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866 results for “closely related species”
Data from: Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives
Premise of the study: Species limits of the emerging model organism Setaria viridis (tribe Paniceae, subtribe Cenchrinae) are not well defined. It is thought to be related to S. adhaerens, S. faberi, S. verticillata, and S. verticilliformis and in North America occurs with the morphologically similar S. pumila. An integrated approach was taken to evaluate its variation and relationships with the other taxa. Methods: Statistical morphology, flow cytometry, molecular phylogenetics, and growth experiments were employed to examine the group's physical variation, polyploidy, evolutionary relationships, and drought ecology, respectively. Key results: Setaria viridis contributed one genome to the tetraploids S. faberi, S. verticillata, and S. verticilliformis; the other genome of the latter two was contributed by S. adhaerens. Setaria pumila is unrelated. Morphologically, S. viridis is most similar to S. faberi, but all tested accessions of S. viridis were diploid, whereas those of S. faberi were all tetraploid. Principal component analysis of 70 morphological characters consistently separated S. viridis from S. faberi, largely by spikelet characters. The diagnostic morphological characters are not affected by watering. Setaria faberi is far more sensitive to drought, in terms of mortality and morphological stunting, than S. viridis or S. pumila. Conclusions: Setaria viridis is a diploid species and has contributed to several polyploid derivatives. The most morphologically similar of the polyploids is S. faberi, which differs in spikelet features, phylogenetics, genome size, and ecological response to drought. Researchers using field-collected S. viridis as a model organism will benefit from the clear delimitation provided in this study.
Data from: Variation in thermal biology of three closely related lizard species across an elevation gradient
The critical thermal limits of organisms and the thermal sensitivity of their performance tends to vary predictably across latitudinal gradients. There has been comparatively less investigation into variation in thermal limits biology with altitude, despite similar gradients in environmental temperatures with elevation. To redress this, we examined species critical thermal limits (CTmin and CTmax); thermal sensitivity of locomotor performance, and shelter site attributes, in three lizard species that replace one another along a contiguous elevation gradient in south eastern Australia. The species examined consisted of a highland specialist, Liopholis guthega, mid elevation species L. montana, and lowland L. whitii. We found similar habitat attributes between the species, but L. guthega predominantly occurred in open habitat which may reflect a strategy for maximising exposure to insolation. We found intraspecific variation in lizard thermal traits, most notably in cold tolerance of L. guthega and in both heat and cold tolerance of L. whitii, suggesting population specific variables acting on thermal physiology rather than a species distribution maintained by distinct thermal tolerances. This study represents one of the few examinations of thermal trait variability within and between species with elevation in a temperate system, and provides evidence for thermal physiology driven by localised adaptation and/or physiological plasticity to local conditions.
Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan
1. To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics. 2. The identification of DNA fragments sampled from a body of water (environmental DNA) has become a popular technique for rapidly determining the distribution of a target species. In this study, we analysed environmental DNA in water samples from 37 sites across the Katsura River basin in Japan. We used TaqMan real-time PCR to distinguish the Japanese giant salamander Andrias japonicus from the closely related Chinese giant salamander Andrias davidianus, which is known to invade Japanese rivers and hybridize with the Japanese species. 3. In environmental samples, we detected mtDNA of the endemic species at 25 sites and mtDNA of the exotic species at nine sites. The DNA detection sites were concentrated in the upstream region. The exotic species DNA was found beyond the limits of an earlier capturing survey. 4. Synthesis and applications. Using environmental DNA to monitor the two salamander species requires less time and effort than traditional surveys, so a wide-ranging survey can be conducted rapidly. Our results showed that performing three environmental DNA surveys for each site between autumn and winter is desirable for giant salamanders. Further collection of environmental DNA, in combination with conventional population surveys, will provide valuable information that can help protect rare endemic species in a variety of aquatic ecosystems and can help monitor the invasion of exotic species.
Data from: Climatic adaptation and ecological divergence between two closely related pine species in Southeast China
Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could have also promoted interspecific divergence through ecological speciation. In this study, we examined genetic variation within and between two closely related pine species, Pinus massoniana and Pinus hwangshanensis. These two species occur in Southeast China and exhibit contrasting ecological preferences, although hybrids are formed where their distributions overlap. We sampled 26 populations of the two species across their distributional ranges and sequenced 25 climate-related candidate genes and 12 reference loci, assumed not to be related to climatic selection. More than half of the 25 candidate genes (17) showed signals of recent and/or ancient selection, as indicated by one or several robust tests at different evolutionary timescales, while selection signals were only detected at three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared history. We compared intra- and interspecific genetic differentiation of loci detected under recent selection (selected loci) with those showing no signals of recent selection (unselected loci). Intraspecific differentiation was reduced, but interspecific differentiation was elevated for selected loci. Under the Isolation with Migration model, climate-related candidate genes had earlier divergence time estimates and more restricted levels of migration in both directions between the two species than reference loci. Taken together, our results suggested that climate-related candidate genes might be commonly shaped by climatic selection and recent divergent selection might have counteracted interspecific gene flow and play an important role during ecological divergence of these two closely related pine species.
Data from: Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?
Obligate mutualistic nursery pollination systems between insects and plants have led to substantial co-diversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases host plants sharing pollinators are allopatric. However in the case of the species group of Ficus auriculata, forms may co-occur over large parts of their range. We show here that the species group of F. auriculata is constituted by four well-defined genetic entities that share pollinators. We detected hybrids in nature mainly when both parental forms were growing nearby. Controlled crosses showed that F1 offspring could be successfully backcrossed. Hence, despite sharing pollinators and despite hybrid viability, the different forms have preserved their genetic and morphological identity. We propose that ecological differentiation among forms, coupled with limited overlap of reproductive season has facilitated the maintenance of these inter-fertile forms. As such, establishment of pollinator host specificity may not be a prerequisite for sympatric diversification in Ficus.
Data from: Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent
The origin of the fungal wheat pathogen Phaeosphaeria nodorum remains unclear despite earlier intensive global population genetic and phylogeographical studies. We sequenced 1,683 bp distributed across three loci in 355 globally distributed Phaeosphaeria isolates, including 74 collected in Iran near the center of origin of wheat. We identified nine phylogenetically distinct clades, including two previously unknown species tentatively named P1 and P2 collected in Iran. Coalescent analysis indicates that P1 and P2 are sister species of P. nodorum and the other Phaeosphaeria species identified in our analysis. Two species, P. nodorum and P. avenaria f. sp. tritici 1 (Pat1), comprised ∼85% of the sampled isolates, making them the dominant wheat-infecting pathogens within the species complex. We designed a PCR-RFLP assay to distinguish P. nodorum from Pat1. Approximately 4% of P. nodorum and Pat1 isolates showed evidence of hybridization. Measures of private allelic richness at SSR and sequence loci suggest that the center of origin of P. nodorum coincides with its host in the Fertile Crescent. We hypothesize that the origin of this species complex is also in the Fertile Crescent, with four species out of nine found exclusively in the Iranian collections.
Data from: Weak coordination between leaf structure and function among closely related tomato species
Theory predicts that natural selection should favor coordination between leaf physiology, biochemistry and anatomical structure along a functional trait spectrum from fast, resource-acquisitive syndromes to slow, resource-conservative syndromes. However, the coordination hypothesis has rarely been tested at a phylogenetic scale most relevant for understanding rapid adaptation in the recent past or for the prediction of evolutionary trajectories in response to climate change. We used a common garden to examine genetically based coordination between leaf traits across 19 wild and cultivated tomato taxa. We found weak integration between leaf structure (e.g. leaf mass per area) and physiological function (photosynthetic rate, biochemical capacity and CO2 diffusion), even though all were arrayed in the predicted direction along a 'fast–slow' spectrum. This suggests considerable scope for unique trait combinations to evolve in response to new environments or in crop breeding. In particular, we found that partially independent variation in stomatal and mesophyll conductance may allow a plant to improve water-use efficiency without necessarily sacrificing maximum photosynthetic rates. Our study does not imply that functional trait spectra, such as the leaf economics spectrum, are unimportant, but that many important axes of variation within a taxonomic group may be unique and not generalizable to other taxa.
Data from: Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex
Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms. Here we studied patterns of reproductive isolation among three taxa, An. coluzzii, An. gambiae s.s. and An. arabiensis, to compare its strength at different spatial scales, to dissect the relative contribution of pre- versus post-mating isolation, and to infer the involvement of ecological divergence on hybridization. Because F1 hybrids are viable, fertile, and not uncommon, understanding the dynamics of hybridization in this trio of major malaria vectors has important implications for how adaptations arise and spread across the group, and in planning studies of the safety and efficacy of gene drive as a means of malaria control. We first performed a systematic review and meta-analysis of published surveys reporting on hybrid prevalence, showing strong reproductive isolation at a continental scale despite geographically restricted exceptions. Second, we exploited our own extensive field datasets collected at a regional scale in two contrasting environmental settings, in order to assess: i) levels of pre-mating isolation; ii) spatio/temporal and frequency-dependent dynamics of hybridization, iii) relationship between reproductive isolation and ecological divergence, and iv) hybrid viability penalty. Results are in accordance with ecological speciation theory predicting a positive association between the strength of reproductive isolation and degree ecological divergence, and indicate that post-mating isolation does contribute to reproductive isolation among these species. Specifically, only post-mating isolation was positively associated with ecological divergence, whereas pre-mating isolation was correlated with phylogenetic distance.
Data from: Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs
The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining region and several genes that are partially sex-linked in Silene latifolia, using Silene dioica, a closely related dioecious plants whose XY sex chromosome system is inherited from a common ancestor. The S. latifolia pseudoautosomal region (PAR) includes several genes extremely closely linked to the fully Y-linked region. These genes were added to an ancestral PAR of the sex chromosome pair in two distinct events probably involving translocations of autosomal genome regions causing multiple genes to become partially sex-linked. Close linkage with the PAR boundary must have evolved since these additions, because some genes added in both events now show almost complete sex linkage in S. latifolia. We compared diversity patterns of five such S. latifolia PAR boundary genes with their orthologues in S. dioica, including all three regions of the PAR (one gene that was in the ancestral PAR and two from each of the added regions). The results suggest recent recombination suppression in S. latifolia, since its split from S. dioica.
FIGURE 5 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 5. Ventral views of representative specimens of three Varanus species. Same individuals as Figure 3.
FIGURE 4 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 4. Dorsal views of representative specimens of three Varanus species. (a) WAM R125521 V. b u s h i sp. nov. Holotype ♂; (b) WAM R135340 V. bushi sp. nov. Paratype Ψ; (c) WAM R75792 V. gilleni Ψ; (d) WAM R135601 V. caudolineatus ♂; (e) WAM R138950 V. caudolineatus ♂.
FIGURE 3 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 3. Details of scalation on dorsal midbody of representative specimens of three Varanus species. (a) WAM R135340 V. b u s h i sp. nov. Paratype Ψ; (b) WAM R75792 V. gilleni Ψ; c) WAM R135601 V. caudolineatus ♂.
FIGURE 7 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 7. Bivariate plots of various external measurements against each of BL and HNL for male specimens of V. caudolineatus: Symbols used on each plot are: TL (triangle);BL (circle); HNL (square); HLL (cross); FLL (diamond).
FIGURE 2 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 2. Relationships among unique mitochondrial haplotypes obtained through sequencing of various individuals of V. caudolineatus, V. gilleni and V. bushi sp. nov. Localities for each specimen are provided in Appendix I. (a). Strict Consensus tree of six equally most parsimonious trees (length of 330 steps). Numbers above branches represent Maximum Parsimony and Minimum Evolution bootstrap proportions (each based on 1000 pseudoreplicates); numbers below branches represent decay indices. (b). Maximum Likelihood tree (InL = 2418.09) obtained using the GTR+I model of nucleotide substitution. Numbers above branches indicate bootstrap proportions (based on 100 pseudoreplicates).
FIGURE 1 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 1. An adult Varanus bushi sp. nov. from near Roebourne, photographed in life by Robert BrowneCooper.
FIGURE 9 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 9. Distribution of the three Varanus species based on examined materials and type localities. The approximate wider distribution of V. g i l l e n i is indicated by the dashed line. Symbols: Stars — V. caudolineatus; Triangles — V. gilleni; Circles — V. b u s h i sp. nov.; Circles with cross — s V. caudolineatus and V. b u s h i sp. nov. in local sympatry; Circles with dot – type localities.
FIGURE 6 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 6. Dorsal views of head and neck of representative specimens of three Varanus species. Same individuals as Figure 3.
FIGURE 8 in A new species of Varanus Merrem (Squamata: Varanidae) from the Pilbara region of Western Australia, with observations on sexual dimorphism in closely related species
FIGURE 8. Bivariate plots of various external measurements of the three taxa, with separate plots for males (a–d) and females (e–h): (a,e) HNL vs BL; (b,f) HNL vs TL; (c,g) HNL vs FLL; (d,h) HNL vs HLL. Symbols used on each plot are V. caudolineatus (cross); V. gilleni (hollow square); V. bushi sp. nov. (solid triangle).
FIGURE 4 in A redescription of Leptodactylus jolyi Sazima and Bokermann (Anura, Leptodactylidae) and the recognition of a new closely related species
FIGURE 4. Leptodactylus sertanejo sp. n.. Holotype ZUEC 13657. A—Dorsal and B—Lateral views of head. C—Palmar and D—Plantar views.
FIGURE 3 in A redescription of Leptodactylus jolyi Sazima and Bokermann (Anura, Leptodactylidae) and the recognition of a new closely related species
FIGURE 3. Advertisement call of two topotypes of Leptodactylus jolyi. A and D—Oscillogram, B and E—Sonogram, and C and F—Power spectrum. A–C—LeptodjolyiSP1cAAGb; 16:53h, air 23.0ºC, 15/Jan/2004. D–F—; LeptodjolyiSP2cAAGb; 17:17h, air 24.0ºC, 15/Jan/2004. A–C, a single-pulsed call; D–F, a three-pulsed call.
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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.