Tree models for difference and change detection in a complex environment

A new family of tree models is proposed, which we call "differential trees." A differential tree model is constructed from multiple data sets and aims to detect distributional differences between them. The new methodology differs from the existing difference and change detection techniques in its nonparametric nature, model construction from multiple data sets, and applicability to high-dimensional data. Through a detailed study of an arson case in New Zealand, where an individual is known to have been laying vegetation fires within a certain time period, we illustrate how these models can help detect changes in the frequencies of event occurrences and uncover unusual clusters of events in a complex environment.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS548 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A demographic study of Crosthwaite parish: some genetic implications

This thesis studies the demographic history of Crosthwaite Parish, Cumberland (Cumbria) during the period 1560-1800, and attempts to assess the factors affecting population change in the region over that period. It uses the demographic material to assess the influence of some of the population changes on the genetic structure of the population. The study starts with a general introduction to the geography and population history of the region. The second chapter describes the methods used to record and cross-reference the Anglican parish registers which were the main source of material for this research. This is followed by an outline of the types of analysis used to obtain demographic information, and by a description of some attempts to assess pre-census population sizes in England and Wales. The main section of the work involves the use of 'cohorts' to study changes in the size of the breeding population, family size, age at marriage, migration rates and the sex ratio of migrants. Indices of genetic isolation are calculated to indicate the likelihood of genetic drift occurring at any point during the period studied. A study of isonymy is used to calculate inbreeding coefficients. The conclusion discusses the results obtained, and assesses the limitations and potential of historical population studies

Growth, age and size of the Jurassic pachycormid Leedsichthys problematicus (Osteichthyes: Actinopterygii)

The Jurassic pachycormid osteichthyan Leedsichthys problematicus is renowned for having been able to achieve prodigious size for a bony fish. Building on work of MARTILL (1986a), a thorough examination of all known material was conducted in order to constrain estimates of the size of this animal and examine its rate of growth. Important specimens of Leedsichthys are described for the first time. The histology of Leedsichthys is reviewed, and the presence of growth annuli is used to establish ages for five specimens. Age and growth data were obtained from gill rakers (n = 4) and lepidotrichia (n = 2). Lepidotrichia show upward curvilinear growth profiles and ages ranging from 21 to 40 annuli, which are assumed to represent years. Both growth profiles start at a small size (0.26 and 0.33 mm radial distance), which is assumed to represent age 1. However, annuli can be lost near the margins of the elements. Gill rakers exhibit a sigmoidal growth profile. Age of gill rakers was estimated by adjusting the alignment of the inflection points of the growth profiles thereby giving adjusted ages. Gill rakers ranged in age from 19–38 annuli, but all show evidence of reabsorption of annuli near the focal points and at the margins of most elements. Sizes for the five individuals range from 8.0-16.5 m for ages of 19-40 years. Growth rate (0.01-0.05 K) was relatively slow as expected for a large, long-lived fish. At age 1, individuals were 1.6 m in length. Estimates for the length of L. problematicus compare well with published lengths of other large suspension feeders such as those for basking and whale sharks

Geosphere and biosphere dynamics during late Ordovician climate change

The late Ordovician was a period of major climatic and biological change, much of which is poorly understood. Global cooling began in the Caradoc (early Katian) with the build-up of ice in southern polar regions of the palaeocontinent of Gondwana. Cooling continued into the Ashgill (late Katian) but may have been interrupted by a brief period of global warming, the Boda Event, in the Cautleyan-Rawtheyan immediately prior to the Hirnantian glacial maximum. The proceeding Hirnantian Stage of the Upper Ordovician was a period of abrupt global change in the biosphere, climate and ocean geochemistry. These events are marked by: (1) an abrupt positive Hirnantian isotopie carbon excursion (HICE); (2) one of the three global Phanerozoic mass extinctions and (3) an extensive drop in sealevel associated with the maximum extent of the Gondwanan ice sheet. Biostratigraphic correlation for the Late Ordovician between basin and shelf sections in the Welsh Basin is limited. The current study describes three new chitinozoan taxa, Spinachitina penbryniensis, Belonechitina reticulatus and Belonechitina ceredigionensis and developed a chitinozan biostratigraphic scheme for the Welsh Basin. Four of the six Avalonian Ashgill chitinozoan biozones are recognized: the bergstroemi fossensis, umbilicata and taugourdeaui Biozones. The Baltoscandian and Laurentian index taxon Hercochitina gamachiana is recorded for the first time in Avalonia and a new lower Hirnantian regional biozone, the new Belonechitina reticulatus n. sp. Biozone is erected. The Cautleyan-Rawtheyan (late Katian) rugata Biozone was not recorded. Four depth-facies biotopes for chitinozoa from the upper Katian-Hirnantian (Upper Ordovician) of Avalonia have been identified herein. These are: 1) an open ocean shallow-water epipelagic biotope which includes Cyathochitina campanulaeformis; 2) an open ocean middle-depth mesopelagic biotope comprising Hercochitina and Spinachitina; 3) an open ocean deep-water meso-bathypelagic biotope characterized by Bursachitina umbilicata and 4) a shelf biotope containing predominantly Desmochitina. The taxonomic composition of the open ocean middle- depth mesopelagic biotope changes from one dominated by Hercochitina and Spinachitina in the Upper Katian to one comprising Ancyrochitina in the Hirnantian post-glacial transgression. The distribution of the deep-water meso- bathypelagic biotope and the shelf biotope is affected by basin hydrography and sea level respectively. Changing hydrography induced by climate belt reconfiguration along the southern margin of lapetus in the Rawthean (late Katian), displaced deep-water taxa into the semi-restricted Welsh Basin. With sea level fall in the early Hirnantian, taxa from the shelf biotope expanded into the shallower basin. Origination of biostratigraphically useful taxa in such segregated environments, e.g. Bursachitina umbilicata, restricts their distribution to periods of climatic and environmental change. Gradual change in climate and, hence, distribution of important biozone taxa, leads to diachroneity of chitinozoan bio-zones. During the Katian and Hirnantian, the Welsh Basin, UK, lay on the northern margin of the palaeocontinent of Avalonia at mid-latitudes (estimated between 32-45 s), within the boundaries of the present-day position of the STHP. It therefore provides a suitable environment to test for sensitivity of palaeo-climate belt movement in a mid-palaeolatitude setting (Armstrong et al, in revision).When the Inter-Tropical Convergence Zone (ITCZ) and Sub-Tropical high pressure belt (STHP) were in a southerly position, mid-palaeolatitudes, which includes the Welsh Basin, were positioned beneath south-easterly trade winds. This climate belt configuration is recorded in the Welsh Basin by the deposition of organic-rich laminated hemipelagites deposited during wind-driven coastal up-welling. Coastal upwelling, increased productivity and organic carbon burial are recorded by increased Ba/Th, increased TOC wt% and negative δ(^13)C. Negative δ (^13)C excursions are interpreted to represent remobilization of (^12)C֊enriched waters during upwelling from the deep-ocean. The onset of the expression of climate belt movement during Boda Event times is later in the Welsh Basin than at low-palaeolatitudes. At low-palaeolatitudes the δ(^18)Ο response to shifting ITCZ occurred in the Cautleyan whilst in the Welsh Basin the isotopic and lithological response to moving STHP began in the Rawtheyan. This delay in expression of events is accounted for by ice-sheet- moderated rectification of insolation in the run-up to the glacial maximum. The onset of the Hirnantian glacial maximum is orbitally-moderated and is interpreted to represent an orbital configuration when eccentricity wag high, obliquity low and aphelion occurred during Austral summer. It represents a threshold at which the Gondwanan ice-sheet was able to survive precession and obliquity-induced ablation. Once this threshold had been reached, global climate belt position stabilized in a position where the ITCZ lay north of the equator and the STHP lay north of Avalonia. Four positive δ (^13)Corp excursions in Hirnantian-age rocks from the Welsh Basin have been recognized in this study and are considered to represent the HICE. They correlate well between basin and shelf environments and also with a proposed sequence stratigraphic model for the Hirnantian in the Welsh Basin. Two excursions of up to 3 %(_00) occur in the lower Hirnantian reticulatus chitinozoan Bio- zone and two excursions of 1 %(_00) are present in the late Hirnantian taugourdeaui Biozone. Higher carbon storage in the basin, coincident with positive δ (^13)Corp excursions during glacial periods, indicate a shift in the locus of carbon burial from the shelf to the basin during low sealevel. The topology of the regional Hirnantian isotope curve for the Welsh Basin compares with only a few curves from other parts of the world indicating strong regional carbon cycling. Comparison of the relative timing of the onset of HICE and peak HICE values from other palaeocontinents demonstrate little, if any, consistency with palaeolatitude or basin setting. It is demonstrated that this chemostratigraphic diachroneity of HICE can be attributed to the process of signal rectification of δ (^13)Corp records most likely due to numerous local carbon cycling processes

The first definitive Middle Jurassic atoposaurid (Crocodylomorpha, Neosuchia), and a discussion on the genus Theriosuchus

Atoposaurids were a clade of semiaquatic crocodyliforms known from the Late Jurassic to the latest Cretaceous. Tentative remains from Europe, Morocco, and Madagascar may extend their range into the Middle Jurassic. Here we report the first unambiguous Middle Jurassic (late Bajocian–Bathonian) atoposaurid: an anterior dentary from the Isle of Skye, Scotland, UK. A comprehensive review of atoposaurid specimens demonstrates that this dentary can be referred to Theriosuchus based on several derived characters, and differs from the five previously recognized species within this genus. Despite several diagnostic features, we conservatively refer it to Theriosuchus sp., pending the discovery of more complete material. As the oldest known definitively diagnostic atoposaurid, this discovery indicates that the oldest members of this group were small-bodied, had heterodont dentition, and were most likely widespread components of European faunas. Our review of mandibular and dental features in atoposaurids not only allows us to present a revised diagnosis of Theriosuchus, but also reveals a great amount of variability within this genus, and indicates that there are currently five valid species that can be differentiated by unique combinations of dental characteristics. This variability can be included in future broad-scale cladistics analyses of atoposaurids and closely related crocodyliforms, which promise to help untangle the complicated taxonomy and evolutionary history of Atoposauridae

Revealing the Archetype: The Journey of a Trecento Madonna and Child at the National Museum of Scotland

The National Museums Scotland Madonna and Child project sought to uncover and document the history of a fine polychrome wood carving attributed to The Master of the Gualino St Catherine and to prepare it for display. A new body of knowledge has been assembled by the interdisciplinary team. The conservation treatment was informed by this work and led to further discoveries: the removal of overpaint exposing a previously hidden underdrawing. The ethics of the treatment decisions, including the removal of the Christ Child’s 1960s’ fingers required team dialogue and was opened up for the public to respond to in a series of blogs. The discovery of a rich polychromy including gold and glazed tin has led to further plans to produce a 3-D colour reconstruction. The collaborations developed during this project will facilitate future joint ventures for polychrome sculpture in Scottish collections

The cranial endocast of the Upper Devonian dipnoan Chirodipterus australis

One of the first endocasts of a dipnoan (lungfish) to be realised was that of the Upper Devonian taxon Chirodipterus australis. This early interpretation was based on observations of the shape of the cranial cavity alone and was not based on a natural cast or 'steinkern' nor from serial sectioning. The validity of this reconstruction is therefore questionable and continued reference to and use of this interpretation in analyses of sarcopterygian cranial evolution runs the risk of propagation of error. Here we describe a new detailed anatomical description of the endocast of Chirodipterus australis and show that it exhibits a suite of characters more typical of Lower and Middle Devonian dipnoan taxa. Notably, the small utricular recess is unexpected for a taxon of this age, whereas the ventral expansion of the telencephalon is more typical of more derived taxa. The presence of such 'primitive' characters in C. australis supports its relatively basal position as demonstrated in the most recent phylogenies of Devonian Dipnoi.</jats:p

Chitinozoan biozonation in the upper Katian and Hirnantian of the Welsh Basin, UK

AbstractHere we present a chitinozoan biostratigraphical framework for the South Wales upper Katian and Hirnantian (Ashgill) succession. The current study indicates that three of the six Avalonian Ashgill chitinozoan biozones are recognised in the Welsh Basin; the bergstroemi, fossensis and umbilicata biozones. The Baltoscandian and Laurentian Hercochitina gamachiana biozone is suggested by the presence of Belonechitina cf. gamachiana and the Spinachitina taugourdeaui biozone is suggested by Spinachitina cf. taugourdeaui. Intervening between these is a newly erected lower Hirnantian regional biozone, the Belonechitina llangrannogensis n. sp. biozone. The late Katian (Cautleyan–Rawtheyan) Conochitina rugata biozone was not recognised, though the index taxon is recorded. The presence of B. cf. gamachiana below the lithological expression of the Hirnantian glacial maximum and alongside Rawtheyan graptolite and trilobite assemblages shows that the local base of the B. cf. gamachiana biozone lies beneath the Katian–Hirnantian boundary. Although at present in open nomenclature, the finds of B. cf. gamachiana and S. cf. taugourdeaui, from sites where these chitinozoans co-occur with graptolites, are potentially important; the area offers the potential to study how B. cf. gamachiana and S. cf. taugourdeaui are taxonomically and stratigraphically linked to the original index species. A composite Katian–Hirnantian chitinozoan biozonation for the Welsh Basin is presented and three new species are defined: Belonechitina llangrannogensis n. sp., Belonechitina ceregidionensis n. sp. and Spinachitina penbryniensis n. sp

A Lungfish survivor of the end-Devonian extinction and an Early Carboniferous dipnoan radiation.

Until recently the immediate aftermath of the Hangenberg event of the Famennian Stage (Upper Devonian) was considered to have decimated sarcopterygian groups, including lungfish, with only two taxa, Occludus romeri and Sagenodus spp., being unequivocally recorded from rocks of Tournaisian age (Mississippian, Early Carboniferous). Recent discoveries of numerous morphologically diverse lungfish tooth plates from southern Scotland and northern England indicate that at least ten dipnoan taxa existed during the earliest Carboniferous. Of these taxa, only two, Xylognathus and Ballgadus, preserve cranial and post-cranial skeletal elements and are yet to be described. Here we present a description of the skull of a new genus and species of lungfish, Limanichthys fraseri gen. et sp. nov. that hails from the very lowest Tournaisian from the Ballagan Formation of Burnmouth, southern Scotland. The new specimen represents the earliest definitive Tournaisian lungfish skull material thus providing valuable insight into the response of this group, and indeed, the Sarcopterygii as a whole, immediately following the Upper Devonian Hangenberg event. Phylogenetic analysis places Limanichthys fraseri within the Devonian ‘phaneropleurid-fleurantiid’ grade of lungfish and that the Carboniferous lungfish represent forms that have their origins deep in the Mid and Late Devonian as well as those from a unique Carboniferous radiation.This work was carried out with the aid of NERC consortium grants NE/J022713/1 (Cambridge), NE/J020729/1 (Leicester) and NE/J021091/1 (Southampton)