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Structure and stability constrained substitution models outperform traditional substitution models used for evolutionary inference
<p>The current knowledge about how protein structures influence sequence evolution is rarely incorporated into substitution models adopted for phylogenetic inference, which are commonly based on independent with the same substitution process and ignore the known variation of the evolutionary rates across sites with different structural properties. In previous works, we presented site-specific substitution models of protein evolution based on selection on the folding stability of the native state (Stab-CPE), which predict more realistically the evolutionary variability across protein sites. However, those Stab-CPE present qualitative differences from observed data, probably because they ignore changes in the native structure, despite empirical studies suggesting that conservation of the native structure is a strong selective force. Here we present novel structurally constrained substitution models (Str-CPE) based on Julián Echave's model of the structural change due to a mutation as the linear response of the protein to a perturbation and on the explicit model of the perturbation generated by a specific amino-acid mutation. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSA) of the wild-type protein, and better predict the observed substitution rates. Next, we combine Str-CPE and Stab-CPE models to obtain structure and stability constrained substitution models (SSCPE) that fit the empirical MSAs even better. Importantly, these SSCPE models present a relevant improvement of the phylogenetic likelihood for all ten protein families that we analyzed with the program RAxML-NG. We implemented the SSCPE models in the program Prot evol, freely available at <a href="https://github.com/ugobas/Prot_evol">https://github.com/ugobas/Prot_evol</a>.</p>
FIGURE 9 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 9 Centroid size differences of (A) The forcipular apparatus; (B) The cephalic capsule; and (C) The ultimate leg among epimorphic groups. The median with the first and third quartiles is shown (in boxes), together with the range of variation and outliers.
FIGURE 8 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 8 Centroid size differences of (A, B) The forcipular apparatus; (C, D) The cephalic capsule; and (E, F) The ultimate leg among sexes in praematurus (left) and maturus (right) epimorphic groups. The median with the first and third quartiles is shown (in boxes), together with the range of variation and outliers.
FIGURE 7 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 7 Position of landmarks (open circles) and semilandmarks (full circles) for analyzed structures in L. melanops: (A) The forcipular apparatus (ventral view); (B) The cephalic capsule (dorsal view); and (C) The ultimate leg (medial view). Scale bar: (A) and (C) – 1 mm; (B) – 0.5 mm.
FIGURE 6 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 6 Development of genital appendages on the postpedal segments in males during epimorphic stages in L. melanops (ventral view). (A) Agenitalis; (B) Immaturus; (C) Praematurus; (D) Pseudomaturus early phase; (E) Pseudomaturus late phase; (F) Maturus. Scale bars: 0.2 mm.
FIGURE 5 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 5 Development of genital appendages on the postpedal segments in females during epimorphic stages in L. melanops (ventral view). (A) Agenitalis; (B) Immaturus early phase; (C) Immaturus late phase; (D) Praematurus early phase; (E) Praematurus middle phase; (F) Praematurus late phase; (G) Pseudomaturus early phase; (H) Pseudomaturus late phase; (I) Maturus. Scale bars: 0.2 mm.
FIGURE 4 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 4 Arrangement of ocelli during post-embryonic development in L. melanops (lateral view). (A) Anamorph 0; (B) Anamorph 1; (C) Anamorph 2; (D) Anamorph 3; (E) Anamorph 4; (F) Agenitalis; Downloaded from Brill.com 06/21/2024 07:44:41PM (G) Immaturus; (H) Praematurusvia; (I) OpenMaturus Access.. Scale Thisbar is: an 0.2 open mm. access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
FIGURE 3 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 3 Development of the forcipular apparatus in L. melanops (ventral view). (A), (B) Anamorph 0; (C), (D) Anamorph 1; (E) Anamorph 2; (F) Anamorph 3; (G) Anamorph 4; (H) Agenitalis; (I) Immaturus; (J) Pseudomaturus; (K) Maturus. Scale bar: 0.2 mm. Specimens colored with toluidine blue: (B) and (D).
FIGURE 1 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 1 Anamorphic post-embryonic developmental stages in L. melanops (dorsal view). Abbreviations: A0 – anamorph 0; A1 – anamorph 1; A2 – anamorph 2; A3 – anamorph 3; A4 – anamorph 4. Scale bar: 1 mm.
FIGURE 2 in Morphological variation during post-embryonic development in the centipede Lithobius melanops: traditional and geometric morphometrics approaches
FIGURE 2 Epimorphic post-embryonic developmental stages in L. melanops (dorsal view). Abbreviations: AG – agenitalis; iM – immaturus; PM – praematurus; PS – pseudomaturus; M – maturus. Scale bar: 5 mm.
FIGURE 3. A plaster and burlap cradle containing MOR 1184 in Non-traditional applications of fire in fossil preparation
FIGURE 3. A plaster and burlap cradle containing MOR 1184 being burned away from the entrapped fossil.
FIGURE 1. A. A in Non-traditional applications of fire in fossil preparation
FIGURE 1. A. A fossil in the field subsequent to flipping the jacket shows the extent of root growth across the surface of the bone, and infiltrating the bone and rock (MWC 9874). B. The same specimen, with the root system highlighted in white to better illustrate the pervasiveness of the root network.
Figure 3. Chromatogram from the sample fairs MAC 02 and ARA 0 in Detection of enteropathogens and research of pesticide residues in Lactuca sativa from traditional and agroecological fairs
Figure 3. Chromatogram from the sample fairs MAC 02 and ARA 0, with the peaks of Diphenoconazole compared with the pattern.
Fig. 4 in Fig. 3 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 4. Unidentified taxa. Blenniidae sp. 1 (a); Blenniidae sp. 2 (b); Coilia sp. 1 (c); Callionymidae sp. 1 (d); Sillaginidae sp. 1 (e); Soleidae sp. 1 (f); Platycephalidae sp. 1 (g).
Fig. 3 in Fig. 3 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 3. Three degrees of pigmentation on the top of head of A. gymnocephalus larvae; heavy pigment (a); moderate pigment (b); sparse pigment (c, d).
Fig. 1 in Fig. 3 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 1. Map of sampling location (left) and enlarged inset box (right) showing five sampling stations (black circles) along the Klang Strait. Right arrow indicates offshore direction of transect line from Kapar power plant.
Fig. 2 in Fig. 3 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 2. Ontogenetic series of E. thoracata at preflexion (a); flexion (b, c); postflexion (d, e); early juvenile (f).
Fig. 4 in Fig. 3 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 4. Unidentified taxa. Trypauchen sp. 1 (h); Gobiidae sp. 1 (i); Gobiidae sp. 2 (j); Gobiidae sp. 3 (k); Gobiidae sp. 4 (l); Gobiidae sp. 5 (m); Gobiidae sp. 6 (n); Gobiidae sp. 7-1 (o); Gobiidae sp. 7-2 (p); Gobiidae sp. 8 (q).
Fig. 4 in Fig. 3 in Fig. 4 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 4. Five developmental stages of feathers and the regulators for natal down growth suppression in zebra finch. (A) Schematic diagram shows the five developmental stages of feathers: LoGZ, invagination, branching, feather β-keratin, and dermal papilla (Wu et al. 2018). (B) A summary of the mRNAs identified in Type I and Type II feather formations in zebra finch (Chen et al. 2016).
Fig. 1. The modified time calibrated Bayesian tree and a in Fig. 3 in Fig. 4 in Fig. 4 in Responses of Phyllostomid Bats to Traditional Agriculture in Neotropical Montane Forests of Southern Mexico.
Fig. 1. The modified time calibrated Bayesian tree and a plot of four major avian developmental modes (Prum et al. 2015). The complete tree is divided into parts A and B. Scale in the Y-axis: millions of years ago.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.