Cryptic Source Research Articles

Pleistocene-dated genomic divergence of avocado trees supports cryptic diversity in the Colombian germplasm

Genomic characterization of ex situ plant collections optimizes the utilization of genetic resources by identifying redundancies among accessions, capturing cryptic variation, establishing reference collections, and ultimately assisting pre-breeding and breeding efforts. Yet, the integration of evolutionary genomic analyses is often lacking when studying the biodiversity of crop gene pools. Such is the case in the avocado, Persea americana Mill., an iconic American fruit tree crop that has seen an unprecedented expansion worldwide because of its nutritional properties. However, given a very restricted number of commercial clones, avocado plantations are becoming more vulnerable to diseases and climate change. Therefore, exploring new sources of evolutionary novelty and genetic diversity beyond the commercial varieties derived from traditional genetic pools in Mexico and Central America is imperative. To fill this gap, we aimed to characterize the genomic diversity of Colombian avocado trees. Specifically, we constructed reduced representation genomic libraries to genotype by sequencing 144 accessions from the Colombian National genebank and 240 materials from local commercial orchards in the Colombian northwest Andes. We merged the resulting reads with available sequences of reference genotypes from known avocado groups (also named as races), Mexican, Guatemalan, and West Indian, to discover 4931 SNPs. We then analyzed the population structure and phylogenetic diversity, and reconstructed evolutionary scenarios, possibly leading to new genetic groups in Colombian germplasm. We detected demographic stratification despite evidence of intergroup gene flow. Besides the classical three avocado groups, we found an exclusive Colombian group with a possible genetic substructure related to the geographical origin (Andean and Caribbean). Phylogenetic and ABC demographic modeling suggested that the Colombian group evolved in the Pleistocene before human agriculture started, and its closest relative from the three recognized races would be the West Indian group. We conclude that northwest South America offers a cryptic source of allelic novelty capable of boosting avocado pre-breeding strategies to select rootstock candidates well adapted to specific eco-geographical regions in Colombia and abroad.

Nectar Source and Pollinator Cross Contamination and Persistence of Pyriproxyfen Associated with the Use of Autodissemination Techniques for Mosquito Control.

Controlling container inhabiting mosquitoes such as Aedes aegypti and Ae. albopictus is often difficult because of the requirement to treat small and inaccessible cryptic sources of water where larvae are located. Autodissemination approaches based on the dissemination of insect growth regulators (IGRs) have been demonstrated as an effective means to treat these cryptic larval habitats and provide population control. Autodissemination approaches are attractive because they are based on the mosquitoes disseminating small amounts of IGRs compared to more traditional insecticide applications. While dissemination of small amounts of IGRs seems like an advantage, these approaches could lead to unintended transfer and effects on nontarget insect pollinators by delivering highly potent IGRs to nectar sources. Here we looked for the indirect and direct transfer of pyriproxyfen (PPF) to natural and artificial nectar sources and painted lady butterflies, Vanessa cardui, in semifield cages using the release of treated Ae. albopictus males or an autodissemination station. We also performed persistence tests of PPF in oviposition containers and natural and artificial nectar sources when exposed to laboratory and natural conditions. The data suggest that there is direct and indirect transfer to nectar sources and V. cardui associated with the use of autodissemination approaches. We discuss the results in the context of using autodissemination approaches for mosquito control and the potential risks these approaches may pose to nontarget insect pollinators.

Zootherapy as a potential pathway for zoonotic spillover: a mixed-methods study of the use of animal products in medicinal and cultural practices in Nigeria

BackgroundUnderstanding how and why people interact with animals is important for the prevention and control of zoonoses. To date, studies have primarily focused on the most visible forms of human-animal contact (e.g., hunting and consumption), thereby blinding One Health researchers and practitioners to the broader range of human-animal interactions that can serve as cryptic sources of zoonotic diseases. Zootherapy, the use of animal products for traditional medicine and cultural practices, is widespread and can generate opportunities for human exposure to zoonoses. Existing research examining zootherapies omits details necessary to adequately assess potential zoonotic risks.MethodsWe used a mixed-methods approach, combining quantitative and qualitative data from questionnaires, key informant interviews, and field notes to examine the use of zootherapy in nine villages engaged in wildlife hunting, consumption, and trade in Cross River State, Nigeria. We analyzed medicinal and cultural practices involving animals from a zoonotic disease perspective, by including details of animal use that may generate pathways for zoonotic transmission. We also examined the sociodemographic, cultural, and environmental contexts of zootherapeutic practices that can further shape the nature and frequency of human-animal interactions.ResultsWithin our study population, people reported using 44 different animal species for zootherapeutic practices, including taxonomic groups considered to be “high risk” for zoonoses and threatened with extinction. Variation in use of animal parts, preparation norms, and administration practices generated a highly diverse set of zootherapeutic practices (n = 292) and potential zoonotic exposure risks. Use of zootherapy was patterned by demographic and environmental contexts, with zootherapy more commonly practiced by hunting households (OR = 2.47, p < 0.01), and prescriptions that were gender and age specific (e.g., maternal and pediatric care) or highly seasonal (e.g., associated with annual festivals and seasonal illnesses). Specific practices were informed by species availability and theories of healing (i.e., “like cures like” and sympathetic healing and magic) that further shaped the nature of human-animal interactions via zootherapy.ConclusionsEpidemiological investigations of zoonoses and public health interventions that aim to reduce zoonotic exposures should explicitly consider zootherapy as a potential pathway for disease transmission and consider the sociocultural and environmental contexts of their use in health messaging and interventions.

Pitfalls and pointers: An accessible guide to marker gene amplicon sequencing in ecological applications

Abstract Next‐Generation Sequencing (NGS) is a powerful tool that has been rapidly adopted by many ecologists studying microbial communities. Despite the exciting demonstration of NGS technology as a tool for ecological research, cryptic pitfalls inherent to its use can obscure correct interpretation of NGS data. Here, we provide an accessible overview of a NGS process that uses marker gene amplicon sequences (MGAS) that will allow scientists, particularly community ecologists, to make appropriate methodological choices and understand limits on inference about community composition and diversity that can be drawn from MGAS data. We describe the MGAS pipeline, focusing specifically on cryptic sources of variation that have received less emphasis in the ecological literature, but which may substantially impact inference about microbial community diversity and composition. By simulating communities from published microbiome data, we demonstrate how these sources of variation can generate inaccurate or misleading patterns. We specifically highlight sample dilution without researcher awareness and lane‐to‐lane variability, two cryptic sources of variation arising during the MGAS pipeline. These sources of variation affect estimates of species presence and relative abundance, particularly for species with moderate to low abundances. Each of these sources of bias can lead to errors in the estimation of both absolute and relative abundance within, and turnover among, microbial communities. Awareness and understanding of what happens and, specifically, why it happens during MGAS generation is key to generating a strong dataset and building a robust community matrix. Requesting sample dilution information from the sequencing centre, including technical replicates across sequencing lanes, and understanding how sampling intensity and community taxa distribution patterns shape the measurement of community richness, evenness and diversity are critical for drawing correct ecological inferences using MGAS data.

Spatial variation in provenance signal: identifying complex sand sourcing within a Carboniferous basin using multiproxy provenance analysis

Multiple factors (e.g. source rock composition, climate, nature/scale of sedimentary system) influence the volume and composition of sediment delivered to basins. Fluctuations in these parameters produce cryptic source signals which can vary within the same sedimentary system. Bespoke multi-proxy provenance approaches, targeted at minerals of variable stability, allow for an assessment of natural biasing (recycling) and intra-basinal spatial variations. Provenance of fluvial/deltaic sandstones (Mullaghmore Sandstone Formation) in the NW Carboniferous Basin, Ireland, has been constrained using zircon and apatite U–Pb geochronology, trace elements in apatite and Pb-in-K-feldspar analysis. Zircon U–Pb grain populations are consistent with feldspar data, suggesting Proterozoic basement highs offshore Ireland and Scotland were the main contributor with minor supply from Archean–Paleoproterozoic rocks of Greenland/NW Scotland and Caledonian-aged rocks. However, apatite data show a much larger proportion of Caledonian-aged grains of metamorphic origin, suggesting significant sediment was recycled from Neopropterozoic metasedimentary rocks. The spatial variation in provenance indicates that, at onset of clastic input, sediment was being routed to the basin through a complex drainage system, comprising several discrete hinterland catchments, rather than supply from a single, large interconnected sedimentary system. Such complexities can only be identified with the careful application of a bespoke multi-proxy provenance approach. Supplementary material: Tables 1-5 and individual Pb-in-K feldspar plots are available at https://doi.org/10.6084/m9.figshare.c.5536691

Microplastic in angling baits as a cryptic source of contamination in European freshwaters

High environmental microplastic pollution, and its largely unquantified impacts on organisms, are driving studies to assess their potential entry pathways into freshwaters. Recreational angling, where many anglers release manufactured baits into freshwater ecosystems, is a widespread activity with important socio-economic implications in Europe. It also represents a potential microplastic pathway into freshwaters that has yet to be quantified. Correspondingly, we analysed three different categories of industrially-produced baits (‘groundbait’, ‘boilies’ and ‘pellets’) for their microplastic contamination (particles 700 µm to 5 mm). From 160 samples, 28 microplastics were identified in groundbait and boilies, with a mean concentration of 17.4 (± 48.1 SD) MP kg−1 and 6.78 (± 29.8 SD) mg kg−1, yet no microplastics within this size range were recorded in the pellets. Microplastic concentrations significantly differed between bait categories and companies, but microplastic characteristics did not vary. There was no correlation between microplastic contamination and the number of bait ingredients, but it was positively correlated with C:N ratio, indicating a higher contamination in baits with higher proportion of plant-based ingredients. We thus reveal that bait microplastics introduced accidentally during manufacturing and/or those originating from contaminated raw ingredients might be transferred into freshwaters. However, further studies are needed to quantify the relative importance of this cryptic source of contamination and how it influences microplastic levels in wild fish.

Clonal diversity impacts coral cover in Acropora cervicornisthickets: Potential relationships between density, growth, and polymorphisms.

As coral reefs decline, cryptic sources of resistance and resilience to stress may be increasingly important for the persistence of these communities. Among these sources, inter‐ and intraspecific diversity remain understudied on coral reefs but extensively impact a variety of traits in other ecosystems. We use a combination of field and sequencing data at two sites in Florida and two in the Dominican Republic to examine clonal diversity and genetic differentiation of high‐ and low‐density aggregations of the threatened coral Acropora cervicornisin the Caribbean. We find that high‐density aggregations called thickets are composed of up to 30 genotypes at a single site, but 47% of genotypes are also found as isolated, discrete colonies outside these aggregations. Genet–ramet ratios are comparable for thickets (0.636) and isolated colonies after rarefaction (0.569), suggesting the composition of each aggregation is not substantially different and highlighting interactions between colonies as a potential influence on structure. There are no differences in growth rate, but a significant positive correlation between genotypic diversity and coral cover, which may be due to the influence of interactions between colonies on survivorship or fragment retention during asexual reproduction. Many polymorphisms distinguish isolated colonies from thickets despite the shared genotypes found here, including putative nonsynonymous mutations that change amino acid sequence in 25 loci. These results highlight intraspecific diversity as a density‐dependent factor that may impact traits important for the structure and function of coral reefs.

Reliable methods for identifying animal deaths in GPS‐ and satellite‐tracking data: Review, testing, and calibration

Abstract Assessing mortality factors and survival rates is a cornerstone for the management of threatened and harvestable species. Modern tracking technologies allow unprecedented opportunities to monitor the mortality of individuals for years. However, the methods employed to separate actual deaths from transmitter failures have rarely been validated. Here, we review these previous methods and exploit an intensive satellite‐tagging programme on raptorial black kites Milvus migrans to examine through tree models whether any tag‐parameter indicators could reliably separate 18 confirmed deaths (recovered corpse) from 32 confirmed cases of radio‐failure (tagged individual subsequently observed alive). Classification keys were validated on 21 confirmed deaths or radio‐failures from an independent tagging study on two other raptor species. Review of tracking studies on mortality showed that they are exponentially increasing and using a wide variety of indicators (e.g., battery charge, stationary locations, fix frequency/quality, sudden tag disappearance, or common sense), with no preponderance of any. Few studies confirmed enough deaths or radio‐failures to validate such methods. For GPS‐satellite tags, we found a reliable classification key that correctly classified 100% of the deaths and radio‐failures in both the calibration and validation datasets through three simple dichotomous indicators: (a) whether GPS locations were stationary or not; (b) whether background Doppler data confirmed them as stationary or not; and (c) whether GPS‐locations’ frequency gave indication of transmitter malfunctioning or not (Figure 3). For tags recording Doppler locations alone, we failed to find a reliable classification key and advise future researchers to use Doppler data very cautiously (e.g., by censoring any uncertain terminal events) because misclassification rates are likely to be high. Synthesis and applications. Refining the death surveillance function of satellite and GPS‐tags will improve the capability of management practitioners to: (a) uncover under‐reported casualties provoked by illegal or conflictual causes (e.g., poisoning, shooting, collision with windmills); and (b) calibrate demographic models which form the basis of management plans (e.g., population viability or sustainable harvest models). Improved exploitation of such remote monitoring will markedly advance the efficiency, planning, and implementation of management projects on imperilled or harvestable species affected by illegal, conflictual, or cryptic sources of mortality.

Influence of Circle Hook Size on Catch Rate and Size of Red Grouper in Shallow Waters of the Southern Gulf of Mexico

AbstractHigh rates of undersized catch and discard mortality are common in fisheries for Red Grouper Epinephelus morio in the Gulf of Mexico and Atlantic Ocean. Reducing undersized catch rate in these fisheries requires more effective regulation of the minimum size limit (MSL). One potential method is to regulate hook selectivity for target species. Three circle hook sizes (11/0, 12/0, and 13/0) were tested to assess the effect of hook size on Red Grouper catch rate and size in the shallow waters of the Yucatan Peninsula coast, which is the primary fishing zone for the region's small‐scale grouper (family Epinephelidae) fishery. Red Grouper was always the numerically dominant species in catches (76–81%) for all hook sizes. Hook size did not affect mean catch rate. Significantly longer fish were caught in the 13/0 hook size treatment than in the 11/0 and 12/0 treatments, which did not differ. Nonetheless, when considering the MSL regulation applicable in Mexico's Red Grouper fishery (36.3 cm TL), high percentages of undersized Red Grouper were still caught, regardless of hook size. The hook sizes required in the Yucatan small‐scale fishery (10/0–12/0) provide little if any improvement in Red Grouper MSL regulation. Real improvement would require the effective release of undersized fish as well as a reduction in the number of undersized specimens caught and in potential cryptic sources of fish release mortality (e.g., barometric trauma). Furthermore, the current applicable Red Grouper MSL only really attempts to control growth overfishing and ignores recruitment overfishing.Received December 22, 2014; accepted September 3, 2015

From continent to intra-oceanic arc: Zircon xenocrysts record the crustal evolution of the Solomon island arc

Research Article| December 01, 2014 From continent to intra-oceanic arc: Zircon xenocrysts record the crustal evolution of the Solomon island arc Simon Tapster; Simon Tapster 1Department of Geology, University of Leicester, Leicester LE1 7RH, UK2NERC Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK Search for other works by this author on: GSW Google Scholar N.M.W. Roberts; N.M.W. Roberts 2NERC Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK Search for other works by this author on: GSW Google Scholar M.G. Petterson; M.G. Petterson 1Department of Geology, University of Leicester, Leicester LE1 7RH, UK Search for other works by this author on: GSW Google Scholar A.D. Saunders; A.D. Saunders 1Department of Geology, University of Leicester, Leicester LE1 7RH, UK Search for other works by this author on: GSW Google Scholar J. Naden J. Naden 3British Geological Survey, Keyworth, Nottingham NG12 5GG, UK Search for other works by this author on: GSW Google Scholar Geology (2014) 42 (12): 1087–1090. https://doi.org/10.1130/G36033.1 Article history received: 29 Jun 2014 rev-recd: 24 Sep 2014 accepted: 25 Sep 2014 first online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share MailTo Twitter LinkedIn Tools Icon Tools Get Permissions Search Site Citation Simon Tapster, N.M.W. Roberts, M.G. Petterson, A.D. Saunders, J. Naden; From continent to intra-oceanic arc: Zircon xenocrysts record the crustal evolution of the Solomon island arc. Geology 2014;; 42 (12): 1087–1090. doi: https://doi.org/10.1130/G36033.1 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract The first U-Pb ages from a ca. 26–24 Ma pluton on Guadalcanal, in the intra-oceanic Solomon island arc (southwest Pacific Ocean), reveal Eocene- to Archean-aged zircon xenocrysts. Xenocryst populations at ca. 39–33 Ma and ca. 71–63 Ma correlate with previously obtained ages of supra-subduction magmatism within the arc. A ca. 96 Ma zircon population may be derived from Cretaceous ophiolite basement crust or region-wide continental rift-related magmatism. Xenocryst age populations alternate with periods of oceanic basin formation that fragmented the East Gondwana margin. Early Cretaceous to Archean zircon xenocryst ages imply continental origins and a cryptic source within the arc crust; they may have been introduced by Eocene interaction of a continental fragment with the arc, and concealed by ophiolite obduction. The data demonstrate that continentally derived zircons may be transported thousands of kilometers from their source and added to intra-oceanic arc magmas, a process likely facilitated by cyclical subduction zone advance and retreat. The findings highlight the continuum of arcs that occurs between continental and oceanic end members, and the caution with which zircons should be used to determine the provenance and setting of ancient arc terranes accreted to the continental crust. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans.

Ribosomes are essential intracellular machines composed of proteins and RNA molecules. The DNA sequences (rDNA) encoding ribosomal RNAs (rRNAs) are tandemly repeated and give origin to the nucleolus. Here we develop a computational method for estimating rDNA dosage (copy number) and mitochondrial DNA abundance using whole-genome short-read DNA sequencing. We estimate these attributes across hundreds of human genomes and their association with global gene expression. The analyses uncover abundant variation in rDNA dosage that is coupled with the expression of hundreds of functionally coherent gene sets. These include associations with genes coding for chromatin components that target the nucleolus, including CTCF and HP1β. Finally, the data show an inverse association between rDNA dosage and mitochondrial DNA abundance that is manifested across genotypes. Our findings uncover a novel and cryptic source of hypervariable genomic diversity with global regulatory consequences (ribosomal eQTL) in humans. The variation provides a mechanism for cellular homeostasis and for rapid and reversible adaptation.

Causes and methods to estimate cryptic sources of fishing mortalitya

Cryptic, not readily detectable, components of fishing mortality are not routinely accounted for in fisheries management because of a lack of adequate data, and for some components, a lack of accurate estimation methods. Cryptic fishing mortalities can cause adverse ecological effects, are a source of wastage, reduce the sustainability of fishery resources and, when unaccounted for, can cause errors in stock assessments and population models. Sources of cryptic fishing mortality are (1) pre-catch losses, where catch dies from the fishing operation but is not brought onboard when the gear is retrieved, (2) ghost-fishing mortality by fishing gear that was abandoned, lost or discarded, (3) post-release mortality of catch that is retrieved and then released alive but later dies as a result of stress and injury sustained from the fishing interaction, (4) collateral mortalities indirectly caused by various ecological effects of fishing and (5) losses due to synergistic effects of multiple interacting sources of stress and injury from fishing operations, or from cumulative stress and injury caused by repeated sub-lethal interactions with fishing operations. To fill a gap in international guidance on best practices, causes and methods for estimating each component of cryptic fishing mortality are described, and considerations for their effective application are identified. Research priorities to fill gaps in understanding the causes and estimating cryptic mortality are highlighted.

Daniel Cavicchi. Listening and Longing: Music Lovers in the Age of Barnum.

Daniel Cavicchi. <i>Listening and Longing: Music Lovers in the Age of Barnum</i>.

Molecular characterization of Vibrio cholerae ΔrelA ΔspoT double mutants

In Escherichia coli cellular levels of pppGpp and ppGpp, collectively called (p)ppGpp, are maintained by the products of two genes, relA and spoT. Like E. coli, Vibrio cholerae also possesses relA and spoT genes. Here we show that similar to E. coli, V. cholerae ΔrelA cells can accumulate (p)ppGpp upon carbon starvation but not under amino acid starved condition. Although like in E. coli, the spoT gene function was found to be essential in V. cholerae relA + background, but unlike E. coli, several V. cholerae ΔrelA ΔspoT mutants constructed in this study accumulated (p)ppGpp under glucose starvation. The results suggest a cryptic source of (p)ppGpp synthesis in V. cholerae, which is induced upon glucose starvation. Again, unlike E. coli ΔrelA ΔspoT mutant (ppGpp0 strain), the V. cholerae ΔrelA ΔspoT mutants showed certain unusual phenotypes, which are (a) resistance towards 3-amino-1,2,4-triazole (AT); (b) growth in nutrient poor M9 minimal medium; (c) ability to stringently regulate cellular rRNA accumulation under glucose starvation and (d) initial growth defect in nutrient rich medium. Since these phenotypes of ΔrelA ΔspoT mutants could be reverted back to ΔrelA phenotypes by providing SpoT in trans, it appears that the spoT gene function is crucial in V. cholerae.

PROMISCUITY DRIVES SEXUAL SELECTION IN A SOCIALLY MONOGAMOUS BIRD

Many socially monogamous species paradoxically show signs of strong sexual selection, suggesting cryptic sources of sexual competition among males. Darwin argued that sexual selection could operate in monogamous systems if breeding sex ratios are biased or if some males attract highly fecund females. Alternatively, sexual selection might result from promiscuous copulations outside the pair bond, although several recent studies have cast doubt on this possibility, in particular by showing that variance in apparent male reproductive success (number of social young) differs little from variance in actual male reproductive success (number of young sired). Our results from a long-term study of the socially monogamous splendid fairy-wren (Malurus splendens) demonstrate that such comparisons are misleading and do not adequately assess the effects of extra-pair paternity (EPP). By partitioning the opportunity for selection and calculating Bateman gradients, we show that EPP has a strong effect on male annual and lifetime fitness, whereas other proposed mechanisms of sexual selection do not. Thus, EPP drives sexual selection in this, and possibly other, socially monogamous species.

Ordovician limestone clasts in the Lower Old Red Sandstone, Pentland Hills, southern Midland Valley Terrane

Synopsis In the southern part of the Scottish Midland Valley Lower Old Red Sandstone sedimentary and volcanic strata of the Lanark Group unconformably overlie inliers of largely marine Silurian rocks. The oldest of the four formations of the Lanark Group is the Greywacke Conglomerate Formation which contains clasts predominantly of greywacke, with subordinate volcanic rocks, cherts and limestones. The greywackes are known to have been derived from a cryptic source which lay to the south and east of the Midland Valley. Contrary to earlier, Silurian, age assessments of limestone clasts from the Greywacke Conglomerate Formation of the Pentland Hills, a conodont faunule described herein belongs in the uppermost Llanvirn to lower Caradoc P. anserinus Biozone. There are no Ordovician rocks exposed within the Pentland Hills inlier, and thus our new age data suggest that along with the other clasts, the limestones in the Greywacke Conglomerate are exotic to the Pentlands Sub-basin. The source area had a cover succession that included mid-Ordovician shallow marine carbonate and flysch.

Reconstructing cave bear paleoecology from skeletons: a cross-disciplinary study of middle Pleistocene bears from Yarimburgaz Cave, Turkey

Cave bears, an extinct subgenus (Spelearctos) of Ursus, were versatile enough to inhabit large areas of the northern hemisphere during the middle and late Pleistocene, yet they had evolved a specialized dentition that emphasized grinding functions, implying a heavy dietary reliance on tough, fibrous foods (i.e., plants). Isotope studies have yielded conflicting results on cave bear diet, however, often without consideration of the provenance of the samples or the possible contradictions that taphonomic and morphologic evidence might pose to dietary interpretations. It is likely that cave bear habits varied somewhat in response to environmental circumstance, and the limits on their abilities to do so remain unknown. If the larger goal of paleontological inquiry is to reconstruct the adaptations of cave bear species, then variation and commonalities among populations must be tracked closely, and the disparate lines of evidence currently available examined together on a case by case basis. Clearly, no single analytical technique can achieve this. By way of example we present the results of a cross-disciplinary collaboration that combines osteometric, isotopic, and taphonomic approaches to studying the paleoecology of a bear assemblage from Yarimburgaz Cave in northwest Turkey. Reference information on the linkages between diet, hibernation, and population structure in modern bears provides test implications for the investigation. Osteometric techniques demonstrate the presence of two coextant middle Pleistocene bear species in the sample–Ursus (Spelearctos) deningeri, a form of cave bear, and U. arctos or brown bear–the former abundant in the sample, the latter rare. An attritional mortality pattern for the bears and the condition of their bones show that most or all of the animals died in the cave from nonviolent causes in the context of hibernation. The study also elucidates several characteristics of the cave bear population in this region. Osteometric techniques show that the adult sex ratio of the cave bears is only slightly skewed toward females. This pattern lies near one extreme of the full range of possible outcomes in modern bear species and can only reflect a strong dietary dependence on seasonally available plants and invertebrates, showing that hibernation was a crucial overwintering strategy for both sexes; the results specifically contradict the possibility of regular, heavy emphasis on large game (hunted or scavenged) as a winter food source. The nature of wear and breakage to the adult cave bear teeth indicates that food frequently was obtained from cryptic sources, requiring digging and prying, and that extensive mastication was necessary, leading to complete obliteration of some cheek tooth crowns in old individuals. The patterns of tooth damage during life corroborate the dietary implications of the adult sex ratio and also argue for a diet rich in tough, abrasive materials such as nuts, tubers, and associated grit. The carbon and oxygen isotopic compositions of cave and brown bear tooth enamel from the site are virtually identical, and there is no evidence of a strong marine signal in either species, despite the cave's proximity to a modern estuary of the Sea of Marmara; nitrogen isotope ratios could not be examined because of poor protein preservation. The isotope results suggest that both bear species were highly omnivorous in the region during the middle Pleistocene and obtained nearly all of their food from terrestrial and fresh-water habitats. Bone pathologies, usually originating from trauma, occur in some of the adult bears, testifying to long lifespans of some individuals in this fossil population. The Yarimburgaz cave bears also exhibit great size dimorphism between the sexes, based on weight-bearing carpal bone dimensions, with adult males attaining roughly twice the body mass of adult females.

MAINTENANCE OF POLYGENIC VARIATION VIA A MIGRATION-SELECTION BALANCE UNDER UNIFORM SELECTION.

Population subdivision is often invoked to explain the large amount of heterozygosity found at single loci in natural populations (Felsenstein 1976; Hedrick et al., 1976; Karlin 1982; Hedrick 1986). Surprisingly, relatively few studies describe the effects of population structure on the maintenance of variance for polygenic (quantitative) traits. Felsenstein (1977) and Slatkin (1978) presented models in which additive variance can be maintained via migration along a cline (see also Barton and Turelli 1989). Goldstein and Holsinger (1992) used simulations to show that variance for quantitative traits could be maintained under uniform selection in a population subject to isolation by distance (see also Lande [1991]), and Slatkin and Lande (1994) demonstrated that the segregation variance generated by betweenpopulation crosses depends on how variance is generated within each population. Here I analyze the amount of variance that can be maintained deterministically via a migration-selection balance under uniform selection and conclude that a potentially large amount of variance can be generated in this way. This is true only when migration is very weak, so as not to overcome the influence of selection. When variance is maintained, it is maximal at the critical balance between migration and selection. The deterministic interaction between migration and selection has been the subject of a great deal of analysis in the context of Wright's shifting-balance theory (Crow et al. 1990; Barton 1992; Kondrashov 1992; Phillips 1993). These studies have shown that migration can be very effective at overcoming the effects of selection and driving populations to uniformity. For the shifting-balance process, this means that once a population has undergone a peak shift, it might be expected to drive peak shifts in neighboring populations, depending on the details of the system and population structure (Barton 1992; Phillips 1993). The purpose here is to explore regions of the parametric space in which this does not happen, but instead both populations remain polymorphic. Results from this deterministic approach will be contrasted with models that include stochastic effects and make somewhat different predictions (Lande 1991; Goldstein and Holsinger 1992; Barton and Rouhani 1993). Uniform stabilizing selection on an additive character generates disruptive selection at the level because various combinations of alleles can yield the same optimal phenotype, but the marginal fitness of any allele depends on the background in which it is found (Wright 1935). This is called genetic redundancy by Goldstein and Holsinger [1992]). Two populations can thus display the same phenotype but be fixed for different genotypes. If these populations were to exchange migrants, the mixing of the different genotypes would generate variance within each population. This would be a somewhat cryptic source of variation because there would be no obvious differentiation between the populations. Depending on the strength of migration, most of the variance generated by migration would then be quickly eliminated by selection, creating a migration-selection balance. This is the multilocus equivalent of a migration-selection polymorphism generated by underdominance at a single locus (Karlin and McGregor 1972). Because many characters are assumed to be under stabilizing selection, and because population structure is undoubtedly an important feature of natural populations, the interaction of migration and selection could obviously be an important influence on the maintenance of variance.

A Summary of the Orogenic Epochs in the Geologic History of North America

Next article FreeA Summary of the Orogenic Epochs in the Geologic History of North AmericaEliot BlackwelderEliot Blackwelder Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The Journal of Geology Volume 22, Number 7Oct. - Nov., 1914 Article DOIhttps://doi.org/10.1086/622180 Views: 389Total views on this site Citations: 17Citations are reported from Crossref PDF download Crossref reports the following articles citing this article:Arlo Brandon Weil, Adolph Yonkee The Laramide orogeny: Current understanding of the structural style, timing, and spatial distribution of the classic foreland thick-skinned tectonic system, (Jan 2023): 707–771.https://doi.org/10.1130/2022.1220(33)Tsilavo Raharimahefa, Bruno Lafrance, Douglas K. Tinkham, Fernando Corfu New structural, metamorphic, and U–Pb geochronological constraints on the Blezardian Orogeny and Yavapai Orogeny in the Southern Province, Sudbury, Canada, Canadian Journal of Earth Sciences 51, no.88 (Aug 2014): 750–774.https://doi.org/10.1139/cjes-2014-0025J. J. Schwartz, A. W. Snoke, F. Cordey, K. Johnson, C. D. Frost, C. G. Barnes, T. A. LaMaskin, J. L. Wooden Late Jurassic magmatism, metamorphism, and deformation in the Blue Mountains Province, northeast Oregon, Geological Society of America Bulletin 123, no.9-109-10 (Jun 2011): 2083–2111.https://doi.org/10.1130/B30327.1Arthur W. Snoke, Calvin G. Barnes The development of tectonic concepts for the Klamath Mountains province, California and Oregon, (Jan 2006): 1–29.https://doi.org/10.1130/2006.2410(01)Gary G. Gray Structural and tectonic evolution of the western Jurassic belt along the Klamath River corridor, Klamath Mountains, California, (Jan 2006): 141–151.https://doi.org/10.1130/2006.2410(07)Charlotte M. Allen, Calvin G. Barnes Ages and some cryptic sources of Mesozoic plutonic rocks in the Klamath Mountains, California and Oregon, (Jan 2006): 223–245.https://doi.org/10.1130/2006.2410(11)Kevin R. Chamberlain, Arthur W. Snoke, Calvin G. Barnes, Jonathan C. Bushey New U-Pb radiometric dates of the Bear Mountain intrusive complex, Klamath Mountains, California, (Jan 2006): 317–332.https://doi.org/10.1130/2006.2410(15)Bradley R. Hacker, Mary M. Donato, Calvin G. Barnes, M. O. McWilliams, W. G. Ernst Timescales of orogeny: Jurassic construction of the Klamath Mountains, Tectonics 14, no.33 (Jul 2010): 677–703.https://doi.org/10.1029/94TC02454Gregory D. Harper, Jason B. Saleeby, Matthew Heizler Formation and emplacement of the Josephine ophiolite and the Nevadan orogeny in the Klamath Mountains, California-Oregon: U/Pb zircon and 40 Ar/ 39 Ar geochronology, Journal of Geophysical Research: Solid Earth 99, no.B3B3 (Sep 2012): 4293–4321.https://doi.org/10.1029/93JB02061Steven H. Edelman Relationships between kinematics of arc-continent collision and kinematics of thrust faults, folds, shear zones, and foliations in the Nevadan orogen, northern Sierra Nevada, California, Tectonophysics 191, no.3-43-4 (Jun 1991): 223–236.https://doi.org/10.1016/0040-1951(91)90058-ZGregory D. Harper, James E. Wright Middle to Late Jurassic tectonic evolution of the Klamath Mountains, California-Oregon, Tectonics 3, no.77 (Jul 2010): 759–772.https://doi.org/10.1029/TC003i007p00759Jason B. Saleeby, Gregory D. Harper, Arthur W. Snoke, Warren D. Sharp Time relations and structural-stratigraphic patterns in ophiolite accretion, west central Klamath Mountains, California, Journal of Geophysical Research 87, no.B5B5 (Jan 1982): 3831.https://doi.org/10.1029/JB087iB05p03831Jason B. Saleeby, Cathy Busby-Spera, J. S. Oldow, G. C. Dunne, J. E. Wright, D. S. Cowan, N. W. Walker, R. W. Allmendinger Early Mesozoic tectonic evolution of the western U.S. Cordillera, (): 107–38.https://doi.org/10.1130/DNAG-GNA-G3.107W. B. Harland Interpretation of stratigraphical ages in orogenic belts, Geological Society, London, Special Publications 3, no.11 (Jun 2022): 115–135.https://doi.org/10.1144/GSL.SP.1969.003.01.07Hans Bürgl The orogenesis in the andean system of colombia, Tectonophysics 4, no.4-64-6 (Oct 1967): 429–443.https://doi.org/10.1016/0040-1951(67)90009-1R. H. Dott Mesozoic-cenozoic tectonic history of the southwestern Oregon coast in relation to cordilleran orogenesis, Journal of Geophysical Research 70, no.1818 (Dec 2012): 4687–4707.https://doi.org/10.1029/JZ070i018p04687Richard A. Sonder Die erdgeschichtlichen Diastrophismen im Lichte der Kontraktionslehre, Geologische Rundschau 13, no.33 (Nov 1922): 217–272.https://doi.org/10.1007/BF01799789