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1,944 results for “Class I”
Data from: No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon
Genes of the major histocompatibility complex (MHC) are a likely target of mate choice because of their role in inbreeding avoidance and potential benefits for offspring immunocompetence. Evidence for female choice for complementary MHC alleles among competing males exists both for the pre- and the postmating stages. However, it remains unclear whether the latter may involve non-random fusion of gametes depending on gametic haplotypes resulting in transmission ratio distortion or non-random sequence divergence among fused gametes. We tested whether non-random gametic fusion of MHC-II haplotypes occurs in Atlantic salmon Salmo salar. We performed in vitro fertilizations that excluded interindividual sperm competition using a split family design with large clutch sample sizes to test for a possible role of the gametic haplotype in mate choice. We sequenced two MHC-II loci in 50 embryos per clutch to assess allelic frequencies and sequence divergence. We found no evidence for transmission ratio distortion at two linked MHC-II loci, nor for non-random gamete fusion with respect to MHC-II alleles. Our findings suggest that the gametic MHC-II haplotypes play no role in gamete association in Atlantic salmon and that earlier findings of MHC-based mate choice most likely reflect choice among diploid genotypes. We discuss possible explanations for these findings and how they differ from findings in mammals.
Data from: Conserved non-exonic elements: a novel class of marker for phylogenomics
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved non-exonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600 - ∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically-derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine+falcon clade, was resolved differently and with moderate (> 70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.
Data from: Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda
Background: Evaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units. Results: Overall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated. Conclusions: The giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend that a captive breeding program be considered for the Qinling panda population.
Data from: Specific MHC class I supertype associated with parasite infection and colour morph in a wild lizard population
The major histocompatibility complex (MHC) is a large gene family that plays a central role in the immune system of all jawed vertebrates. Non-avian reptiles are under-represented within the MHC literature and little is understood regarding the mechanisms maintaining MHC diversity in this vertebrate group. Here, we examined the relative roles of parasite-mediated selection and sexual selection in maintaining MHC class I diversity of a colour polymorphic lizard. We discovered evidence for parasite-mediated selection acting via rare-allele advantage or fluctuating selection as ectoparasite load was significantly lower in the presence of a specific MHC supertype (functional clustering of alleles); supertype four. Based on comparisons between ectoparasite prevalence and load, and assessment of the impact of ectoparasite load on host fitness, we suggest that supertype four confers quantitative resistance to ticks or an intracellular tick-borne parasite. We found no evidence for MHC-associated mating in terms of pair genetic distance, number of alleles or specific supertypes . An association was uncovered between supertype four and male throat colour morph. However, it is unlikely that male throat colouration acts as a signal of MHC genotype to conspecifics because we found no evidence to suggest that male throat colouration predicts male mating status. Overall, our results suggest that parasite-mediated selection plays a role in maintaining MHC diversity in this population via rare allele advantage and/or fluctuating selection. Further work is required to determine whether sexual selection also plays a role in maintaining MHC diversity in agamid lizards.
Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects
Cell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shaped Escherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell: the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that aPBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level, we then present evidence that PBP1b, the major aPBP, contributes to cell-wall integrity by repairing cell wall defects.
Data from: Estimating age and age class of harvested hog deer from eye lens mass using frequentist and Bayesian methods
Estimation of the age or age class of harvested animals is often necessary to interpret the condition and dynamics of wildlife populations. The mammalian eye lens continues to grow until death and hence the dry mass of the eye lens has commonly been used to estimate the age of mammals. The method requires the relationship between eye lens mass and age to be parameterized using individuals of known age. However, predicting age is complicated by the curvilinear relationship between eye lens mass and age. We used frequentist and Bayesian methods to predict the ages and age classes of harvested hog deer Axis porcinus from eye lens mass. Deer were tagged as calves and harvested 4–177 months later in southeastern Australia. Lenses were extracted, fixed and oven-dried. Of the five growth models evaluated, the Lord model best described the relationship between age and eye lens dry mass (R2 = 95%). The precision of age predictions obtained using the Lord model in a Bayesian mode of inference decreased with increasing eye lens dry mass, with the size of the 95% CI equaling or exceeding predicted age for hog deer > 6 years. However, most predictions of hog deer age will have reasonable precision because few animals > 6 years are harvested. Linear discriminant analysis had high predictive power for classifying hog deer to four widely-used age classes (juvenile, yearling, prime-age and senescent). The Bayesian method is recommended for inverse non-linear prediction of age and the frequentist linear discriminant analysis method is recommended for estimating age class. We provide tables of correspondence between hog deer eye lens dry mass and predicted age and age class. Our statistical methods can be used to estimate age and age class for other mammalian species, including from other ageing techniques such as tooth eruption-wear criteria.
Data from: Discrimination of hybrid classes using cross-species amplification of microsatellite loci: methodological challenges and solutions in Daphnia
Microsatellite markers are important tools in population, conservation and forensic studies and are frequently used for species delineation, the detection of hybridization and introgression. Therefore, marker sets that amplify variable DNA regions in two species are required; however, cross-species amplification is often difficult, as genotyping errors such as null alleles may occur. In order to estimate the level of potential misidentifications based on genotyping errors, we compared the occurrence of parental alleles in laboratory and natural Daphnia hybrids (Daphnia longispina group). We tested a set of twelve microsatellite loci with regard to their suitability for unambiguous species and hybrid class identification using F1 hybrids bred in the laboratory. Further, a large set of 44 natural populations of D. cucullata, D. galeata and D. longispina (1715 individuals) as well as their interspecific hybrids were genotyped to validate the discriminatory power of different marker combinations. Species delineation using microsatellite multi-locus genotypes produced reliable results for all three studied species using assignment tests. D. galeata x cucullata hybrid detection was limited due to three loci exhibiting D. cucullata specific null alleles which most likely are caused by differences in primer binding sites of parental species. Overall discriminatory power in hybrid detection was improved when a subset of markers was identified that amplifies equally well in both species.
Data from: Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forest
A variety of ecological processes influence diversity and species composition in natural communities. Most of these processes, whether abiotic or biotic, differentially filter individuals from birth to death, thereby altering species' relative abundances. Nonrandom outcomes could accrue throughout ontogeny, or the processes that generate them could be particularly influential at certain stages. One long-standing paradigm in tropical forest ecology holds that patterns of relative abundance among mature trees are largely set by processes operating at the earliest life cycle stages. Several studies confirm filtering processes at some stages, but the longevity of large trees makes a rigorous comparison across size classes impossible without long-term demographic data. Here, we use one of the world's longest-running, plot-based forest dynamics projects to compare nonrandom outcomes across stage classes. We considered a cohort of 7,977 individuals in 186 species that were alive in 1971 and monitored in 13 mortality censuses over 42 y to 2013. Nonrandom mortality with respect to species identity occurred more often in the smaller rather than the larger size classes. Furthermore, observed nonrandom mortality in the smaller size classes had a diversifying influence; species richness of the survivors was up to 30% greater than expected in the two smallest size classes, but not greater than expected in the larger size classes. These results highlight the importance of early life cycle stages in tropical forest community dynamics. More generally, they add to an accumulating body of evidence for the importance of early-stage nonrandom outcomes to community structure in marine and terrestrial environments.
Data from: Very high MHC Class IIB diversity without spatial differentiation in the Mediterranean population of Greater Flamingos
Background: Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. Results: We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Conclusion: Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity appears to be maintained by population wide pathogen-mediated selection rather than local pathogen-mediated selection. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in species with large panmictic populations and high dispersal rates.
Data from: Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3
Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful toolfor the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds.
Data from: Low major histocompatibility complex class II variation in the endangered Indo-Pacific humpback dolphin (Sousa chinensis): inferences about the role of balancing selection
It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy–Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis.
Data from: Relatedness within and between leks of golden-collared manakin differ between sexes and age classes
Several hypotheses have been advanced to explain the evolution of leks, a mating system in which males aggregate at display sites where females choose their mates. Only a small proportion of males obtain copulations, and why other males join the lek remains unexplained. One hypothesis has called kin selection into play: if juvenile males join leks where their relatives display and contribute to attract females to the lek, they can gain indirect fitness benefits. We investigated the genetic structure of eight leks of golden-collared manakin, a tropical Passerine. Adult court-holder males, females, and immature males were caught within lek boundaries and the geographical location of the courts was recorded. For court-holding males, within-lek relatedness among four leks was significantly higher than average across-lek relatedness. Courts of more closely related males were not spatially associated within leks. Relatedness among immature males was relatively lower, yet higher within than between leks. Values of relatedness and genetic differentiation among leks were even lower for females. Thus, leks were composed of males that were more related to each other than to other males of the population, and the degree of relatedness decreased from court holding males to immature males to females. This suggests that immature males explore several leks and eventually join those where their relatives display, whereas females appear to visit leks randomly with respect to relatedness. Our results provide support for the hypothesis that kin selection influences the evolution of lekking behavior in this species.
Formaston Class II Pictish Cross Slab, Aboyne
Formaston 1 (St Adomnan), Aboyne, Aberdeenshire, Pictish cross-slab with ogham inscription. Measurements: H 1.12m, W 0.43m, D 0.12m Class II symbol stone bearing mirror, interlace-filled cross-shaft and incised Ogham inscription Place of discovery: NJ 5412 0014 Present location: Victory Hall, Aboyne Found lying in the kirkyard at Formaston before 1874 and moved to the grounds of Aboyne Castle by 1883. It was taken to Inverurie Museum in 1974 and thence to the Victory Hall, Aboyne. The outer line of ogham runs along the roll moulding on the edge of the slab. The oghams are in Irish script and language and include the Pictish names Nehht and Talorc. Date: eighth or ninth century. The slab is in a protective glass case in Victory Hall, Aboyne which makes 3D modelling difficult and it was only possible to model front face. Canmore ID 17507 Source: Objaverse 1.0 / Sketchfab
BindingDB activity classes
<p>A collection of 120 activity classes extracted from BindingDB and their ECFP4, GpiDAPH3, and MACCS fingerprint representations are provided.</p>
Data for Automatic recognition of element classes and boundaries in the birdsong with variable sequences
<p>Data for Automatic recognition of element classes and boundaries in the birdsong with variable sequences</p>
Amino acid variation in HLA class II proteins is a major determinant of humoral response to common viruses - GWAS summary results
<p>Online Supplementary Dataset of the manuscript "Amino acid variation in HLA class II proteins is a major determinant of humoral response to common viruses": http://www.cell.com/ajhg/fulltext/S0002-9297(15)00372-9</p>
FIGURE 1. African mammal species described between January 1 1989 and December 31 2008 in A synthesis of African and western Indian Ocean Island mammal taxa (Class: Mammalia) described between 1988 and 2008: an update to Allen (1939) and Ansell (1989)
FIGURE 1. African mammal species described between January 1 1989 and December 31 2008, per year. The spike in 2006 is due largely to Louis et al. (2006b).
FIGURE 2 in A synthesis of African and western Indian Ocean Island mammal taxa (Class: Mammalia) described between 1988 and 2008: an update to Allen (1939) and Ansell (1989)
FIGURE 2. Accrual of newly described species per year, by Order, between January 1 1989 and December 31 2008.
FIGURE 17 in The tantulocarid genus Arcticotantalus removed from Basipodellidae into Deoterthridae (Crustacea: Maxillopoda) after the description of a new species from Greenland, with first live photographs and an overview of the class
FIGURE 17. Developmental stages of Arcticotantulus kristenseni sp. nov. (LM). A. Parthenogenetic female (arrow points at head of female) attached to host (ZMUC CRU4872). B. Parthenogenetic female with embryos inside (enlargement of A). C. Living female in late stage of development, probably a sexual female (see Discussion), with developing abdomen (arrow) (ZMUC CRU4873). D. Live male in late stage of development (LM) attached to cephalon of harpacticoid host (ZMUC CRU4877). E. Close-up of D. Abbreviations: cephalic stylet in larval head (cs), male antennular aesthetascs (aes).
FIGURE 15 in The tantulocarid genus Arcticotantalus removed from Basipodellidae into Deoterthridae (Crustacea: Maxillopoda) after the description of a new species from Greenland, with first live photographs and an overview of the class
FIGURE 15. Live tantulus larvae and some developing males of Arcticotantulus kristenseni sp. nov. (LM). Animals in A, B, D, F were alive when the pictures were taken. A. Tantulus larva attached dorsally to harpacticoid host (arrow) (ZMUC CRU4882). B. Three tantulocaridans at different stages of development attached to harpacticoid host (arrows); the most developed tantulus has a male inside (ZMUC CRU4885). C. Detached tantulus larva, ventral view (ZMUC CRU4887). D. Attached tantulus larva, lateral view (ZMUC CRU4884). E. Detached tantulus larva, ventral view (same specimen as in C). F. Attached tantulus larva (close-up of specimen in A). G. Lateral view of detached tantulus larva (ZMUC CRU4887).
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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.