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Fig. 2. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 2. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among five novel Limosilactobacillus species, six L. reuteri subspecies and other recognized species in the genus Limosilactobacillus. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].
Fig. 3. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies. The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54].
Fig. 4 in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts
Fig. 4. Pairwise average nucleotide identity values (ANI; %) of genome sequences belonging to the same or different L. reuteri subspecies. ANI values within the same subspecies and between different subspecies were calculated for 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium). Further information on the involved genome sequences is listed in Table S1.
Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species - Datasets and scripts
<p>Datasets and scripts from "Local adaptation to hosts and parasitoids shape <em>Hamiltonella defensa</em> genotypes across aphid species"</p>
Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations
The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulfide, and represent highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).
Data from: On the equivalence of host local adaptation and parasite maladaptation: an experimental test
In spatio-temporally varying environments, host-parasite coevolution may lead to either host or parasite local adaptation. Using reciprocal infestations over 11 pairs of plots, we tested local adaptation in the hen flea and its main host, the great tit. Flea reproductive success (number of adult at host fledging) was lower on host individuals from the same plot compared to foreign hosts (from another plot), revealing flea local maladaptation. Host reproductive success (number of fledged young) was lower for nests infested by foreign fleas compared to controls, with an intermediate success for nests infested by local fleas. This suggests host local adaptation although the absence of local adaptation could not be excluded. However, fledglings were heavier and larger when reared with foreign compared to local fleas, which could also indicate host local maladaptation if the fitness gain in offspring size offsets the potential cost in offspring number. Our results therefore challenge the traditional view that parasite local maladaptation is equivalent to host local adaptation. The differences in fledgling morphology between nests infested with local and foreign fleas suggest that flea origin affects host resource allocation strategy between nestling growth and defense against parasites. Therefore determining the mechanisms that underlie these local adaptation patterns requires the identification of the relevant fitness measures and life-history trade-offs in both species.
Data from: Dissecting the contributions of plasticity and local adaptation to the phenology of a butterfly and its host plants
Phenology affects the abiotic and biotic conditions that an organism encounters and consequently its fitness. For populations of high latitude species, spring phenology often occurs earlier in warmer years and regions. Here we apply a novel approach to decompose spatiotemporal covariation between spring temperature and the phenology of two flowering plants, Cardamine pratensis and Alliara petiolata, and a Lepidopteran herbivore, Anthocharis cardamines, across the UK, into the contributions of plasticity and local adaptation. All three species overlap in the time-window over which mean temperatures best predict variation in phenology and we find little evidence that the position of time-windows varies latitudinally, as expected if they were initiated by day-length. The focal species show pronounced temperature-mediated phenological plasticity of similar magnitude. While we find no evidence for local adaptation in the flowering times of the plants, geographic variation in the phenology of the butterfly reveals countergradient local adaptation. Geographic variation in the butterfly's phenology appears to be more sensitive to variation in temperature than the flowering times of the host plants and we find no evidence that coevolution has generated geographic variation in adaptive phenological plasticity.
Data from: Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts
<p>Several studies have demonstrated the ecological consequences of genetic variation within a single plant species. For example, these studies show that individual plant genotypes support unique composition of the plants' associated arthropod community. By contrast, fewer studies have explored how plant genetic variation may influence evolutionary dynamics in the plant's associated species. Here, we examine how aphids respond evolutionarily to genetic variation in their host plant. We conducted two experiments to examine local adaptation and rapid evolution of the free-feeding aphid <i>Chaitophorus populicola</i> across genetic variants of its host plant, <i>Populus angustifolia</i>. To test for local adaptation, we collected tree cuttings and aphid colonies from three sites along an elevation / climate gradient and conducted a reciprocal transplant experiment. In general, home aphids (aphid transplanted onto trees from the same site) produced 1.7-3.4 times as many offspring as foreign aphids (aphids transplanted onto trees from different sites). To test for rapid evolution, we used 4 clonally replicated aphid genotypes and transplanted each onto 5 clonally replicated <i>P. angustifolia</i> genotypes. Each tree genotype started with the same aphid genotype composition. After 21 days (~two aphid generations), aphid genotype composition changed (i.e. aphids evolved) and some tree genotypes supported unique evolutionary trajectories of aphids. These results suggest that plant evolution in response to human perturbation, such as climate change and invasive species will also result in evolutionary responses in strongly interacting species that could cascade to affect whole communities.</p>
Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence
<p><span><span><span><span><span><span><span><span><span><span><span>Three subspecies of Northern Bahamian Rock Iguanas, <i>Cyclura cychlura</i>, are currently recognized: <i>C. c. cychlura,</i>restricted to Andros Island, and <i>C. c. figginsi</i> and <i>C. c. inornata,</i> native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of <i>C. cychlura</i> are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: <i>C. cychlura</i> iguanas, their ticks (genus <i>Amblyomma</i>, preferentially parasitizing these reptiles), and <i>Rickettsia </i>spp. endosymbionts (within tick ectoparasites). Our results indicate that while <i>C. c. cychlura</i> on Andros is consistently supported as a separate clade, patterns of relatedness among populations of <i>C. c. figginsi</i> and <i>C. c. inornata</i> within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and <i>Rickettsia</i> spp., supports the evolutionary independence of <i>C. c. inornata</i>. Further, these patterns are also consistent with two independent evolutionarily significant units within <i>C. c. figginsi</i>. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.</span></span></span></span></span></span></span></span></span></span></span></p>
Host plant adaptation during recent global range expansion in the monarch butterfly
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Data from: Spatiotemporal variation in local adaptation of a specialist insect herbivore to its long-lived host plant
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Data from: Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts
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Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence
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Data from: Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts
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Local adaptation of a parasite to solar radiation impacts disease transmission potential, spore yield, and host fecundity
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Data from: Host coevolution alters the adaptive landscape of a virus
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Data from: Host defense triggers rapid adaptive radiation in experimentally evolving parasites
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Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations
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Data from: Host-adapted aphid populations differ in their migratory patterns and capacity to colonize crops
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Allen Brain Atlas
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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
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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
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