In this paper, we address a conjecture of Fill [Fill03] about the spectral gap of a nearest-neighbor transposition Markov chain ℳ_nn over biased permutations of [n]. Suppose we are given a set of input probabilities 𝒫 = {p_{i,j}} for all 1 ≤ i, j ≤ n with p_{i, j} = 1-p_{j, i}. The Markov chain ℳ_nn operates by uniformly choosing a pair of adjacent elements, i and j, and putting i ahead of j with probability p_{i,j} and j ahead of i with probability p_{j,i}, independent of their current ordering.

We build on previous work [S. Miracle and A.P. Streib, 2018] that analyzed the spectral gap of ℳ_nn when the particles in [n] fall into k classes. There, the authors iteratively decomposed ℳ_nn into simpler chains, but incurred a multiplicative penalty of n^-2 for each application of the decomposition theorem of [Martin and Randall, 2000], leading to an exponentially small lower bound on the gap. We make progress by introducing a new complementary decomposition theorem. We introduce the notion of ε-orthogonality, and show that for ε-orthogonal chains, the complementary decomposition theorem may be iterated O(1/√ε) times while only giving away a constant multiplicative factor on the overall spectral gap. We show the decomposition given in [S. Miracle and A.P. Streib, 2018] of a related Markov chain ℳ_pp over k-class particle systems is 1/n²-orthogonal when the number of particles in each class is at least C log n, where C is a constant not depending on n. We then apply the complementary decomposition theorem iteratively n times to prove nearly optimal bounds on the spectral gap of ℳ_pp and to further prove the first inverse-polynomial bound on the spectral gap of ℳ_nn when k is as large as Θ(n/log n). The previous best known bound assumed k was at most a constant.