The performance of PREPARE on realistic simulation is comparable to polygamous Wright-Fisher simulations.

<p>The simulated population grew from 160 individuals of the and HapMap populations to 846 individuals in 200 years. This simulation accounts for IBD detection errors, asynchronous mating and dynamic population size.</p

Distribution of relationship scores under specific true relationships.

<p>Distribution of relationship scores under specific true relationships.</p

Examples for possible ancestry structures created for individuals and in order to test the relationship between them.

<p>The triangles under and represent their existing descendants, edges represent parent-offspring relationship.</p

Depicting cases where edge removal rules are required in polygamous pedigree reconstruction.

<p>Redundant graph edges are dashed red, correct edges in solid black.</p

Souvenir Postcard Folder: Souvenir Folder of Beautiful Jacksonville, Florida

Souvenir Postcard Folder: Souvenir Folder of Beautiful Jacksonville, Florida; 1915 (134)https://digitalcommons.unf.edu/mette_postcardimages/1224/thumbnail.jp

Intuition for sibling assignment, depicting the potential-siblings graph , the contracted graph , and assigned graph .

<p>In both examples ,, are parent couples with extant descendants in the observed population. A. For the case where , are full-siblings, the contraction will end in composed of three super-vertices, connected by two edges; the assignment algorithm will assign each edge to a disjoint clique. B. If are also full-siblings, a 3-clique is formed in ; the assignment algorithm assigns all edges to a corresponding 3-clique of siblings.</p

Attempting to reconstruct the simple pedigree on the left, from the genotypes of extant generation (bright blue).

<p>Considering observed genetic similarity of extant descendants only, we cannot distinguish which of the four parents in the second generation are siblings (Correctly inferred sibling relationship are colored blue, and wrong potential sibling-relationships in dashed red).</p

Running times of PREPARE on 1.6GHz Intel Core i5-2467M machine with 4G RAM using a single thread.

<p>The two parameters affecting the running time of prepare is the population size, and whether PREPARE is run on monogamous or polygamous mode. Most of the running time is spent on reconstructing the fifth generation.</p

Four examples of vertex contractions, typical for first, second, and third generations.

<p>Founders are filled with Grey. Extant individuals are outlined in blue. Green arrows stand for the contraction action.</p

Simulated IBD feature distribution in monogamous and polygamous populations.

<p>The overlap in polygamous distributions is the main challenge in reconstructing pedigrees of real populations.</p