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The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern
<p>Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.</p>
FIG. 7. — Deutonura jeromoltoi n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 7. — Deutonura jeromoltoi n. sp.: A, central area of head; B, genal and posterior areas of head. Scale bars: A, B, 50 µm.
FIG. 9. — A, C, Deutonura jeromoltoi n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 9. — A, C, Deutonura jeromoltoi n. sp.; B, D, D. igilica Dallai, 1983; A, B, reticulations of antenno-frontal tubercle; C, D reticulations of dorso-internal tubercle of Abd. V. Scale bars: 50 µm.
FIG. 1. — Orogastrura tetrophthalma n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 1. — Orogastrura tetrophthalma n. sp.: habitus, specimens from sample M090608-DB18. Body size: 650-800 µm.
FIG. 4. — Orogastrura tetrophthalma n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 4. — Orogastrura tetrophthalma n. sp.: A, dorsal side of Abd. V-VI; B, ventral side of Abd. VI; C, posterior side of furca. Scale bars: A, 30 µm; B, 20 µm; C, 25 µm.
FIG. 2. — Orogastrura tetrophthalma n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 2. — Orogastrura tetrophthalma n. sp.: A, dorsal chaetotaxy; B, maxillary outer lobe; C, ocular area; D, labrum; E, right antenna in dorsal view with numbers of Ant. IV S-chaetae; F, apical vesicle of Ant. IV; G, s-microchaeta of Ant. IV; H, s-microchaeta of Ant. III organ. Abbreviations: see material and methods.Scale bars: A, 150 µm; C, E, 20 µm; B, D, 10 µm.
FIG. 3. — Orogastrura tetrophthalma n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 3. — Orogastrura tetrophthalma n. sp. leg II. Pale grey, area without secondary granules (primary granules only). Scale bar: 20 µm.
FIG. 8. — Deutonura jeromoltoi n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 8. — Deutonura jeromoltoi n. sp.: abdominal sternite chaetotaxy. Grey areas, muscular insertions; Black spots, pseudopores. Scale bar: 100 µm.
FIG. 5. — Deutonura jeromoltoi n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 5. — Deutonura jeromoltoi n. sp.: habitus, in dorsal view, of three specimens. Body size 1150 to 1800 µm.
FIG. 6. —A-C, E-G, Deutonura jeromoltoi n in Two new species of Poduromorpha (Collembola) from the Mercantour National Park (Alpes-Maritimes, France), with comments on pseudopore patterns
FIG. 6. —A-C, E-G, Deutonura jeromoltoi n. sp.; D, D. gibbosa Porco, Bedos & Deharveng, 2010: A, dorsal chaetotaxy, Black spots, pseudopores; B, labrum chaetotaxy; C, ventro-distal sclerification of labrum in D. jeromoltoi n. sp.; D, idem in D. gibbosa; E, labium; F, left Ant. III-IV in dorsal view; G, left Ant. III-IV in ventral view. Names of antennal chaetae after Smolis, 2008. Scale bars: A, 100 µm; B-E, 20 µm.
FIG. 4 in Descriptions of two new species of Empidinae Schiner, 1862 (Diptera: Empididae) from the Mercantour National Park, France
FIG. 4. — Rhamphomyia (Lundstroemiella) brevis n. sp. Male hypopygium in lateral view. Scale Bar: 0.1 mm
FIG. 3 in Rodents in grassland habitats: does livestock grazing matter? A comparison of two Alpine sites with different grazing histories
FIG. 3. — Rank/abundance plots for the Carex sempervirens (CS) and Dactylis glomerata (DG) pastoral types. Plots are based on data published by Cavallero et al. (2003, 2007) and refer to: A, the pastoral type of the lightly grazed areas (CS type); B, the abandoned, formerly intensively grazed areas (DG type).
FIG. 2 in Rodents in grassland habitats: does livestock grazing matter? A comparison of two Alpine sites with different grazing histories
FIG. 2. — Box and whisker plots showing the median, first and third quartile and the minimum and maximum values for the log of the captured animals in each plot. Outliers are plotted as open circles.
FIG. 1 in Rodents in grassland habitats: does livestock grazing matter? A comparison of two Alpine sites with different grazing histories
FIG. 1. — Simplified land use in the study area overlaid onto a topographic map. Sampling plots were located within the lightly grazed and in the intensively grazed areas. For the latter areas, in particular, plots were located in sites not used by cattle at present. Plot locations are approximate since we could not leave traps unattended between sessions, with the result that, for each session, plots were not exactly in the same locations as the one before.
FIG. 4 in Groundwater oligochaetes (Annelida, Clitellata) from the Mercantour National Park (France), with the descriptions of one new genus and two new stygobiont species
FIG. 4. — Marionina sambugarae Schmelz, n. sp.: A, segments IV-VI, lateral view (facing left) (paratype MNHN HEL 11.262.01d); B, clitellar region, lateral view (holotype MNHN HEL 11.262.01c); C, clitellar region, dorsal view, showing dorsally interrupted clitellum (paratype IRScNB I.G. 32392 slide 11.264.02e). Symbols: Ü, dorsal lobe of pharyngeal gland in VI. Scale bars: 100 µm.
FIG. 3 in Groundwater oligochaetes (Annelida, Clitellata) from the Mercantour National Park (France), with the descriptions of one new genus and two new stygobiont species
FIG. 3. — Geographical distribution of groundwater Aberrantidrilus Martin, 2015 species in Southern Europe. The shaded patterns indicate the areas of carbonate rock outcrops (exposed karst terrains; Williams & Fong 2010).
FIG. 2 in Groundwater oligochaetes (Annelida, Clitellata) from the Mercantour National Park (France), with the descriptions of one new genus and two new stygobiont species
FIG. 2. — Aberrantidrilus stephaniae Martin, n. gen., n. sp.: A, male genitalia (paratype MNHN HEL 524 slide 11.007.04); B, detailed sketch of the pseudopenis area, showing posterior prostate (ppr) and penial seta (ps) (paratype IRScNB I.G. 32392 slide 11.019.06); C, spermathecae in segment XII (paratype IRScNB I.G. 32392 slide 11.017.01c); D, D', unmodified and penial setae (ps) (D. IRScNB paratype I.G. 32392 slide 11.017.01b; D'. IRScNB holotype I.G. 32392 slide 11.019.01). Abbreviations: see Material and methods. Scale bars: A, C, 100 µm; B, D, D', 50 µm.
Figures 43-46 in Two new species of Chrysina Kirby (Coleoptera: Scarabaeidae: Rutelinae) from Mexico
Figures 43-46. Female inferior genital plates of Chrysina spp. 43) C. blackalleri. 44) C. donthomasi. 45) C. beyeri. 46) C. nogueirai.
Figures 25-42 in Two new species of Chrysina Kirby (Coleoptera: Scarabaeidae: Rutelinae) from Mexico
Figures 25-42. Male genital capsule of Chrysina spp. 25-30) Dorsal habitus. 25) C. blackalleri. 26) C. dianae. 27) C. taylori. 28) C. donthomasi. 29) C. beyeri. 30) C. nogueirai. 31-36)Ventral habitus. 31) C. blackalleri. 32) C. dianae. 33) C. taylori. 34) C. donthomasi. 35) C. beyeri. 36) C. nogueirai. 37-42) Lateral habitus. 37) C. blackalleri. 38) C. dianae. 39) C. taylori. 40) C. donthomasi. 41) C. beyeri. 42) C. nogueirai.
Figures 21-24 in Two new species of Chrysina Kirby (Coleoptera: Scarabaeidae: Rutelinae) from Mexico
Figures 21-24. Pygidium of male Chrysina spp. 21) C. blackalleri. 22) C. donthomasi. 23) C. beyeri. 24) C. nogueirai.
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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.