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Figure 7 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 7. Plot of first two canonical axes from quadratic discriminant analysis of degree of fossoriality (non-burrowing versus fossorial versus subterranean) in mammals based on an expanded version of the "limbs only" dataset of Hopkins and Davis (2009). Non-burrowing species are represented by green circles, fossorial species by pink squares and subterranean species by blue asterisks. Inner ellipses represent 95% confidence intervals for the means for each class, whilst the outer ellipses represent the 50% prediction intervals.Naraboryctes philcreaseri is represented by a black triangle and was treated as unknown, but falls among subterranean species and is predicted to be subterranean with very high probability (p = 1.0). Abbreviations: F, fossorial; N, non-burrowing; S, subterranean.
Figure 9 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 9. Part of the dated total evidence phylogeny shown in Figure 8, restricted to the clade Agreodontia (which includes Notoryctemorphia), with divergence dates compared to global temperatures and environmental change in Australia. The estimated time of inactivation of the RBP3 gene in the Notoryctes lineage is indicated: the black bar represents the point estimate (5.4 MYA), whilst the grey bars represent 95% HPDs (4.5-6.3 MYA). The global temperature curve is modified from Zachos et al. (2001). The date for the major increase in grass pollen is taken from Martin and McMinn (1994: fig. 2) whilst the date for the onset of major aridity in Australia (~1.4-1.5 MYA) is taken from McLaren and Wallace (2010).
Figure 2 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 2. Comparison of humeri of Naraboryctes philcreaseri and Notoryctes typhlops: a, left humerus of Naraboryctes philcreaseri (QM F57719) in cranial view; b, right humerus (reversed) of Notoryctes typhlops (SAM M637) in cranial view; c, QM F57719 in caudal view; d, SAM M637 (reversed) in caudal view. Abbreviations: bg, bicipital groove; cap, capitulum; dpc, deltopectoral crest; gtu, greater tuberosity; hh, humeral head; lsr, lateral supracondylar ridge; ltu, lesser tuberosity; mep, medial epicondyle; stf, supratrochlear foramen; tro, trochlea.
Figure 6 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 6. Comparison of tibiae of Naraboryctes philcreaseri and Notoryctes typhlops: a, left femur of Naraboryctes philcreaseri (QM F57686) in medial view; b, left femur of Notoryctes typhlops (SAM M637) in medial view; c, QM F57686 in lateral view; d, SAM M637 in lateral view. Abbreviations: mma, medial malleolus; pltp, posterolateral tibial process for articulation with lateral femoral condyle and fibula; sup, sulcus for patella; tc, tibial crest.
Figure 5 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 5. Comparison of femora of Naraboryctes philcreaseri and Notoryctes typhlops: a, right femur of Naraboryctes philcreaseri (QM F57678) in cranial view; b, right femur of Notoryctes typhlops (SAM M637) in cranial view; c, QM F57678 in caudal view; d, SAM M637 in caudal view. Abbreviations: fh, femoral head; gtr, greater trochanter; icg, intercondylar groove; ltr, lesser trochanter; trf, trochanteric fossa; ttr, third trochanter.
Figure 8 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 8. Dated total evidence phylogeny based on 259 morphological characters and 9012 bp of sequence data from five nuclear genes (APOB, BRCA1, RBP3, RAG1, and VWF) analysed using MrBayes 3.2.2 assuming the Independent Gamma Rates (IGR) clock model, with topological and temporal constraints applied to selected internal nodes (see supplementary information). Notoryctes and Naraboryctes are indicated in bold. Blue bars represent 95% highest posterior density intervals (HPDs) on the divergence times. Nodes without Bayesian posterior probability (BPP) were constrained a priori.
Figure 1 in Going underground: postcranial morphology of the early Miocene marsupial mole Naraboryctes philcreaseri and the evolution of fossoriality in notoryctemorphians
Figure 1. Comparison of scapulae of Naraboryctes philcreaseri and Notoryctes typhlops in lateral view: a, left scapula of Naraboryctes philcreaseri (QM F57716); b, right scapula (reversed) of Notoryctes typhlops (SAM M637). Abbreviations: acr, acromion process; cau, "caudal" angle; cor, coracoid process; cra, "cranial" angle; inf, infraspinous fossa; psf, postscapular fossa; ssf, supraspinous fossa; ssp, scapular spine; sssp, secondary scapular spine.
Fig. 5 in Deep-water fossorial shrimps from the Oligocene Kiscell Clay of Hungary: Taxonomy and palaeoecology
Fig. 5. Minor chelae of fossorial shrimp Ctenocheles rupeliensis (Beurlen, 1939), Óbuda in Budapest, Late Kiscellian. A. Left minor propodus (HNHM M.59.4700). B. Right minor propodus (HNHM M.59.4869). C. Minor propodus articulated with dactylus (HNHM M.59.4691). D. Articulated left minor chela (HNHM M.59.4682). All specimens are paralectotypes selected herein. All specimens are figured to the same scale and were covered with ammonium chloride (except D) prior to photography. Photographs by MH.
Fig. 2 in Deep-water fossorial shrimps from the Oligocene Kiscell Clay of Hungary: Taxonomy and palaeoecology
Fig. 2. Fossorial shrimp Lepidophthalmus crateriferus (Lőrenthey in Lőrenthey and Beurlen, 1929) comb. nov., Óbuda in Budapest, Late Kiscellian. A. Left major cheliped of presumed male (HNHM M.59.4684b). B. Isolated left major propodus (HNHM M.59.4690). C. Left major cheliped of presumed male (C 1); neotype herein designated (lectotype of Callianassa brevimanus Beurlen, 1939) (HNHM M.59.4684a). Detail of C 1 under different light angle showing carpus and merus (C 2). Line drawing of merus depicted in C 2 (C 3). Note presence of distal meral hook and blade (see also white arrows in A and C 1). D. Presumed female specimen with both chelae (HNHM M.59.4720). E. Imprint of mesial surface of right major propodus (HNHM M.59.4683). Note setal pits close to upper margin of the chela. All specimens except HNHM M.59.4684a are paralectotypes of C. brevimanus selected herein. All specimens are figured to the same scale and were covered with ammonium chloride (except C ) prior to photography. Photographs by MH.
Fig. 3 in Deep-water fossorial shrimps from the Oligocene Kiscell Clay of Hungary: Taxonomy and palaeoecology
Fig. 3. Fossorial shrimp Lepidophthalmus crateriferus (Lőrenthey in Lőrenthey and Beurlen, 1929) comb. nov., Óbuda in Budapest, Late Kiscellian; presumed male morphotypes unless stated otherwise. A. Right major propodus (KGP-MH OT-007). B. Left major propodus articulated with dactylus of presumed female (KGP-MH OT-003). C. Left major propodus (KGP-MH OT-009). D. Left major propodus (KGP-MH OT-006). E. Fragmentary left major propodus (KGP-MH OT-008). F. Right major propodus (KGP-MH OT-010). G. Right major propodus (KGP-MH OT-001). H. Right major propodus of presumed female (KGP-MH OT-002). I. Right minor propodus of indeterminate sex (KGP-MH OT-011). J. Left major propodus of presumed female KGP-MH OT-005). K. Right minor propodus of indeterminate sex (KGP-MH OT-004). L. Left major dactylus (KGP-MH OT-017). M. Right major dactylus (KGP-MH OT-013). N. Right minor(?) dactylus (KGP-MH OT-012). O. Left major dactylus (KGP-MH OT-016). All elements are depicted in lateral aspect except D–F and J which are depicted in mesial view. All specimens are figured to the same scale and were covered with ammonium chloride prior to photography. Photographs by MH.
Climate-associated decline of body condition in a fossorial salamander
<p><strong>Climate-associated decline of body condition in a fossorial salamander</strong></p> <p><strong>Abstract </strong>Temperate ectotherms have responded to recent environmental change, likely due to the direct and indirect effects of temperature on key life-cycle events. Yet, a substantial number of ectotherms are fossorial, spending the vast majority of their lives in subterranean microhabitats that are assumed to be buffered against environmental change. Here we examine whether seasonal climatic conditions influence body condition (a measure of general health and vigor), reproductive output, and breeding phenology in a northern population of fossorial salamander (Spotted Salamander,<em>Ambystoma maculatum</em>). We found that breeding body condition declined over a 12 year monitoring period (2008–2019) with warmer summer and autumn temperatures at least partly responsible for the observed decline in body condition. Our findings are consistent with the hypothesis that elevated metabolism drives the negative association between temperature and condition. Population-level reproduction, assessed via egg mass counts, showed high interannual variation and was weakly influenced by autumn temperatures. Salamander breeding phenology was strongly correlated with lake ice-melt but showed no long-term temporal trend (1986–2019). Climatic warming in the region, which has been and is forecasted to be strongest in the summer and autumn, is predicted to lead to a 5 to 27% decline in salamander body condition under realistic near-future climate scenarios. Although the subterranean environment offers a thermal buffer, the observed decline in condition and relatively strong effect of summer temperature on body condition suggest that fossorial salamanders are sensitive to the effects of a warming climate. Given the diversity of fossorial taxa, heightened attention to the vulnerability of subterranean microhabitat refugia and their inhabitants is warranted amid global climatic change.</p> <p> </p> <p>The dataset and corresponding R script are split into five parts, consistent with the presentation of Methods/Results in Moldowan et al.</p> <p><strong>Part 1 of 5: Body condition data and analysis files</strong></p> <ul> <li>2008.2019.female.SMI.CONSTANTSVL.csv</li> <li>2008.2019.male.SMI.CONSTANTSVL.csv</li> <li>2009.2019.female.SMI.CONSTANTSVL.csv</li> <li>2009.2019.male.SMI.CONSTANTSVL.csv</li> <li>BodyCondition.TimeSeries.WeightedRegression.csv</li> <li>SMAregression.Female.2009.2019.R</li> <li>SMAregression.Male.2009.2019.R</li> <li>ModelSel.Avrg.Forecast.AutoCor.FemaleBodyCondition.climate.R</li> <li>ModelSel.Avrg.Forecast.AutoCor.MaleBodyCondition.climate.R</li> <li>WeightedRegression.BodyCondition.TimeSeries.R</li> <li>YearEffects-Njal_PDM update (20 March 2021)</li> </ul> <p> </p> <p><strong>Part 2 of 5: Forecast body condition under climate change files</strong></p> <ul> <li>2009.2019.male.SMI.CONSTANTSVL.csv (as above in Part 1)</li> <li>HeatMap.Forecast.MaleSMI.04 Feb 2021.R</li> </ul> <p> </p> <p><strong>Part 3 of 5: Reproductive output (egg mass) data and analysis files</strong></p> <ul> <li>2009.2019.EggCount.Climate.csv</li> <li>ReproductiveOutput.climate.R</li> </ul> <p> </p> <p><strong>Part 4 of 5: Breeding phenology data and analysis files</strong></p> <ul> <li>2008.2019.BreedingPhenology.Climate.csv</li> <li>Opeongo.Two Rivers.Bat.IceOff.csv</li> <li>BreedingPhenology.climate.R</li> </ul> <p> </p> <p><strong>Part 5 of 5: Temperature dataloggers and salamander metabolic rate estimation files</strong></p> <ul> <li>HOBO_Bat_Lake_Underground_Temperatures.csv</li> <li>WhitfordHutchison1967Data.csv</li> <li>WhitfordHutchison1967DataExplainer.xlsx</li> <li>Metabolic Rate Prediction_PDM, 21 Feb 2021.R</li> </ul> <p> </p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "New species of fossorial salamanders of the genus Oedipina (Plethodontidae) from the northwestern Ecuador"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "New species of fossorial salamanders of the genus Oedipina (Plethodontidae) from the northwestern Ecuador". The matrix is in NEXUS format.</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>16S = 4- 789 1761- 1891 ;<br> ND1-codonPos1 = 790-1759\3;<br> ND1-codonPos2 = 791-1760\3;<br> ND1-codonPos3 = 792-1758\3;<br> CytB-codonPos1 = 1893-2274\3;<br> CytB-codonPos2 = 1894-2275\3;<br> CytB-codonPos3 = 1892-2276\3;</p>
Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent - nuclear genomic genotypes
<p>Genotype likelihood (GMR_minind40_mmaf0.05_glf2.beagle.gz) and pseudohaploid calls (GMR_minind40_mmaf0.05_glf2.haplo.gz) used for the nuclear genomic analyses in the manuscript "Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent".</p><p>The order of the individuals in each file is listed in Names.txt</p><p> </p>
Different selection regimes explain morphological evolution in fossorial lizards
<p>Independent origins of similar phenotypes are ubiquitous to the evolutionary process and evoke strong and recurrent environmental associations. Snakelike lizards evolved multiple times and are often portrayed as limb-reduced and body-elongated outcomes from shared selection associated with fossoriality. However, a refined evaluation including specific head traits and subtle differences in subterranean microhabitats unveils some degree of uniqueness even among lineages traditionally interpreted as phenotypically similar. Here we address regimes of selection in fossorial lizards accounting for differences in the burrowing substrate and emphasizing head shape in addition to body and limbs. We assembled an ecomorphological database comprising 213 species from all major lizard clades, and then characterized contemporary morphological diversity and modeled phenotypic evolution to test the hypothesis that fossoriality encompasses at least two distinct selection regimes. We identified two ecomorphological groups within the fossorial lizards: moist-soil fossorial and dry-soil fossorial. Both groups evolved towards distinct adaptive optima concerning head shape and limb size. Despite some degree of uniqueness, these groups also share similar patterns in specific traits. Dry-soil fossorial lizards present less morphological variation than moist-soil fossorial, possibly due to the combination of distinct sets of selective pressures with shared ancestry. Our study provides evidence that an often-interpreted general adaptive regime (e.g., fossoriality) may in fact comprise enough ecological and functional diversity to elicit several distinct ecomorphological associations despite overall convergence among phenotypic traits.</p>
Fig. 155 in Karakumosa gen. nov., a new Central Asian genus of fossorial wolf spiders (Araneae: Lycosidae: Lycosinae)
Fig. 155. Localities of four species in the genus Karakumosa gen. nov.
Fig. 1 in Karakumosa gen. nov., a new Central Asian genus of fossorial wolf spiders (Araneae: Lycosidae: Lycosinae)
Fig. 1. Geographical range of the genus Karakumosa gen. nov.
Fig. 76 in Karakumosa gen. nov., a new Central Asian genus of fossorial wolf spiders (Araneae: Lycosidae: Lycosinae)
Fig. 76. Localities of five species in the genus Karakumosa gen. nov.
Discrete element models for understanding the biomechanics of fossorial animals
<p><span>The morphological features of fossorial animals have continuously evolved in response to the demands of survival. However, </span><span>existing methods for animal burrowing mechanics are not capable of addressing the large deformation of substrate. T</span><span>he discrete element method (DEM) is able to overcome this limitation. In this study, we used DEM </span><span>to develop a general model to simulate the motion of an animal body part and its interaction with the substrate. The DEM also allowed us to easily change the forms of animal body parts to examine how those different forms affected the biomechanical functions. These capabilities of the DEM were presented through a case study of modelling the burrowing process of North American Badger. In the case study, the dynamics (forces, work, and soil displacements) of burrowing were predicted for different forms of badger claw and manus, using the model. Results showed that when extra digits are added to a manus, the work required for a badger to dig increases considerably, while the mass of soil dug only increases gradually. According to the proposed efficiency index (ratio of the amount of soil dug to the work required), the modern manus with 5 digits has indeed biomechanical advantage for their fossorial lifestyle, and the current claw curvature (25.3 mm in radius) is indeed optimal. The DEM is able to predict biomechanical relationships between functions and forms for any fossorial animals. Results can provide biomechanical evidences for explaining how the selective pressures for functions influence the morphological evolution in fossorial animals.</span></p>
Data from: Integrating niche and occupancy models to infer the distribution of an endemic fossorial snake (Atractus lasallei)
<p>Understanding species distribution and habitat preferences is crucial for effective conservation strategies. However, the lack of information about population responses to environmental change at different scales hinders effective conservation measures. In this study, we estimate the potential and realized distribution of <em>Atractus lasallei</em>, a semi-fossorial snake endemic to the northwestern region of Colombia. We modelled the potential distribution of <em>A. lasallei</em> based on ecological niche theory (using maxent), and habitat use was characterized while accounting for imperfect detection using a single-season occupancy model. Our results suggest that <em>A. lasallei</em> selects areas characterized by slopes below 10°, with high average annual precipitation (>2500mm/year) and herbaceous and shrubby vegetation. Its potential distribution encompasses the northern Central Cordillera and two smaller centers along the Western Cordillera, but its habitat is heavily fragmented within this potential distribution. When the two models are combined, the species' realized distribution sums up to 935 km<sup>2</sup>, highlighting its vulnerability. We recommend approaches that focus on variability at different spatio-temporal scales to better comprehend the variables that affect species' ranges and identify threats to vulnerable species. Prompt actions are needed to protect herbaceous and shrub vegetation in this region, highly demanded for agriculture and cattle grazing.</p>
The evolution of fossorial locomotion in the transition from tetrapod to snake-like in lizards
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