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196 results for “population comparison”
Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.
Data from: Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America
We investigate population genetic structuring in Margaritifera falcata, a freshwater mussel native to western North America, across the majority of its geographical range. We find shallow rangewide genetic structure, strong population-level structuring and very low population diversity in this species, using both mitochondrial sequence and nuclear microsatellite data. We contrast these patterns with previous findings in another freshwater mussel species group (Anodonta californiensis/A. nuttalliana) occupying the same continental region and many of the same watersheds. We conclude that differences are likely caused by contrasting life history attributes between genera, particularly host fish requirements and hermaphroditism. Further, we demonstrate the occurrence of a 'hotspot' for genetic diversity in both groups of mussels, occurring in the vicinity of the lower Columbia River drainage. We suggest that stream hierarchy may be responsible for this pattern and may produce similar patterns in other widespread freshwater species.
Data from: Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genome-wide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (1) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (2) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (3) whole-genome relatedness at 37,037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.
A comparison of neutral genetic differentiation and genetic diversity among migratory and resident populations of Golden-crowned-Kinglets (Regulus satrapa)
<p>Many animals migrate seasonally between breeding and non-breeding territories and these annual movements can have a profound effect on population genetic structure. We genotyped 283 individuals from 11 populations at seven variable microsatellite loci and compared patterns of neutral genetic differentiation and neutral genetic diversity among migratory and resident breeding populations of the Golden-crowned Kinglet (Regulus satrapa), a widespread North American songbird. We predicted that resident populations would exhibit greater genetic differentiation and lower genetic diversity than migratory populations because migratory behaviour is thought to enhance gene flow. The magnitude of genetic differentiation and genetic diversity among migratory and resident populations was comparable, and the greatest levels of differentiation were observed for pairwise comparisons between Ontario and all western populations. Distance-based redundancy models and redundancy models revealed that patterns of neutral genetic differentiation and neutral genetic diversity follow an isolation-by-distance model and are not correlated with migratory behaviour. Overall it appears that genetic patterns are more closely associated with Pleistocene glacial history as proposed in a previous study.</p>
FIGURE 2. Artemia persimilis female. A in Comparison of the amplexial morphology of two Argentine populations of Artemia (Crustacea, Anostraca, Artemiidae): a reliable taxonomical tool
FIGURE 2. Artemia persimilis female. A: Brood pouch, dorsal view (50x); B: Brood pouch, lateral view (50x). Abbreviations: FP: flattened projection; TP: tergal projection.
FIGURE 6. A in Comparison of the amplexial morphology of two Argentine populations of Artemia (Crustacea, Anostraca, Artemiidae): a reliable taxonomical tool
FIGURE 6. A. franciscana mating arrangement successive crosssections micrographs. Abbreviations: DA: distal articles of male second antennae; FK: frontal knobs; BP: brood pouch.
FIGURE 5. Artemia male heads anterior view. A in Comparison of the amplexial morphology of two Argentine populations of Artemia (Crustacea, Anostraca, Artemiidae): a reliable taxonomical tool
FIGURE 5. Artemia male heads anterior view. A: A. persimilis; B: A. franciscana. Abbreviations: DA: distal articles of second antennae.
FIGURE 7. A in Comparison of the amplexial morphology of two Argentine populations of Artemia (Crustacea, Anostraca, Artemiidae): a reliable taxonomical tool
FIGURE 7. A. persimilis mating arrangement successive crosssections micrographs. Abbreviations: DA: distal articles of male second antennae; FK: frontal knobs; FP: flattened projections; SM: Spiny mound.
FIGURE 4. Artemia male heads with second antennae extended forwards. A in Comparison of the amplexial morphology of two Argentine populations of Artemia (Crustacea, Anostraca, Artemiidae): a reliable taxonomical tool
FIGURE 4. Artemia male heads with second antennae extended forwards. A: A. persimilis; B: A. franciscana. Abbreviations: BA: basal articles of second antennae; DA: distal articles of second antennae; FK: frontal knobs.
FIGURE 5 in What is Pseudopotamilla reniformis (Sabellidae)? Comparisons of populations from Britain, Iceland and Canada with comments on Eudistylia and Schizobranchia
FIGURE 5. Pseudopotamilla saxicava (Quatrefages, 1866) (NMW.Z.2009.038.0903). A) Whole worm; B) thorax and crown, lateral view; C) same, dorsal view; D) same, ventral view; E) dorsal lip; F) superior thoracic chaeta; G) inferior thoracic chaeta; H) thoracic uncinus (right) and companion chaeta (left); J) abdominal uncini, three-quarter view. Not scaled: H, K.
FIGURE 4 in What is Pseudopotamilla reniformis (Sabellidae)? Comparisons of populations from Britain, Iceland and Canada with comments on Eudistylia and Schizobranchia
FIGURE 4. Pseudopotamilla aspersa (Krøyer, 1856). A–J & P, N: Type ZMUC POL-00523; K, L, M: lost Syntype, after Krøyer: A) 'whole' worm, left crown missing, posterior damaged; B) antero-lateral detail of A; C) anterior thorax, dorsal view; D) same, ventral view; E) superior thoracic chaeta; F) inferior thoracic chaeta, front view; G) same, side view; H) side views of thoracic uncinus (left) and companion chaeta (right); J) view of companion chaeta showing teardrop-shaped 'blade'; K) uncinus and companion chaeta (after Krøyer); L) same, but part of torus; M) left side of crown; N) and P) two views of abdominal chaetae. Not scaled: H, J. Krøyer gave no scales for K–M.
FIGURE 2 in What is Pseudopotamilla reniformis (Sabellidae)? Comparisons of populations from Britain, Iceland and Canada with comments on Eudistylia and Schizobranchia
FIGURE 2. Pseudopotamilla reniformis (Bruguiére, 1789), Neotype (NMW.Z.2001.042.0001). Anterior of neotype in A) dorsal view; B) ventral view; C) lateral view.
FIGURE 3 in What is Pseudopotamilla reniformis (Sabellidae)? Comparisons of populations from Britain, Iceland and Canada with comments on Eudistylia and Schizobranchia
FIGURE 3. Developing abdominal fragments of Pseudopotamilla reniformis. A) Dorsal view of Icelandic fragment with anterior radiolar buds and new posterior with pygidium; B) same, but ventral view; C) developing fragments within posterior of tube from Nova Scotia.
FIGURE 1 in What is Pseudopotamilla reniformis (Sabellidae)? Comparisons of populations from Britain, Iceland and Canada with comments on Eudistylia and Schizobranchia
FIGURE 1. Pseudopotamilla reniformis (Bruguiére, 1789), Neotype (NMW.Z.2001.042.0001). A) Whole worm; B) radiolar compound eye; C) cross section of radiole; D) dorsal view of anterior thorax and crown base; E) same, ventral view; F) dorsal lip and dorsal radiolar appendage; G–H, J) collar chaetae; K) superior thoracic chaeta; L) inferior thoracic chaeta; M) abdominal chaeta; N) thoracic uncinus (right) and companion chaeta (left); P) different view of companion chaeta; Q) abdominal uncinus; R) tube showing distal enrolling and the branch of an offspring. Not scaled: B–C, Q & R.
Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Supplementary material 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 9 in Redescription of the terrestrial isopod Armadillo mayeti Simon, 1885 and its comparison with Armadillo officinalis Duméril, 1816 from Tunisian populations
Figure 9. Male Armadillo officinalis. (A) Telson with uropods, dorsal view. (B) Uropod exopodite insertion, dorsal view. (C) Pleopod 2. (D) Pleopod 1.
Figure 5 in Redescription of the terrestrial isopod Armadillo mayeti Simon, 1885 and its comparison with Armadillo officinalis Duméril, 1816 from Tunisian populations
Figure 5. Male Armadillo mayeti. (A) Pereopod 1. (B) Pereopod 7. (C) Exopodite pleopod 1. (D) Endopodite pleopod 1. (E) Pleopod 2.
Figure 6 in Redescription of the terrestrial isopod Armadillo mayeti Simon, 1885 and its comparison with Armadillo officinalis Duméril, 1816 from Tunisian populations
Figure 6. Male Armadillo mayeti. (A) Stridulation apparatus on propodus 5. (B) Enlarged scale. (C) Scale-setae on tergite I enlarged scale.
Figure 2 in Redescription of the terrestrial isopod Armadillo mayeti Simon, 1885 and its comparison with Armadillo officinalis Duméril, 1816 from Tunisian populations
Figure 2. Male Armadillo mayeti. (A) Cephalon and tergite I dorsal view with numerous setae. (B) Pereonite I and II with lateral groove. (C) Pleotelson ventral view (pereopods 7 removed) with bilobed caudal process, pereopods 6, pleopods 1 and 2, uropods, telson apex.
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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
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.