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477 results for “Molecular evolution”
Data from: Do saline taxa evolve faster? comparing relative rates of molecular evolution between freshwater and marine eukaryotes
The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline vs. freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein-coding and non-coding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein-coding genes in freshwater taxa—the comparisons mainly involving bony fish—compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.
Data from: High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders
Background: Spiders are known for their predatory efficiency and for their high capacity of digesting relatively large prey. They do this by combining both extracorporeal and intracellular digestion. Whereas many high throughput ("-omics") techniques focus on biomolecules in spider venom, so far this approach has not yet been applied to investigate the protein composition of spider midgut diverticula (MD) and digestive fluid (DF). Results: We here report on our investigations of both MD and DF of the spider Nephilingis (Nephilengys) cruentata through the use of next generation sequencing and shotgun proteomics. This shows that the DF is composed of a variety of hydrolases including peptidases, carbohydrases, lipases and nuclease, as well as of toxins and regulatory proteins. We detect 25 astacins in the DF. Phylogenetic analysis of the corresponding transcript(s) in Arachnida suggests that astacins have acquired an unprecedented role for extracorporeal digestion in Araneae, with different orthologs used by each family. The results of a comparative study of spiders in distinct physiological conditions allow us to propose some digestion mechanisms in this interesting animal taxon. Conclusion: All the high throughput data allowed the demonstration that DF is a secretion originating from the MD. We identified enzymes involved in the extracellular and intracellular phases of digestion. Besides that, data analyses show a large gene duplication event in Araneae digestive process evolution, mainly of astacin genes. We were also able to identify proteins expressed and translated in the digestive system, which until now had been exclusively associated to venom glands.
Data from: Mitochondrial phylogeny of notothenioids: a molecular approach to Antarctic fish evolution and biogeography
Antarctic waters represent a unique marine environment delimited by an oceanographic barrier, the Polar Front Zone, and characterized by constant subzero temperatures and presence of sea ice. A group of teleost fish, the Notothenioidei, have adapted to these challenging environmental conditions, undergoing a remarkable diversification. In the present study a total of 798 base pairs, generated from partial sequencing of 16S and 12S mitochondrial ribosomal RNA genes, were examined in 33 notothenioid species representative of all families included in the suborder Notothenioidei. Phylogenetic trees, reconstructed on the basis of sequence data using different methods, indicate that traditional hypotheses on notothenioid systematics and biogeography might be in need of reexamination. Molecular evidence suggests that vicariant speciation could be invoked to explain the early divergence of Eleginops maclovinus, a species previously included in the family Nototheniidae, which is now proposed as the closest sister group to all the rest of notothenioids apart from bovichtids. On the other hand, repeated, independent dispersal through the Polar Front is proposed for the divergence of other subantarctic notothenioid species. Likewise, multiple, independent transitions from benthic to pelagic habit are inferred from molecular data, at variance with the more conservative hypothesis based on cladograms reconstructed from morphological data.
Data from: Molecular palaeontology illuminates the evolution of ecdysozoan vision
Colour vision is known to have arisen only twice – once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders and crustaceans. Here we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously-unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications were fixed in a period of 35 to 71 Million years (Ma) along the stem-arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.
Data from: The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees
Rates of molecular evolution vary substantially between lineages, and a growing research effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test which can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.
Data from: Combining and Comparing Morphometric Shape Descriptors with a Molecular Phylogeny: The Case of Fruit Type Evolution in Bornean Lithocarpus (Fagaceae)
Fruit type in the genus Lithocarpus (Fagaceae) includes both classic oak acorns and novel modifications. Bornean taxa with modified fruits can be separated into two sections (Synaedrys and Lithocarpus) based on subtle shape differences. Following strict criteria for homology and representation, this variation in shape can be captured and the sections distinguished using elliptic Fourier or eigenshape analysis. Phenograms of fruit shape, constructed using restricted maximum likelihood techniques and these morphometric descriptors, were incorporated into combined and comparative analyses with molecular sequence data from the internal transcribed spacer (ITS) region of the nuclear rDNA using branch-weighted matrix representation. The combined analysis strongly suggested independent derivation of the novel fruit type in the two sections from different acorn-like ancestors, while the comparative analysis indicated frequent decoupling between the molecular and morphological change as inferred at well-supported nodes. The acorn fruit type has undergone little modification between ingroup and outgroup, despite large molecular distance. Greater morphological than molecular change was inferred at critical transitions between acorn and novel fruit types, particularly for section Lithocarpus. The combination of these two different types of data improved our understanding of the macroevolution of fruit type in this difficult group and the comparative analysis highlighted the significant incongruities in evolutionary pattern between the two datasets.
Supplementary material 1 from: Parasram N, Santana W, Vallès Y, Windsor AМ, Vallès H (2024) Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species. Zoosystematics and Evolution 100(1): 15-30. https://doi.org/10.3897/zse.100.109192
Phylogenetic trees of individual datasets of 12S, 16S, and ITS-1 genes
Supplementary material 8 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Table of coordinates used
Figure 3 from: Parasram N, Santana W, Vallès Y, Windsor AМ, Vallès H (2024) Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species. Zoosystematics and Evolution 100(1): 15-30. https://doi.org/10.3897/zse.100.109192
Figure 3 Amphithrax aculeatus (Herbst, 1790) adult male (BLSZ 331). A. Habitus, dorsal; B. Ventral view, locality: Barbados; C. Pleonal view of right G1 (BLSZ 222); D. Distal third of the right G1. Scale bars: 20 mm (A, B); 10 mm (C). Photos: Nadeshinie Parasram.
Supplementary material 7 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Haplotype network of the COI data analyzed of D. pampeana
Supplementary material 2 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Scree plots obtained from the morphometric and meristic data analyzed
Figure 2 from: Parasram N, Santana W, Vallès Y, Windsor AМ, Vallès H (2024) Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species. Zoosystematics and Evolution 100(1): 15-30. https://doi.org/10.3897/zse.100.109192
Figure 2 A.BI molecular phylogenetic tree for Amphithrax verrucosus, A. aculeatus and other selected species within the family Mithracidae MacLeay, 1838. Based on GTR+G nucleotide substitution model on the concatenated dataset for two mitochondrial (12S, 16S) and one nuclear (ITS-1) genes, represented as a maximum likelihood phylogram with Bayesian posterior probabilities and maximum likelihood bootstrap values (black diamond = ≤ 50% support, * = 16S sequences only). Note: ULLZ's 9148 and 4534, of Windsor and Felder (2014) and 13596 all re-identified as Amphithrax verrucosus (H. Milne Edwards, 1832); B.Amphithrax verrucosus (H. Milne Edwards, 1832), male (CW: 40.7 mm; CL: 29.5 mm), Barbados (BLSZ 218); C.Amphithrax aculeatus (Herbst, 1790), juvenile female (CW: 53.8 mm; CL: 44.0 mm), Barbados (BLSZ 217).
Supplementary material 5 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Tukey box plot of most distinctive meristic data observed in analyzed specimens of Diapoma pampeana
Figure 6 from: Parasram N, Santana W, Vallès Y, Windsor AМ, Vallès H (2024) Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species. Zoosystematics and Evolution 100(1): 15-30. https://doi.org/10.3897/zse.100.109192
Figure 6 Colour in life. Young female of Amphithrax aculeatus (Herbst, 1790) (BLSZ 217), Barbados. A. Habitus dorsal view; B. Ventral view. Adult male of Amphithrax aculeatus (Herbst, 1790) (MNHN-IU-2013-5929), Guadeloupe; C. Habitus, dorsal view; D. Ventral view. Adult male of Amphithrax verrucosus (H. Milne Edwards, 1832) (GIC 072), Venezuela; E. Habitus, dorsal view; F. Ventral view. Female of Amphithrax verrucosus (H. Milne Edwards, 1832) (BLSZ 328), Barbados; G. Habitus, dorsal view; H. Ventral view. Scale bars: 20 mm. Photos: A, B, G, H. Nadeshinie Parasram. C, D. Joseph Poupin. E, F. William Santana.
Figure 4 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Figure 4 Most discriminant axes obtained from the PCA analyses performed using morphometric and meristic data of studied specimens of Diapoma pampeana (in each plot, the loadings are scaled to 90% of the PC scores). Size-corrected measurements: A. PC1 vs. PC2 plot; B. PC3 vs. PC4 plot. Meristic data; C. PC1 vs. PC2 plot; D. PC3 vs. PC4 plot. Only these variables that most loaded the components are indicated as follows: E- depth at dorsal-fin origin; F- snout to dorsal-fin origin; G- snout to pelvic-fin origin; H- Snout to anal-fin origin; I- distance between dorsal- and adipose-fin origins; J- dorsal fin to caudal-fin base; K- anal-fin base length; L- caudal peduncle length; M- longitudinal scales; N- lateral-line scales; P- scales between lateral line-dorsal origin; Q- scales between lateral line-pelvic origin; R- circumpeduncular scales; S- predorsal scales; T- number of branched anal-fin rays; U- gill rakers on upper limb of branchial arch; V- gill rakers on lower limb of branchial arch; W- number of maxillary teeth; X- number of dentary teeth.
Figure 3 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Figure 3 Geographic distribution of Diapoma pampeana. A. View within South America; B. View within Brazil and Uruguay. All studied specimens from the Pando (Circle), Santa Lucía (triangle), Yi (diamond), and Upper Negro (star; holotype represented by not-filled pattern) are depicted. Other records presented by Ito et al. (2022) are also included.
Figure 1 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Figure 1 Coloration in life of D. pampeana (A, B) from the Pando stream, Canelones Uruguay. Photo by J. Pfleiderer.
Figure 6 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Figure 6 Bayesian topology of phylogenetic relationships among the analyzed Diapoma species (comparing specimens of D. pampeana from the Pando stream and Upper Negro basin) based on COI sequence data. Numbers at nodes correspond to posterior probabilities.
Figure 5 from: Parasram N, Santana W, Vallès Y, Windsor AМ, Vallès H (2024) Morphological and molecular support for Amphithrax verrucosus (H. Milne Edwards, 1832) and Amphithrax aculeatus (Herbst, 1790) (Crustacea, Decapoda, Brachyura) as valid species. Zoosystematics and Evolution 100(1): 15-30. https://doi.org/10.3897/zse.100.109192
Figure 5 Type specimens. A. Paralectotype of Cancer aculeatus, Herbst, 1790, dry preserved carapace without setae and with most of the spines broken (ZMB Herbst 79), locality: Antilles; B. Holotype of Mithrax plumosus Rathbun, 1901 (USNM 23775), ovig. female (CW: 37.0 mm; CL: 29.0 mm), locality: Puerto Rico; C. Holotype of Mithrax pilosus Rathbun, 1892, setae on carapace removed (USNM 16299), male (CW: 30.0 mm; CL: 28.0 mm), locality: Bahamas; D. Distal third of the right G1 of the holotype of Mithrax pilosus (USNM 16299) in pleonal view. Photos: A Kristina von Rintelen. B, C, D Amanda Windsor.
Supplementary material 6 from: Vanegas-Ríos JA, Serra Alanís WS, Azpelicueta MM, Litz T, Malabarba LR (2024) Population variation of Diapoma pampeana (Characiformes, Characidae, Stevardiinae) from an isolated coastal drainage in Uruguay, with new records: comparing morphological and molecular data. Zoosystematics and Evolution 100(1): 69-85. https://doi.org/10.3897/zse.100.112778
Uncorrected pairwise genetic distances using the COI data matrix
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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)
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DANDI Archive for NWB datasets
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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.
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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.