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Urbanization shapes the relation between density and melanin-based colouration in bird communities

Growing urbanization increasingly influences ecosystems worldwide. While the effects of urban conditions within species (through either plastic or evolutionary responses) have been widely studied, their potential influences among species (through environmental filter), especially concerning their colouration, remain poorly known. Here, we investigated whether avian communities breeding inside and outside a major European city (Paris) differ with regards to melanin-based plumage colouration. Melanins are heritable pigments present in many taxa and have a series of unique properties that may allow coping with urban conditions. Using melanic-based colouration as an integrative phenotypic marker, we predicted (i) that the probability of breeding inside the city should increase with the intensity of species melanin-based colouration, (ii) that for species breeding both inside and outside the city, density should increase with the intensity of dark colouration inside the city, but not outside the city, and (iii) that species not breeding inside the city should not exhibit this positive relation between density and colouration. Our results confirmed these predictions. In addition, the density of species not breeding inside the city decreased with the darkness of their plumage. Altogether, these results suggest that bird species experience a balance between costs and benefits of melanin-based colouration shaped by environmental conditions. Both the environmental filtering and the urbanisation-shaped relation between density and colouration evidenced here are likely a general trend, however possibly modulated by additional local environmental conditions. Their importance may even be underestimated given the restricted geographical scale and the overall urbanization rate of the region studied. Further studies involving regions with contrasted environmental conditions should gain insight into the consequences of urbanization worldwide on traits associated with melanin-based colouration.

Stay in shape: assessing the adaptive potential of shell morphology and its sensitivity to temperature in the invasive New Zealand Mud Snail Potamopyrgus antipodarum through phenotypic plasticity and natural selection in Europe

Climate change may force organisms to adapt genetically or plastically to new environmental conditions. Invasive species show a remarkable potential for rapid adaptation. The ovoviviparous New Zealand mud snail (NZMS), Potamopyrgus antipodarum, has successfully established across Europe with two clonally reproducing mitochondrial lineages since its arrival in the first half of the 19th century. Its remarkable variation in shell morphology was shown to be fitness relevant. We investigated the effects of temperature on shell morphology across eleven populations from Germany and the Iberian Peninsula in a common garden across three temperatures. We analysed size and shape using geometric morphometrics. For both, we compared reaction norms and estimated heritabilities. For size, the interaction of temperature and haplotype explained about 50% of the total variance. We also observed more genotype by environment interactions indicating a higher degree of population differentiation than in shape. Across the three temperatures, size followed the expectations of the temperature-size rule, with individuals growing larger in cold environments. Changes in shape may have compensated changes in size affecting space for brooding embryos. Heritability estimates were relatively high. As indicated by the very low coefficients of variation for clonal repeatability (CVA), they can probably not be compared in absolute terms. However, they showed some sensitivity to temperature, in haplotype t more so than in z, which was only found in Portugal. The low CVA-values indicate that genetic variation among European populations is still restricted with low potential to react to selection. A considerable fraction of the genetic variation was due to differences between the clonal lineages. The NZMS has apparently not been long enough in Europe to accumulate significant genetic variation relevant for morphological adaptation. As temperature is obviously not the sole factor influencing shell morphology, their interaction will probably not be a factor limiting population persistence under a warming climate in Europe.

Evolutionary rates and shape variation along the anuran vertebral column with attention to phylogeny, body size, and ecology

The vertebral column is critical to a vertebrate species' flexibility and skeletal support, making vertebrae a clear target for selection. Anurans (frogs and toads) have a unique, truncated vertebral column that appears constrained to provide axial rigidity for efficient jumping. However, no study has examined how presacral vertebrae shape varies among anuran species at the macroevolutionary scale nor how intrinsic (developmental and phylogenetic) and extrinsic (ecological) factors may have influenced vertebrae shape evolution. We used microCT scans and phylogenetic comparative methods to examine the vertebrae of hundreds of anuran species that vary in body size as well as adult and larval ecology. We found variation in shape and evolutionary rates among anuran vertebrae, dispelling any notion that trunk vertebrae evolve uniformly. We discovered the highest evolutionary rates in the cervical vertebrae and in the more caudal trunk vertebrae. We found little evidence for selection pressures related to adult or larval ecology affecting vertebrae evolution, but we did find body size was highly associated with vertebrae shape and microhabitat (mainly burrowing) affected those allometric relationships. Our results provide an interesting comparison to vertebrae evolution in other clades and a jumping-off point for studies of anuran vertebrae evolution and development.

opencc-by-4.0Jul 2022View details →

Temporal FEL Pulse Shaping and Diagnostics at SwissFEL with Tilted Electron Beams

Data for all results shown in my Dissertation. It is a large file archive with simulation and measurement data. Furthermore, almost all analysis scripts are included. The only analysis software missing is the photon spectrum spike analysis, which was written by Adrian Rutschmann. The archive also includes the tex files and a Makefile. From the information (starting from main.tex) one can find the analysis scripts that correspond to each plot. The data was also used for the conference contribution MOP51 to the FEL conference 2022 (fel2022.org).

Data from: Interactive effects of wildfires, season, and predator activity shape mule deer movements

Wildfires are increasing in size, frequency, and severity due to climate change and fire suppression, but the direct and indirect effects on wildlife remain largely unresolved. Fire removes forest canopy, which can improve forage for ungulates but also reduce snow interception, leading to a deeper snowpack and potentially increased vulnerability to predation in winter. If ungulates exhibit predator-mediated foraging, burns should generally be selected for in summer to access high-quality forage and avoided in winter to reduce predation risk in deep snow. Fires also typically increase the amount of deadfall and initiate growth of dense understory vegetation, creating obstacles that may confer a hunting advantage to stalking predators and a disadvantage to coursing predators. To minimize risk, ungulates may therefore avoid burns when and where stalking predators are most active, and use burns when and where coursing predators are most active. We used telemetry data from GPS-collared mule deer (Odocoileus hemionus), cougars (Puma concolor), and wolves (Canis lupus) to develop step selection functions to examine how mule deer navigated species-specific predation risk across a landscape in northern Washington, USA that has experienced substantial wildfire activity during the past several decades. We considered a diverse array of wildfire impacts, accounting for both the severity of the fire and time since the burn (1 to 35 years) in our analyses. We observed support for the predator mediating foraging hypothesis: mule deer generally selected for burned areas in summer and avoided burns in winter. In addition, deer increased use of burned areas when and where wolf activity was high and avoided burns when and where cougar use was high in winter, suggesting the hunting mode of resident predators mediated the seasonal response of deer to burns. Deer were not more likely to die by predation in burned than in unburned areas, indicating that they adequately manage fire-induced changes to predation risk. As fire activity increases with climate change, our findings indicate the impact on ungulates will depend on tradeoffs between enhanced summer forage and functionally reduced winter range, mediated by characteristics of the predator community.

Data from: Empirically testing the influence of light regime on diel activity patterns in a marine predator reveals complex interacting factors shaping behaviour

Diel cycles in marine predator diving behaviour centre around the light-mediated diel vertical migration (DVM) of prey, and are considered critical for optimizing foraging and limiting competition across global seascapes. Yet our understanding of predator diel behaviour is based primarily on examining relative depth usage between constant day/night cycles with no formal investigation of how varying light regimes interact with abiotic factors to shape diel activity. The extreme seasonal light regimes (midnight sun, polar night, day/night cycle) in the Arctic provide a unique natural experimental setting to empirically investigate the occurrence and intensity of diel behaviour in marine predators relative to changing light levels while concomitantly assessing interacting abiotic factors. Depth time series data from satellite-linked tags deployed on six belugas for up to 12 months were used to quantify diel behaviour by calculating dissimilarity in time-at-depth between periods of low and high solar altitude on each day. Generalized additive mixed effects models were used to examine the influence of hours of daylight across extreme light cycles, coupled with bathymetry and sea ice concentration; focal diel patterns were further examined relative to the thermal structure of the water column. As predicted, belugas exhibited cathemerality during the midnight sun, and initiated diel behaviour with the onset of the fall day/night cycle, with a marked increase in its intensity with the progression to equal day/night length. Occurrence of diel patterns, however, was complex; ceasing in regions with seafloor depths < 700 m, and occurring with greatest intensity when the water column was thermally homogeneous within the upper 150 m. Through empirical investigation, this study demonstrates that the onset of day/night light cycles and presumably associated prey DVM can modulate predator diel dive behaviour under certain circumstances, but highlights how the complex interaction of abiotic factors with light regime shape dynamic spatiotemporal patterns. These findings, building on a body of recent work, emphasize that the traditional view of the ubiquitous occurrence of diel behaviour tied to DVM at the base of the food web oversimplifies vertical predator-prey interactions, identifying the need for more structured investigation.

opencc-zeroSep 2022View details →

Environmental data from: Feeding strategy and dietary preference shape the microbiome of epipelagic copepods in a warm nutrient-impoverished ecosystem

Copepods provide a rich organic microenvironment allowing the settlement and proliferation of microorganisms, forming dynamic microbial hotspots in the oceans. Such symbiotic associations in the plankton were previously hypothesized to be especially developed in warm oligotrophic seas, as they may serve as alternative sources of nutrients in biologically-poor waters. Aiming to better understand how copepod microbiomes are shaped in an oligotrophic sea, we characterized microbiota associated with three dominant coastal epipelagic copepod species in the ultra-oligotrophic Eastern Mediterranean Sea using amplicon sequencing of the 16S rRNA gene. Our results show that copepod-associated microbial communities were host-specific rather than determined by seasonal environmental changes. In the filter-feeding copepod with a tendency to herbivory, Temora stylifera, microbial diversity was low and relatively stable throughout the year. In contrast, omnivorous copepods, the ambush-feeding Oithona nana, and the mixed-feeding Centropages ponticus harbored more diverse microbiomes dominated by transient taxa. We suggest that filter-feeding strategy and narrow food spectrum can limit copepod-microbe interactions, while the ambush and mixed feeding strategies combined with omnivory confer higher microbial diversity. Filter feeders may reduce the recruitment of opportunistic microbes by maintaining high fidelity associations, as indicated by the large number of core taxa in T. stylifera. We underline the importance of the copepod-microbe associations in nutrient-impoverished ecosystems, based on predicted enrichment of nitrogen metabolism in the core microbiome, mostly during summer when the shallow coastal waters are nitrogen-depleted.

opencc-by-4.0Sep 2022View details →

Taxonomic classification of seabird long bones using 3D shape: A method with wider potential in zooarchaeology

Dataset of manually-placed landmark (.pts) files.  Fixed landmarks and semilandmarks were placed on 3D digitised (.ply) models and exported in .pts file format from Landmark Editor 3.0 (Institute of Data Analysis and Visualization IDAV, University California Davis, USA) (Wiley et al., 2005). The .pts files can be read into R (R Core Team., 2021) using the Morpho::read.pts function (Schlager, 2017).     R Core Team. (2021). R: A language and environment for statistical computing. (Version 4.0.2). R Foundation for Statistical Computing, Vienna, Austria. <a href="https://www.r-project.org/">https://www.r-project.org/.</a> Schlager, S. (2017). Morpho and Rvcg–Shape Analysis in R: R-Packages for geometric morphometrics, shape analysis and surface manipulations. In Statistical shape and deformation analysis (pp. 217-256). Elsevier. Wiley, D. F., Amenta, N., Alcantara, D. A., Ghosh, D., Kil, Y. J., Delson, E., Harcourt-Smith, W., Rohlf, F. J., St. John, K., & Hamann, B. (2005). Evolutionary morphing. IEEE Visualization 2005 - (VIS'05), pp.55.

opencc-zeroSep 2022View details →

Functional constraints channel mandible shape ontogenies in rodents

In mammals, postnatal growth plays an essential role in the acquisition of the adult shape. During this period, the mandible undergoes many changing functional constraints, leading to spatialization of bone formation and remodelling to accommodate various dietary and behavioural changes. The interactions between the bone, muscles and teeth drive this developmental plasticity, which, in turn, could lead to convergences in the developmental processes constraining the directionality of ontogenies, their evolution and thus the adult shape variation. To test the importance of the interactions between tissues in shaping the ontogenetic trajectories, we compared the mandible shape at five postnatal stages on three rodents: the house mouse, the Mongolian gerbil and the golden hamster, using geometric morphometrics. After an early shape differentiation, either by longer gestation and allometric scaling in gerbils or early divergence of postnatal ontogeny in hamsters in comparison to the mouse, the ontogenetic trajectories appear more similar around weaning. The changes in muscle load associated to new food processing and new behaviours at weaning seem to impose similar physical constraints on the mandible driving the convergences of the ontogeny at that stage despite an early anatomical differentiation. Nonetheless, mice present a rather different timing compared to gerbils or hamsters.

opencc-by-4.0Sep 2022View details →

Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids

Orthogroups and species tree Proteomes included in the analysis: proteomes.tar.gz Orthogroups: Orthogroups.txt Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa Species tree: SpeciesTree_rooted.txt Whole genome alignment of S. avenae, S. miscanthi, M. dirhodum and A. pisum Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz Haplotype divergence analysis (whole genome sequences) VCF files of HapCUT2 phased variants for S. miscanthi Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9): Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz VCF files of HapCUT2 phased variants for S. avenae JIC1 chromosomes (Siave_v2.1 assembly scaffolds 1 to 9): JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz Haplotype resolved assemblies of S. avenae JIC1 and S. miscanthi Langfang-1 based on HapCUT2 phasing results: JIC1_H1.Hapcut2.fa JIC1_H2.Hapcut2.fa Langfang1_H1.Hapcut2.fa Langfang1_H2.Hapcut2.fa SibeliaZ whole genome alignment of S. avenae JIC1 and S. miscanthi Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf Filtered VCF files used for population genomics analysis S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf S. avenae and S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf S. avenae and S. miscanthi GBS samples + JIC1, Langfang1 and M. dirhodum WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf S. miscanthi GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf SNAPP phylogenetic analysis configuration file and trees SNAPP configuration file: snapp.xml SNAPP log file: ut.log SNAPP posterior sample of trees: ut.trees SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc

opencc-zeroOct 2022View details →

Data and scripts from: Replacement drives native β-diversity of British avifauna, while richness differences shape alien β-diversity

Aim: We explored the range shifts of alien and native birds, the responses of alien and native β-diversity to abiotic factors, and the effect of native diversity on alien β-diversity in two time periods. Location: Great Britain. Time period: 1968–1972, 2007–2011. Taxa studied: Breeding birds. Methods: We estimated range shifts of alien and native species between the periods 1968–1972 and 2007–2011. Following, β-diversity of alien and native communities was estimated by Jaccard pairwise index (βtot) and partitioned into richness difference and replacement component for each period. We built abiotic Generalized Dissimilarity Models including abiotic factors for alien and native βtot and their components and a biotic model for aliens including native taxonomic and functional diversity as predictors. Results: Most alien and half native species expanded into new regions during the 40-year period. The native species range shifts did not exhibit a clear pattern along the longitudinal or latitudinal gradient, while alien species tended to move north-westwards. The richness difference was the dominant component of alien β-diversity, and the replacement component contributed mostly to native β-diversity. Alien β-diversity responded similarly, but less strongly than native β-diversity, to the abiotic gradients. Temperature-related variables, distance, and precipitation were the most important abiotic drivers of native and alien β-diversity. The biotic model of alien β-diversity explained more deviance than the abiotic model. Main conclusions: Alien species expanded into new regions over the 40 years, with alien β-diversity driven mostly by species gains. The effect of environmental filtering on alien communities was weaker compared to native communities but was slightly reinforced in the second period compared to the first period, highlighting the role of environmental change in shaping diversity patterns. Native diversity played a key role in driving alien β-diversity, through biotic interactions or/and by reflecting climatic suitability or niche availability for aliens.

Figure 46 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 46. Field records of predation on ants by a male Jotus remus at Barrington Tops (1), a female Anasaitis canosa from Greenville County, South Carolina (2), and a male Naphrys pulex, also from Greenville County (3). Although found on a different continent, Naphrys is thought to be more closely related to the Australian Jotus than to the Anasaitis that shares its leaf-litter habitat (Zhang & Maddison 2013). 2-3, Scale = 1 mm.

Figure 45 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 45. Take-off sequence by an adult male Jotus remus based on analysis of high-speed (sequential frames at 1000 FPS), low resolution video frames. Note the paddles on legs III. In this sequence, the spider crouched (1-4), then sprung off of the surface in a near-vertical trajectory, extending all four hind legs in about 3 msec.

Figure 43 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 43. Take-off sequence by an adult male Jotus auripes based on analysis of high-speed (1000 FPS) video frames. In this example, legs IV accelerated the spider to ~50 cm/s, then to ~55 cm/s, and extension of legs III brought this up to ~90 cm/s.

Figure 42 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 42. Take-off sequence by an adult male Jotus auripes based on analysis of high-speed (1000 FPS) video frames. In this example, legs IV accelerated the spider to ~40 cm/s, then to ~60 cm/s, and extension of legs III brought this up to ~90 cm/s.

Figure 41 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 41. Take-off sequence by an adult male Jotus auripes based on analysis of high-speed (1000 FPS) video frames. In this example, legs IV accelerated the spider to ~55 cm/s, then to ~70 cm/s, and extension of legs III brought this up to ~80 cm/s. Since vertical deceleration due to gravity takes place as the spider is accelerating, the actual acceleration due to vertical extension of the legs is somewhat greater than this.

Figure 39 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 39. Take-off sequence by an adult male Jotus auripes based on analysis of high-speed (1000 FPS) video frames. In this example, legs IV accelerated the spider to ~50 cm/s, then to ~60 cm/s, and extension of legs III brought this up to ~80 cm/s.

Figure 37 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 37. Selected composite images showing successive positions of a jumping male Jotus remus (1000 FPS video). The position of the pedicel was plotted with small circles a 1 msec intervals, superimposed on a grid of 1 mm squares (1 mm/msec corresponds to 100 cm/s). The take-off velocity (at position 7 at right side of grid) shown here was ~79 cm/s in a direction of 18.4° above horizontal (horizontal velocity ~75 cm/s, vertical velocity ~25 cm/s). The red line represents a ballistic flight trajectory from the take-off position, and the actual flight path (small circles) approximates this. Like other jumping spiders, Jotus use their dragline during these targeted jumps. Note the reversal of pitch (backward to forward) at the end of this jump.

Figure 38 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 38. Take-off sequence by an adult male Jotus auripes based on analysis of high-speed (1000 FPS) video frames. In this and in subsequent figures (Figures 31-36), four frames are shown to represent [1] the start position when extension of legs IV begins, [2] the start of extension of legs III, as legs IV continue to extend, [3] the end of extension of legs IV, when only legs III are still extending, and [4] the take-off position at which legs III are completely extended. Small circles show the position of a reference position on the spider (identifed by the presence of the lateral band of white scales on the carapace) for each frame, separated by 1 msec. In the background is a 1 mm grid. In this example, the spider accelerated to ~60 cm/s with legs IV, then to ~70 cm/s with legs III and IV, and finally to ~80 cm/s with only legs IV. In this and in subsequent examples the spider crouched down against the surface before extending its legs.

Figure 44 in Males of a new species of Jotus from Australia wave a paddle-shaped lure to solicit nearby females (Araneae: Salticidae: Euophryini)

Figure 44. Take-off sequence by an adult male Jotus remus based on analysis of high-speed (sequential frames at 1000 FPS), low resolution video frames. In this species legs III and IV are also close in length and both contribute to acceleration.