furthermore, these results suggest a potential new avenue through which environmental pollution with veterinary deworming agents may affect dung beetles and their ecosystem services.

Climate change impacts are driving forest fires worldwide and reducing snowfall in temperate countries. Whether these impacts result in a significant alteration of winter soil respiration (Rs) rates and temperature in the postfire and the undisturbed black pine (Pinus nigra) forests remain poorly understood. A field experiment was conducted in the postfire and the undisturbed black pine forests during a winter period in Türkiye to quantify Rs rates as affected by lack of snow and snow cover. Four treatments were applied: snow-exclusion postfire (SEPF), snow postfire (SPF), snow-exclusion undisturbed forest (SEUF), and snow-undisturbed forest (SUF). The SEPF exhibited the significantly lowest mean Rs rates (0.71 µmol m-2 s-1) compared to the SPF (1.02 µmol m-2 s-1), SEUF (1.44 µmol m-2 s-1, and SUF (1.48 µmol m-2 s-1). The Rs also showed significant variations with time (p <.0001). However, treatments and time exhibited no statistically significant interaction effects (p = 0.6801). Total amounts of winter Rs (January to March) ranged from 4.92 to 5.07 Mt CO2 ha-1 in the undisturbed forest and 2.53 to 3.51 Mt CO2 ha-2 in the postfire site. The Rs showed a significantly positive relationship (p <.0001) with the soil (0.59) and air (0.46) temperatures and a significantly negative relationship (p = 0.0017) with the soil moisture (-0.20) at the 5 cm depth. In contrast, the Rs showed a negative, but not statistically significant relationship (p = 0.0932) with the soil moisture (-0.16) at the 10 cm soil depth. The combined effects of lack of snow and forest fire resulted in a significant decrease of Rs. In contrast, a warmer winter significantly increased Rs rates in the undisturbed forest, suggesting that a warmer winter could potentially accelerate soil organic carbon losses in naturally growing undisturbed forest ecosystems, thus, providing positive feed backs to climate change.