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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.
... Sets of 13 predictor variables were generated from PCA and all PCA factor scores were used as input variables for DFA to determine the classification success of our samples. PCA and DFA were performed using the statistical software PAST 4.11 (Hammer et al., 2001). ...
The Western and Eastern Ghats of the Peninsular India are known for their high biological diversity, which is shaped due to various geological barriers and environmental parameters. Scorpion diversity in Peninsular India remains poorly known thereby warranting a need to undertake rigorous arachnological surveys. In our continued effort to discover scorpion lineages hitherto unknown to science, we describe five new species of the genus Isometrus Ehrenberg, 1828 which were obtained from southern India, and discuss morphological, molecular and ecological discordance within this genus. The validity of Reddyanus atherii Amir and Kamaluddin, 2008, Isometrus liaqatii Amir and Kamaluddin, 2008 and Isometrus formosus Pocock, 1894 is also commented upon, with implications to propose taxonomic changes within the genus.
... Statistical tests were performed using nonparametric or parametric tests, chosen based on the data dis- Analysis (PAST), version 4.09 (Hammer et al., 2001), was used to conduct the statistical analyses. Graphs were generated using Microsoft ® Excel Version 16.52. ...
Phthalates are a group of chemicals used as plasticisers, and are easily released into the environment , where they degrade over time. We investigated the concentrations of phthalates in sediments, seawater, and the cockle Anadara antiquata from beaches at Dar es Salaam, Mtwara, Tanga and Zanzibar in Tanzania. A dispersive liquid-liquid microextraction method was used to extract analytes from samples, whereafter they were analysed with a gas chromatograph coupled to a mass spectrophotometer. Concentrations of diisobutyl phthalate (DiBP), dibutyl phthalate (DBP) and Bis(2-ethylhexyl) phthalate (DEHP) were determined. DiBP concentrations were highest at Dar es Salaam (11.5-12.4 ng/mL in seawater; 11.5-13.6 ng/g dry weight in sediments), compared to the other three sites, where minimum and maximum concentrations in sediments were 3.5 ng/g dw (Mtwara) and 10.7 ng/g dw (Tanga). DBP concentrations were also highest at Dar es Salaam (12.4-20.6 ng/mL in seawater; 12.1-18.7 ng/g dw in sediments) compared to 2.7 (minimum, Mtwara) and 11.2 ng/g dw (maximum, Tanga). DEHP at Dar es Salaam ranged from un-detected to 12.6 ng/mL in seawater and to 12.6 ng/g dw in sediments. It was further revealed that A. antiquata from Kawe Beach (Dar es Salaam) had higher concentrations of DiBP, DBP, and DEHP compared to other sites. Monitoring of phthalate concentrations will indicate pollution hotspots and trends in the region.
... Since multiple t-tests were completed, we corrected for family-wise error rates using sequential Bonferroni correction. Statistical analysis was performed in PAST 4.03 (Hammer et al., 2001). ...
KEYWORDS Thalassoma lunare is one of the most popular species of the family Laridae, and it has several attractive colour patterns in addition to a longer life span in the aquarium. In some species of Labridae, there is a colour pattern that enables discrimination between sexes and that colour variation, is missing in T. lunare. Therefore, it is challenging to distinguish sexes through colour patterns or external markings. The study aims to clarify the morphometric differences between the sexes of moon wrasses and detect the most valuable characters which assist in discriminating between males and females. All transformed relative percentages of morphometric values concerning standard length, head length, and body depth were subjected to non-metric multidimensional scaling (NMDS) for examining the parameters that help discrimination between sexes. The sex determination of the moon wrasse Thalassoma lunare was confirmed after a histological examination of gonads, and the samples were sorted into primary males, secondary males, and females. In multivariate morphometric space, primary males and females formed different clusters. Comparison of size-corrected morphometric characters between sexes suggested that two characters, longer caudal fin, and pelvic fin in males, were significant even after adjusting for family-wise error rate and indicated some degree of sexual dimorphism in primary males and females. Such differences represent an important criterion for selecting large male individuals for sexual selection in mating. Both primary and secondary males are found, indicating that this is a diandric species, and there is a remarkable variation in the histological structure between the two types of male testes; the study confirmed the sex reverse of female to secondary male.
... The spectrograms were created in Syrinx 2.5s (software developed by John M. Burt; University of Washington, Department of Psychology, Seattle, WA 98195, USA) with settings FFT = 512 and Blackman window. We used the software packages STATISTICA V. 8.0 (StatSoft, Inc.USA) and PAST V. 2.13 (Hammer et al. 2001) for statistical data processing. For each population, we calculated the variety of song types and the number of males performing them (in percentage of the total number of males studied in this population). ...
We analyze the variability of the Chaffinch’s (Fringilla coelebs) song and rain calls in 20 populations localized along a transect of about 3,000 km, crossing the territory of European Russia between the White Sea, Crimean Peninsula and the Caucasus Mountains. Three subspecies of Chaffinch inhabit this area: European (F. c. coelebs) , Caucasian (F. c. caucasicus) , and Crimean (F. c. solomkoi) . The results of cluster analysis based on song show that the populations of Crimea and southeastern Dagestan stand out the most. All other populations fall clearly into two clusters corresponding to the European and Caucasian subspecies. In most of the European subspecies vast range in Russia, the “buzzing” dialect of the rain call is widespread. Only in the extreme northwest of Russia, it is replaced by a whistling dialect. In most of the Caucasus and in the Ciscaucasia, Chaffinches also emit exclusively whistling sounds, but of a completely different structure. In the Western Caucasus, Chaffinches perform also a whistling call having a unique two-syllable structure. The Crimean peninsula is inhabited by whistling Chaffinches as well, although the frequency modulation of its call is different from that of Caucasian subspecies. We discuss the spatial distribution of song types and of rain calls dialects within the ranges of subspecies and in the contact zones between them.
... A hierarchical cluster analysis (with Euclidean distance) was used to detect similarities between the productivity of the studied species in consecutive years. All data analyses were conducted using the Past program version 4.03 (Hammer et al. 2001). ...
This study aimed to monitor the demographic changes of some closely related species based on bird ringing data from the CES (Constant Effort Sites) program in Hungary between 2007 and 2018, and to explore the reasons for these demographic changes. The CES program tracks breeding bird populations with standard methods. The studied species breeding in Hungary were from genera Sylvia , Curruca, and Phylloscopus . Among these species, the trends of some forest birds, like Eurasian Blackcap (Sylvia atricapilla) , Lesser Whitethroat (Curruca curruca) , Common Chiffchaff (Phylloscopus collybita) and Willow Warbler ( Ph. trochilus) showed no substantial changes, and one of the open-habitat species, the Barred Warbler (Curruca nisoria) – a long distant migrant – showed decreasing trends. The Garden Warbler (Sylvia borin) – a trans-Saharan migrant but forest dweller – also experienced population declines. Short-distance migrants maintained stable populations. Common Whitethroat productivity displayed an increasing trend to compensate for population decline. Upon examining the Eurasian Blackcap, this study detected a strong relationship between the number of adult birds, productivity, and the number of adults captured the following year.
... For this reason, the number of adult birds caught in a given year was divided by two, and the number of juvenile birds caught in that year was then divided by this value. For statistical analyses, the program Past 3.14 was used (Hammer et al. 2001). ...
In recent years, the breeding populations of many migratory songbird species have declined in the Carpathian Basin. However, there may be significant differences between different geographical regions, as most species have a much higher chance of successful breeding in protected areas. This is also the case for the Moustached Warbler, one of the most habitat-specialist passerine. It colonises only perennial, unharvested reedbeds, therefore its conservation management is essential. We studied the population changes of this species between 2001 and 2022 at Lake Kolon in Izsák, based on bird ringing data from 10–24 July. Data of 12,817 ringed and 5,075 recaptured birds were used in the analyses. The annual capture rate decreased significantly during the study period. The proportion of juveniles was higher at higher water levels during the whole breeding season. In contrast, when looking at winter and first and second broods separately, water level had no effect on the juvenile/adult ratio. This is because the birds compensate for unsuccessful first broods by increasing the proportion of second and replacement broods. If the first broods are successful, the ratio of second and replacement broods will be lower. As reed management is practically non-existent in this area, the perennial reedbeds provide suitable nesting conditions for the species. Changes in the wintering sites may be responsible for the declining trend. Protection of the area is of particular importance for the conservation of the species.
In the highlands of Costa Rica, poorly studied ecological formations such as the paramo and peatbogs are present. Peatbogs in Costa Rica are located in the Tapantí- Macizo de la Muerte National Park in the Cordillera de Talamanca. The aim of our study was to characterize the soil of high peatbogs with the purpose of providing scientific information of these ecosystems as framework for future research. Vegetation description and soil samples were collected from four peatbogs (T1, T2, T3 and T4) at different depths (20, 30 and 60 cm) in an altitudinal gradient ranging from 2400 to 3100 m. Physical and chemical analyses of the soil were carried out in the laboratory of the CIA-UCR, and the vegetation of the peatbogs was described. The soils in the peatlands correspond to the histosol order with a sandy loam texture, which predominate in cold and swampy areas. The percentage of carbon and organic matter was high in T3, with 32.90 and 47.05%, respectively, while the C/N ratio was higher in T1, with a ratio of 22.3%. The sites with the highest similarity were T2 and T4 by 99%. The vegetation characterization was represented by vascular plants, bryophytes, especially of the genus Sphagnum, and lichens that contribute to the formation of the peaty soil. Peatlands are efficient in accumulating carbon in the soil due to the accumulated organic matter. The lack of previous studies prevented us from comparing the results obtained here. As this is an unprecedented study, our research is a valuable scientific contribution that can be used to consolidate the conservation of the small extension of high peatbogs in the country.
Extended Abstract
Introduction and Objective: Obtaining information and identifying the changes and dynamics of forest ecosystems in different developmental stages is necessary for optimal management, restoration and improvement of forests. The aim of This research was to investigate the effect of different development stages of the stand on tree regeneration and understory species in the mixed hornbeam stand in spring and summer (due to the beginning of vegetative activities until the optimal vegetative stage of herbaceous plants) in the forestry plan of Gorgan Shasat-Kalate district two was done.
Material and Methods: In order to investigate development stages, after forest surveying, three rectangular half-hectare sample plots with dimensions of 50 x 100 meter for each development stage based on the characteristics provided by Leibundgut and Korpel in the field of the structure pattern of development stages and phases in natural forests were used. In order to study and investigate the vegetation cover, five small sample plots (20x20 meters), one of them in the center and four other in the four corners. In each sample plot, the percentage of herbaceous species cover and the tree regeneration frequency were recorded. To investigate and compare diversity in different development stages, use the diversity indices of Simpson and Shannon-Wiener, and to calculate the richness, use the richness indices of Margalf and Manhinik, and for evenness, use the evenness indices of Smith-Wilson and Evenness in PAST and R software (package Adiv software and specieseve function( were used.
Results: The results showed that the number of plant species in the degradation stage is more than the initial and optimal stages. Diversity indices of understory species and tree regeneration species showed that the diversity of Shannon and Simpson in the two seasons of spring and summer in the optimal stage was lower than the initial and degradation stages. Also, Smith-Wilson and Evenness indices had the highest values in both spring and summer in the optimal stage. The highest value of the Menhinic richness index of understory species was determined in the optimal stage in the spring season, while no significant difference was observed between the different stages in the summer season. The highest value of Margalef richness index of tree species regeneration in both seasons was also observed in the degradation stage.
Conclusion: Based on the results of the present research, it can be stated that different development stages have an effect on the diversity of herbaceous species and forest regeneration. Therefore, there are significant implications of sustainable management on the vegetation layer, which should be considered in future of forest management strategies.
Keywords: Developmental stages, Diversity, Evenness, Forest regeneration, Richness
We investigated the distribution patterns of galling insects in veredas with varying degrees of drying in the Brazilian Cerrado. We tested if the insect gall diversity is higher in degraded veredas (dry veredas ) compared to preserved (wet veredas ) ones, as predicted by the hygrothermal stress hypothesis. Additionally, we also tested whether the composition of galling insects varied along the veredas and if species richness and abundance of galling insects are higher in the upstream zone of the veredas . In total, we recorded 99 species of galling insects, distributed across 54 plant species and 24 botanical families. We found that galling species richness was high in degraded veredas compared to preserved ones, while the abundance of galling insects was higher in preserved veredas than in degraded ones. When examining the different zones along the veredas , we observed variations in the richness and abundance of galling insects in preserved veredas . Specifically, the galling insect richness was higher in the upstream and middle zones compared to the downstream zone, while the abundance of galling insects was higher in the middle zone compared to the upstream zone. However, in the degraded veredas , there were no significant differences in galling species richness and abundance among the zones studied. The composition of galling insect species differed significantly between degraded and preserved veredas , with a higher faunal similarity observed in preserved veredas for both the downstream and upstream zones compared to degraded vereda s (upstream zone). Our results indicate a preference of galling insects for more hygrothermally stressed environments, such as dry veredas and upstream zones of wet veredas.
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.
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.
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.