The hierarchical structure of organisms: a scale and documentation of a trend in the maximum

Paleobiology ◽  
2001 ◽  
Vol 27 (2) ◽  
pp. 405-423 ◽  
Author(s):  
Daniel. W. McShea

The degree of hierarchical structure of organisms—the number of levels of nesting of lower-level entities within higher-level individuals—has apparently increased a number of times in the history of life, notably in the origin of the eukaryotic cell from an association of prokaryotic cells, of multicellular organisms from clones of eukaryotic cells, and of integrated colonies from aggregates of multicellular individuals. Arranged in order of first occurrence, these three transitions suggest a trend, in particular a trend in the maximum, or an increase in the degree of hierarchical structure present in the hierarchically deepest organism on Earth. However, no rigorous documentation of such a trend—based on operational and consistent criteria for hierarchical levels—has been attempted. Also, the trajectory of increase has not been examined in any detail. One limitation is that no hierarchy scale has been developed with sufficient resolution to document more than these three major increases. Here, a higher-resolution scale is proposed in which hierarchical structure is decomposed into levels and sublevels, with levels reflecting number of layers of nestedness, and sublevels reflecting degree of individuation at the highest level. The scale is then used, together with the body-fossil record, to plot the trajectory of the maximum. Two alternative interpretations of the record are considered, and both reveal a long-term trend extending from the Archean through the early Phanerozoic. In one, the pattern of increase was incremental, with almost all sublevels arising precisely in order. The data also raise the possibility that waiting times for transitions between sublevels may have decreased with increasing hierarchical level (and with time). These last two findings—incremental increase in level and decreasing waiting times—are tentative, pending a study of possible biases in the fossil record.

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150223 ◽  
Author(s):  
Clive N. Trueman ◽  
Ming-Tsung Chung ◽  
Diana Shores

The fossil record provides the only direct evidence of temporal trends in biodiversity over evolutionary timescales. Studies of biodiversity using the fossil record are, however, largely limited to discussions of taxonomic and/or morphological diversity. Behavioural and physiological traits that are likely to be under strong selection are largely obscured from the body fossil record. Similar problems exist in modern ecosystems where animals are difficult to access. In this review, we illustrate some of the common conceptual and methodological ground shared between those studying behavioural ecology in deep time and in inaccessible modern ecosystems. We discuss emerging ecogeochemical methods used to explore population connectivity and genetic drift, life-history traits and field metabolic rate and discuss some of the additional problems associated with applying these methods in deep time.


2020 ◽  
Vol 117 (16) ◽  
pp. 8966-8972 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Christine Strullu-Derrien ◽  
Tomasz Góral ◽  
Alexander J. Hetherington ◽  
Christine Thompson ◽  
...  

Identifying marine or freshwater fossils that belong to the stem groups of the major terrestrial arthropod radiations is a longstanding challenge. Molecular dating and fossils of their pancrustacean sister group predict that myriapods originated in the Cambrian, much earlier than their oldest known fossils, but uncertainty about stem group Myriapoda confounds efforts to resolve the timing of the group’s terrestrialization. Among a small set of candidates for membership in the stem group of Myriapoda, the Cambrian to Triassic euthycarcinoids have repeatedly been singled out. The only known Devonian euthycarcinoid, Heterocrania rhyniensis from the Rhynie and Windyfield cherts hot spring complex in Scotland, reveals details of head structures that constrain the evolutionary position of euthycarcinoids. The head capsule houses an anterior cuticular tentorium, a feature uniquely shared by myriapods and hexapods. Confocal microscopy recovers myriapod-like characters of the preoral chamber, such as a prominent hypopharynx supported by tentorial bars and superlinguae between the mandibles and hypopharynx, reinforcing an alliance between euthycarcinoids and myriapods recovered in recent phylogenetic analysis. The Cambrian occurrence of the earliest euthycarcinoids supplies the oldest compelling evidence for an aquatic stem group for either Myriapoda or Hexapoda, previously a lacuna in the body fossil record of these otherwise terrestrial lineages until the Silurian and Devonian, respectively. The trace fossil record of euthycarcinoids in the Cambrian and Ordovician reveals amphibious locomotion in tidal environments and fills a gap between molecular estimates for myriapod origins in the Cambrian and a post-Ordovician crown group fossil record.


2016 ◽  
Vol 3 (8) ◽  
pp. 160222 ◽  
Author(s):  
Jennifer Anné ◽  
Brandon P. Hedrick ◽  
Jason P. Schein

Identification and interpretation of pathologies in the fossil record allows for unique insights into the life histories of extinct organisms. However, the rarity of such finds limits not only the sample size for palaeopathologic studies, but also the types of analyses that may be performed. In this study, we present the first occurrence of a palaeopathology in a vertebrate from the Mesozoic of the East Coast of North America (Appalachia), a pathologic ulna and radius of an indeterminate hadrosaur from the Navesink Formation (New Jersey). X-ray microtomography allowed for both detailed and more accurate diagnosis of the pathologic condition as well as virtual conservation of the specimen. Based on extant archosaurian comparisons, the hadrosaur was diagnosed with severe septic arthritis affecting the proximal ulna and radius. Diagnosis was based on erosion of the joint and highly reactive periosteal bone growth and fusion of the elements. To the best of our knowledge, this is the first recorded account of septic arthritis in dinosaurs. The severity of the pathology suggests the animal suffered with this condition for some time before death. Unfortunately, only the ulna and radius were found. Thus, the extent to which the condition spread to other parts of the body is unknown.


2016 ◽  
Vol 371 (1685) ◽  
pp. 20150287 ◽  
Author(s):  
Graham E. Budd ◽  
Illiam S. C. Jackson

Simulation studies of the early origins of the modern phyla in the fossil record, and the rapid diversification that led to them, show that these are inevitable outcomes of rapid and long-lasting radiations. Recent advances in Cambrian stratigraphy have revealed a more precise picture of the early bilaterian radiation taking place during the earliest Terreneuvian Series, although several ambiguities remain. The early period is dominated by various tubes and a moderately diverse trace fossil record, with the classical ‘Tommotian’ small shelly biota beginning to appear some millions of years after the base of the Cambrian at ca 541 Ma. The body fossil record of the earliest period contains a few representatives of known groups, but most of the record is of uncertain affinity. Early trace fossils can be assigned to ecdysozoans, but deuterostome and even spiralian trace and body fossils are less clearly represented. One way of explaining the relative lack of clear spiralian fossils until about 536 Ma is to assign the various lowest Cambrian tubes to various stem-group lophotrochozoans, with the implication that the groundplan of the lophotrochozoans included a U-shaped gut and a sessile habit. The implication of this view would be that the vagrant lifestyle of annelids, nemerteans and molluscs would be independently derived from such a sessile ancestor, with potentially important implications for the homology of their sensory and nervous systems.


Author(s):  
Julián Simón López-Villalta

Abstract During the Stage 3 of the Cambrian, several siliciclastic formations were deposited in a shallow platform that would become part of the Iberian Massif, containing abundant trace fossils and the conspicuous ichnospecies Astropolichnus hispanicus, endemic to southwestern Europe during the regional Ovetian stage. The fossil record of these formations has been explored mainly in northern Spain; in southern Spain, the Azorejo Formation (Azorejo Sandstone) is the only unit of this kind, but its paleobiological content has never been described in detail. In this work, the fossil record of the Azorejo Formation is documented from one of its least known outcrops: the Guadiana river section at Picón, Ciudad Real. In this section, the Azorejo Forma- tion contains a diverse trace fossil record for a neritic environment, comprising Agrichnium?, Astropolichnus hispanicus, Belorhaphe, Bergaueria cf. hemispherica, Cochlichnus, Conichnus conicus, Cruziana, Dimorphichnus, Diplichnites, Diplocraterion, Monocraterion, Monomorphichnus bilinearis, Monomorphichnus lineatus, Monomorphichnus lineatus var. giganticus, Palaeophycus, Palaeophycus cf. imbricatus, Planolites, Psammichnites, Rusophycus avalonensis?, Skolithos, Treptichnus pedum, and trace fossils similar to Nereites and Zoophycos. A structure interpreted as the body fossil of a radial organism is also described. Some of these fossils are firstly cited to the Azorejo Formation and the Lower Cambrian of the Iberian Massif. Resumen Durante la Edad 3 del Cámbrico, varias formaciones siliciclásticas fueron depositadas en una plataforma somera que habría de convertirse en parte del Macizo Ibérico, conteniendo abundantes pistas fósiles y la icnoespecie Astropolichnus hispanicus, endémica del sudoeste europeo durante el piso regional Ovetiense. El registro fósil de estas formaciones ha sido explorado principalmente en el norte de España; en el sur, la Formación Azorejo (Areniscas del Azorejo) es la única unidad de este tipo, pero su contenido paleobiológico nunca ha sido descrito en detalle. En este trabajo, el registro fósil de la Formación Azorejo es documentado para uno de sus afloramientos menos conocidos: la sección del río Guadiana en Picón, Ciudad Real. En él la Formación Azorejo contiene variadas pistas fósiles, incluyendo Agrichnium?, Astropolichnus hispanicus, Belorhaphe, Bergaueria cf. hemispherica, Cochlichnus, Conichnus conicus, Cruziana, Dimorphichnus, Diplichnites, Diplocraterion, Monocraterion, Monomorphichnus bilinearis, Monomorphichnus lineatus, Monomorphichnus lineatus var. giganticus, Palaeophycus, Palaeophycus cf. imbricatus, Planolites, Psammichnites, Rusophycus avalonensis?, Skolithos, Treptichnus pedum, una pista similar a Nereites y otra a Zoophycos. Se describe una estructura interpretada como el fósil corporal de un organismo radial. Algunos de estos fósiles se citan por primera vez para las Areniscas del Azorejo y el Cámbrico Inferior del Macizo Ibérico.


2019 ◽  
Vol 32 (15) ◽  
pp. 11579-11596
Author(s):  
Anjan Dutta ◽  
Pau Riba ◽  
Josep Lladós ◽  
Alicia Fornés

AbstractDespite being very successful within the pattern recognition and machine learning community, graph-based methods are often unusable because of the lack of mathematical operations defined in graph domain. Graph embedding, which maps graphs to a vectorial space, has been proposed as a way to tackle these difficulties enabling the use of standard machine learning techniques. However, it is well known that graph embedding functions usually suffer from the loss of structural information. In this paper, we consider the hierarchical structure of a graph as a way to mitigate this loss of information. The hierarchical structure is constructed by topologically clustering the graph nodes and considering each cluster as a node in the upper hierarchical level. Once this hierarchical structure is constructed, we consider several configurations to define the mapping into a vector space given a classical graph embedding, in particular, we propose to make use of the stochastic graphlet embedding (SGE). Broadly speaking, SGE produces a distribution of uniformly sampled low-to-high-order graphlets as a way to embed graphs into the vector space. In what follows, the coarse-to-fine structure of a graph hierarchy and the statistics fetched by the SGE complements each other and includes important structural information with varied contexts. Altogether, these two techniques substantially cope with the usual information loss involved in graph embedding techniques, obtaining a more robust graph representation. This fact has been corroborated through a detailed experimental evaluation on various benchmark graph datasets, where we outperform the state-of-the-art methods.


2020 ◽  
Vol 133 (1-2) ◽  
pp. 91-99 ◽  
Author(s):  
Mao Luo ◽  
Luis A. Buatois ◽  
G.R. Shi ◽  
Zhong-Qiang Chen

Abstract The end-Permian mass extinction (EPME) profoundly shaped shallow marine ecosystems. Although much has been learned about this event based on the body-fossil record, the global infaunal response to the EPME, as represented by ichnofossils, is much less understood. Here we analyze secular changes in ichnodiversity and ichnodisparity from the late Permian to the Middle Triassic based on a global trace-fossil data set. Results show that, in contrast to the body-fossil record, late Permian global ichnodiversity and ichnodisparity maintained their level until the Griesbachian, followed by a sharp loss in the Dienerian. Notably, the Griesbachian shows an unusual dominance of shallower tiers. The discrepancy between the body- and trace-fossil record is interpreted to be the result of the resurgence of widespread microbial matgrounds in the Griesbachian that aided the preservation of surface, semi-infaunal, and shallow-tier ichnofossils. Our study shows that the EPME strongly affected the sediment mixed layer, allowing the preservation of shallower tier trace fossils. The disappearance of the mixed layer in the earliest Triassic may have enhanced pyrite burial in sediments and inhibited its further re-oxidation, therefore impacting sea water sulfate concentrations.


2016 ◽  
Vol 20 (1) ◽  
pp. 77-87 ◽  
Author(s):  
Iván ARRIBAS ◽  
Fernando GARCÍA ◽  
Francisco GUIJARRO ◽  
Javier OLIVER ◽  
Rima TAMOŠIŪNIENĖ

Mass appraisal, or the automatic valuation of a large number of real estate assets, has attracted the attention of many researchers, who have mainly approached this issue employing traditional econometric models such as Ordinary Least Squares (OLS). However, this method does not consider the hierarchical structure of the data and therefore assumes the unrealistic hypothesis of the independence of the individuals in the sample. This paper proposes the use of the Hierarchical Linear Model (HLM) to overcome this limitation. The HLM also gives valuable information on the percentage of the variance error caused by each level in the hierarchical model. In this study HLM was applied to a large dataset of 2,149 apartments, which included 17 variables belonging to two hierarchical levels: apartment and neighbourhood. The model obtained high goodness of fit and all the estimated variances of the parameters in HLM were lower than those calculated by OLS. It can be concluded as well that no further neighbourhood variables need be added to the model to improve the goodness of fit, since almost all the residual variance can be attributed to the first hierarchical level of the model, the apartment level.


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