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ADAPTS (Analysis of Diversity, Asymmetry of Phylogenetic Trees, and Survivorship): A new software tool fo ranalysing stratigraphic range data

Alistair J. McGowan and Paul N. Pearson

Plain Language Abstract

The character of palaeotology has changed considerably in the past 25 years. Much more emphasis is now placed on investigating patterns in the fossil record using numerical and statistical techniques to consider such topics as rates of evolution in the fossil record. Description of fossils is still an important part of palaeontology, but has not been subject to such radical changes. The advent of the microcomputer has greatly expanded the ability of palaeontologists to handle large amounts of data and ask very different questions from the qualitative (non-numerical) ones that dominated palaeontology before.

This paper presents a computer program called ADAPTS (Analysis of Diversity, Asymmetry of Phylogenetic Trees, and Survivorship) that was developed to analyse stratigraphic range data, which is the raw material that palaeontologists use to ask questions about rates of evolution in the fossil record. The stratigraphic range of a group (taxon) is the time from when it first appears in the fossil record (the oldest occurrence) until the last time it appears (the youngest occurrence). A rate is simply the amount of change in a given period of time. So, if you look at how the number of groups (taxa) alive every million years changes over fifty million years, you are considering changes in the diversity. Similarly rates of origination and extinction can be studied with the same sort of approach.

Survivorship is a way of looking at how long taxa live for in the fossil record. To do this a life table is required. To construct a life table you must first decide on the age class size that you will use. An age class is just a length of time, say 0-5 years old in humans. You would then see how many people fell into that particular class, and all the other classes from 0-5 upwards. Then you would see how many people died in each age class and this allows you to get some idea of the probability of an individual dying, or living to a certain age.

For fossil taxa the same sort of thing can be done, only across entire species and millions of years. The shape of the curve that appears when a life table is made into a graph can also distinguish whether taxa in a group are more or less likely to become extinct as they get older.

If a phylogenetic tree is available for the group, then aspects of that tree can also be analysed. A phylogenetic tree is a bit like a family tree, but instead of human relatives in a family the branches are taxa, such as genera of dinosaurs. It has been proposed that differential rates of extinction and origination in the fossil record will be recorded as asymmetry in the shape of the tree. One part of the tree will have many more branches than the other, generating a "lop-sided" tree. ADAPTS has a test which examines whether such unbalanced patterns are the results of unbalanced numbers of originations and/or extinctions and whether there are biases for parent or offspring taxa to preferentially go extinct first or give rise to new species. If evolution was "random" in this respect then a 50:50 split would be expected and the tree would be balanced.

By bringing all of these methods together in one package that interfaces with spreadsheets, this program should be of use to palaeontologists in general, many of whom are interested in rates of evolution. By automating these routines hopefully a lot of time consuming, and frankly boring, calculations can be done easily with this software tool. It also means that it is possible to carry out calculations across different intervals of time, say looking at rates for every two million years, rather than every one million, which can be used to check if the patterns are robust or just caused by timescale effects. The fact that several less used methods are available in the package may also serve to encourage workers to use tests that they have not applied before, due to the lengthy calculations involved, which could lead to the discovery of new patterns in the fossil record.

Resumen en Español

ADAPTS (Análisis de la diversidad, asimetría de árboles filogenéticos y supervivencia): un nuevo programa informático para el análisis de datos sobre extensiones estratigráficas

Se ha desarrollado un programa informático, ADAPTS (análisis de la diversidad, asimetría de árboles filogenéticos y supervivencia) con el fin de realizar el análisis automático de datos sobre distribuciones estratigráficas. ADAPTS realiza medidas de las tasas de evolución taxonómica, analiza la supervivencia y examina si hay sesgos en las tasas de especiación y extinción de ancestrales y descendientes, sesgos que deben quedar registrados en los árboles filogenéticos en forma de ramificación asimétrica. ADAPTS requiere sólo cinco datos sobre cada uno de los taxones de un grupo: un número de identificación (I.D.), edad de la primera aparición (FAD), edad de la última aparición (LAD), extensión estratigráfica y número de identificación del antecesor. El fichero de datos se puede introducir bajo el formato de cualquier hoja de cálculo estándar y los resultados son suministrados también con formato de hoja de cálculo. Para someter a prueba el funcionamiento de ADAPTS se analizó una filogenia aleatoria generada con el programa TREE GROWTH. La señal aleatoria, conocida de antemano, fue reconocida y, además, se puso de manifiesto que ADAPTS puede procesar rápidamente grandes conjuntos de datos.

PALABRAS CLAVE: extensiones estratigráficas, supervivencia, tasas evolutivas

Traducción: Prof. José Mª González-Donoso; Depto. de Ecología y Geología, Facultad de Ciencias; Universidad de Málaga; Campus de Teatinos s/n; E-29071 Málaga

Résumé en Français

ADAPTS (ANALYSE DE LA DIVERSITÉ, L’ASSYMÉTRIE DES ARBRES PHYLOGÉNÉTIQUES, ET LA SURVIVANCE): UN NOUVEAU LOGICIEL POUR L’ANALYSE DES DONNÉES RELATIFS À LA PORTÉE STRATIGRAPHIQUE

Afin d’automatiser l’analyse des données relatives à la portée stratigraphique, un nouveau logiciel fut développé: ADAPTS (analyse de la diversité, l’assymétrie des arbres phylogénétiques, et la survivance). ADAPTS exécute trois sortes d’analyses: des métriques taxonomiques relatives au taux de l’évolution, des analyses de survivance, et des tests pour des biais dans les taux de spéciation et d’extinction entre les ancêtres et les descendants, ce qui devrait prendre la forme de branchages assymétriques dans l’arbre phylogénétique. Pour ces tests, ADAPTS n’a besoin que cinqs informations au sujet de chaque taxon: un numéro d’identification (ID), une date de première apparition (FAD) et dernière apparition (LAD) du taxon, sa portée stratigraphique, et le numéro d’identification (ID) de son ancêtre. Ces données sont entrés à l’aide de n’importe quel logiciel de feuille de calcul, et ADAPTS les lit, et inscrit les résultats dans une feuille de calcul. Pour tester la performance d’ADAPTS, une phylogénie aléatoire fut construite avec TREE GROWTH, et le produit anyalysé par ADAPTS. Ce test confirme qu’ADAPTS est capable de détecter un signal aléatoire connu et d’analyser rapidement une grand nombre de données.

MOTS CLÉS: portée stratigraphique, survivance, taux d’évolution

Deutsche Zusammenfassung

ADAPTS (Analyse von Diversität, Asymmetrie phylogenetischer Bäume und üerlebenden): Eine neue Software für die Analyse von stratigraphischen Reichweiten

Für die automatische Analayse von stratigraphischen reichweiten wurde eine neue Software ADAPTS (Analyse von Diversität, Asymmetrie phylogenetischer Bäume und üerlebenden) entwickelt. ADAPTS erzeugt drei Gruppen von Analysen: Masse für taxonomische Evolutionsraten, überlebens-Analayse und Abweichungen in Entstehungs- und Aussterberaten zwischen Stammformen und Abkömmlingen, die als asymmetrische Verzweigung in phylogenetischen Bäumen aufgezeichnet sind. Um alle diese Tests in der Anwendung durchzuführen, braucht ADAPTS nur fünf Angaben über jedes Taxon in der Gruppe: eine Identifikationszahl (I,D.), das Erstauftreten (FAD) und das Letztauftreten (LAD) des Taxons, seine stratigraphische Reichweite und die Identifikationszahl seiner Stammform. Diese Daten werden in ein beliebiges Standardprogramm für Tabellenkalkulation eingegeben und ADAPTS liest die Daten nach der Aktivierung automatisch ein und gibt die Resultate an eine Tabellenkalkulation aus. Um die Leistungsfähigkeit von ADAPTS zu testen, wurde eine bekannte zufällige Phylogenie mit einem anderen Programm, TREE GROWTH, erzeugt und das Ergebnis untersucht. Der Test bestätigt, dass ADAPTS in der Lage ist, ein bekanntes Zufallssignal zu erkennen und grosse Datensätze schnell zu verarbeiten.

Italiano

ADAPTS (ANALISI DELLA DIVERSITÀ, DELLA ASIMMETRIA DEGLI ALBERI FILOGENETICI E DELLA SOPRAVVIVENZA): UN NUOVO PROGRAMMA PER ANALIZZARE I DATI SULL'ESTENSIONE STRATIGRAFICA

Allo scopo di automatizzare l'analisi di dati di estensione stratigrafica (range), è stato sviluppato il programma ADAPTS. Questo programma permette di effettuare analisi di tre grandi tipi: dalle metriche relative al tasso di evoluzione tassonomico, all'analisi della sopravvivenza, a test per la ricerca di errori pregiudiziali di base nei tassi di speciazione ed estinzione tra antenati e discendenti, come ad esempio quelli che causano ramificazioni asimmetriche negli alberi filogenetici. Per potere effettuare queste analisi, ADAPTS ha bisogno solamente di cinque tipi di informazione per ogni taxon in un gruppo: un numero di identificazione (I.D.), una data di prima (FAD) e di ultima comparsa (LAD), la sua estensione stratigrafica, ed il numero di identificazione (I.D.) dell'antecessore. Questi dati possono essere inseriti in un qualsiasi foglio di calcolo. Il programma ADAPTS legge automaticamente questi dati, effettua i calcoli e scrive i risultati di nuovo sul foglio di calcolo. Per verificare le capacità di ADAPTS, abbiamo generato, per mezzo del programma TREE GROWTH, una filogenia casuale ma conosciuta, ed abbiamo analizzato i risultati. Questo test ha confermato che ADAPTS è stato in grado di riconoscere un tipo di segnale casuale conosciuto e di analizzare rapidamente grandi insiemi di dati.

Una versione dimostrativa di ADAPTS è disponibile in questi siti:

Sito 1, Stati Uniti
Sito 2, Regno Unito.

Una versione finale verrà resa disponibile in futuro.

Parole chiave: estensione stratigrafica, sopravvivenza, tassi evolutivi

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