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Fig. 4 in Divergence in energy sources for Prochilodus lineatus (Characiformes: Prochilodontidae) in Neotropical floodplains
Fig. 4. The average percentage contribution of each carbon source in different subsystems. The width of arrows represents the strength of resource utilization in each environment studied (MB = microbial biomass).
Fig. 6 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 6. Scatter plot of PCA results on shape variables of the (A) ventral, (B) dorsal and (C) lateral sides of Meriones crassus Sundevall, 1842 specimens. Legends: ○ = Iranian Plateau, ● = Western Zagros, * = Kuwait, Δ = Arabian, ▲ = Jeddah, □ = Jordan/NW Arabia, ■ = African. Deformation grids (two times magnified) along the first principal components, representing shape differences between configurations corresponding to minimal and maximal scores, are shown to the right of each plot. For the numbering of landmarks, see Fig. 2.
Fig. 4 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 4. Scatter plot of the CVA results of the (A) ventral and (B) dorsal shape data of Meriones crassus Sundevall, 1842 (two groups) and M. libycus Lichtenstein, 1823. Legends: ○ = M. crassus (other than Western Zagros), ● = M. crassus of Western Zagros, □ = M. libycus. The grids below show deformation along the arrows, when moving from the M. crassus group mean shape to the Western Zagros group mean shape (A1 and B1), and from the M. libycus mean shape to the mean shape of the Western Zagros (A2 and B2) (shape differences magnified three times for better visualization). For the numbering of landmarks, see Fig. 2.
Fig. 3 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 3. Scatter plot of RW1 versus RW2 of the (A) ventral and (B) dorsal cranium of Meriones crassus Sundevall, 1842 and M. libycus Lichtenstein, 1823. Legends: ○ = M. crassus (other than Western Zagros), ● = M. crassus of Western Zagros, □ = M. libycus. Below: thin-plate spline deformation grids visualize shape variation as expressed by the first two RWs axes (grids represent shape difference between configurations corresponding to lowest and highest RW-values). For the numbering of landmarks, see Fig. 2.
Fig. 7 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 7. CVA scatter plot (axes 1 and 2) on shape variables of the (A) ventral, (B) dorsal and (C) lateral side of the Meriones crassus groups (Jeddah group not included). Legends: ○ = Iranian plateau, ● = Western Zagros, Δ = Arabian and ■ = African. Grids show deformation (3 x magnified) when following the trajectory within the morphospace along the arrows and between the groups' consensus (from African to Western Zagros – A1, B1 and C1; and from Iranian plateau to Western Zagros – A2, B2 and C2). For the numbering of landmarks, see Fig. 2.
Fig. 1 in Cranial phenotypic variation in Meriones crassus and M. libycus (Rodentia, Gerbillinae), and a morphological divergence in M. crassus from the Iranian Plateau and Mesopotamia (Western Zagros Mountains)
Fig. 1. Map showing the sampling localities of Meriones crassus Sundevall, 1842 (circles) and M. libycus Lichtenstein, 1823 (squares) and groups of sampling localities indicated by ellipses (see more detail about the grouping in Material and Methods). The dark closed symbols are the sampling localities of the type specimens (synonyms of Meriones crassus and M. libycus, see Table 1). The ellipses (from left to right) show the following groups: African, Jeddah, Arabian, Western Zagros and Iranian Plateau.
Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
<p>Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of <i>Rhagoletis pomonella </i>to their sibling species <i>R. mendax</i> that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and <i>R. mendax</i> show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on <i>R. mendax</i> revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in <i>Rhagoletis</i>. The generality of this result is placed in the context of other similar systems.</p>
Divergence, gene flow and the origin of leapfrog geographic distributions: the history of color pattern variation in Phyllobates poison-dart frogs
<p>The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between "leapfroging" taxa has not played a prominent role as a driver of phenotypic diversity in <i>Phyllobates</i>. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.</p>
Figure 6 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 6. Relative warps analysis (RWA) of 13 dorsal cranial landmarks from 22 individuals of R. hildebrandtii s.l. belonging to two molecular clades and two lineages of Clade 1 (see Fig. 3). Revised taxon names are provided in parentheses (see Taxonomic Conclusions). Skulls which were included in this analysis are indicated in Table S1. Symbols as in Fig. 5. Thin plate splines (grids) show landmark distortions represented by extremes of variation on RW1 (left = negative; right = positive) and RW2 (bottom = negative; top = positive) axes. The two skull photographs at the bottom are of actual specimens representing the negative (left: TM 41997ı smithersi from Pafuri) and positive (right: DM 11560ı cohenae from Mayoı Mpumalanga Province) extremes of variation on RW1. Landmark positions (filled circles) are shown in the photograph in the centre. doi:10.1371/journal.pone.0041744.g006
Figure 9 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 9. Dorsal (D), ventral (V) and lateral (L) view of bacula (tips on right) from four individuals (a–d) from Mpumalanga (Clade 1a = cohenae sp. nov.), two (e–f) from lowland sites in Mozambique (Clade 2 = mossambicus sp. nov.) and one (g) from Mt Mabu in Mozambique (Clade 1b = mabuensis sp. nov.). a = DM 11558 (Sudwala); b = DM 11620 (Barberton Tunnel; Topotype of cohenae); c = DM 11560 (Mayo); d = DM 11618 (Barberton Tunnel); e = DM 8580 (Gorongosa); f = DM 8578 (Niassa GR; Holotype of mossambicus); g = DM 10842 (Mt Mabu; Holotype of mabuensis). Bacula of Clade 1a (cohenae sp. nov.) have spatulate tip (rounded in Clades 2 (mossambicus sp. nov.) and 1b (mabuensis sp. nov.))ı typically emarginated basal portion (less so in Clades 2 and 1b) and shaft laterally compressed (cylindrical in Clades 2 and 1b) and sloping downwards in lateral view (horizontal in Clades 2 and 1b). doi:10.1371/journal.pone.0041744.g009
Figure 5 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 5. Canonical variates analysis (CVA) (a) of 10 cranial variables in five groups of the Rhinolophus hildebrandtii complex defined by molecular analysis; and PCA (b) of five cranial variables for sample in (a) with type series of hildebrandtii (''H¹'') and eloquens (''E¹'') added. Open circles = Clade 1a (= cohenae sp. nov.); closed circles = Clade 1b (= mabuensis sp. nov.); shaded circles = Clade 1d (= smithersi sp. nov.; Pafuri); asterisk enclosed in circle = Clade 1e (= smithersi sp. nov.; Zimbabwe); open squares = Clade 2 (mossambicus sp. nov.; Mozambique); shaded squares = Clade 2 (mossambicus sp. nov.; Lutopeı Zimbabwe); open diamonds = R. eloquens type series (Clade 3); crosses in circles = R. hildebrandtii type and co-type (Clade 1c). doi:10.1371/journal.pone.0041744.g005
Figure 1 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 1. Portraits of (a) Rhinolophus smithersi species novo, and (b) Rhinolophus mossambicus species novo, two of four new cryptic species described herein within the R. hildebrandtii complex. doi:10.1371/journal.pone.0041744.g001
Figure 4 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 4. Morphometric variation in a series representing the R. hildebrandtii complex from Lutope-Ngolangola, Zimbabwe: a) biplot of forearm length versus noseleaf width and b) PCA of five craniometric variables (M3M3, CM3, IOC, NW, NH) in 26 individuals of known (37 or 46 kHz) and unknown (?) frequency. Females indicated by open circlesı males by closed circles or crosses or asterisk. Voucher specimens for molecular sequencing study indicated by asterisk (Clade 1e: = smithersii sp. nov.; see Taxonomic Conclusions) and crosses (Clade 2: = mossambicus sp. nov.; see Taxonomic Conclusions). Hereafterı all individuals with a frequency of 37 kHz were assumed to belong to Clade 2 (mossambicus sp. nov.) and the 46 kHz individual was assumed to belong to Clade 1e (smithersi sp. nov.). doi:10.1371/journal.pone.0041744.g004
Figure 3. Consensus tree for the cytochrome b in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 3. Consensus tree for the cytochrome b dataset for representative genotyped specimens of the Rhinolophus hildebrandtii complex. The topology represents the consensus topology from a 20 million MCMC run implemented in BEAST. Estimates of divergence times (million years ago; Mya) are indicated adjacent to nodes or above branches and grey bars indicate 95% HPD values. The split between the Hipposideridae and Rhinolophidae was used as the calibration point. Taxa names include museum/field numbers which correspond to Appendix S1 or GenBank accession numbers and abbreviations are: RcfH - R. cf. hildebrandtiiı RD - R. darlingiı RE - R. eloquensı RF - R. fumigatusı RH - R. hildebrandtii s.l.ı RL - R. landeri and RR - R. ruwenzorii. Localitiesı where availableı are providedı abbreviations include SA - South Africaı MZ - Mozambiqueı and ZW - Zimbabweı and the numbers in parentheses correspond with place names in Table S1 and Fig. 2 for Clade 1 and 2 individuals. doi:10.1371/journal.pone.0041744.g003
Figure 7 in Four New Bat Species (Rhinolophus hildebrandtii Complex) Reflect Plio-Pleistocene Divergence of Dwarfs and Giants across an Afromontane Archipelago
Figure 7. Relative warps analysis (RWA) of 12 lateral cranial landmarks from 23 individuals of R. hildebrandtii s.l. belonging to two molecular clades and two lineages of Clade 1 (see Fig. 3). Revised taxon names are provided in parentheses (see Taxonomic Conclusions). Skulls which were included in this analysis are indicated in Table S1. Symbols as is in Fig. 5. Thin plate splines (grids) show landmark distortions represented by extremes of variation on RW1 (left = negative; right = positive) and RW2 (bottom = negative; top = positive) axes. The two skull photographs at the bottom are of actual specimens representing the negative (left: DM 8577ı mossambicus from Namapaı Mozambique) and positive (right: DM 11560ı cohenae from Mayoı Mpumalanga Province) extremes of variation on RW1. Landmark positions (filled circles) are shown in the photograph in the centre. doi:10.1371/journal.pone.0041744.g007
Allopatric divergence of cooperators confers cheating resistance and limits the effects of a defector mutation
<p>Studies of microbial social defectors that 'cheat' on cooperative genotypes generally focus on interactions with their cooperative parents, yet in nature defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting the cheaters' spread and potentially the overall equilibrium frequency of cheaters. The bacterium Myxococcus xanthus undergoes cooperative multicellular development upon starvation, but some developmental defectors can cheat on cooperators, outcompeting them within mixed groups. We show that a defector disrupted at the signaling gene csgA has a narrow cheating range among diverse natural cooperators owing to antagonisms not specifically targeted at defectors. More strikingly, lab-evolved cooperators only slightly differentiated from the defector have allopatrically evolved beyond its cheating range by accumulating fewer than 20 mutations when development was not directly under selection. Cooperators might diversify not only with respect to which defectors cheat on them, but also in the potential for a particular mutation to reduce expression of cooperative trait or generate a cheating phenotype. We tested this by constructing a new csgA mutation in several highly diverged cooperators. The mutation generated very different sporulation phenotypes – from a complete defect to no defect – indicating that genetic background effects can limit the set of genomes for which a given mutation creates a defector and potentiates cheating. Our results suggest that natural populations feature geographic mosaics of cooperators diversified in susceptibility to cheating by any given defector and in the social phenotypes generated by any given mutation in a cooperation gene.</p>
Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common "most genes conserved–few genes adaptive" genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.
Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities
1. Anthropogenic environmental changes are known to affect the Earth's ecosystems. However, how these changes influence assembly trajectories of the impacted communities remains a largely open question. 2. In this study, we investigated the effect of elevated nitrogen (N) deposition and increased precipitation on plant taxonomic and phylogenetic β-diversity in a 9-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China. 3. We found that both N and water addition significantly increased taxonomic β-diversity, whereas N, not water, addition significantly increased phylogenetic β-diversity. After the differences in local species diversity were controlled using null models, the standard effect size of taxonomic β-diversity still increased with both N and water addition, while water, not N, addition, significantly reduced the standard effect size of phylogenetic β-diversity. The increased phylogenetic convergence observed in the water addition treatment was associated with the colonization of different, but phylogenetically closely related, species into different replicate plots of the treatment. Species colonization in this treatment was found to be trait-based, with leaf nitrogen concentration being the key functional trait. 4. Synthesis. Our analyses demonstrate that anthropogenic environmental changes may affect the assembly trajectories of plant communities at both taxonomic and phylogenetic scales. Our results also suggest that while stochastic processes may cause communities to diverge in species composition, deterministic process could still drive communities to converge in phylogenetic community structure.
Divergent molecular networks program functionally distinct CD8+ skin-resident memory T cells
<p>Skin-resident CD8+ T cells comprise distinct IFN-γ- (TRM1) and IL-17-producing (TRM17) subsets that differentially contribute to immune responses. However, whether these populations employ common mechanisms to establish tissue residence is unknown. Here, we show that TRM1 and TRM17 cells navigate divergent trajectories to acquire tissue residency in skin. While TRM1 cells depend on a T-bet-Hobit-IL-15 axis, TRM17 cells develop independently of these factors. Instead, c-Maf commands a tissue-resident program in TRM17 cells parallel to that induced by Hobit in TRM1 cells, with an ICOS-c-Maf-IL-7 axis pivotal to TRM17 cell commitment. Accordingly, targeting this pathway enables ablation of skin TRM17 cells without compromising their TRM1 counterparts. Thus, skin-resident T cells rely on distinct molecular circuitries, which can be exploited to strategically modulate local immunity.</p>
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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.