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Source code for R tutorials and dataset for empirical case study on Malurus elegans (red-winged fairy wren)
<p>Biological processes exhibit complex temporal dependencies due to the sequential nature of allocation decisions in organisms' life-cycles, feedback loops, and two-way causality. Consequently, longitudinal data often contain cross-lags: the predictor variable depends on the response variable of the previous time-step. Although statisticians have warned that regression models that ignore such covariate endogeneity in time series are likely to be inappropriate, this has received relatively little attention in biology. Furthermore, the resulting degree of estimation bias remains largely unexplored.</p> <p>We use a graphical model and numerical simulations to understand why and how regression models that ignore cross-lags can be biased, and how this bias depends on the length and number of time series. Ecological and evolutionary examples are provided to illustrate that cross-lags may be more common than is typically appreciated and that they occur in functionally different ways.</p> <p>We show that routinely used regression models that ignore cross-lags are asymptotically unbiased. However, this offers little relief, as for most realistically feasible lengths of time series conventional methods are biased. Furthermore, collecting time series on multiple subjects–such as populations, groups or individuals—does not help to overcome this bias when the analysis focusses on within-subject patterns (often the pattern of interest). Simulations (R tutorial 1 & 2), a literature search and a real-world empirical example on fairy wrens (data archived here with analyses presented in R-tutorial 3) together suggest that approaches that ignore cross-lags are likely biased in the direction opposite to the sign of the cross-lag (e.g. towards detecting density-dependence of vital rates and against detecting life history trade-offs and benefits of group living). Next, we show that multivariate (e.g. structural equation) models can dynamically account for cross-lags, and simultaneously address additional bias induced by measurement error, but only if the analysis considers multiple time series.</p> <p>We provide guidance on how to identify a cross-lag and subsequently specify it in a multivariate model, which can be far from trivial. Our tutorials with data and R code of the worked examples provide step‐by‐step instructions on how to perform such analyses.</p> <p>Our study offers insights into situations in which cross-lags can bias analysis of ecological and evolutionary time series and suggests that adopting dynamical models can be important, as this directly affects our understanding of population regulation, the evolution of life histories and cooperation, and possibly many other topics. Determining how strong estimation bias due to ignoring covariate endogeneity has been in the ecological literature requires further study, also because it may interact with other sources of bias.</p>
3D Parameter Maps of Red Clump Stars in the Milky Way -- Absolute Magnitudes and Intrinsic Colors
<p>Catalog, application and supplementary figures for the RC paper.</p> <p>1100mRC_WC2021new.fits.zip -- RC catalog</p> <p>Gaia photometric RC sample with 11 million RCs selected based on {\it Gaia}'s EDR3 parallax, our 3D parameter maps, and extinction--distance profile.</p> <p>ra, dec -- position; dm -- distance modulus; av -- V-band extinction</p> <p>dm1 -- corrected distance modulus; av1 -- corrected extinction. used for low-extinction RCs</p> <p>edm -- uncertainty of distance modulus; flag -- 1: high probability RCs, 0: low probability RCs.</p> <p> </p> <p>RC_calculator_linux.zip -- application RC2021 and installer for linux</p> <p>RC_calculator_mac.zip -- application RC2021 and installer for mac </p> <p>The application to estimate the absolute magnitudes and intrinsic colors for RCs with the APOGEE or LAMOST parameters</p> <p> </p> <p>eps -- the best applicable ranges for using application.</p> <p>pd_APOGEE.eps and pd_LAMOST.eps -- Probability densities of each parameter for absolute magnitude training set (orange) and the whole sample (blue). </p> <p>pd_APOGEE_color.eps and pd_LAMOST_color.eps -- Probability densities of each parameter for intrinsic color training set (orange) and the whole sample (blue). </p>
Figure 3 in Morphometric structure and allometry profiles of the giant red shrimp Aristaeomorpha foliacea (Risso, 1827) in the eastern Mediterranean
Figure 3. Relationship between carapace length and other measurements (mm) (logarithmic plots) of females of Aristaeomorpha foliacea (Risso, 1827) (data pooled for all the sampling periods).
Figure 2 in Morphometric structure and allometry profiles of the giant red shrimp Aristaeomorpha foliacea (Risso, 1827) in the eastern Mediterranean
Figure 2. Morphometric measurements taken on Aristaeomorpha foliacea (Risso, 1827). CL, carapace length; T, telson; U, uropodal exopodite; S, scaphocerite; P, third pereiopod; R, rostrum; ABD, abdomen.
Figure 1 in Morphometric structure and allometry profiles of the giant red shrimp Aristaeomorpha foliacea (Risso, 1827) in the eastern Mediterranean
Figure 1. Map of the sampling area and the depth range of the sampling stations of Aristaeomorpha foliacea (Risso, 1827) in the Greek Ionian Sea.
Figure 4 in Morphometric structure and allometry profiles of the giant red shrimp Aristaeomorpha foliacea (Risso, 1827) in the eastern Mediterranean
Figure 4. Relationship between carapace length and other measurements (mm) (logarithmic plots) of males of Aristaeomorpha foliacea (Risso, 1827) (data pooled for all the sampling periods).
Figure 3. Richalpheus dahabensis n in Description of a new species of Richalpheus Anker and Jeng, 2006 (Crustacea: Decapoda: Alpheidae) from the Red Sea
Figure 3. Richalpheus dahabensis n. sp., female holotype (NHMW 21600). (A, B) Left (major) cheliped, mesial and lateral view, respectively; (C) right (minor) cheliped, lateral view; (D) same, carpus and chela, mesial view; (E) same, chela fingers opened. Scale bars: 1 mm.
Figure 1. Richalpheus dahabensis n in Description of a new species of Richalpheus Anker and Jeng, 2006 (Crustacea: Decapoda: Alpheidae) from the Red Sea
Figure 1. Richalpheus dahabensis n. sp., female holotype (NHMW 21600). (A, B) Frontal region, dorsal and lateral view, respectively; (C) same, frontal margin of carapace and first segments of antennular peduncles, dorsal view; (D) right antennule, tooth on ventromesial carina of first segment, lateral view; (E) right cardiac notch, lateral view; (F) sixth pleomere and tail fan, right lateral view; (G) telson and left uropod, dorsal view; (H) right uropod, dorsal view. Scale bars: 1 mm.
Figure 2. Richalpheus dahabensis n in Description of a new species of Richalpheus Anker and Jeng, 2006 (Crustacea: Decapoda: Alpheidae) from the Red Sea
Figure 2. Richalpheus dahabensis n. sp., female holotype (NHMW 21600). (A) Right mandible, mesial view; (B) right maxillule, lateral view; (C) right maxilla, lateral view; (D) right first maxilliped, lateral view; (E) right second maxilliped, lateral view; (F) right third maxilliped, lateral view; (G) right second pereiopod, lateral view; (H) same, detail of carpus and chela; (I) right third pereiopod, lateral view; (J) same, detail of dactylus, mesial view; (K) right fifth pereiopod, lateral view; (L) same, detail of distal propodus and dactylus. Scale bars: 1 mm.
Fig. 7. Red-backed Dwarf Kingfisher Ceyx rufidorsa. a–c in A taxonomic and conservation re-appraisal of all the birds on the island of Nias
Fig. 7. Red-backed Dwarf Kingfisher Ceyx rufidorsa. a–c, an individual of the Nias endemic Ceyx [rufidorsa] captus caught at Bawolato; d, nominate subspecies Ceyx rufidorsa rufidorsa caught on neighbouring Tuangku Island. Photographs by Chyi Yin Gwee (a–c) and Elize Ying Xin Ng (d).
Red-green opponency in the long visual fibre photoreceptors of brushfoot butterflies (Nymphalidae)
<p>In many butterflies, the ancestral trichromatic insect colour vision, based on UV-, blue- and green-sensitive photoreceptors, is extended with red-sensitive cells. Physiological evidence for red receptors has been missing in Nymphalid butterflies, although some species can discriminate red hues well. In eight species from genera Archaeoprepona, Argynnis, Charaxes, Danaus, Melitaea, Morpho, Heliconius and Speyeria we found a novel class of green-sensitive photoreceptors that have hyperpolarising responses to stimulation with red light. These green-positive, red-negative (G+R–) cells are allocated to positions R1/2, normally occupied by UV and blue-sensitive cells. Spectral sensitivity, polarisation sensitivity and temporal dynamics suggest that the red opponent units (R–) are the basal photoreceptors R9, interacting with R1/2 in the same ommatidia via direct inhibitory synapses. We found the G+R– cells exclusively in butterflies with red-shining ommatidia containing longitudinal screening pigments. The implementation of the red colour channel with R9 is different from Pierid and Papilionid butterflies, where cells R5-8 are the red receptors. The Nymphalid red-green opponent channel and the potential for tetrachromacy seem to have been switched on several times during evolution, balancing between the cost of neural processing and the value of extended colour information.</p>
Fig. 4. A in First record of the nesting biology of the red-vented barbet, Megalaima lagrandieri (Aves: Piciformes: Megalaimidae), an Indochinese endemic
Fig. 4. A, Parent red-vented barbet on the nesting hole. B–F, with different food items: B, lizard Bronchocela smaragdina; C, figs; D, fruit of Knema sp.; E, bush cricket Zabalius sp.; and F, cicada.
Fig. 3 in First record of the nesting biology of the red-vented barbet, Megalaima lagrandieri (Aves: Piciformes: Megalaimidae), an Indochinese endemic
Fig. 3. Frequency of parental feeding visits during the early nestling period (average for seven days of observation, from 2nd to 13th day of feeding) in the red-vented barbet.
Fig. 1 in First record of the nesting biology of the red-vented barbet, Megalaima lagrandieri (Aves: Piciformes: Megalaimidae), an Indochinese endemic
Fig. 1. Longitudinal and transversal sections of the nest of the redvented barbet. All distances are given in millimetres (mm). "A" stands for the level of the transversal section.
Text-fig. 7. Temporal distribution of the described taxa from the Plio-Pleistocene localities of Turkey. The described localities are marked in red. in Plio-Pleistocene Amphibians And Reptiles From Central Turkey: New Faunas And Faunal Records With Comments On Their Biochronological Position Based On Small Mammals
Text-fig. 7. Temporal distribution of the described taxa from the Plio-Pleistocene localities of Turkey. The described localities are marked in red.
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone. in Mortality Profiles Of Castor And Trogontherium (Mammalia: Rodentia, Castoridae), With Notes On The Site Formation Of The Mid-Pleistocene Hominin Locality Bilzingsleben Ii (Thuringia, Central Germany)
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone.
Text-fig. 1. Geographic position of the beaver-bearing sites discussed in this paper. Red triangles – records of Castor, blue dots – records of Trogontherium. Bilz II – Bilzingsleben II, Ehr – Weimar-Ehringsdorf, Mosb 2 – Mosbach 2, Taub – Weimar-Taubach, Teg – Tegelen. (This map was created using ArcGIS® software by Esri. ArcGIS® and ArcMap™ are the intellectual property of Esri and are used herein under license. Copyright © Esri). in Mortality Profiles Of Castor And Trogontherium (Mammalia: Rodentia, Castoridae), With Notes On The Site Formation Of The Mid-Pleistocene Hominin Locality Bilzingsleben Ii (Thuringia, Central Germany)
Text-fig. 1. Geographic position of the beaver-bearing sites discussed in this paper. Red triangles – records of Castor, blue dots – records of Trogontherium. Bilz II – Bilzingsleben II, Ehr – Weimar-Ehringsdorf, Mosb 2 – Mosbach 2, Taub – Weimar-Taubach, Teg – Tegelen. (This map was created using ArcGIS® software by Esri. ArcGIS® and ArcMap™ are the intellectual property of Esri and are used herein under license. Copyright © Esri).
Figure 2 A in First evidence of predation of the ant species Lasius alienus on the poultry red mite Dermanyssus gallinae
Figure 2 A pile of dry hen feces colonized byD. gallinae was divided into two pieces in Experiment 3. The left one was exposed to ants for 24 hours. The right one was not exposed to ants and was used as a negative control after being kept at 20oC to hold the mites inactive. A: adult mite, B: early biological forms, C: egg, D: white residues of PRM aggregate.
Figure 1 in First record of two insects preying on the red tomato spider mite Tetranychus evansi (Acari: Tetranychidae) in Latakia governorate, Syria
Figure 1 Life stages ofStethorus gilvifrons feeding on all developmental stages ofTetranychus evansi: A – Larva feeding on adult; B – Pupa; C – Adult feeding on eggs; D – Adult feeding on nymph.
Text-fig. 2. A – First small excavation trench in the newly discovered fossiliferous outcrop area of the Ploužnice lake horizon, locality "Small Ravine" south of the village Ploužnice on the slope of road No. 286. Typical are the red, violet and varicoloured tuffaceous siltstones. Semily Formation, Late Stephanian, Krkonoše Piedmont Basin. B – Basal part of fossiliferous 12 cm to14 cm thick reddish to purple-red tuffaceous siltstone bed from the trench in Text-fig. 2A. Internal bedding is expressed as horizontal but with diffuse changes in grain size from fine silt to coarse, fine sandy silt. Intercalated in places are 3 to 5 mm thick layers (indicated by arrows) with patchy concentrations of isolated fish remains, especially in the first 3 centimetres of this siltstone layer. The large white spot at 2.5 cm is a coprolite fragment. in Fossil Fauna And Flora Of A Re-Discovered Locality In The Late Carboniferous Ploužnice Horizon Of The Krkonoše Piedmont Basin, Bohemian Massif
Text-fig. 2. A – First small excavation trench in the newly discovered fossiliferous outcrop area of the Ploužnice lake horizon, locality "Small Ravine" south of the village Ploužnice on the slope of road No. 286. Typical are the red, violet and varicoloured tuffaceous siltstones. Semily Formation, Late Stephanian, Krkonoše Piedmont Basin. B – Basal part of fossiliferous 12 cm to14 cm thick reddish to purple-red tuffaceous siltstone bed from the trench in Text-fig. 2A. Internal bedding is expressed as horizontal but with diffuse changes in grain size from fine silt to coarse, fine sandy silt. Intercalated in places are 3 to 5 mm thick layers (indicated by arrows) with patchy concentrations of isolated fish remains, especially in the first 3 centimetres of this siltstone layer. The large white spot at 2.5 cm is a coprolite fragment.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.