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Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g., the bombycid, Arotros Schaus) were misplaced and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
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Closely related populations often display similar patterns of genomic differentiation, yet it remains an open question which ecological and evolutionary forces generate these patterns. The leading hypothesis is that this similarity in divergence is driven by parallel natural selection. However, several recent studies have suggested that these patterns may instead be a product of the depletion of genetic variation that occurs as result of background selection (i.e. linked negative selection). To date, there have been few direct tests of these competing hypotheses. To determine the relative contributions of background selection and parallel selection to patterns of repeated differentiation, we examined 24 independently derived populations of freshwater stickleback occupying a variety of niches and estimated genomic patterns of differentiation in each relative to their common marine ancestor. Patterns of genetic differentiation were strongly correlated across pairs of freshwater populations adapting to the same ecological niche, supporting a role for parallel natural selection. In contrast to other recent work, by examining populations adapting to the same niche we did not find evidence that similar patterns of genomic differentiation are generated by background selection. We also found that overall patterns of genetic differentiation were considerably more similar for populations found in closer geographic proximity. In fact, the effect of geography on the repeatability of differentiation was greater than that of parallel selection. Our results suggest that shared selective landscapes and ancestral variation are the key drivers of repeated patterns of differentiation in systems that have recently colonized novel environments.
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Spring heat accumulation plays a major role in the timing of events such as leaf-out, leaf expansion, flowering, and insect hatch in temperate systems. Accordingly, heat accumulation can serve as a proxy for the timing of plant and insect phenological activity and can be used in a predictive way when the timing of heat accumulation thresholds being reached can be anticipated. This has strong value for a host of planning and management applications. If relationships exist between earlier- and later-season thresholds at a location, then the timing of later-season phenological events that are forced by the accumulation of warmth could be anticipated based on when earlier-season thresholds are met. Using high-resolution daily temperature data, we calculated the coherence in pairs of spring-season heat accumulation (growing degree day) threshold anomalies over 1948-2016. Overall, relationships between thresholds spanning the entire spring season were relatively low, while later season thresholds exhibited much higher correlations. This pattern is generally the result of decreasing variability in heat accumulation with season progression. However, correlation strengths did not follow latitudinal or gradients, revealing that within-season heat accumulation and interannual variability in threshold timing are unique to the specified base temperature and thresholds being compared. We show that the relationships between earlier- and later-season heat accumulation thresholds were sufficient to accurately predict the timing of phenological events in plants in two case examples.
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Ecological communities are constantly being reshaped in the face of environmental change and anthropogenic pressures. Yet, how food webs change over time remains poorly understood. Food web science is characterized by a trade-off between complexity (in terms of the number of species and feeding links) and dynamics. Topological analysis can use complex, highly resolved empirical food web models to explore the architecture of feeding interactions but is limited to a static view, whereas ecosystem models can be dynamic but use highly aggregated food webs. Here, we explore the temporal dynamics of a highly resolved empirical food web over a time period of 18 years, using the German Bight fish and benthic epifauna community as our case study. We relied on long-term monitoring ecosystem surveys (from 1998 to 2015) to build a metaweb, i.e. the meta food web containing all species recorded over the time span of our study. We then combined time series of species abundances with topological network analysis to construct annual food web snapshots. We developed a new approach, “node-weighted” food web metrics by including species abundances to represent the temporal dynamics of food web structure, focusing on generality and vulnerability. Our results suggest that structural food web properties change through time; however, binary food web structural properties may not be as temporally variable as the underlying changes in species composition. Further, the node-weighted metrics enabled us to detect that food web structure was influenced by changes in species composition during the first half of the time series and more strongly by changes in species dominance during the second half. Our results demonstrate how ecosystem surveys can be used to monitor temporal changes in food web structure, which are important ecosystem indicators for building marine management and conservation plans.
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In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.
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In Drosophila, long sperm are favoured in sperm competition based on the length of the female’s primary sperm storage organ, the seminal receptacle (SR). This sperm-SR interaction, together with a genetic correlation between the traits, suggests that the coevolution of exaggerated sperm and SR lengths may be driven by Fisherian runaway selection. Here, we explore the costs and benefits of long sperm and SR genotypes, both in the sex that carries them and in the sex that does not. We measured male and female fitness in inbred lines of D. melanogaster derived from four populations previously selected for long sperm, short sperm, long SRs, or short SRs. We specifically asked: what are the costs and benefits of long sperm in males and long SRs in females? Furthermore, do genotypes that generate long sperm in males or long SRs in females impose a fitness cost on the opposite sex? Answers to these questions will address whether long sperm are an honest indicator of male fitness, if male post-copulatory success is associated with male pre-copulatory success, if female choice benefits females or is costly, and whether intra-genomic conflict could influence evolution of these traits. We found that both sexes have increased longevity in long sperm and long SR genotypes. Males, but not females, from long SR lines had higher fecundity. Our results suggest that sperm-SR coevolution is facilitated by both increased viability and indirect benefits of long sperm and SRs in both sexes.
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Recent theoretical and experimental models have evidenced the role played by evolution during species spread, and particularly question the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences on genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Brière, northwestern France). Despite the small spatial scale of our study (15 km²), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonisation through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a two-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights in the current context of profound rearrangements in species distributions due to global change.
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Forests globally are subject to multiple disturbances such as logging and fire that create complex temporal variation in spatial patterns of forest cover and stand age. However, investigations that quantify temporal changes in biodiversity in response to multiple forms of disturbance in space and time are relatively uncommon. Over a 10-year period, we investigated the response of bird species to spatio-temporal changes in cover associated with logging and wildfire in the Mountain Ash (Eucalyptus regnans) forests of south-eastern Australia. Specifically, we examined how bird occurrence changed with shifts in the proportion of area burnt or logged in a 4.5km radius surrounding each of 87 field survey sites. Overall species richness was greatest in older forest patches. Bird species richness declined as the amount of fire around each site increased. At the individual species level, most species were more likely to be found in old growth than younger forest. Twenty-five of 36 bird species we modeled, exhibited a negative response to the amount of fire in the surrounding landscape (while two species responded positively to fire). Only nine species exhibited signs of post-fire recovery. Ten species were more likely to be recorded as the proportion of logged forest surrounding a site increased, suggesting a possible “concentration effect” with displaced birds moving into unlogged areas following harvesting of adjacent areas. In contrast to predictions from the disturbance-congruence hypothesis, no bird species exhibited similar responses to fire and logging in the landscape surrounding our sites. Similarly, no bird life history traits were associated with burned or logged forest, although insectivorous birds were more likely to be found in old growth forests and increased over time. Birds in Mountain Ash forests are strongly associated with old growth stands and exhibit complex, time-dependent and species-specific responses to landscape disturbance. Despite logging and fire both being high-severity perturbations, species responses to one kind of landscape-scale disturbance are not readily predictable based on an understanding of the responses to another kind of (albeit superficially similar) disturbance.
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Background: Animal-borne data loggers today often house several sensors recording simultaneously at high frequency. This offers opportunities to gain fine-scale insights into behaviour from individual-sensor as well as integrated multi-sensor data. In the context of behaviour recognition, even though accelerometers have been used extensively, magnetometers have recently been shown to detect specific behaviours that accelerometers miss. The prevalent constraint of limited training data necessitates the importance of identifying behaviours with high robustness to data from new individuals, and may require fusing data from both these sensors. However, no study yet has developed an end-to-end approach to recognise common animal behaviours such as foraging, locomotion, and resting from magnetometer data in a common classification framework capable of accommodating and comparing data from both sensors. Methods: We address this by first leveraging magnetometers’ similarity to accelerometers to develop biomechanical descriptors of movement: we use the static component given by sensor tilt with respect to Earth’s local magnetic field to estimate posture, and the dynamic component given by change in sensor tilt with time to characterise movement intensity and periodicity. We use these descriptors within an existing hybrid scheme that combines biomechanics and machine learning to recognise behaviour. We showcase the utility of our method on triaxial magnetometer data collected on ten wild Kalahari meerkats (Suricata suricatta), with annotated video recordings of each individual serving as groundtruth. Finally, we compare our results with accelerometer-based behaviour recognition. Results: The overall recognition accuracy of >94% obtained with magnetometer data was found to be comparable to that achieved using accelerometer data. Interestingly, higher robustness to inter-individual variability in dynamic behaviour was achieved with the magnetometer, while the accelerometer was better at estimating posture. Conclusions: Magnetometers were found to accurately identify common behaviours, and were particularly robust to dynamic behaviour recognition. The use of biomechanical considerations to summarise magnetometer data makes the hybrid scheme capable of accommodating data from either or both sensors within the same framework according to each sensor’s strengths. This provides future studies with a method to assess the added benefit of using magnetometers for behaviour recognition.
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Neusticemys neuquina is a turtle from the Upper Jurassic of the Neuquén Basin, Patagonia, Argentina. Here we describe in detail a new skull, lower jaw, and a vertebra, utilizing both traditional anatomical description and computed tomography (CT). New diagnostic cranial characters of Ne. neuquina are: a round depression on the ventral surface of the basisphenoid, a relatively larger oval foramen nervi trigemini and reduced and steepened triturating surfaces on both the maxilla and dentary. The new morphological information presented in this study was included in a phylogenetic analysis, the primary result of which was recovery of Ne. neuquina within Thalassochelydia. Characters recognized as synapomorphies of this clade include (1) anterolateral recess of the anterior surface of the quadrate positioned lateral to the processus trochlearis oticum, (2) presence of a fossa on the supraoccipital-opisthotic-exoccipital contact area, (3) foramina anterius caroticus cerebralis located close together but independently perforating the basisphenoid, and (4) presence of the splenial in the mandible. Two contrasting dispersal scenarios may explain how this species of Thalassochelydia can be found outside of Europe. The presence of Ne. neuquina in the Neuquén Basin could be the consequence of an early dispersion event, for which we lack intermediate forms, or it may be the result of a later event once the clade was already established in Europe.
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