Gaming artificial phylogenies

in Language Dynamics and Change
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The reconstruction of phylogenies of cultural artefacts represents an open problem that mixes theoretical and computational challenges. Existing benchmarks rely on simulated phylogenies, where hypotheses on the underlying evolutionary mechanisms are unavoidable, or on real data phylogenies, for which no true evolutionary history is known. Here we introduce a web-based game, Copystree, where users create phylogenies of manuscripts through successive copying actions in a fully monitored setup. While players enjoy the experience, Copystree allows to build artificial phylogenies whose evolutionary processes do not obey any predefined theoretical mechanisms, being generated instead with the unpredictability of human creativity. We present the analysis of the data gathered during the first set of experiments and use the artificial phylogenies gathered for a first test of existing phylogenetic algorithms.

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    Figure 1

    User interface of Copystree. The challenge of the game consists in copying a text to the best of the players’ ability, with time constraints and the readability of the text progressively reduced in an artificial way. The text to be copied is presented to the player in a non-editable graphic format, to avoid cut and paste actions, and input is allowed only through a standard HTML text field. At the end of each gaming session, players are given a score based on the similarity between the copy they produced and the text they were prompted with. Higher similarities result in higher scores. The scoring system is not explicitly available to players.

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    Figure 2

    Evolution of a single copy. To mimic the degradation processes that manuscripts and old books undergo during their lifetime, each copy of a text is associated with an independent phylogenetic lineage, through which the text is progressively degraded. Each fragment can thus be copied several times, each time with a different level of degradation, each new copy being the starting point of a new lineage. Because of the reduced readability of the original text, several variants, for example new words (here highlighted in red), may emerge in the new copies.

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    Figure 3

    Phylogenetic structures of the artificial phylogenies. A: Schematic illustration of the creation of an artificial phylogeny. Starting from the original text (the root, brown circle), a binary tree is generated via successive copying actions. In each round, a player is presented with a text to copy, chosen from among the elements of the tree available for copying (represented by empty red squares). When copying is completed, the empty square becomes a solid red square and branches into two new nodes of the tree: the copy of the text entered by the player (a green circle) and another empty red square representing the degraded version of the text just copied. This operation is repeated through the successive rounds of the game. At each point in time, the phylogeny consists of a set of artificial texts (squares) and a set of copies (green circles). Only the artificial texts not yet copied (the empty red squares) are available for further copying. Artificial texts are generated to mimic the aging process of each copy, while each copy represents a new phylogenetic lineage (as shown in Fig. 2). Lineages in the tree can be declared inactive and will not be available anymore for copy (black square) if the same fragment is skipped by users more than 3 times. B: A non-binary tree embeds the evolutionary relationship between all the copies of Fig. A. The fact that, in the topology shown in Fig. 3B, the copies 1, 5 and 7 are actually ancestral nodes of the copies below is made explicit by setting the branches above them to have a length = 0. In this way, in the “true phylogeny,” which we will use as reference for the inference, all the copies are treated as terminal nodes (this is needed because all inference algorithms will infer a tree where all the copies are leaves), but, on the other hand, we correctly report them as identical to the internal nodes above them.

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    Figure 4

    Degradation processes simulating the aging process of a text. Top: Dots, where circular colored spots of different sizes are randomly located at different positions to cover portions of the text. Center: Deletion of single characters in random positions of the text and replacement with blank spaces. Bottom: Multiple Deletions, with the deletion of up to three neighboring characters in randomly chosen locations of the text.

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    Figure 5

    Statistics of the database collected in the preliminary session. A: Scatter plot for the size of the artificial phylogenies (x axis) for the three languages adopted to generate the phylogenies. Different colors denote different degradation processes (see legend). B: Histogram of the cumulative gaming time per user. C: Histogram of the number of copies per user.

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    Figure 6

    An example of artificial phylogeny. A: The root of the artificial phylogeny, taken from Hero and Leander by Christopher Marlowe. During the gaming sessions, this text was copied 10 times, following the scheme illustrated in Fig. 3. Here we report the non-binary phylogeny describing the diversification process of the set of copies. B: Examples of two copies belonging to this artificial phylogeny. The texts differ from the root due to accidental typos (marked in blue) and because new words have emerged during the evolution (marked in red). C: Variants that emerged during the evolution of the text. Numbers indicate the tree branch (as marked in the A panel) where the variant appeared. Several events of parallel evolution can be identified, where the same word has emerged in two independent lineages (words marked in orange).

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    Figure 7

    Mutation rates. A: Mean value and standard deviation of the edit distance (top) and number of variants (i.e. different words) measured between two consecutive copies (bottom), for the three different degradation processes considered. B: Same information as in A but evaluated as a function of the number of copies away from the original text. We show in grey the expected value (plus/minus standard deviation) of both the edit distance and the number of observed variants, under the hypothesis of independent changes (i.e. linear extrapolations of the values of A after many copies). C: Examples of the evolution of a text after multiple copies; changes are highlighted in blue. In the first case, a typo introduced after the first copy is restored in the subsequent one. In the second case, the introduction of a new variant in the first copy induces a change of the semantic content of the sentence, which is retained in the subsequent copy. These examples are taken from the tree of copies of Hero and Leander by Christopher Marlowe (same as Fig. 6).

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    Figure 8

    Comparison between binary and non-binary trees. Top: Example of a compatible (blue) and a non-compatible (red) edge between a non-binary tree (left, orange) and a binary tree, as considered in the Generalized Robinson-Foulds distance. Bottom: Example of a compatible (blue) and a non-compatible (red) quartet between a non-binary tree (left, orange) and a binary tree, as considered in the Generalized Quartet Distance.

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    Figure S1

    Accuracy of the reconstruction. We study here the accuracy of the reconstructed phylogenetic trees of our dataset as a function of the size of the phylogeny, i.e., the amount of copied text. In this plot we include all the phylogenies of our dataset (i.e., all three degradation processes considered together); trees are then grouped into classes of 5 elements, for which we show the mean value of the GQD and GRF (y axis) as a function of the mean size of the phylogeny N (x axis). Trees were reconstructed with the three distance-based algorithms considered in this context (see main text): FastME, Neighbor-Joining (NJ) and Fast-SBiX.

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