# On the statistical inconsistency of Maximum Parsimony for $k$-tuple-site data

## TL;DR

This paper demonstrates that Maximum Parsimony remains statistically inconsistent for $k$-tuple-site data with five taxa, extending previous four-taxa results and highlighting limitations in phylogenetic reconstruction methods.

## Contribution

It proves the statistical inconsistency of Maximum Parsimony for $k$-tuple-site data with five taxa, showing limitations beyond four-taxa cases.

## Key findings

- Maximum Parsimony is statistically inconsistent for 5 taxa with $k$-tuple data.
- Inconsistency persists even when moving from site-based to $k$-tuple analyses.
- The equivalence between site-based and $k$-tuple data breaks down for more than four taxa.

## Abstract

One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the evolutionary relationships of these species. Maximum Parsimony is one such criterion for tree reconstruction and, it is the one which we will use in this paper. However, it is well-known that tree reconstruction methods can lead to wrong relationship estimates. One typical problem of Maximum Parsimony is long branch attraction, which can lead to statistical inconsistency. In this work, we will consider a blockwise approach to alignment analysis, namely so-called $k$-tuple analyses. For four taxa it has already been shown that $k$-tuple-based analyses are statistically inconsistent if and only if the standard character-based (site-based) analyses are statistically inconsistent. So, in the four-taxon case, going from individual sites to $k$-tuples does not lead to any improvement. However, real biological analyses often consider more than only four taxa. Therefore, we analyze the case of five taxa for $2$- and $3$-tuple-site data and consider alphabets with two and four elements. We show that the equivalence of single-site data and $k$-tuple-site data then no longer holds. Even so, we can show that Maximum Parsimony is statistically inconsistent for $k$-tuple site data and five taxa.