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Data from: Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield
<p>The nine-banded armadillo (<em>Dasypus novemcinctus</em>) is the most widespread xenarthran species across the Americas. Recent studies have suggested it is composed of four morphologically and genetically distinct lineages of uncertain taxonomic status. To address this issue, we used a museomic approach to sequence 80 complete mitogenomes and capture 997 nuclear loci for 71 <em>Dasypus</em> individuals sampled across the entire distribution. We carefully cleaned up potential genotyping errors and cross contaminations that could blur species boundaries by mimicking gene flow. Our results unambiguously support four distinct lineages within the <em>D. novemcinctus</em> complex. We found cases of mito-nuclear phylogenetic discordance but only limited contemporary gene flow confined to the margins of the lineage distributions. All available evidence including the restricted gene flow, phylogenetic reconstructions based on both mitogenomes and nuclear loci, and phylogenetic delimitation methods consistently supported the four lineages within <em>D. novemcinctus</em> as four distinct species. Comparable genetic differentiation values to other recognized <em>Dasypus</em> species further reinforced their status as valid species. Considering congruent morphological results from previous studies, we provide an integrative taxonomic view to recognise four species within the <em>D. novemcinctus </em>complex: <em>D. novemcinctus</em>, <em>D. fenestratus</em>, <em>D. mexicanus</em>, and <em>D. guianensis </em>sp. nov.<em>, </em>a new species endemic of the Guiana Shield that we describe here. The two available individuals of <em>D. mazzai</em> and <em>D. sabanicola</em> were consistently nested within <em>D. novemcinctus </em>lineage and their status remains to be assessed. The present work offers a case study illustrating the power of museomics to reveal cryptic species diversity within a widely distributed and emblematic species of mammals.</p>
Excavation data from Eripe 1 rock shelter, Papua New Guinea
<p>Data from archaeological excavations made in 2024 at the Eripe 1 rockshelter, Gulf Province, Papua New Guinea, by the <a href="https://papuanpast.hypotheses.org/2908" target="_blank" rel="noopener"><em>Papuan Past Project</em></a> team. This dataset can be visualised using the online <a href="https://analytics.huma-num.fr/archeoviz/eripe1" target="_blank" rel="noopener"><em>archeoViz</em></a> application.</p> <p>This dataset includes piece-plotted objects and some objects from the sieved materials (note that pebbles were piece-plotted in spit 1 and then retrieved from the sieve). The archaeological assemblage includes mainly lithic and faunal remains, some beads, and charcoal samples.</p> <ul> <li><strong>id</strong>: unique identifier in the dataset</li> <li><strong>id_plot</strong>: unique identifier attributed during excavation</li> <li><strong>layer</strong>: number of the 10 cm spits, defined from objects' altitude</li> <li><strong>layer_recorded</strong>: spit recorded during the excavation</li> <li><strong>object_type</strong>: type of archaeological remain</li> <li><strong>object_subtype</strong>: subtype of archaeological remain</li> <li><strong>object_fauna.anatomy</strong>: when available about faunal remains, anatomical parts</li> <li><strong>object_lithic.material</strong>: lithic raw material</li> <li><strong>object_local.interpretation</strong>: description of objects by local Pawaian helpers during the excavation</li> </ul>
Composition-based estimates of the thermal properties of New Zealand basement rocks: data used for calculations and figures
<p>This archive contains four files with compositional data (mineralogical and geochemical) used to estimate thermal conductivity and heat production in New Zealand basement terranes (Kirkby et al., 2024).</p> <p><br>HPR_source_data.csv - contains K, Th, and U concentrations and calculated heat production rates.</p> <p>Longitude - longitude (New Zealand Geodetic Datum)<br>Latitude - latitude(New Zealand Geodetic Datum)<br>K_wtpct - K concentration in weight percent<br>Th_ppm - Th concentration in ppm<br>U_ppm - U concentration in ppm<br>Heat_production_uW/m3 - heat production calculated from K, Th and U concentrations, in microWatts per meter cubed<br>Terrane - name of basement terrane that sample has been assigned to<br>Source - source of data, either PetLAB (Strong et al. 2016), PMAP (Turnbull ref) or separate compilation for this study<br>Reference - Reference citation for data as listed in PetLAB/PMAP or added for this study</p> <p> </p> <p>TC_from_majors_PMAP.csv - contains thermal conductivity estimated from major element geochemistry (Kirkby et al., 2024) using method of, Jennings et al. (2019).<br>Columns are as follows:</p> <p>Collection - collection that sample is contained in within the PetLAB database (Strong et al., 2016)<br>Collection_Number - sample number within the collection above<br>Sample_ID - unique sample ID in PetLAB<br>Analysis_ID - unique analysis ID in PetLAB<br>Longitude - longitude (New Zealand Geodetic Datum)<br>Latitude - latitude(New Zealand Geodetic Datum)<br>**_wtpct - major oxide concentration in weight percent (normalised to non-volatile component)<br>Terrane - name of basement terrane that sample has been assigned to<br>Analysis_Method - analysis method for major oxide concentrations<br>Thermal_conductivity_pred - calculated estimate of thermal conductivity based on major oxide composition, W/mK<br>Bib_ref - analysis source reference, direct copy of Bib_ref field in PetLAB<br>Reference - analysis source reference, direct copy of Reference field in PetLAB</p> <p><br>TC_from_modal_mineralogy.csv - contains thermal conductivity estimated from modal mineralogy (Kirkby et al., 2024).<br>Columns are as follows:</p> <p>Longitude - longitude (New Zealand Geodetic Datum)<br>Latitude - latitude(New Zealand Geodetic Datum)<br>Analysis_ID - unique analysis ID in PetLAB<br>Collection - collection that sample is contained in within the PetLAB database (Strong et al., 2016)<br>Collection_ID - sample number within the collection above<br>Subsample - in the case of thermal conductivity, sometimes two samples were measured. This column distinguishes the two measurements<br>Mineralogy_method - method of determining mineralogy, either point count or QEMSCAN<br>Quartz - percentage of quartz in sample<br>Olivine - percentage of olivine in sample<br>Pyroxene - percentage of pyroxene in sample<br>Other - percentage of other minerals in sample<br>Thermal_conductivity_grain_pred - estimated thermal conductivity (W/mK) from mineralogy (Kirkby et al, 2024), W/mK<br>Thermal_conductivity_dry_measured - measured dry thermal conductivity (W/mK) for samples reported by Sanders et al (2024), W/mK<br>Porosity_measured_pct - measured porosity (percent) for samples reported by Sanders et al (2024)<br>Thermal_conductivity_grain_measured - grain thermal conductivity (W/mK) calculated from measured dry thermal conductivity and porosity<br>Terrane - name of basement terrane that sample has been assigned to<br>Bib_ref - analysis source reference, direct copy of Bib_ref field in PetLAB<br>Reference - analysis source reference, direct copy of Reference field in PetLAB</p> <p><br>TC_from_normative_mineralogy.csv</p> <p>Longitude - longitude (New Zealand Geodetic Datum)<br>Latitude - latitude(New Zealand Geodetic Datum)<br>Analysis_ID - unique analysis ID in PetLAB<br>Collection - collection that sample is contained in within the PetLAB database (Strong et al., 2016)<br>Collection_ID - sample number within the collection above<br>Mineralogy_method - method of determining mineralogy, either Mesonorm or CIPWnormhb (CIPW norm with hornblende)<br>Quartz - percentage of quartz in sample<br>Olivine - percentage of olivine in sample<br>Pyroxene - percentage of pyroxene in sample<br>Other - percentage of other minerals in sample<br>Thermal_conductivity_grain_pred - estimated thermal conductivity (W/mK) from mineralogy (Kirkby et al, 2024)<br>Thermal_conductivity_dry_measured - measured dry thermal conductivity (W/mK) for samples reported by Sagar et al (2022)<br>Porosity_measured_pct - measured porosity (percent) for samples reported by Sagar et al (2024)<br>Thermal_conductivity_grain_measured - grain thermal conductivity (W/mK) calculated from measured dry thermal conductivity and porosity<br>Terrane - name of basement terrane that sample has been assigned to<br>Bib_ref - analysis source reference, direct copy of Bib_ref field in PetLAB<br>Reference - analysis source reference, direct copy of Reference field in PetLAB</p> <p> </p> <p>tc_by_terrane.csv</p> <p>Contains thermal conductivity, standard deviation, and standard error of thermal conductivity estimates by terrane as shown in Figure 7 of Kirkby et al (2024)</p> <p> </p> <p>hpr_by_terrane.csv</p> <p>Contains thermal conductivity, standard deviation, and standard error of thermal conductivity estimates by terrane as shown in Figure 7 of Kirkby et al (2024).</p> <p> </p> <p><br>References</p> <p>Jennings, S., Hasterok, D., & Payne, J. (2019). A new compositionally based thermal conductivity model for plutonic rocks. Geophysical Journal International, 219(2), 1377-1394. https://doi.org/10.1093/gji/ggz376<br>Kirkby, A., N. Mortimer, R. Funnell, M. Sagar, A. Seward, K. Faure and F. Sanders (2024). Composition-based estimates of the thermal properties of New Zealand basement rocks, New Zealand Journal of Geology and Geophysics.<br>Sagar, M. W., Funnell, R., Randell, K., Faure, K., Seward, A., Sanders, F., & Stratford, W. R. (2022). Physical properties of Te Riu-a-Māui / Zealandia crustal rocks: Reconnaissance study and future research. (GNS Science Internal Report 2022/05. <br>Sanders, F., Seward, A., Sagar, M., & Faure, K. (2024). Thermal Properties of Zealandia Basement Rocks: results of Thermal Conductivity Scanner measurements 2023. Lower Hutt. (GNS Science Report. <br>Strong, D. T., Turnbull, R. E., Haubrock, S., & Mortimer, N. (2016). Petlab: New Zealand’s national rock catalogue and geoanalytical database. New Zealand Journal of Geology and Geophysics, 59(3), 475-481. https://doi.org/10.1080/00288306.2016.1157086 </p>
Figure 6 in Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran
Figure 6: (A–E) Xiphinema index Thorne and Allen, 1950, (A) Anterior end; (B) Tubular part of uterus; (C) Vagina; (D) Pars dilatata oviductus; (E) Tail, (F–H) X. pachtaicum (Tulaganov, 1938) Kirjanova, 1951, (F) Anterior end; (G) Anterior genital branch; (H) Tail, (I–N) X. vuittenezi Luc, Lima, Weischer and Flegg, 1964, (I) Anterior end; (J, L) Uterine differentiation spines; (K) Vagina; (M, N) Tail. (Scale bars =10 μm).
Figure 5 in Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran
Figure 5: Bayesian tree inferred under the GTR + I + G model from 28S rDNA D2–D3 expansion domains of X. barooghii n. sp. and X. index (−lnL = 9,085.8555; AIC = 18,191.7109; freqA = 0.2402; freqC = 0.2341; freqG = 0.2885; freqT = 0.2373; R (a) = 1.0503; R (b) = 2.8325; R (c) = 2.6784; R (d) = 0.5047; R (e) = 4.0878; R (f) = 1.0000). Posterior probabilities are given for appropriate clades. Newly obtained sequences are indicated by bold letters.
Figure 1 in Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran
Figure 1: Xiphinema barooghii n. sp. (A) Amphidial pouch; (B) Entire body; (C) Neck region; (D) Female tail; (E) Anterior end; (F) Posterior genital branch; (G–J) Tail of juveniles from J1–J4, respectively.
Figure 3 in Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran
Figure 3: Juvenile stages of Xiphinema barooghii n. sp. Anterior region and tail shape of (A, B) first; (C, D) second; (E, F) third and (G, H) fourth juvenile stages, respectively (Scale bars =10 μm).
Figure 2 in Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran
Figure 2: Xiphinema barooghii n. sp. Female (A, B) anterior end; (C, G) uterine differentiation spines; (D) entire body; (E) reproductive system; (F) vagina; (H) tail; (I) caudal pores in lateral optical view; (J) amphidial pouch; (K) pharyngeal expansion. (Scale bars: A–K = 10 μm, D = 70 μm).
Figure 4 in Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran
Figure 4: Xiphinema barooghii n. sp. Graph of correlation of functional and replacement odontostyle to body length in all developmental stages from Jl to mature females.
Fig. 13 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 13. The vesicomyid bivalve Hubertschenckia ezoensis (Yokoyama, 1890), from the upper Eocene Poronai Formation in Hokkaido, Japan. A. NRM Mo 204823, very large RV; external sculpture (A1) and hinge (A2) views. B. NRM Mo 204821, small articulated specimen; showing ligament (B1) and external ornament and posterior ridge (B2). C. NRM Mo 204824, internal mold of large RV, showing anterior adductor muscle scar; view on right valve (C1) and close-up on hinge area (C2). D. NRM Mo 204825, large articulated specimen, mostly an internal mold; view on right valve (D1) and left valve (D2). E. NRM Mo 204822, hinge of LV.
Fig. 14 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 14. Stratigraphic ranges of vesicomyid bivalve species in western Washington State, USA (reported herein and by Amano and Kiel 2007).
Fig. 11 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 11. The vesicomyid bivalve Pleurophopsis thieli sp. nov., from the upper Eocene Whiskey Creek seep deposit in the Pysht Formation in western Washington State, USA. A. NRM Mo 204797, small articulated specimen, showing inflation; left valve (A1) and dorsal (A2) views. B. NRM Mo 204795, semi-articulated specimen; left valve (B1) and right valve (B2) views. C. NRM Mo 204796, small left valve, showing lack of lunular incision. D. NRM Mo 204794, LV showing shell outline. E. NRM Mo 204799, hinge area and anterior adductor muscle scar of LV. F. NRM Mo 204800, hinge plate of right valve. G. NRM Mo 204801, hinge plate and ligament nymph of RV. H. NRM Mo 204802, hinge plate and ligament nymph of LV. All specimens are paratypes.
Fig. 10 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 10. The vesicomyid bivalve Pleurophopsis chinookensis (Squires and Goedert, 1991), from the upper Eocene Bear River seep deposit in western Washington State, USA. A. NRM Mo 204815, semi-articulated specimen with preserved shell material; view on LV (A1); dorsal view showing short ligament (A2). B. NRM Mo 204816, largely an internal mold, view on LV showing anterior adductor muscle scar. C. NRM Mo 204817, closely articulated specimen in dorsal view, showing true width. D. NRM Mo 204818, view on RV of internal mold showing internal posterior ridge. E. NRM Mo 204819, anterior part of RV with preserved shell, showing lack of lunular incision (E1, E2) and hinge dentition (E3). Abbreviations: aprs, anterior pedal retractor scar; sub. pit., subumbonal pit.
Fig. 9 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 9. The vesicomyid bivalve Squiresica yooni sp. nov., from the Middle Miocene Duho Formation, loc. 18 of Yoon (1976b), South Korea. A. Holotype, NRM Mo 204829, an articulated specimen with preserved cast of RV hinge area; close-up on hinge area (A1), view on right valve and exposed hinge of left valve (A2), and view on left valve (A3). B. Paratype, NRM Mo 204832, articulated specimen, mostly an internal mold; dorsal view showing inflation (B1); view on exterior of RV (B2); close-up on anterior part of LV showing the lack of a lunular incision (B3). C. Paratype, NRM Mo 204831, articulated specimen with some shell preserved; dorsal view showing inflation (C1); lateral view on RV showing fine growth increments (C2).
Fig. 7 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 7. The vesicomyid bivalve Squiresica cf. knapptonensis (Amano and Kiel, 2007) from upper Eocene seep deposits of the Siltstone Unit B along the West Fork of Grays River in western Washington State, USA. A. NRM Mo 204773, internal mold of RV showing adductor muscle scars and pallial line. B. NRM Mo 204808, internal mold of semi-articulated specimen; view on RV (B1); close-up on lunular incision (B2). C. NRM Mo 204776, internal mold of LV showing anterior adductor muscle scar, onset of pallial line, and the short ligament. D. NRM Mo 204775, internal mold of RV showing adductor muscle scars and pallial line. E. NRM Mo 204809, anterior half of RV showing external shell sculpture. F. NRM Mo 204805, view on internal mold of posterior adductor muscle scar. G. NRM Mo 204807I, internal mold of semi-articulated specimen, view on LV. H. NRM Mo 204806, close-up on lunular incision of LV.
Fig. 6 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 6. The vesicomyid bivalve Pliocardia? guthrieorum sp. nov., from the Oligocene seep deposits at UWMB loc. B7452, Lincoln Creek Formation, western Washington State, USA. A. Paratype, NRM Mo 204779, large specimen showing outline, inflation, and ligament; left valve (A1) and dorsal (A2) views. B. Paratype, NRM Mo 204784, showing outline, inflation, and anterior adductor muscle scar; left valve (B1) and dorsal (B2) views. C. Paratype, NRM Mo 204780, small, elongate specimen; right valve (C1) and dorsal (C2) views; digital sections through the hinge area, with our interpretation of the hinge teeth indicated (C3, C4). D. Paratype, NRM Mo 204782, showing ligament. E. Holotype, NRM Mo 204785, showing inflation (E1) and both adductor muscle scars and the pallial line in the RV (E2). F. Paratype, NRM Mo 204781, large specimen with particularly large and blunt umbo. G. Paratype, NRM Mo 204814, small specimen in dorsal view, showing inflation and lunular incision (G1) and the lack of an escutcheon (G2). H. Paratype, NRM Mo 204786, showing lunular incision. I. Paratype, NRM Mo 204813, showing lunular incision. Abbreviation: pams, posterior adductor muscle scar.
Fig. 8 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 8. The vesicomyid bivalve Squiresica plana sp. nov., from Oligocene seep deposits in the Lincoln Creek Formation in western Washington State, USA. Specimens from UWBM loc. B7452 (A–C) and LACMIP loc. 17426 (= SR4) (D–F). A. Paratype, NRM Mo 204772, exterior of LV showing fine growth increments. B. Paratype, NRM Mo 204771, exterior of LV showing shell outline and fine growth increments. C. Paratype, NRM Mo 204770, close-up on anterior part of RV showing near absence of a lunular incision. D. Holotype, NRM Mo 204704, articulated specimen with preserved shell; lateral view on RV (D1) and dorsal view, showing inflation and ligament (D2). E. Paratype, NRM Mo 204705, specimen with partially preserved shell, showing anterior adductor muscle scar and onset of pallial line. F. Paratype, NRM Mo 204706, semi-articulated specimen; F1, close-up on LV hinge area; F2, lateral view on LV.
Fig. 5 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 5. The vesicomyid bivalve Pliocardia kawadai (Aoki, 1954), from Middle Miocene seep deposit at Frankfort of the Astoria Formation in western Washington State, USA. NRM Mo 204713, polished sections of the hinge area in the RV (A) and LV (B). Photographs (A1, B1) and their interpretation (A2, B2).
Fig. 4 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 4. The vesicomyid bivalve Pliocardia kawadai (Aoki, 1954), from Middle Miocene seep deposits of the Astoria Formation in western Washington State, USA. A. NRM Mo 204714, Rocky Point, internal mold showing muscle scars and pallial line. B. NRM Mo 204719, Frankfort, specimen with partially preserved shell (LV) showing the fine, irregular growth lines and the anterior adductor muscle scar. C. NRM Mo 204709, Frankfort, mostly an internal mold, showing the anterior adductor muscle scar and the posterior ridge. D. NRM Mo 204720, Frankfort, mostly an internal mold, note naticid drill hole on posterodorsal margin. E. LACMIP 6132.2, LACMIP loc. 6132, specimen with partially preserved shell; view of RV showing muscle scars E1); anterodorsal view showing elongate lunular incision (E2); posterodorsal view showing ligament (E3). F. NRM Mo 204711, Frankfort, internal mold of left valve, showing pallial line and posterior adductor muscle scar. G. NRM Mo 204712, Frankfort, specimen with partially preserved shell (RV) showing the fine, irregular growth lines and the anterior adductor muscle scar.
Fig. 1 in New taxa, records, and data for vesicomyid bivalves from Cenozoic strata of the North Pacific region
Fig. 1. Map showing localities in western Washington State, USA. 1, coastal sites between Rasmussen Creek and Jansen Creek (Makah Formation); 2, Whiskey Creek site (Pysht Formation); 3–5, sites LACMIP loc. 12385, CSUN loc. 1583, "East Fork Bridge site" (Humptulips Formation); 6, UWBM loc. B7452 in the Canyon River (Lincoln Creek Formation); 7, SR2 and SR4, Satsop River (Lincoln Creek Formation); 8, Bear River seep deposit; 9, West Fork of Grays River (Siltstone of Unit B); 10, Frankfort (Astoria Formation); 11, sites around Rocky Point (Astoria Formation).
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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.