A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes

Abstract

The evolution of multicellular organisms involved the evolution of specialized cell types performing distinct functions; and specialized cell types presumably arose from more generalized ancestral cell types as a result of mutational event, such as gene duplication and changes in gene expression. We used characters based on gene expression data to reconstruct evolutionary relationships among 11 types of lymphocytes by the maximum parsimony method. The resulting phylogenetic tree showed expected patterns including separation of the lymphoid and myeloid lineages; clustering together of granulocyte types; and pairing of phenotypically similar cell types such as T-helper cells type 1 and T-helper cells type 2 (Th1 and Th2). We used phylogenetic analyses of sequence data to determine the time of origin of genes showing significant expression difference between Th1 and Th2 cells. Many such genes, particularly those involved in the regulation of gene expression or activation of proteins, were of ancient origin, having arisen by gene duplication before the most recent common ancestor (MRCA) of tetrapods and teleosts. However, certain other genes with significant expression difference between Th1 and Th2 arose after the tetrapod-teleost MRCA, and some of the latter were specific to eutherian (placental) mammals. This evolutionary pattern is consistent with previous evidence that, while bony fishes possess Th1 and Th2 cells, the latter differ phenotypically in important respects from the corresponding cells of mammals. Our results support a gradualistic model of the evolution of distinctive cellular phenotypes whereby the unique characteristics of a given cell type arise as a result of numerous independent mutational changes over hundreds of millions of years.

Fig. 1

(A) Cluster analysis of gene expression data in 11 human leukocyte types. The distance (Y-axis) is 1 minus the correlation coeffcient. (B) Maximum parsimony tree based on 22,215 characters derived from gene expression data (tree length = 54,501 changes; overall consistency index = 0.678). The numbers on the branches represent the percentage of 1000 bootstrap samples supporting that branch. BC, B-cells; NK, natural killer cells; CMEM, central memory cells; EFM, effector memory cells; Th1, T-helper cells type 1; Th2, T-helper cells type 2; MAC, macrophages; CMAS, cord-blood mast cells; BAS, basophils.

Fig. 2

Neighbor-joining tree of vertebrate proline 4-hydroxylases, rooted with invertebrate homologs, based on the JTT amino acid distance at 380 aligned amino acid positions. Sequences are identified by species and by accession number. The numbers on the branches represent the percentage of 1000 bootstrap samples supporting that branch.

Fig. 3

Neighbor-joining tree of zinc finger protein 215 (ZNF215) and related zinc finger proteins, based on the JTT amino acid distance at 111 aligned amino acid positions. Sequences are identified by species and by accession number. The numbers on the branches represent the percentage of 1000 bootstrap samples supporting that branch; only values ≥ 50% are shown.

Fig. 4

Interaction graphs, for significant gene by cell type interactions, illustrating mean expression scores in Th1 and Th2 cells of three pairs of related genes: (A) ARID3A and ARID3B; (B) GFPT1 and GFPT2; and (C) RBPJ and RBPJL.

Fig. 5

Neighbor-joining tree of ARID family of vertebrates, rooted with invertebrate sequences, based on the JTT amino acid distance at 248 aligned amino acid positions. Sequences are identified by species and by accession number. The numbers on the branches represent the percentage of 1000 bootstrap samples supporting that branch.

Fig. 6

Neighbor-joining tree of RBPJ and RBPJL of vertebrates and invertebrates, based on the JTT amino acid distance at 399 aligned amino acid positions. Sequences are identified by species and by accession number. The numbers on the branches represent the percentage of 1000 bootstrap samples supporting that branch; only values ≥ 50% are shown.