Multipoint gene mapping using seriation. I. General methods.

Initial and accurate inference of locus order and estimates of interlocus distances and interference can be obtained using seriation techniques. The analysis requires a matrix of recombination values that can be estimated by standard pairwise linkage analysis. This allows combination of results from individual investigators without reanalysis of basic pedigree material. Seriation can be performed without the use of a computer.     

Multipoint gene mapping using seriation. II. Analysis of simulated and empirical data.

Seriation methods provide an accurate and efficient means of constructing preliminary multilocus genetic maps. By using both simulated and previously published empirical data, multipoint mapping by seriation was critically evaluated. Analysis of the simulated data sets showed that the seriation methodology could accurately estimate order and interlocus distances. Application to the empirical data demonstrated that seriation could obtain results directly comparable with those of other multipoint mapping methods. Techniques such as seriation can produce preliminary genetic maps that may be used as starting points for more computer-intensive maximum-likelihood multipoint techniques.     

Environmental distribution of colony growth form in the favositid Pleurodictyum americanum

Pandolfi, John M. & Burke, Collette D. 1989 01 15: Environmental distribution of colony growth form in the favositid Pleurodictyum americanum. Lethaia , Vol. 22, pp. 69–84. Oslo. ISSN 0024–1164.
Colony growth form is of fundamental importance to understanding the ecology of both modern and ancient marine sessile colonial animals. Fourier shape analysis of the coral Pleurodictyun americantum (Tabulata: Favositida) from the Middle Devonian Hamilton Group of New York State, indicates that colony growth form is variable between environments. Discriminate function analysis of harmonics 2–6 of 51 assemblages of Pleurodictyum americanum (N = 1900) shows that this species displays an onshore to offshore gradient in colony shape. Offshore environments characterized by low levels of turbidity, oxygen, and light contain more flattened, less hemispherical growth forms, whereas onshore environments characterized by high levels of turbidity, oxygen, and light contain more hemispherical, less flattened growth forms. Harmonic shape analysis detected subtle differences among samples of P. americanum from different environments, but also showed that distinctive morphotypes are distributed within horizons. as well as between them. In fact, no one-to-one correspondence in growth form to environment is apparent; growth forms are distributed within environments, suggesting that genetic factors may have had a greater influence over coral growth form than environment. In tabulate corals, patterns of within species variability must be determined before growth form may be useful in interpreting ancient environments. □ Tabulate coral, Fourier shape analysis, morphological variability, growth form, Devonian, Hamilton Group, New York .     

Diversity dynamics of Zosterophyllopsida

The Zosterophyllopsida were major contributors to the diversification of early land plants. We present the first detailed analysis of the diversity dynamics of these plants from an updated database of all currently recognized zosterophyllopsid species. A set of quantitative methods classically used in palaeodiversity studies was applied to two data sets. The first one, ‘Zosterophyllopsida sensu stricto’, corresponds to the clade identified by Hao & Xue (The Early Devonian Posongchong Flora of Yunnan. (2013), Science Press). In the second, called ‘Zosterophyllopsida sensu lato’, barinophytalean‐type plants and taxa for which zosterophyllopsid affinities are suspected are added. The number of localities is used to explore sampling bias. Results show that sampling effect is minimal for the Early Devonian. For this time interval, both data sets record consistent patterns of changes suggesting that, whatever their affinities, all taxa included in the Zosterophyllopsida sensu lato show similar evolutionary trends. The diversity dynamics of zosterophyllopsids are characterized by a radiation during the Lochkovian, maximal values in the Pragian and a decline starting in the Emsian. The proportion of zosterophyllalean taxa with terminal sporangia is high until the Late Lochkovian when gosslingialean taxa without terminal sporangia evolved. During the Middle and Late Devonian, when diversity patterns are strongly affected by sampling, zosterophyllopsid diversity is low and characterized by a high proportion of barinophytacean and gosslingialean taxa, the latter becoming extinct in the Early Frasnian.     

A Factor Analytic Approach to Seriation

Abstract

Seriation, a unidimensional ordering technique, is one of archaeology’s oldest and most useful tools. Its mathematical aspects have drawn the attention of mathematicians and statisticians in recent years, even as archaeologists themselves have begun to question its underlying assumptions. In this paper I describe some techniques appropriate at each step in the mathematical seriation problem: discovering trendsensitive variables and ordering items on the basis of these variables.     

A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data

Background

Serial Analysis of Gene Expression (SAGE) is a DNA sequencing-based method for large-scale gene expression profiling that provides an alternative to microarray analysis. Most analyses of SAGE data aimed at identifying co-expressed genes have been accomplished using various versions of clustering approaches that often result in a number of false positives.

Principal Findings

Here we explore the use of seriation, a statistical approach for ordering sets of objects based on their similarity, for large-scale expression pattern discovery in SAGE data. For this specific task we implement a seriation heuristic we term ‘progressive construction of contigs’ that constructs local chains of related elements by sequentially rearranging margins of the correlation matrix. We apply the heuristic to the analysis of simulated and experimental SAGE data and compare our results to those obtained with a clustering algorithm developed specifically for SAGE data. We show using simulations that the performance of seriation compares favorably to that of the clustering algorithm on noisy SAGE data.

Conclusions

We explore the use of a seriation approach for visualization-based pattern discovery in SAGE data. Using both simulations and experimental data, we demonstrate that seriation is able to identify groups of co-expressed genes more accurately than a clustering algorithm developed specifically for SAGE data. Our results suggest that seriation is a useful method for the analysis of gene expression data whose applicability should be further pursued.     

Fluctuations in a late devonian-early Mississippian phytoplankton flora of Ohio,U.S.A

Fossil diversity and abundance fluctuations of Late Devonian (Famennian)—Early Mississippian (Tournaisian) phytoplankton assemblages were determined in a stratigraphic sequence of samples in Barberton test core 3, from northeast Ohio. Both diversity and abundance were relatively high during deposition of the lower Chagrin Shale (Upper Devonian) and both decreased during deposition of the upper Chagrin Shale. The overlying Cleveland Shale (Upper Devonian) is characterized by sharply increased abundance with a corresponding (although less marked) increase in diversity; in contrast, both abundance and diversity were at relatively low levels during deposition of the Lower Mississippian Bedford Shale, the uppermost unit of the sequence. These trends agree with the phytoplankton periodicity model presented by Tappan, which indicates large-scale extinction at the end of the Devonian.Many of the acritarch and prasinophycean algal taxa have restricted stratigraphic occurrences within the section studied, making them useful for local and perhaps worldwide correlation. The stratigraphically restricted taxa provide a basis for the proposal of five biostratigraphic zones within the Upper Famennian (Upper Devonian) and a portion of the Lower Mississippian. In ascending order occur: the Gorgonisphaeridium ohioense Assemblage Zone, the Acriora petala Assemblage Zone, the Muraticavea enteichia Range Zone, the Cymatiosphaera labyrinthica Range Zone, and the Navifusa drosera Assemblage Zone.     

Composition and community structure of the coralline algal reefs from Atol das Rocas, South Atlantic, Brazil

 Coralline-algal frameworks from Atol das Rocas reefs were sampled along windward and leeward transects, and multivariate statistical analysis was used to investigate the composition and community structure of the encrusting community. The following components of the reefs were identified in slabbed and polished reef blocks sampled along each transect: encrusting coralline algae dominated by Porolithon cf. pachydermum, vermetid gastropods, Homotrema rubrum, acervulinid foraminiferans, molluscs, corals, polychaete tubes, clionid sponge borings, polychaete/sipunculid borings, cemented sediments, and growth cavities. Q-mode cluster analysis correctly classified 78% of all windward samples and 69% of all leeward samples, and R-mode separated reef components adapted to high wave energy environments from those adapted to low wave energy. Separate classification and ordination of samples from each transect indicate that seriation breakdown occurs in the windward reef between 25 and 45 m from the reef front. In the leeward reef between 75 and 90 m from the leeward reef front, seriation breakdown was not found to be significant. These results confirm that seriation (zonation) is best developed in the windward reef, as has been documented in coral-dominated reefs. Accepted: 28 February 2000     

Substrate specificity in the Devonian tabulate coral Pleurodictyum

The tabulate coral Pleurodictyum americanum Roemer has been cited as an example of a host-specific organism occurring exclusively on the shells of gastropods, particularly Palaeozygopieura hamiltoniae (Hall). Examination of over 1600 specimens of P. americanum, from the Middle Devonian Hamilton Group of western New York, reveals additional complexities which require reinterpretation. While substrate selectivity for Palaeozygopieura shells is evident in all 42 subsamples, a variety of other substrates were also utilized by Pleurodictyum including corals, brachiopods, other molluscs and pebbles. Recent scleractinian corals inhabiting soft bottoms show similar substrate preference, selecting for the tubes of live serpulids, or gastropod shells (invariably with a secondary sipunculid host), but also occasionally settling on unoccupied shells or pebbles. Shell surfaces of P. hamiltoniae, preserved as external molds on the Pleurodictyum epitheca, exhibit encrustation by worm tubes and bryozoans as well as borings and mechanical shell damage, suggesting that these were not the shells of live gastropods. However, the invariant aperture-downward orientation and the high degree of selectivity of P. americanum strongly suggest that the shells were occupied by secondary hosts. □ Substrate specificity, commen-salism, tabulate coral, gastropod, sipunculid, Devonian, Hamilton Group, New York.     

Thelodont Scales from the Lower Devonian Red Bay Group, Spitsbergen

Scales of nine thelodont taxa are described from the Red Bay Group of Spitsbergen, also characterized by its assemblage of other typical Early Devonian vertebrates. The four thelodont–bearing horizons of the lower Fraenkelryggen Formation yield typical Lochkovian thelodont assemblages, containing Boreania minima , Canonia grossi , Nikolivia depressa sp. nov., Nikolivia elongata , Nikolivia gutta and Turinia pagei . One horizon from the younger Ben Nevis Formation has a similar thelodont assemblage, except for two new taxa; Apalolepis angelica sp. nov. and Turinia barentsia sp. nov. The appearance of Turinia polita and the disappearance of Boreania minima is also characteristic for this assemblage. Comparison with similar faunas from the Northern Hemisphere supports this faunal change and allows further elaboration of Early Devonian thelodont biostratigraphy.     

A test of a new technique illustrating faunal dominance trends: Application to the 'Trilobite Beds' interval of the Middle Devonian Wanakah Shale in western New York

Batt, R.J. 1995 11 30 A test of a new technique illustrating faunal dominance trends: Application to the 'Trilobite Beds' interval of the Middle Devonian Wanakah Shale in western New York. Lethaia , Vol. 28, pp. 245–258. Oslo. ISSN 0024–1164.
A new graphic technique illustrating species relative abundance trends through stratigraphic sections facilitates recognition of subtle temporal and geographic changes in environment. This technique is illustrated by application to three closely spaced sections through the 'Trilobite Beds' interval of the Wanakah Shale of western New York. Graphic representation of faunal data from bed-by-bed sampling of these sections allows recognition of water depth changes that may be related to small-scale cyclic eustatic sealevel fluctuations. Comparison of graphs for neighboring sections, aided by excellent chronostratigraphic control, allows delineation of seafloor topography. During deposition of the study interval, the seafloor was consistently shallowest at the western section and deepest at the middle site. □ Wanakah Shale, Hamilton Group, Devonian, Darien Center Submember, 'Trilobite Beds', Expanded Bandygram .     

The Dinosauria,an updated compendium that matches its subject in scale and scope

The palaeoecology of a sequence of five closely spaced mammalian assemblages in the English Late Eocene Bembridge Limestone Formation is studied using cladistic, seriation and ecological diversity methods, after assessing the collecting and taphonomic biases. Analysis of this sequence is important as it is temporally close to the terminal Eocene global cooling event. It is concluded that the assemblages probably reflect quite closely the species composition of the original living communities and that they indicate habitats ranging from an open wooded environment to dense forest. The oldest assemblage (limestone facies) indicates open wooded habitat and contains earliest occurrences of certain taxa in the English Eocene; these represent northward dispersal from southwestern Europe in response to changing climate. The more forested habitats occur higher in the sequence and are characterised by ‘Lazarus’ taxa, suggesting reversion to earlier existing environments. Small scale changes appear to relate to local events, whereas more major ones may result from global climate change. Certain pairs of closely related species are segregated in different assemblages which are habitat distinctive, a conclusion not available from their morphologies.     

Coenocorrelation: gradient analysis of fossil communities and its applications in stratigraphy

Coenocorrelation is the correlation of positions in a stratigraphic sequence with corresponding positions along a paleoenvironmental gradient through gradient analysis of fossil communities. By ordination of community samples, the distribution and abundance of taxa along a depth gradient can be translated into a continuous scale that accurately measures the gradient and thus makes possible analysis of facies change on a continuum. The procedure is tested using data on marine benthic invertebrates along ten time-parallel transects down an Ordovician basin slope (Trenton Group, New York). Reversals between transgression and regression revealed in coenocorrelation curves served nearly as well as bentonite beds in time-correlation of sections. Ordinations gave estimates of depositional strike in close agreement with estimates from physical indicators. Walther's Law of Facies is evidently a more rigorous, quantifiable generalization than it has been revealed to be through classificatory approaches to communities and environments.     

Mitochondrial phylogeny of the Chrysisignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction

The ignita species group within the genus Chrysis includes over 100 cuckoo wasp species, which all lead a parasitic lifestyle and exhibit very similar morphology. The lack of robust, diagnostic morphological characters has hindered phylogenetic reconstructions and contributed to frequent misidentification and inconsistent interpretations of species in this group. Therefore, molecular phylogenetic analysis is the most suitable approach for resolving the phylogeny and taxonomy of this group. We present a well-resolved phylogeny of the Chrysis ignita species group based on mitochondrial sequence data from 41 ingroup and six outgroup taxa. Although our emphasis was on European taxa, we included samples from most of the distribution range of the C. ignita species group to test for monophyly. We used a continuous mitochondrial DNA sequence consisting of 16S rRNA, tRNA(Val), 12S rRNA and ND4. The location of the ND4 gene at the 3' end of this continuous sequence, following 12S rRNA, represents a novel mitochondrial gene arrangement for insects. Due to difficulties in aligning rRNA genes, two different Bayesian approaches were employed to reconstruct phylogeny: (1) using a reduced data matrix including only those positions that could be aligned with confidence; or (2) using the full sequence dataset while estimating alignment and phylogeny simultaneously. In addition maximum-parsimony and maximum-likelihood analyses were performed to test the robustness of the Bayesian approaches. Although all approaches yielded trees with similar topology, considerably more nodes were resolved with analyses using the full data matrix. Phylogenetic analysis supported the monophyly of the C. ignita species group and divided its species into well-supported clades. The resultant phylogeny was only partly in accordance with published subgroupings based on morphology. Our results suggest that several taxa currently treated as subspecies or names treated as synonyms may in fact constitute separate species. Our study provides a solid basis for further systematic investigations of this enigmatic insect group.     

Modern pollen rain from the Biligirirangan-Melagiri hills of southern Eastern Ghats, India

A total of 39 soil surface samples collected between 11 degrees 30'N 76 degrees 45'E and 12 degrees 45'N 78 degrees 15'E from the mainly deciduous forests in the Biligirirangan-Melagiri hills of the southern Eastern Ghats were analysed for their pollen content. The samples are distributed among four different deciduous and evergreen vegetation types between 210 and 1700m altitudes and fall within three distinct rainfall regimes. The aims of this paper are to provide new data on the modern pollen rain from the Southern Eastern Ghats, a region characterized by a unique and complex climate and vegetation, and to interpret these data using multivariate statistics and the diagram of pollen percentages. We could distinguish first between the deciduous and the evergreen forests and then also between different types of deciduous forest. The distinction between the evergreen and deciduous forests was based on a humidity gradient and that among the deciduous forests on a physiognomic gradient identified through correspondence analysis. The above analysis also allowed us to identify a set of 14 pollen taxa markers and 11 associated pollen taxa that help differentiate the evergreen from deciduous forests. Similarly, a set of 12 pollen taxa markers and six associated pollen taxa was demarcated to help distinguish woodland formations from scrub and thicket formations, among the deciduous vegetation. We could also differentiate amongst the four distinct vegetation types sampled, on the basis of distinct associations of both tree and herb pollen taxa according to their relative abundance in the pollen diagram as well as on the proportion of total arboreal pollen. The ground cover of grasses and other herbaceous plants in the deciduous forests is effectively demonstrated by percentages of non-arboreal pollen varying between 40 and 70%. The 1000m altitude limit reflecting a gradient of humidity and the physiognomic gradient among deciduous forests seem to be important in this region.     

Effects of the number of presences on reliability and stability of MARS species distribution models: the importance of regional niche variation and ecological heterogeneity

Question: What are the effects of the number of presences on models generated with multivariate adaptive regression splines (MARS)? Do these effects vary with data quality and quantity and species ecology? Location: Spain and Ecuador. Methods: We used two data sets: (1) two trees from Spain, representing high‐occurrence number data sets with real absences and unbalanced prevalence; (2) two herbs from Ecuador, representing low‐occurrence number data sets without real absences and balanced prevalence. For model quality, we used two different measures: reliability and stability. For each sample size, different replicates were generated at random and then used to generate a consensus model. Results: Model reliability and stability decrease with sample size. Optimal minimum sample size varies depending on many factors, many of which are unknown. Regional niche variation and ecological heterogeneity are critical. Conclusions: (1) Model predictive power improves greatly with more than 18‐20 presences. (2) Model reliability depends on data quantity and quality as well as species ecological characteristics. (3) Depending on the number of presences in the data set, investigators must carefully distinguish between models that should be treated with skepticism and those whose predictions can be applied with reasonable confidence. (4) For species combining few initial presences and wide environmental range variation, it is advisable to generate several replicate models that partition the initial data and generate a consensus model. (5) Models of species with a narrow environmental range variation can be highly stable and reliable, even when generated with few presences.     

Application of two-part statistics for comparison of sequence variant counts

Investigation of microbial communities, particularly human associated communities, is significantly enhanced by the vast amounts of sequence data produced by high throughput sequencing technologies. However, these data create high-dimensional complex data sets that consist of a large proportion of zeros, non-negative skewed counts, and frequently, limited number of samples. These features distinguish sequence data from other forms of high-dimensional data, and are not adequately addressed by statistical approaches in common use. Ultimately, medical studies may identify targeted interventions or treatments, but lack of analytic tools for feature selection and identification of taxa responsible for differences between groups, is hindering advancement. The objective of this paper is to examine the application of a two-part statistic to identify taxa that differ between two groups. The advantages of the two-part statistic over common statistical tests applied to sequence count datasets are discussed. Results from the t-test, the Wilcoxon test, and the two-part test are compared using sequence counts from microbial ecology studies in cystic fibrosis and from cenote samples. We show superior performance of the two-part statistic for analysis of sequence data. The improved performance in microbial ecology studies was independent of study type and sequence technology used.