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PAST: Paleontological Statistics Software Package for Education and Data Analysis
Abstract
A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheettype data entry with univariate and multivariate statistics, curve fitting, time-series analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
... Data analyses were performed by using PAST ver. 2.17 (HAMMER et al., 2012). ...
New advancements in tissue culture techniques have resulted in vitro propagation of several regenerations of horticultural crops. The somaclonal variation which occurs during plant tissue culture is a potential source for inducing new genetic variability in such crops. Several approaches have been utilized to ascertain the occurrence of somaclonal variation. The pomegranate plant can adapt to various environmental conditions and grow well in different kinds of soil and climate. Pomegranate Zagheh cultivar is mainly cultivated in the state of Esfehan, Kashan city in Iran. The present study was performed to investigate the potential occurrence of somaclonal variation in tissue culture regenerated plants of the cultivar Zagheh and provide morphological, cytological and molecular evidences for its occurrence. Nodal segments were chosen for the in vitro propagation of pomegranate. Explants were cultured on MS basal medium. We carried out both molecular (ISSR) and karyological studies in propagation collected. In the present study, we observed variation in both morphological (length of shoot, branch, internode, leaf and root and number of branch and root) and genetic features of the tissue culture regenerated plants. The regenerated plants of the third sub-culture differed from mother plants in the ISSR marker. We observed frequent occurrence of cells with different chromosome numbers, ranging from normal diploid 2n = 2x = 16 to tetraploid 2n = 32 chromosome number.
... Spearman Correlation Coefficient was used to verify correlations between the abundances observed for each species and the averages of the monthly records of the macroclimatic variables of rainfall, temperature and relative humidity. The calculations of the similarity indexes and Spearman coefficient were performed using the PAST 3.26b program (Hammer et al., 2001) . (Table 2). ...
Objective: To describe and analyze the diversity of mosquitoes in urban areas of the Federal District (DF), Brazil, the types of breeding sites, and the relationships between climatic variables and the abundance of the main vector species. Theoretical Framework: The potential distribution, endemicity, emergence, and re-emergence of pathogens transmitted by mosquitoes is regulated by fluctuations in potential vector Culicidae communities. Studies on the diversity of culicids are important to understand the ecological relationships between species and the environment they occupy. However, information on diversity patterns and the structure of the culicid fauna in the DF is still scarce and dispersed in the literature. Method: Mosquito larvae collected and identified in urban areas of the DF between January 2014 and December 2018 were evaluated for abundance, constancy, dispersal capacity, similarity of specific composition among Administrative Regions, and abundance by type of breeding site. The influence of macroclimatic factors was verified using the Spearman coefficient. Results and Discussion: The results revealed 12 species of mosquitoes, with higher abundance, constancy, and dispersion among Aedes aegypti and Culex quinquefasciatus. Precipitation and relative humidity were the abiotic factors that most influenced total abundance, with similar results recorded in other studies. Research Implications: Understanding the structure of the Culicidae fauna, and in particular, the identification of local parameters that shape these communities are important for adequate approaches to control vector species. Originality/Value: Shows the benefits that disease-vectoring mosquito species find in the Federal District.
Differences between the lines of aggressive and tame American minks that arose as a result of selection for traits of defensive behavior (16–17 generations) were revealed based on the biomechanic indices of the mandible characterizing the mechanic potentials of the canine and carnassial teeth. The results are consistent with D. K. Belyaev’s theory of destabilizing selection: along with an increase in the variability of functions and the destabilization of the historically established system of their sexual differences (sexual dimorphism), new biomechanic features of the mandible were formed in the line of tame minks. In contrast, the control line of non-selected minks unaffected by selection retained significant sex differences in biomechanic indices. Between the American minks from a Canadian natural population and the lines of aggressive and tame individuals, the differences in biomechanic indicators were less pronounced than between the lines themselves. Differences between the American mink, the European mink (Mustela lutreola L. 1758) and the Siberian weasel (M. sibirica Pallas 1773) in the biomechanic potentials of the canine and predatory teeth of the mandible which reflect specializations in the genus Neogale and the specifics of the hunting behavior of the species were found. In the invasive American mink, the mechanic potential (MP) of the canine tooth prevails, vs the MP of the carnassial tooth both in the European mink and the Siberian weasel, this trait being capable of ensuring the divergence of their trophic niches and contribute to the preservation of native species in areas of their sympatry with N. vison.
The present study was conducted to detect Pb metal content in sediment and muscle of fish (Mystus gulio Ham. – Buch.) of the of the river Hooghly, West Bengal, India. The study sites were selected at Batanagar (Bt), Budge Budge (Bg) and Birlapur (Br) sites. The samples viz. sediment and muscle of fish were collected and estimated by using atomic absorption spectrophotometer. The Pb content in sediments gradually significantly increasing trend towards downstream in the river Hooghly and winter season observed higher values in all the sites. But the content was found within the prescribed limit. The study sites observed significantly higher level of Pb accumulation in the muscle of the fish specimen (Mystus gulio) during summer compared to winter. The findings pose the risk of accumulation may be lower in fish muscle as per BSAF value. In future, this study may be beneficial to determine the water and sediment quality status in different stations of river Hooghly as well as other metals content in different fish species.
A detailed diversity analysis of the prokaryotic and fungal communities in soil impacted by an underground fire located in the Trans-Mexican volcanic belt, Mexico, is described. Microbial diversity data obtained from soils at different depths and temperatures (27 °C, 42 °C, 50 ºC and 54 ºC) were analyzed, and Firmicutes increased in abundance as the temperature augmented, and Proteobacteria mainly decreased in abundance at high temperatures compared to unaffected soils. The fungal phylum Ascomycota was the most abundant, with no significant changes. A clear impact on the richness of prokaryotic and eukaryotic operational taxonomic units (OTUs) was observed. At the genus level, bacilli were the ones that increased in abundance, while Aspergillus, Penicillium, and Mortierella were also among the most abundant at high temperatures. Interestingly, the physicochemical parameters of the affected soils modified organic matter, which was indirectly correlated with the presence of some microbial taxa. Likewise, we obtained 308 soil bacterial isolates from both control and affected soils. Among these, the taxa from the phyla Actinobacteria and Firmicutes demonstrated the highest thermotolerance in the affected soils. Our findings shed light on the impact of underground fires on the structure of microbial communities, favoring an abundance of thermotolerant microbes.
Antecedentes y Objetivos: El matorral xerófilo en México cubre 40% de su superficie y es el más vasto de todos los tipos de vegetación. En Aguascalientes, ocupa 21.52% del territorio y presenta fuerte grado de impacto debido a la influencia humana. El objetivo del estudio fue determinar la composición florística de herbáceas en dos subtipos de vegetación xerófila y conocer los años de abandono y el tipo de cultivo que se sembraba, con la finalidad de comparar frecuencia y diversidad de herbáceas en sitios con vegetación primaria y secundaria en áreas agrícolas.Métodos: Se realizaron inventarios florísticos en matorral espinoso crasicaule y pastizal con arbustos, en sitios con vegetación primaria y secundaria ubicadas en áreas agrícolas. Se determinó el número de taxones, se calculó la frecuencia de especies herbáceas, diversidad alfa (D0), índices de Shannon-Wiener (H’), Simpson (D) y Equidad de Pielou (J’). También se realizó un análisis comparativo de los índices de diversidad.Resultados clave: Se registraron 219 especies de herbáceas pertenecientes a 140 géneros y 45 familias. En los sitios con vegetación primaria, Bouteloua chondrosioides fue la especie más frecuente y en vegetación secundaria Eragrostis mexicana. El matorral espinoso crasicaule primario tuvo la mayor riqueza con 138 especies y H’=3.49, el menos diverso es el matorral espinoso crasicaule secundario con 98 y H’=2.92. El matorral espinoso crasicaule primario tiene menos especies dominantes con D=0.05 y J’=0.83 mientras que el pastizal con arbustos primario y matorral espinoso crasicaule secundario presentan más taxones dominantes con D=0.10 y J’=0.74 en ambas condiciones. Conclusiones: En la vegetación xerófila de Aguascalientes, el estrato herbáceo tiene un índice de diversidad medio; su composición, frecuencia y diversidad están directamente afectadas por el impacto agrícola. La información generada en este estudio puede ser utilizada en la restauración de las zonas áridas impactadas por la agricultura.
The Guadalupian Khuff Formation of the Huqf area (Sultanate of Oman) is composed of marine marls and bioclastic limestones which yield a rich brachiopod fauna associated with conodonts, foraminifers, ostracods, bivalves, gastropods, and cephalopods. The brachiopod fauna of the Khuff Fm. includes Perigeyerella raffaellae nov. sp., Derbyia sp. cf. D. diversaReed, 1944, Neochonetes (Sommeriella) arabicus(Hudson & Sudbury, 1959), Celebetes manarollai nov. sp., Haydenella sp., Chonetellini? gen. and sp. indet., Dyschrestia rugosa nov. sp., Kozlowskia tescorum(Hudson & Sudbury, 1959), Calliprotonia sp., Juresania omanensisHudson & Sudbury, 1959,Bilotina yanagidai nov. sp., Linoproductus sp. aff. L. kasetiGrant, 1976,Grandaurispina ghabaensis nov. sp., Magniplicatina sp., Cyclacantharia sp., Acritosia sp., Orthotichia sp. cf. O. bistriataReed, 1944,Cleiothyridina sp. cf. C. seriataGrant, 1976,Pennospiriferinoidea genus and species undetermined, Dielasma sp. A, Dielasma sp. B, Dielasma sp. C, D. sp. aff. D. minorWaagen, 1882 and Hemiptychina sp. This fauna shows strong affinities with that of the Amb Fm. (Salt Range, Pakistan) and that of the Rat Buri Limenstone of southern Thailand. Analysis of the brachiopod data of the Khuff Fm by means of the Unitary Association method (Guex 1991) leads to the construction of a local biochronological sequence of eight faunal associations. Strictly based on a bed rock-controlled sampling, this result provides a firm basis and a first step for future correlations with other Guadalupian brachiopod sequences. It also suggests that species diversity and rates of faunal turnovers are only partly controlled by the vertical succession of depositional environments, which reflects an intra-Khuff asymmetric transgressive-regressive cycle. A full evaluation of the biochronologic component of the Guadalupian brachiopod faunas still requires further tests against other similarly well-documented sequences.
Following the end-Ordovician extinction, global clade diversity of Silurian trilobites dropped to about half of Ordovician levels. Although clade diversity failed to recover, this extinc-tion had surprisingly little long-term impact on the number of trilobite species that occupied local habitats (alpha diversity). A new compilation of data from Laurentia and other continents indicates that Silurian trilobite alpha diversities in all major environments were comparable to those of the Late Cambrian and Ordovician; shallow subtidal diversity reached an all-time high during the Late Ordovician. The profound differences in patterns at local and global levels demonstrate the neces-sity for a hierarchical approach to analyses of diversity. Factors governing global clade diversity are lodged at hierarchical levels beyond those controlling local species richness and must be sought in studies of between-habitat (beta) or geographic (gamma) diversity.
Detrended correspondence analysis (DCA) is an improvement upon the reciprocal averaging (RA) ordination technique. RA has two main faults: the second axis is often an arch or horseshoe distortion of the first axis, and distances in the ordination space do not have a consistent meaning in terms of compositional change (in particular, distances at the ends of the first RA axis are compressed relative to the middle). DCA corrects these two faults. Tests with simulated and field data show DCA superior to RA and to nonmetric multidimensional sealing in giving clear, interpretable results. DCA has several advantages. (a) Its performance is the best of the ordination techniques tested, and both species and sample ordinations are produced simultaneously. (b) The axes are scaled in standard deviation units with a definite meaning, (c) As implemented in a FORTRAN program called DECORANA, computing time rises only linearly with the amount of data analyzed, and only positive entries in the data matrix are stored in memory, so very large data sets present no difficulty. However, DCA has limitations, making it best to remove extreme outliers and discontinuities prior to analysis. DCA consistently gives the most interpretable ordination results, but as always the interpretation of results remains a matter of ecological insight and is improved by field experience and by integration of supplementary environmental data for the vegetation sample sites.
Spatial statistics on the positions of trilobite tubercles indicate the existence of a developmental spacing mechanism. Similar spacing between sensory bristles, due to lateral inhibition, is well known in insects, and the genetic basis for these patterns has been thoroughly studied. Tubercles (granules) in the Middle Cambrian trilobite Paradoxides forchhammeri are spaced out, but otherwise randomly positioned. Assuming that similar genetic principles are in operation for the positioning of peripheral neuronal elements in all arthropods, it can even be speculated that genes with functions similar to Delta, Notch, achaete and scute were active in trilobite cuticular patterning. Also, in P. forchhammeri, terrace lines (ridges) seem to display transitions into granulation, indicating that these two types of structure share an underlying pattern formation mechanism.
Size and shape are analyzed for Pliocene lineages of the rodent genus Stephanomys Schaub 1938. Previous phylogenetic studies were based mainly on size variation and descriptive comparisons, without any attempt to quantify shape changes. Hence, on the basis of regular size increase, Stephanomys has been considered a prime example of phyletic gradualism. In order to quantify morphological variation within the lineage, a method for analyzing complex outlines, the elliptic Fourier transform, was applied to tooth contour (upper and lower first molars). It was then possible to compare evolution in size, estimated by tooth area, as well as evolution of shape, represented by Fourier coefficients.
While size seems to change gradually through time, morphology gives a rather discontinuous evolutionary pattern for both the upper and lower molar. Such a discrepancy between the evolution of size and shape of a single structure suggests that different genetic determinisms and mechanical constraints may act on size and shape. Hence it may be misleading to infer generalized evolutionary processes from either size or shape alone.
Seriation of an original data matrix provides the paleoecologist with a simple and powerful tool for data manipulation. The data matrix lists the presences and absences of taxa in samples. The strategy is to generate a unidimensional sequence by rearranging the taxa and samples so that the presences are blocked along the matrix diagonal. The method is illustrated with two case studies from the Middle Devonian Hamilton Group of New York. The first represents a regressive interval and the seriation sequence summarizes the changes in fauna and samples which can be explained by falling sea level. The second example embraces a much wider range of variation. Seriation mainly recovers a first-order pattern related to depth and correlated variables. This seriation does not reveal parameters such as the nature of the substrate, turbidity, habitat stability and distance offshore. These data cannot be reduced to one dimension. In all cases, seriation yields results similar to those of cluster analysis and the first axis of multivariate ordinations frequently used by ecologists and paleoecologists. Seriation, paleoecology, Devonian, Hamilton Group, multivariate analysis.