A general reaction norm model of any order can be formulated as a linear mixed model. From this follows that estimates of mean phenotypic traits in a population (fixed effects), and predictions of individual additive genetic deviations from mean reaction norm parameter values (random effects), can be found from the best linear unbiased predictions (BLUP) equation in matrix form. The resulting BLUP model is dynamical in the sense that the incidence matrix varies with time. This leads to a straightforward and multivariate alternative to infinite-dimensional and random regression modeling of reaction norms. Based on such a BLUP model, the within-generation changes in predicted mean reaction norm parameter values can be found by use of the Robertson-Price identity, applied on the predicted random effects. From this follows that the between-generation change in the mean values are found from Robertson’s secondary theorem of natural selection, applied on the predicted random effects. This explains why and to which extent the variances of BLUP random effects are underestimated, which is a well-known observation. The dynamical BLUP model will thus produce the mean reaction norms over time, which makes it possible to disentangle the microevolutionary and plasticity components in for example climate change responses. The BLUP responses will depend on the additive genetic relationship matrix A_t. When A_t is an identity matrix, the results will be identical to the results from a variant of the multivariate breeder’s equation, based on the selection gradient with respect to the individual phenotypic trait values. Parameters are assumed to be known and constant, but it is discussed how they can be estimated by means of a prediction error method. Generations are assumed to be non-overlapping, but adjustments for overlapping generations can easily be done.
Sharks, rays and chimaera form the clade Chondrichthyes, an ancient group of morphologically and ecologically diverse vertebrates that has played an important role in our understanding of gnathostome evolution. Increasingly studies have are seeking to investigate evolutionary processes operating within the chondrichthyan crown group, with the broad aim of understanding the driving forces behind the vast phenotypic diversity observed amongst its constituent taxa. Genetic, morphological and behavioural studies have all contributed to our understanding of phenotypic evolution yet are typically considered in isolation in the context of Chondrichthyes. I argue that integrating these core fields of organismal biology is vital if we are to understand the evolutionary processes operating in contemporary chondrichthyan taxa, and how such processes have contributed to past phenotypic evolution. In light of the global extinction crisis facing this clade, this understanding is crucial if we are to successfully conserve rapidly declining chondrichthyan populations.
Ontogenetic color change in animals is an interesting evolution-related phenomenon that has been studied by evolutionary biologists for decades. However, the performance of quantitative and continuous color measurements throughout the life cycle of animals is a challenge. To understand the rhythm of change in tail color and sexual dichromatism, we used a spectrometer to measure the tail color of blue-tailed skink (Plestiodon elegans) from birth to sexual maturity. Lab color space was selected due to its simple, fast, and accurate and depends on the visual sense of the observer for measuring the tail color of skinks. A strong relationship was observed between color indexes (values of L*, a*, b*) and growth time of skink. The luminance of tail color decreased from juveniles to adults in both sexes. Moreover, we observed differences in color rhythms between the sexes, which may be influenced by different behavioral strategies employed by them. This study provides continuous measurements of change in tail color in skinks from juveniles to adults and offers insights into their sex-based differences. Our findings explain the potential factors that drive dichromatism between the sexes of lizards and is expected to serve as a reference for future studies that explore possible mechanisms of ontogenetic color change in reptiles.
The complete mitochondrial genomes of two Prophantis species in the tribe Trichaeini (Lepidoptera: Crambidae) were sequenced using high-throughput sequencing technology. They were assembled and annotated: the complete mitogenomes of P. octoguttalis and P. adusta were 15,197 bp and 15,714 bp, respectively, and contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. Their arrangement was consistent with the first sequenced mitogenome of Lepidoptera, from Bombyx mori (Bombycidae). The nucleotide composition was obviously AT-biased, and all protein-coding genes, except for the cox1 gene (CGA), used ATN as the start codon. Except for trnS1, which lacked the DHU arm, all tRNA genes could fold into the clover-leaf structure. Phylogenetic trees of Crambidae were reconstructed based on mitogenomic data using Maximum likelihood (ML) and Bayesian inference (BI) analysis methods. Results showed that Trichaeini in this study robustly constitute a monophyletic group in Spilomelinae, with the relationships (Trichaeini + Nomophilini) + ((Spilomelini + (Hymeniini + Agroterini)) + Margaroniini). However, the affinities of the six subfamilies Acentropinae, Crambinae, Glaphyriinae, Odontiinae, Schoenobiinae and Scopariinae within the “non-PS Clade” in Crambidae remained doubtful with unstable topologies or low supports.
Inter-specific adoption is an intriguing topic in behavioural and evolutionary ecology. Being a rare phenomenon is rarely documented in the literature and thus reports of inter-specific adoption based on solid data are particularly valuable. Here, owing to a long-term and extensive monitoring of a local population of the European blackbird (Turdus merula, hereafter blackbird), we describe observations of alloparental behaviour exhibited by blackbirds towards fieldfare (Turdus pilaris) nestlings (single nest, first record ever) and fledglings (twelve cases in total). We discuss the observations in respect to available literature.
Many reef invertebrates reproduce through simultaneous broadcast spawning, with an apparent advantage of overwhelming potential predators and maximizing propagule survival. Although reef fish have been observed to consume coral gamete bundles during spawning events, there are no published records of such predation by benthic invertebrates. Here, we document several instances of the ruby brittle star, Ophioderma rubicundum, capturing and consuming egg-sperm bundles of the mountainous star coral, Orbicella faveolata, and the symmetrical brain coral, Pseudodiploria strigosa, during spawning events in the Cayman Islands in 2012 and the Florida Keys in 2022. These observations are widely separated in space and time (>600 km, 10 years), suggesting that this behavior may be ubiquitous on western Atlantic reefs. Since O. rubicundum spawns on the same or subsequent nights as these coral species, we hypothesize that this opportunistic feeding behavior takes advantage of the coral’s lipid-rich bundles to recover energy reserves expended by the brittle star during gametogenesis. The consumption of coral gametes by adult brittle stars suggests a novel trophic link between reef invertebrates, and also provides evidence that ophiuroid-coral symbioses may oscillate between commensalism and parasitism depending on the ontogeny and reproductive status of both animals. Our observations provide insights into the nuanced, dynamic associations between coral reef invertebrates and may have implications for coral fecundity and resilience.
Avian diet can be affected by site-specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi-marker faecal metabarcoding to provide in-depth dietary analysis of a declining passerine, the Hawfinch (Coccothraustes coccothraustes). We collected faecal samples from (n=262) UK Hawfinches prior to, and during the breeding seasons in 2016-2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilise multiple resources within their foraging environments.
The interaction of recent orographic uplift and climate heterogeneity acted as a key role in the East Himalaya-Hengduan Mountains (EHHM) has been reported in many studies. However, how exactly the interaction promotes clade diversification remains poorly understood. Here, we both studied genetic structure of the chloroplast trnT-trnF region and 11 nuclear microsatellite loci in Hippophae gyantsensis and examined what role geological barriers or ecological factors play in the spatial genetic structure. The results showed that this species had a strong east-west phylogeographic structure, with several mixed populations identified from microsatellite data in central location. The intraspecies divergence time was estimated to about 3.59 Ma, corresponding well with the recent uplift of the Tibetan Plateau. Between the two lineages there was significant climatic differentiation without geographic barriers. High consistency between lineage divergence, climatic heterogeneity and Qingzang Movement demonstrated that climatic heterogeneity but not geographic isolation drives the divergence of H. gyantsensis, and the recent regional uplift of the QTP, as the Himalayas, create heterogeneous climates by affecting the flow of the Indian monsoon. The east group of H. gyantsensis experienced population expansion c. 0.12 Ma, closely associated with the last interglacial interval. Subsequently, a genetic admixture event between east and west groups happened at 26.90 ka, a period corresponding to the warm inter-glaciation again. These findings highlight the importance of the Quaternary climatic fluctuations in the recent evolutionary history of H. gyantsensis. Our study will improve the understanding of the history and mechanisms of biodiversity accumulation in the EHHM region.
The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate areas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we characterized and compared eight complete mitochondrial genomes for five Gempylidae species [Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun] using Ion-Torrent sequencing. Using Bayesian Inference and Maximum-Likelihood tree search methods, we investigated the evolutionary relationships of seventeen Gempylidae species using mitogenome data. In addition, we estimate divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89 – 52.04 mya) million years ago; Gempylidae 1 [Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis], and Gempylidae 2 [Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus]. The present study demonstrates the superior performance of complete mitogenome data compared to individual genes in phylogenetic reconstruction. In addition to Cytochrome c oxidase subunit 1, NADH dehydrogenase subunit 2, and Cytochrome b, which are frequently employed in phylogenetic investigations, NADH dehydrogenase subunit 5 provided adequate resolving power. Analyses of selection pressure revealed purifying selection is predominant in Gempylidae mitogenomes. By including T. atun individuals from different regions we demonstrate the potential for the application of mitogenomes in species phylogeography.
The climate drives species distribution and genetic diversity; the latter defines the adaptability of populations and species. The ongoing climate crisis induces tree decline in many regions, compromising the mitigation potential of forests. Scientific-based strategies for prioritising forest tree populations are critical to managing the impact of climate change. Identifying future climate refugia, which are locations naturally buffering the negative impact of climate change, may facilitate local conservation. In this work, we conducted the populations’ prioritisation for Castanea sativa (sweet chestnut), a Neogene relict growing in the Caucasus global biodiversity hotspot. We generated genetic and ecological metrics for 21 sites in Georgia and Azerbaijan, which cover the natural range of sweet chestnut across the region. We demonstrated that climate primarily drives the pattern of genetic diversity in C. sativa, proved with a significant Isolation-by-Environment model. In future, climate change may significantly reorganise the species genetic diversity, inducing even some genetic loss, especially in the very distinct eastern fringe of the species range in Azerbaijan. Based on our combined approach, we mapped populations suitable for ex-situ and in-situ conservation, accounting for genetic variability and the location of future climate refugia.
Workers in the ant genus Pheidole show an extreme degree of morphological differentiation, with at least two distinct subcastes: minor workers are smaller and perform most of the colony tasks, whereas majors are larger, display disproportionately massive heads, and specialize in roles as defense and food processing. There is considerable interspecific variation in head shape within worker subcastes of Pheidole, which could affect how the stresses generated by the mandibular closing muscle contraction (0md1) spread throughout the head and influence bite force. To assess the role of head shape in stress patterns of Pheidole workers, we solve a set of Finite Element Analysis (FEA) while exploring variation in Pheidole worker head morphospace. We hypothesize that majors possess head shapes optimized for the generation of stronger bites. In addition, we expect that head shapes corresponding to the edges of morphological space in the genus would show mechanical limitations that could prevent further expanding the occupied morphospace. We vectorized Pheidole head shapes based on images of worker heads, considering species that represent mean shapes and the edges of the two main axes of each morphospace, for a total of five head shapes for each worker subcaste. We performed linear static FEA simulating the contraction of 0md1. Our results demonstrate that head shapes of majors are optimized to generate stronger bites given that stress generated on those shapes is distinctly directed towards the mandibles. Head shapes of minors tended to concentrate stresses around the mandibular articulations, with substantially lower and more diffuse stresses spreading throughout the head, indicating that such shapes are associated with weaker bites. Our results agree with the expectations regarding the main colony tasks performed by each worker subcaste, and we find some evidence of biomechanical limitations on extreme head shapes for majors and minors.
1. The structure, composition, and shape of teeth have been related to dietary specialization in many vertebrate species, except snakes. Yet, snakes have diverse dietary habits that may impact the shape of their teeth. We hypothesize that prey properties, such as hardness and shape, as well as feeding behavior, such as aquatic or arboreal predation, or holding vigorous prey, impose constraints on the evolution of tooth shape in snakes. 2. We compared the morphology of the dentary teeth of 63 species that cover the phylogenetic and dietary diversity of snakes, using 3D geometric morphometrics and linear measurements. 3. Our results show that prey hardness, foraging substrate and the main mechanical challenge are important drivers of tooth shape, size, and curvature. 4. Overall, long, slender, curved teeth with a thin layer of hard tissue are observed in species that need to maintain a grip on their prey. Short, stout, less curved teeth are associated with species that undergo high or repeated loads. 5. Our study demonstrates the diversity of tooth morphology in snakes and the need to investigate its underlying functional implications to better understand the evolution of teeth in vertebrates.
1. High latitude ecosystems are experiencing the most rapid warming on earth, expected to trigger a diverse array of ecological responses. Climate warming affects the ecophysiology of fish, and fish close to the cold end of their thermal distribution are expected to increase somatic growth from increased temperatures and a prolonged growth season, which in turn affects maturation schedules, reproduction and survival, boosting population growth. Accordingly, fish species living in ecosystems close to their northern range edge should increase in numerical importance and possibly displace cold-water adapted species. 2. We aim to document if and how population level effects of warming mediated by individual level responses to increased temperatures, shift community structure and composition in high latitude ecosystems. 3. We studied 11 cool-water adapted freshwater fish populations in communities dominated by cold-water adapted species to investigate changes in the relative importance of cool-water fish during the last 30 years of rapid warming in high latitude lakes. In addition, we studied the individual level responses to warming to clarify the potential mechanisms underlying the population effects. 4. Our long-term series‘ (1991-2020) reveal a marked increase in numerical importance of the cool-water fish species, perch, in ten out of eleven populations, and in most fish communities the cool-water species is now dominant. Moreover, we show that climate warming affects population level processes via direct and indirect temperature effects on the individuals. Specifically, the increase in abundance arises from increased survival of 0+ individuals, faster juvenile growth and ensuing earlier maturation, all boosted by climate warming. 5. The speed and magnitude of the response to warming in these high latitude fish communities strongly suggest that cold-water fish will be displaced by fish adapted to warmer water. Consequently, management should focus on climate adaptation limiting future introductions and invasions of cool-water fish and mitigating harvesting pressure on cold-water fish.
Passive acoustic monitoring (PAM) is a cost-effective method for monitoring cetacean populations compared to techniques such as aerial and ship-based surveys. The C-POD (Cetacean POrpoise Detector) has become an integral tool in monitoring programmes globally for over a decade, providing standardised metrics of occurrence that can be compared across time and space. However, the phasing out of C-PODs following development of the new F-POD (Full waveform capture Pod) with increased sensitivity, improved train detection, and reduced false positive rates, represents an important methodological change in data collection, particularly when being introduced into existing monitoring programmes. Here, we compare the performance of the C-POD with that of its successor, the F-POD, co-deployed in a field setting for 15 months, to monitor harbour porpoise (Phocoena phocoena). While similar temporal trends in detections were found for both devices, the C-POD detected only 58% of the detection positive minutes (DPM), recorded by the F-POD. Differences in detection rates were not consistent through time making it difficult to apply a correction factor or directly compare results obtained from the two PODs. To test whether these differences in detection rates would have an effect on analyses of temporal patterns and environmental drivers of occurrence, generalised additive models (GAMs) were applied. No differences were found in seasonal patterns or the environmental correlates of porpoise occurrence (month, diel period, temperature, environmental noise, and tide). However, the C-POD failed to detect sufficient foraging buzzes to identify temporal patterns in foraging behaviour that were clearly shown by the F-POD. Our results suggest that the switch to F-PODs will have little effect on determining broad-scale seasonal patterns of occurrence, but may improve our understanding of fine-scale behaviours such as foraging. We highlight how care must be taken interpreting F-POD results as indicative of increased occurrence when used in time-series analysis.
Connectivity maintains the spatial dynamics of metapopulations by promoting dispersal between habitat patches, potentially buffering populations and communities against continued global change. However, this function is threatened by habitats becoming increasingly fragmented, and habitat matrices becoming increasingly inhospitable, potentially reducing the resilience and persistence of populations. Yet, we lack a clear understanding of how reduced connectivity interacts with rates of environmental change to destabilise populations. Using laboratory microcosms containing metapopulations of the Collembola Folsomia candida, we investigate the impact of habitat connectivity on metapopulation persistence under a range of simulated droughts, a key stressor for this species. We manipulated both drought severity and the number of patches affected by drought across landscapes connected by either good or poor-quality corridors. We measured the time of population extinction, the maximum rate of population decline, and the variability of abundance among patches as criteria to evaluate the persistence ability of metapopulations. We show that whilst drought severity and number of drought-affected patches negatively influenced population persistence, these results were mitigated by increased habitat connectivity, which increased population persistence time and decreased both how fast populations declined and the variability in abundance among patches. Our results suggest that enhancing spatial connectivity can increase the persistence of metapopulations, increasing the time available for conservation actions to take effect, and/or for species to adapt or move in the face of continued stress. Given that fragmentation increases the isolation of habitats, improving habitat connectivity by using good quality corridors may provide a useful strategy to enhance the resistance of spatially structured populations.
Recent declines in eastern wild turkeys (Meleagris gallopavo silvestris) has prompted increased interest in management and research of this important game species. However, the mechanisms underlying these declines are unclear, leaving uncertainty in how best to manage this species. Foundational to effective management of wildlife species is understanding the biotic and abiotic factors that influence demographic parameters and the contribution of vital rates to population growth. Our objectives for this study were to: 1) conduct a literature review to collect all published vital rates for eastern wild turkey over the last 50 years, 2) perform a scoping review of the biotic and abiotic factors that have been studied relative to wild turkey vital rates and highlight areas that require additional research, and 3) use the published vital rates to populate a life-stage simulation analysis (LSA) and identify the vital rates that make the greatest contribution to population growth. Based on published vital rates for eastern wild turkey, we estimated a mean asymptotic population growth rate (λ) of 0.91 (95% CI = 0.71, 1.12). Vital rates associated with after second year (ASY) females were most influential in determining population growth. Survival of ASY females had the greatest elasticity (0.53), while reproduction of ASY females had lower elasticity (0.21), but high process variance, causing it to explain a greater proportion of variance in λ. Our scoping review found that most research has focused on the effects of habitat characteristics at nest sites and the direct effects of harvest on adult survival, while research on topics such as disease, weather, predators, or anthropogenic activity on vital rates have received less attention. We recommend that future research take a more mechanistic approach to understanding variation in wild turkey vital rates as this will assist managers in determining the most appropriate management approach.
Seed dormancy contributes greatly to successful establishment and community stability and shows large variation over a continuous status scale in mountain ecosystems. Although empirical studies have shown that seed dormancy status (SDS) is shaped by elevation and phylogenetic history in mountain ecosystems, few studies have quantified their combined effects on SDS. Here, we collected mature seeds from 51 populations of 11 Impatiens species (Balsaminaceae) along an elevational gradient in the Gaoligong Mountains of southwest China and downloaded 19 bioclimatic variables from WorldClim v.2.1 for each Impatiens population. We used internal transcribed spacer (ITS), atpB-rbcL, and trnL-F molecular sequences from the GenBank nucleotide database to construct a phylogenetic tree of the 11 species of Impatiens. SDS was estimated using mean dormancy percentage of fresh seeds germinated at three constant temperatures (15, 20, and 25 °C). Logistic regression model analysis was performed to quantify the effects of phylogeny and environment on SDS. Results showed that there was a significant phylogenetic signal of SDS in the Impatiens species. Furthermore, elevation and phylogeny accounted for 63.629% of the total variation in SDS among the Impatiens populations. The logistic model indicated that climatic factors accounted for 20.832% of the total variation in SDS among the Impatiens species, and model residuals were significantly correlated with phylogeny, but not with elevation. Our results indicated that seed dormancy is phylogenetically conserved, and climate drives elevational patterns of SDS variation in mountain ecosystems. This study provides new insights into the response of seed plant diversity to climate change.
Quantifying spatiotemporally explicit interactions within animal populations facilitates the understanding of social structure and its relationship with ecological processes. Data from animal tracking technologies (Global Positioning Systems [“GPS”]) can circumvent longstanding challenges in the estimation of spatiotemporally explicit interactions, but the discrete nature and coarse temporal resolution of data mean that ephemeral interactions that occur between consecutive GPS locations go undetected. Here, we developed a method to quantify individual and spatial patterns of interaction using continuous-time movement models (CTMMs) fit to GPS tracking data. We first applied CTMMs to infer the full movement trajectories at an arbitrarily fine temporal scale before estimating interactions, thus allowing inference of interactions occurring between observed GPS locations. Our framework then infers indirect interactions – individuals occurring at the same location, but at different times– while allowing the identification of indirect interactions to vary with ecological context based on CTMM outputs. We assessed the performance of our new method using simulations and illustrated its implementation by deriving disease-relevant interaction networks for two behaviorally differentiated species, wild pigs (Sus scrofa) that can host African Swine Fever and mule deer (Odocoileus hemionus) that can host Chronic Wasting Disease. Simulations showed that interactions derived from observed GPS data can be substantially underestimated when temporal resolution of movement data exceeds 30-minute intervals. Empirical application suggested that underestimation occurred in both interaction rates and their spatial distributions. CTMM-Interaction method, which can introduce uncertainties, recovered the majority of true interactions. Our method leverages advances in movement ecology to quantify fine-scale spatiotemporal interactions between individuals from lower temporal resolution GPS data. It can be leveraged to infer dynamic social networks, transmission potential in disease systems, consumer-resource interactions, information sharing, and beyond. The method also sets the stage for future predictive models linking observed spatiotemporal interaction patterns to environmental drivers.