On the accuracy of paleodiversity reconstructions: a case study in Antarctic Neogene radiolarians

Paleobiology ◽  
10.1666/12016 ◽  
2013 ◽  
Vol 39 (3) ◽  
pp. 491-509 ◽  
Author(s):  
Johan Renaudie ◽  
David B. Lazarus
Keyword(s):  
Environmental Changes ◽  
Ecological Change ◽  
Significant Drop ◽  
Data Set ◽  
Species Abundances ◽  
History Of ◽  
Ecological Event ◽  
Plankton Diversity ◽  
Paleoceanographic Change ◽  
Species Occurrences

The deep-sea Cenozoic planktonic microfossil record has the unique characteristics of continuously well-preserved populations of most species, with virtually unlimited sample size, and therefore constitutes, in principle, a major resource for macroevolutionary research. Antarctic Neogene radiolarians in particular, are diverse, abundant and consistently well-preserved and evolved rapidly. This fauna is, in theory, a near-perfect testing ground for paleodiversity reconstructions. In this study we determined the diversity history of these faunas from a new quantitative, taxonomically complete data set from Neogene and Quaternary sections at several Antarctic sites. The pattern retrieved by our whole-fauna data set shows a significant, largely extinctionless ecological change in faunal composition and decrease in the evenness of species' abundances during the late Miocene, followed 3 Myr later, at around 5 Ma, by a significant drop in diversity. We tentatively associate this ecological event with a synchronous, regional change in the composition of the primary producers, but as yet cannot identify any environmental changes associated with the later extinction. Further, our whole-fauna diversity history was compared to diversity computed from much less complete, biostratigraphically oriented studies of species' occurrences, compiled in the Neptune database and reconstructed by using subsampling methodologies. Comparison of our whole-fauna and subsampling-reconstructed diversity patterns shows that the first-order trends are the same in both, suggesting that, to some degree, such literature compilations can be used to explore diversity history of plankton. However, our results also highlight substantial errors and distortions in the reconstructed diversity which make it poorly suited to more-detailed studies (e.g., for comparison of diversity history with paleoenvironmental history). We conclude that detailed studies of plankton diversity, and particularly those attempting to understand the relation between diversity and paleoceanographic change, should be based on taxonomically comprehensive, quantitative data.

scholarly journals Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble

2021 ◽  
Vol 17 (12) ◽  
pp. e1008906
Author(s):  
Icíar Civantos-Gómez ◽  
Javier García-Algarra ◽  
David García-Callejas ◽  
Javier Galeano ◽  
Oscar Godoy ◽  
...  
Keyword(s):  
Species Composition ◽  
Species Interactions ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Predictive Accuracy ◽  
Data Driven ◽  
Soil Conditions ◽  
Fine Scale ◽  
Data Set ◽  
Species Abundances

Prediction is one of the last frontiers in ecology. Indeed, predicting fine-scale species composition in natural systems is a complex challenge as multiple abiotic and biotic processes operate simultaneously to determine local species abundances. On the one hand, species intrinsic performance and their tolerance limits to different abiotic pressures modulate species abundances. On the other hand there is growing recognition that species interactions play an equally important role in limiting or promoting such abundances within ecological communities. Here, we present a joint effort between ecologists and data scientists to use data-driven models to predict species abundances using reasonably easy to obtain data. We propose a sequential data-driven modeling approach that in a first step predicts the potential species abundances based on abiotic variables, and in a second step uses these predictions to model the realized abundances once accounting for species competition. Using a curated data set over five years we predict fine-scale species abundances in a highly diverse annual plant community. Our models show a remarkable spatial predictive accuracy using only easy-to-measure variables in the field, yet such predictive power is lost when temporal dynamics are taken into account. This result suggests that predicting future abundances requires longer time series analysis to capture enough variability. In addition, we show that these data-driven models can also suggest how to improve mechanistic models by adding missing variables that affect species performance such as particular soil conditions (e.g. carbonate availability in our case). Robust models for predicting fine-scale species composition informed by the mechanistic understanding of the underlying abiotic and biotic processes can be a pivotal tool for conservation, especially given the human-induced rapid environmental changes we are experiencing. This objective can be achieved by promoting the knowledge gained with classic modelling approaches in ecology and recently developed data-driven models.

scholarly journals Current understanding on the Cambrian Explosion: questions and answers

PalZ ◽  
2021 ◽  
Author(s):  
Xingliang Zhang ◽  
Degan Shu
Keyword(s):  
Environmental Changes ◽  
Size Variation ◽  
Progressive Increase ◽  
Cambrian Explosion ◽  
Time Interval ◽  
Early Cambrian ◽  
Ecological Processes ◽  
Questions And Answers ◽  
Evolutionary Event ◽  
History Of

AbstractThe Cambrian Explosion by nature is a three-phased explosion of animal body plans alongside episodic biomineralization, pulsed change of generic diversity, body size variation, and progressive increase of ecosystem complexity. The Cambrian was a time of crown groups nested by numbers of stem groups with a high-rank taxonomy of Linnaean system (classes and above). Some stem groups temporarily succeeded while others were ephemeral and underrepresented by few taxa. The high number of stem groups in the early history of animals is a major reason for morphological gaps across phyla that we see today. Most phylum-level clades achieved their maximal disparity (or morphological breadth) during the time interval close to their first appearance in the fossil record during the early Cambrian, whereas others, principally arthropods and chordates, exhibit a progressive exploration of morphospace in subsequent Phanerozoic. The overall envelope of metazoan morphospace occupation was already broad in the early Cambrian though it did not reach maximal disparity nor has diminished significantly as a consequence of extinction since the Cambrian. Intrinsic and extrinsic causes were extensively discussed but they are merely prerequisites for the Cambrian Explosion. Without the molecular evolution, there could be no Cambrian Explosion. However, the developmental system is alone insufficient to explain Cambrian Explosion. Time-equivalent environmental changes were often considered as extrinsic causes, but the time coincidence is also insufficient to establish causality. Like any other evolutionary event, it is the ecology that make the Cambrian Explosion possible though ecological processes failed to cause a burst of new body plans in the subsequent evolutionary radiations. The Cambrian Explosion is a polythetic event in natural history and manifested in many aspects. No simple, single cause can explain the entire phenomenon.

Economics of respiratory disease in dairy replacement heifers

2020 ◽  
Vol 21 (2) ◽  
pp. 143-148
Author(s):  
Michael W. Overton
Keyword(s):  
Respiratory Disease ◽  
Milk Production ◽  
Incident Case ◽  
Data Set ◽  
Dairy Heifers ◽  
The Usa ◽  
History Of ◽  
On Farm ◽  
The Impact ◽  
Selective Culling

AbstractBovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

Three Cases of Pyogenic Granuloma of the Gastrointestinal Tract

2019 ◽  
Vol 152 (Supplement_1) ◽  
pp. S119-S119
Author(s):  
Yukihiro Nakanishi ◽  
Preeti Behl ◽  
Byron Crawford
Keyword(s):  
Gastrointestinal Tract ◽  
Pyogenic Granuloma ◽  
Right Hemicolectomy ◽  
Capillary Hemangioma ◽  
Deficiency Anemia ◽  
Significant Drop ◽  
Massive Gastrointestinal Bleeding ◽  
History Of ◽  
Mixed Inflammatory Infiltrate ◽  
Pedunculated Polyp

Abstract Pyogenic granuloma also known as lobular capillary hemangioma occurs commonly in the skin and oral mucosa. This entity has been rarely reported in the gastrointestinal tract. We herein report three cases of pyogenic granuloma, located in the duodenum, ileum, and rectum, respectively. Case 1 is a 54-year-old female with a history of angioimmunoblastic T-cell lymphoma who underwent an esophagogastroduodenoscopy for severe heartburn. The endoscopy showed a 13-mm nonbleeding, pedunculated polyp in the second portion of duodenum, which was removed using a hot snare after injection of epinephrine. The patient had an episode of massive gastrointestinal bleeding postpolypectomy, with a significant drop of her hemoglobin, which was managed with blood transfusion. Case 2 is a 68-year-old male with a history of right hemicolectomy due to trauma who had a colonoscopy for chronic diarrhea. The colonoscopy revealed a 14-mm, nonbleeding, pedunculated polyp in the ileum, located 3 cm from the ileocolonic anastomosis. The polyp was removed with hot snare, without complications. Case 3 is a 44-year-old female with morbid obesity who underwent a colonoscopy for iron-deficiency anemia. The colonoscopy showed an 8-mm multilobulated sessile lesion in the distal rectum, which was completely removed using hot snare. No complications were seen postpolypectomy. Histological examination of all the three polyps showed a proliferation of capillary-sized blood vessels with a mixed inflammatory infiltrate, resembling granulation tissue. Additionally, the ileal polyp in our case had marked eosinophilic infiltrate, the etiology of which remains unknown. In conclusion, pyogenic granuloma, given its vascular nature, can be a cause of bleeding in the gastrointestinal tract. Awareness regarding this rare entity is important for its proper diagnosis and treatment.

scholarly journals Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Daniele Raimondi ◽  
Antoine Passemiers ◽  
Piero Fariselli ◽  
Yves Moreau
Keyword(s):  
Data Sets ◽  
Precision Oncology ◽  
Complex Task ◽  
Excellent Performance ◽  
Driver Genes ◽  
Significant Drop ◽  
Data Set ◽  
Gene Effects ◽  
Cancer Driver ◽  
Functional Variants

Abstract Background Identifying variants that drive tumor progression (driver variants) and distinguishing these from variants that are a byproduct of the uncontrolled cell growth in cancer (passenger variants) is a crucial step for understanding tumorigenesis and precision oncology. Various bioinformatics methods have attempted to solve this complex task. Results In this study, we investigate the assumptions on which these methods are based, showing that the different definitions of driver and passenger variants influence the difficulty of the prediction task. More importantly, we prove that the data sets have a construction bias which prevents the machine learning (ML) methods to actually learn variant-level functional effects, despite their excellent performance. This effect results from the fact that in these data sets, the driver variants map to a few driver genes, while the passenger variants spread across thousands of genes, and thus just learning to recognize driver genes provides almost perfect predictions. Conclusions To mitigate this issue, we propose a novel data set that minimizes this bias by ensuring that all genes covered by the data contain both driver and passenger variants. As a result, we show that the tested predictors experience a significant drop in performance, which should not be considered as poorer modeling, but rather as correcting unwarranted optimism. Finally, we propose a weighting procedure to completely eliminate the gene effects on such predictions, thus precisely evaluating the ability of predictors to model the functional effects of single variants, and we show that indeed this task is still open.

Characteristics and Care of U.S. Nursing Home Residents with a History of Chronic Mental Illness

2000 ◽  
Vol 19 (S2) ◽  
pp. 1-17 ◽  
Author(s):  
Charles D. Phillips ◽  
Kathleen M. Spry
Keyword(s):  
Nursing Home ◽  
Nursing Home Residents ◽  
Minimum Data Set ◽  
Chronic Mental Illness ◽  
Data Set ◽  
Minimum Data ◽  
Troubles Mentaux ◽  
History Of ◽  
Resident Assessment ◽  
Medicaments Psychotropes

RÉSUMÉTrès peu de recherches ont été effectuées sur les pensionnaires des maisons de soins ayant manifestés des troubles mentaux chroniques sans démence avant leur entrée en institution. Les données du Minimum Data Set for Nursing Home Resident Assessment and Care Screening (MDS) de 1993 ont été utilisées pouranalyser les différences dans les caractéristiques et les soins se rapportant à ce type de pensionnaires par rapport aux autres pensionnaires. Cette enquête portait sur 70 000 pensionnaires du Kansas, du Maine, du Mississippi et du Dakota du Sud. Les caractéristiques des pensionnaires qui éprouvaient ce type de troubles mentaux chroniques étaient plus fréquemment les suivantes: sexe masculin, 65 ans et plus, bénéficiaires de Medicaid, moins médicalement inaptes et niveau plus élevé de problèmes de comportements. Ces pensionnaires reçoivent aussi davantage de médicaments psychotropes et suivant une thérapie, la prévalence de la thérapie étant cependant moins éleveé. Les informations recueillies pourraient laisser croire que les soins accordés à ces pensionnaires ne sont pas des plus appropriés.

Environmental evolution and anthropogenic forcing in the Garigliano coastal plain (Italy) during the Holocene

The Holocene ◽  
2021 ◽  
pp. 095968362110032
Author(s):  
Halinka Di Lorenzo ◽  
Pietro Aucelli ◽  
Giuseppe Corrado ◽  
Mario De Iorio ◽  
Marcello Schiattarella ◽  
...  
Keyword(s):  
Human Activity ◽  
Coastal Plain ◽  
Forest Cover ◽  
Environmental Changes ◽  
Pollen Data ◽  
Human Environment ◽  
The Holocene ◽  
Natural Processes ◽  
History Of ◽  
The Rich

The Garigliano alluvial-coastal plain, at the Latium-Campania border (Italy), witnessed a long-lasting history of human-environment interactions, as demonstrated by the rich archaeological knowledge. With the aim of reconstructing the evolution of the landscape and its interaction with human activity during the last millennia, new pollen results from the coastal sector of the Garigliano Plain were compared with the available pollen data from other nearby sites. The use of pollen data from both the coastal and marine environment allowed integrating the local vegetation dynamics within a wider regional context spanning the last 8000 years. The new pollen data presented in this study derive from the analysis of a core, drilled in the coastal sector, which intercepted the lagoon-marshy environments that occurred in the plain as a response to the Holocene transgression and subsequent coastal progradation. Three radiocarbon ages indicate that the chronology of the analyzed core interval ranges from c. 7200 to c. 2000 cal yr BP. The whole data indicate that a dense forest cover characterized the landscape all along the Prehistoric period, when a few signs of human activity are recorded in the spectra, such as cereal crops, pasture activity and fires. The main environmental changes, forced by natural processes (coastal progradation) but probably enhanced by reclamation works, started from the Graeco-Roman period and led to the reduction of swampy areas that favoured the colonisation of the outer plain.

scholarly journals The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fan Li ◽  
Yunyun Lv ◽  
Zhengyong Wen ◽  
Chao Bian ◽  
Xinhui Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Physiological Activity ◽  
Complete Mitochondrial Genome ◽  
Dynamic Environment ◽  
Data Set ◽  
History Of ◽  
Complete Mitogenome ◽  
Selection Signal ◽  
Positive Selection Signal

Abstract Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

Heterogeneity of reasons for attendance in frequent attenders of emergency departments and its relationship to future attendance

2021 ◽  
pp. emermed-2020-210412
Author(s):  
Richard Hotham ◽  
Colin O'Keeffe ◽  
Tony Stone ◽  
Suzanne M Mason ◽  
Christopher Burton
Keyword(s):  
Mental Health ◽  
Mental Disorder ◽  
Emergency Care ◽  
Health Problem ◽  
Patient Characteristics ◽  
Health Needs ◽  
Data Set ◽  
Frequent Attenders ◽  
History Of ◽  
Ed Visits

BackgroundEDs globally are under increasing pressure through rising demand. Frequent attenders are known to have complex health needs and use a disproportionate amount of resources. We hypothesised that heterogeneity of patients’ reason for attendance would be associated with multimorbidity and increasing age, and predict future attendance.MethodWe analysed an anonymised dataset of all ED visits over the course of 2014 in Yorkshire, UK. We identified 15 986 patients who had five or more ED encounters at any ED in the calendar year. Presenting complaint was categorised into one of 14 categories based on the Emergency Care Data Set (ECDS). We calculated measures of heterogeneity (count of ECDs categories and entropy of categories) and examined their relationship to total number of ED visits and to patient characteristics. We examined the predictive value of these and other features on future attendance.ResultsMost frequent attenders had more than one presenting complaint type. Heterogeneity increased with number of attendances, but heterogeneity adjusted for number of attendances did not vary substantially with age or sex. Heterogeneity was associated with the presence of one or more contacts for a mental health problem. For a given number of attendances, prior mental health contact but not heterogeneity was associated with further attendance.ConclusionsHeterogeneity of presenting complaint can be quantified and analysed for ED use: it is increased where there is a history of mental disorder but not with age. This suggests it reflects more than the number of medical conditions.

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