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Size-dependent costs of migration: migrant bird species are subordinate to residents, but only at small body sizes
Martin, Paul; Kenyon, Haley; Hayes, Leah — 2020-01-07 <p>Migrant species are commonly thought to be poor competitors in aggressive interactions with resident species. However, no studies have tested if this relationship is widespread. Here we compare the behavioural dominance of closely-related species of migratory and non-migratory birds, testing if migrants are consistently subordinate to resident species in aggressive contests. We compiled published behavioural dominance data involving migrant and resident congeners, gathering additional data on the body mass and migratory distance of each species. Focal species included a diverse array of birds (28 taxonomic families, 12 orders) from around the world. We found that migrant species are usually subordinate to resident species, but that this relationship disappears at larger body sizes. For smaller birds (&lt; 500g), resident species were behaviourally dominant in 83-88% of comparisons; for larger birds (&gt; 500g), resident species were dominant in only 25-30% of comparisons. The relative difference in body mass best predicted dominance relationships among species, with larger species dominant in 80-84% of comparisons. When migrant and resident masses were equal, however, resident species were still more likely to be dominant in smaller birds, suggesting that other factors may also contribute to the subordinate status of migrants. Overall, our results suggest that in smaller species, the evolution of migration is associated with lighter weights and other traits that compromise the competitive abilities of migrants relative to residents. In contrast, larger species appear able to evolve migration without compromising their size or competitive abilities in aggressive contests, suggesting size-dependent constraints on the evolution of migration.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Phylogenetic tree shape and the structure of mutualistic networks
Chamberlain, Scott; Vázquez, Diego P.; Carvalheiro, Luisa; Elle, Elizabeth; Vamosi, Jana C. — 2014-06-27 Species community composition is known to alter the network of interactions between two trophic levels, potentially affecting its functioning (e.g. plant pollination success) and the stability of communities. Phylogenies vary in shape with regard to the rate of evolutionary change across a tree (influencing tree balance) and variation in the timing of branching events (affecting the distribution of node ages in trees), both of which may influence the structure of species interaction networks. Because related species are likely to share many of the traits that regulate interactions, the shape of phylogenetic trees may provide some insights into the distribution of traits within communities, and hence the likelihood of interaction among species. However, little attention has been paid to the potential effects of changes in phylogenetic diversity (PD) on interaction networks. Phylogenetic diversity is influenced by species diversity within a community, but also how distantly-related the constituent species are from one another. Here, we evaluate the relationship between two important measures of phylogenetic diversity (tree shape and age of nodes) and the structure of plant-pollinator interaction networks using empirical and simulated data. Whereas the former allows us to evaluate patterns in real communities, the latter allows us to evaluate more systematically the relationship between tree shape and network structure under three different models of trait evolution. In empirical networks, less balanced plant phylogenies were associated with lower connectance in interaction networks indicating that communities with the descendants of recent radiations are more diverged and specialized in their partnerships. In simulations, tree balance and the distribution of nodes through time were included in the best models for modularity, and the second best models for connectance and nestedness. In models assuming random evolutionary change through time (i.e., Brownian motion), less balanced trees and trees with nodes near the tips exhibited greater modularity, whereas in models with an early burst of radiation followed by relative stasis (i.e. early-burst models) more balanced trees and trees with nodes near roots had greater modularity. Synthesis: Overall, these results suggest that the shape of phylogenies can influence the structure of plant-pollinator interaction networks. However, the mismatch between simulations and empirical data indicate that no simple model of trait evolution mimics that observed in real communities. https://creativecommons.org/publicdomain/zero/1.0/
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The impact of methanol on behaviour: Dataset from zebrafish (Danio rerio) behavioural research
Hamilton, Trevor; Krook, Jeffrey; Szaszkiewicz, Joshua; Burggren, Warren — 2021-04-23 <p class="Body" style="border:medium none;text-align:justify;margin-bottom:13px;"><span>In many pharmacological and toxicological studies solvents are used as vehicles for the compound of interest.  The solvents themselves may have effects on their own, therefore, it is important to test the impact of the solvent on the preparation prior to conducting the study.  Methanol, (CH<sub>3</sub>OH), is a solvent used in many studies, and one we have used as a vehicle for benzo[a]pyrene. This data contains raw videos of zebrafish after exposure to 0, 0.25%, or 2.5% vol/vol, for 30 minutes prior to behavioral testing.  Immediately after exposure, the individual zebrafish were moved to an open field test to quantify movement and location preference and were recorded for 10 minutes.  Following the open field trial, a novel object was placed into the center of the arena to examine the exploratory response (boldness) of the fish for a second 10 minute trial.  Motion-tracking software (EthoVision XT) was used to quantify the dependent variables (distance moved, time in outer 'thigmotaxis' zone, 'inner' zone, and 'transition' zone). </span>There were no significant differences between groups for any of the variables in either the open field or novel object approach tests.  This data suggests that 0.25% and 2.5% methanol does not alter locomotion or location preference in these two tests.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Latitudinal limit not a cold limit: Cold temperatures do not constrain an endangered tree species at its northern edge
Clason, Alana J.; McIntire, Eliot J. B.; Burton, Philip J. — 2021-03-20 <h4>Aim</h4> <p>A strong influence of climate on species’ range is often assumed, and forms the basis for projecting many future range shifts with changing climate. Particularly at poleward latitudinal or elevational edges, abiotic conditions are thought to play a major role in limiting distributions. We estimated the roles of climate and landscape features in shaping habitat at the northern distributional edge of a critically threatened mountain tree species.</p> <h4>Location</h4> <p>British Columbia and Alberta, Canada.</p> <h4>Taxon</h4> <p><i>Pinus albicaulis</i> (Engelm.)</p> <h4>Methods</h4> <p>We used a hierarchical Bayesian model (HBM) to combine multiple scales, sources, qualities and types of species data. We jointly examined the climate influence on occupancy across scales, and on juvenile and adult abundance to quantify habitat quality at two life history stages.</p> <h4>Results</h4> <p>We found that cold temperature was the strongest predictor of whitebark pine occurrence at regional scales, with colder areas being better (i.e. the sign was negative). Occupancy at local scales was best predicted by low growing degree‐days and declining precipitation as snow. These relationships with occupancy across scales indicate that suitable climatic and topographic habitats currently exist beyond the northern edge of whitebark pine's current range. We found high adult abundance was predicted in sunny, cool habitats with little climatic drought, whereas high juvenile densities were associated with higher precipitation as snow and more climatic drought.</p> <h4>Main conclusions</h4> <p>The negative relationship to temperature and the ample suitable habitats predicted to exist poleward of the current species’ range limit indicates whitebark pine is not limited by cold temperatures. We suggest that not all species’ ranges are cold limited at high latitudes or elevations. For whitebark pine this means warming temperatures may not directly result in a northern range expansion as a result of warming habitat.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Data from: How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Graham, Carly F; Boreham, Douglas R; Manzon, Richard G; Stott, Wendylee; Wilson, Joanna Y; Somers, Christopher M — 2020-03-16 Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Hippocampal neurogenesis regulates forgetting during adulthood and infancy
Akers, Katherine G.; Martinez-Canabal, Alonso; Restivo, Leonardo; Yiu, Adelaide P.; De Cristofaro, Antonietta; Hsiang, Hwa-Lin (Liz); Wheeler, Anne L.; Guskjolen, Axel; Niibori, Yosuke; Shoji, Hirotaka; Ohira, Koji; Richards, Blake A.; Miyakawa, Tsuyoshi; Josselyn, Sheena A.; Frankland, Paul W. — 2015-04-02 Throughout life, new neurons are continuously added to the dentate gyrus. As this continuous addition remodels hippocampal circuits, computational models predict that neurogenesis leads to degradation or forgetting of established memories. Consistent with this, increasing neurogenesis after the formation of a memory was sufficient to induce forgetting in adult mice. By contrast, during infancy, when hippocampal neurogenesis levels are high and freshly-generated memories tend to be rapidly forgotten (infantile amnesia), decreasing neurogenesis after memory formation mitigated forgetting. In precocial species, including guinea pigs and degus, the majority of granule cells are generated prenatally. Consistent with reduced levels of postnatal hippocampal neurogenesis, infant guinea pigs and degus did not exhibit forgetting. However, increasing neurogenesis after memory formation induced infantile amnesia in these species. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Mechanisms underlying spruce budworm outbreak processes as elucidated by a 14-year study in New Brunswick, Canada
Royama, T.; Eveleigh, Eldon S.; Morin, J. R. B.; Pollock, S. J.; McCarthy, P.C.; McDougall, G. A.; Lucarotti, C. J.; McCarthy, P. C. — 2017-09-26 We conducted a 14-year intensive study of spruce budworm (Choristoneura fumiferana (Clem.)) survivorship at three study plots in largely balsam fir (Abies balsamea (L.) Mill.) stands in New Brunswick, Canada, to elucidate certain key mechanisms underlying spruce budworm outbreak cycles. The study covered a peak-to-declining phase (from 1981 and 1994) of the budworm outbreak cycle that had started in the early 1960s. Frequent sampling was carried out in each plot-year to construct a practically continuous survivorship curve, and the annual variation in population density was estimated. We found a high level of correlation between the studied phase of the outbreak cycle and annual variations in the survivorship over the postdiapause period, suggesting that postdiapause survivorship was the chief determinant of the cycle. We found the annual changes in population density in the present study to be closely similar in pattern to those from the provincial budworm surveys conducted in much larger areas. This implies that the mechanism underlying the population process found in the few study plots in largely balsam fir stands also applies to the process in much larger areas of diverse stand types. The main source of postdiapause mortality is found to be natural enemies. The impacts of parasitoids and disease are evaluated by rearing budworm samples in the laboratory. Hymenopteran and dipteran parasitoids are by far the major sources of mortality, and microsporidians are the most prevalent pathogen. Occurrences of other entomopathogenic fungi and viruses were insignificant throughout the study. Seasonal changes in laboratory survivorship are compared with the corresponding field survivorship to estimate the effect of predation. No major mortality factor is found to singly play a predominant role in determining the outbreak cycle. Conversely, some minor factors are shown to have played significant roles. Thus, the importance of recognizing the action of natural enemies as a complex is emphasized for understanding the budworm outbreak cycle. Finally, centered around the roles played by the chronological succession of natural enemies in the present study, the results of budworm research in New Brunswick since the mid-1940s are synthesized to outline basic mechanisms underlying the outbreak processes as a guide for further studies. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs
Sze, Marc A.; Tsuruta, Masashi; Yang, Shun-Wei Julia; Oh, Yeni; Man, S. F. Paul; Hogg, James C.; Sin, Don D. — 2015-09-30 Introduction: Previous reports have shown that the gastrointestinal (GI) bacterial microbiota can have profound effects on the lungs, which has been described as the “gut-lung axis”. However, whether a “lung-gut” axis exists wherein acute lung inflammation perturbs the gut and blood microbiota is unknown. Methods: Adult C57/Bl6 mice were exposed to one dose of LPS or PBS instillation (n = 3 for each group) directly into lungs. Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation. We then investigated the effects of oral neomycin and streptomycin (n = 8) on the microbiota at 4 and 24 hours post LPS instillation versus control treatment (n = 5 at baseline and 4 hours, n = 7 at 24 hours). Results: At 24 hours post LPS instillation, the total bacterial count was significantly increased in the cecum (P<0.05); whereas the total bacterial count in blood was increased at 4, 48, and 72 hours (P<0.05). Antibiotic treatment reduced the total bacteria in blood but not in the cecum. The increase in total bacteria in the blood correlated with Phyllobacteriaceae OTU 40 and was significantly reduced in the blood for both antibiotic groups (P<0.05). Conclusion: LPS instillation in lungs leads to acute changes in the bacterial microbiota in the blood and cecum, which can be modulated with antibiotics. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea
Stock, Amanda J.; Campitelli, Brandon E.; Stinchcombe, John R. — 2015-05-27 Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. https://creativecommons.org/publicdomain/zero/1.0/
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Taurine depletion impairs cardiac function and affects tolerance to hypoxia and high temperatures in brook char (Salvelinus fontinalis)
Dixon, Toni-Anne M.; Rhyno, Emma-Lee M.; El, Nir; McGaw, Samuel P.; Otley, Nathan A.; Parker, Katya S.; Buldo, Elena C.; Pabody, Claire M.; Savoie, Mireille; Cockshutt, Amanda; Morash, Andrea J.; Lamarre, Simon G.; MacCormack, Tyson J. — 2023-02-16 <p>Physiological and environmental stressors can cause osmotic stress in fish hearts, leading to a reduction in intracellular taurine concentration. Taurine is a beta amino acid known to regulate cardiac function in other animal models but its role in fish has not been fully elucidated. We generated a model of cardiac taurine-deficiency (TD) by feeding brook char (<em>Salvelinus</em> <em>fontinalis</em>) a diet enriched in β-alanine, which inhibits cardiomyocyte taurine uptake. Cardiac taurine levels were reduced by 21%, and stress-induced changes in normal taurine handling were observed in TD brook char. Responses to exhaustive exercise and acute thermal and hypoxia tolerance were then assessed using a combination of in vivo, in vitro, and biochemical approaches. Critical thermal maximum was higher in TD brook char despite significant reductions in maximum heart rate. In vivo, TD brook char exhibited a lower resting heart rate, blunted hypoxic bradycardia, and a severe reduction in time to loss of equilibrium under hypoxia. In vitro function was similar between control and TD hearts under oxygenated conditions, but stroke volume and cardiac output were severely compromised in TD hearts under anoxia. Aspects of mitochondrial structure and function were also impacted in TD permeabilized cardiomyocytes, but overall effects were modest. High levels of intracellular taurine are required to achieve maximum cardiac function in brook char and cardiac taurine efflux may be necessary to support heart function under stress. Taurine appears to play a vital, previously unrecognized role in supporting cardiovascular function and stress tolerance in fish.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Climate oscillations drive millennial-scale changes in seabird colony size
Robertson, Gregory; Hedd, April; Montevecchi, William; Kimpe, Linda; Duda, Matthew; Cyr, Frédéric; Michelutti, Neal; Blais, Jules; Smol, John; Meyer-Jacob, Carsten — 2022-03-21 <p>Seabird population size is intimately linked to the physical, chemical, and biological processes of the oceans. Yet, the overall effects of long-term changes in ocean dynamics on seabird colonies are difficult to quantify. Here, we used dated lake sediments to reconstruct ~10,000-years of seabird dynamics in the Northwest Atlantic to determine the influences of Holocene-scale climatic oscillations on colony size. On Baccalieu Island (Newfoundland and Labrador, Canada) – where the world’s largest colony of Leach’s storm-petrel (<em>Hydrobates leucorhous</em> Vieillot 1818) currently breeds – our data track seabird colony growth in response to warming during the Holocene Thermal Maximum (ca. 9,000 to 6,000 BP). From ca. 5,200 BP to the onset of the Little Ice Age (ca. 550 BP), changes in colony size were correlated to variations in the North Atlantic Oscillation (NAO). By contrasting the seabird trends from Baccalieu Island to millennial-scale changes of storm-petrel populations from Grand Colombier Island (an island in the Northwest Atlantic that is subjected to different ocean climate), we infer that changes in NAO influenced the ocean circulation, which translated into, among many things, changes in pycnocline depth across the Northwest Atlantic basin where the storm-petrels feed. We hypothesize that the depth of the pycnocline is likely a strong bottom-up control on surface-feeding storm-petrels through its influence on prey accessibility. Since the Little Ice Age, the effects of ocean dynamics on seabird colony size have been altered by anthropogenic impacts. Subsequently, the colony on Baccalieu Island grew at an unprecedented rate to become the world’s largest resulting from favourable conditions linked to climate warming, increased vegetation (thereby nesting habitat), and attraction of recruits from other colonies that are now in decline. We show that although ocean dynamics were an important driver of seabird colony dynamics, its recent influence has been modified by human interference.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Synchrotron imagery of phosphatized eggs in Waptia cf. W. fieldensis from the middle Cambrian (Miaolingian; Wuliuan) Spence Shale of Utah
Moon, Justin — 2021-07-25 <p style="margin-bottom:11px;">Exceptionally preserved fossil eggs and embryos provide critical information regarding paleoembryogenesis, reproductive strategies, and the early ontogeny of early arthropods, but the rarity of preservation of both eggs and egg-bearing organisms in situ limits their use in detailed evo-devo studies. Burgess Shale-type deposits preserve rare instances of egg-bearing arthropods as carbonaceous compressions, however, the eggs are usually poorly preserved with no compelling evidence of embryos. We describe the first record of a brooding specimen of <i>Waptia </i>cf. <i>fieldensis</i> from the Spence Shale, a Cambrian (Wuliuan stage) Burgess Shale-type deposit in northeastern Utah and southeastern Idaho. This is the first record of an egg-bearing arthropod from the Spence Shale and it exhibits two distinct modes of preservation among eggs within the single clutch: carbonization and phosphatization. Unlike the egg-bearing Burgess Shale specimens, many eggs of this Utah specimen are also preserved three-dimensionally. In addition, synchrotron radiation X-ray tomographic microscopy reveals internal distributions of mineral phases, along with potential remnants of the egg membrane and attachment structures but, as in the Burgess Shale, no explicit traces of developing embryos. The distinct modes of preservation highlight the existence of diagenetic microenvironments within some eggs but not in others during fossilization.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Expanded consumer niche widths may signal an early response to spatial protection
Olson, Angeleen M.; Trebilco, Rowan; Salomon, Anne K. — 2019-10-18 <p class="Normal1" style="margin-bottom:13px;">Marine management interventions are increasingly being implemented with the explicit goal of rebuilding ocean ecosystems, but early responses may begin with alterations in ecological interactions preceding detectable changes in population-level characteristics. To establish a baseline from which to monitor the effects of spatial protection on reef fish trophic ecology and track future ecosystem-level changes, we quantified temperate reef fish densities, size, biomass, diets and isotopic signatures at nine sites nested within two fished and one five-year old marine protected area (MPA) on the northwest coast of Canada. We calculated rockfish (Sebastes spp.) community and species-specific niche breadth for fished and protected areas based on δ<sup>13</sup>C and δ<sup>15</sup>N values. We found that rockfish community niche width was greater inside the MPA relative to adjacent fished reefs due to an expanded nitrogen range, possibly reflecting early changes in trophic interactions following five years of spatial protection. Our data also demonstrated that the MPA had a positive effect on the δ<sup>15</sup>N signature of rockfish (i.e., trophic position), but the effect of rockfish length on its own was not well-supported. In addition, we found a positive interaction between rockfish length and δ<sup>15</sup>N signature, such that δ<sup>15</sup>N signatures of rockfish caught within the MPA increased more rapidly with body size than those caught in fished areas. Differences in rockfish size structure and biomass among fished and unfished areas were not clearly evident. Species of rockfish and lingcod varied in trophic and size responses, indicating that life-history traits play an important role in predicting MPA effects. These results may suggest early changes in trophic behavior of slow-growing rockfish due to predation risk by faster growing higher trophic level predators such as lingcod inside MPAs established on temperate reefs. Consequently, spatial protection may restore both the trophic and behavioral roles of previously fished consumers earlier and in measurable ways sooner than observable changes in abundance and size.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Examination of a historic collection of isolated cranial and appendicular hadrosaurid material from the lower Kirtland Formation of the San Juan Basin, New Mexico
Wosik, Mateusz; Guenther, Merrilee F. — 2017-03-30 The Field Museum of Natural History collection contains several isolated hadrosaurid specimens collected by Charles H. Sternberg from the lower Kirtland Formation of the San Juan Basin, New Mexico, that have been previously overlooked. Cranial elements described herein consist of a dentary and three jugals while appendicular material is limited to two humeri and two pubes. Many of the specimens preserve taxonomically informative characters that show strong affinities with Kritosaurini but are distinct from Kritosaurus navajovius (Brown, 1910) suggesting that the saurolophine-dominated San Juan Basin diversity is greater than currently recognized. Future examination of currently unprepared material will add to our developing understanding of the ambiguous hadrosaurid diversity of the San Juan Basin. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Enamel hypoplasia and dental wear of North American late Pleistocene horses and bison: an assessment of nutritionally-based extinction models
Barrón-Ortiz, Christina I.; Jass, Christopher N.; Barrón-Corvera, Raúl; Austen, Jennifer; Theodor, Jessica M. — 2019-03-27 Approximately 50,000 – 11,000 years ago many species around the world became extinct or were extirpated at a continental scale. The causes of the late Pleistocene extinctions have been extensively debated and continue to be poorly understood. Several extinction models have been proposed, including two nutritionally-based extinction models: coevolutionary disequilibrium and mosaic-nutrient models. These models draw upon the individualistic response of plant species to climate change to present a plausible scenario in which nutritional stress is considered one of the primary causes for the late Pleistocene extinctions. In this study, we tested predictions of the coevolutionary disequilibrium and mosaic-nutrient extinction models through the study of dental wear and enamel hypoplasia of Equus and Bison from various North American localities. The analysis of the dental wear (microwear and mesowear) of the samples yielded results which are consistent with predictions established for the coevolutionary disequilibrium model, but not for the mosaic-nutrient model. These ungulate species show statistically different dental wear patterns (suggesting dietary resource partitioning) during preglacial and full-glacial time intervals, but not during the postglacial in accordance with predictions of the coevolutionary disequilibrium model. In addition to changes in diet, these ungulates, specifically the equid species, show increased levels of enamel hypoplasia during the postglacial indicating higher levels of systemic stress, a result which is consistent with the models tested and with other climate-based extinction models. The extent to which the increase in systemic stress was detrimental to equid populations remains to be further investigated, but suggests that environmental changes during the late Pleistocene significantly impacted North American equids. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: No evidence that sex and transposable elements drive genome size variation in evening primroses
Ågren, J. Arvid; Greiner, Stephan; Johnson, Marc T. J.; Wright, Stephen I. — 2015-01-29 Genome size varies dramatically across species, but despite an abundance of attention there is little agreement on the relative contributions of selective and neutral processes in governing this variation. The rate of sex can potentially play an important role in genome size evolution because of its effect on the efficacy of selection and transmission of transposable elements. Here, we used a phylogenetic comparative approach and whole genome sequencing to investigate the contribution of sex and transposable element content to genome size variation in the evening primrose (Oenothera) genus. We determined genome size using flow cytometry for 30 species that vary in genetic system and find that variation in sexual/asexual reproduction cannot explain the almost two-fold variation in genome size. Moreover, using whole genome sequences of three species of varying genome sizes and reproductive system, we found that genome size was not associated with transposable element abundance; instead the larger genomes had a higher abundance of simple sequence repeats. Although it has long been clear that sexual reproduction may affect various aspects of genome evolution in general and transposable element evolution in particular, it does not appear to have played a major role in genome size evolution in the evening primroses. https://creativecommons.org/publicdomain/zero/1.0/
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Dataset on how mesopredator-mediated trophic cascade can break persistent phytoplankton blooms in coastal waters
Berthold, Maximilian; Schumann, Rhena; Reiff, Volker; Wulff, Rita; Schubert, Hendrik — 2022-11-29 <p>Managing eutrophied systems using only nutrient decreases to impose bottom-up control can be economically and ecologically challenging. Top-down controls through increased consumption have sometimes effectively controlled phytoplankton blooms. However, mechanistic insights, especially on possible trophic cascades, are less understood in brackish, species-poor coastal waters, where large cladocera are absent. In this study, we set up large mesocosms for three consecutive years during the growing season. One set of mesocosms contained mesopredators (gobies and shrimps), whereas the other mesocosms had no such mesopredator present. The results were standardized to monitoring data from the ecosystem to track possible differences between treatments and the system. We found that mesopredator mesocosms showed lower turbidity, phytoplankton biomass, and nutrients compared to no-mesopredator mesocosms, and compared to the ecosystem. This decrease allowed macrophytes to colonize water depths only sparsely colonized in the ecosystem. Rotifer biomass increased in mesopredator mesocosms compared to the ecosystem and to the no-mesopredator mesocosms. Likewise, copepod biomass that potentially grazes upon rotifers and other microzooplankton decreased in mesopredator mesocosms. No-mesopredator mesocosms were colonized by an omnivorous mesograzer (<em>Gammarus</em> <em>tigrinus</em>), potentially creating additional pressure on macrophytes and increasing grazing-mediated nutrient release. Zooplankton was not able to control the non-nutrient-limited phytoplankton. We propose a new mechanism, where a higher mesopredator density will increase grazing on phytoplankton by promoting microzooplankton capable of grazing on picophytoplankton. This proposed mechanism would contrast with freshwater systems, where a decrease of zooplanktivorous fish would promote larger phytoplankton grazer like cladocerans. Biomanipulation in such species-poor eutrophic coastal waters may be more successful, due to fewer trophic pathways, that can cause complex top-down controls like in other systems. Stocking eutrophic coastal waters with gobies and shrimps may be an alternative biomanipulative approach rather than selectively removing large piscivorous or omnivorous fish from eutrophic coastal waters.</p> https://creativecommons.org/publicdomain/zero/1.0/
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A dynamic ancestral graph model and GPU-based simulation of a community based on metagenomic sampling
Griswold, Cortland — 2022-03-21 <p>In this paper we present an ancestral graph model of the evolution of a guild in an ecological community. The model is based on a metagenomic sampling design in that a random sample is taken at the community, as opposed the taxon, level and species are discovered by genetic sequencing. The specific implementation of the model envisions an ecological guild that was founded by colonization at some point in the past that then potentially undergoes diversification by natural selection. Within the graph, species emerge and evolve through the diversification process and their densities in the graph are dynamic and governed by both ecological drift and random genetic drift, as well as differential viability. We employ the 3% sequence divergence rule at a marker locus to identify Operational Taxonomic Units. We then explore approaches to see if there are indirect signals of the diversification process, including population genetic and ecological approaches. In terms of population genetics, we study the joint site frequency spectrum of OTUs, as well its associated statistics. In terms of ecology, we study the species (or OTU) abundance distribution. For both we observe deviations from neutrality, which indicates that there may be signals of diversifying selection in metagenomic studies under certain conditions. The model is available as a GPU-based computer program in C/C++ and using OpenCL, with the long-term goal of adding functionality iteratively to model large-scale eco-evolutionary processes for metagenomic data.</p> https://creativecommons.org/publicdomain/zero/1.0/
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Data for: Causes and consequences of variation in diet composition of nestling Canada jays
Freeman, Nikole — 2021-06-28 <p>Diet quality during development can impact growth, physiology, behaviour, and survival. The Canada jay is a resident boreal passerine that caches a wide variety of perishable food items in late summer and autumn for its over-winter survival and late-winter reproduction. A previous experiment found evidence that food supplementation of Canada jay pairs during the nestling period had a positive effect on the condition of their nestlings. However, given that foods cached by adults vary widely in nutritional content, the composition of nestling diets could also have an important influence on offspring development. In a population of Canada jays in Algonquin Provincial Park, Ontario, Canada, we investigated the influence of environmental conditions before and during the breeding season on nestling diet composition and the consequences of nestling diet composition on the body condition of nestlings and on their subsequent survival. Using stable-carbon (δ13C) and -nitrogen (δ15N) isotopes, we estimated the proportion of three food groups (vertebrates+human food, invertebrates and plants) in feathers from almost 200 nestlings. Nestling diet in March and April was influenced by environmental conditions 5 – 6 months prior to hatching, with warmer and more variable autumn temperatures associated with a greater proportion of vertebrate flesh and human food in the diet. However, the proportion of vertebrates and human food in the diet had no influence on nestling body condition or whether an individual was observed the following fall. Our results, in conjunction with previous work on Canada jays, suggest that the quantity of food available to a nestling during development may be more important than diet composition.</p> <p> </p> https://creativecommons.org/publicdomain/zero/1.0/

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