The Proceedings of the Eighth International Conference on Creationism (2018)

Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism , ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. AN OVERVIEW OF THE INDEPENDENT HISTORIES OF THE HUMAN Y CHROMOSOME AND THE HUMAN MITOCHONDRIAL CHROMOSOME Robert W. Carter , FMS Foundation, 877 Marshall Rd, Waterloo, NY 13165, USA, rcarter@FMSFound.org Stephen S. Lee , Statistical Science Department, University of Idaho, Moscow, ID 83843, USA, stevel@uidaho.edu John C. Sanford , FMS Foundation, 877 Marshall Rd, Waterloo, NY 13165, USA, rcarter@FMSFound.org ABSTRACT The existence of a literal Adam and Eve is hotly debated, even within the Christian body. Now that many full-length human Y (chrY) and mitochondrial (chrM) chromosome sequences have been sequenced and made publicly available, it may be possible to bring clarity to this question. We have used these data to comprehensively analyze the historical changes in these two chromosomes, starting with the sequences of people alive today, and working backwards to the ancestral sequence of the family groups to which they belong. The analyses of the chrY and chrM histories were done separately and in parallel. Remarkably, both analyses gave very similar results. First, the pattern displayed in both datasets supports a massive expansion of the human lineage, with multiple new branches forming from closely- related individuals. Second, for both chromosomes, the mutation rate along each branch has not been the same through time. Third, both phylogenetic trees display a starburst pattern that centers around specific historical individuals, nearly all of whom lived in the Middle East. Fourth, we can know with a very high degree of confidence the actual sequences of the historical individuals that gave rise to each branch in both family trees. Fifth, within a reasonable margin of error we can approximate the sequence of Y chromosome Adam/Noah and Mitochondrial Eve. Sixth, given a few reasonable assumptions, we can estimate the time to Y Chromosome Adam/Noah and Mitochondrial Eve. Both individuals lived less than 10,000 years ago, which is most consistent with a biblical timeframe. Lastly, recurrent mutations are extremely common, and many of them are associated with epigenetic CpG sites, meaning mutation accumulation is not free of environmental influence and many mutations may have accumulated in different lineages in parallel. The genetic evidence strongly suggests that Y Chromosome Adam/Noah and Mitochondrial Eve were not just real people, they were the progenitors of us all. In this light, there is every reason to believe that they were the Adam/Noah and Eve of the Bible. KEY WORDS Adam, Eve, genetics, mutation, Y chromosome, mitochondria, ancestral reconstruction, molecular clock Copyright 2018 Creation Science Fellowship, Inc., Pittsburgh, Pennsylvania, USA www.creationicc.org 133 INTRODUCTION The Bible describes the creation of a first founding couple of all humanity, Adam and Eve.  Even though the early church readily accepted the reality of Adam and Eve, this has been a highly controversial subject for the past several centuries, specifically after the rise of Darwinism. One of the more controversial aspects of this debate deals with the evidence pointing back to a single man (“Y chromosome Adam”,  c.f.  Karafet et al. 2008) and a single woman (“mitochondrial Eve”,  c.f.  Cann et al. 1987) who supposedly lived one to two hundred thousand years ago, much further back than the biblical timescale allows. In this paper, we will analyze these claims and attempt to show that 1) Adam and Eve are a concrete reality, 2) the timeframe in which they lived is much more recent than evolutionary calculations suggest, and 3) variable branch lengths on the Y and mitochondrial family tree strongly indicate that mutations have not accumulated at the same rate across time or geography. This last point is a direct challenge to the “molecular clock hypothesis” that is, in turn, behind all evolutionary speculations about the timing of genetic events, including the “Out-of-Africa” dispersion and the time when Y chromosome Adam and mitochondrial Eve lived. Rapid advances in DNA sequencing have led to an enormous wealth of genomic data, including “whole-chromosome” databases such as the 1000 Genomes Project (2010) and the Simons Genome Diversity Project (Malik et al. 2016). These new data have opened an unprecedented window into human genetic history. For example, a recently published study of over 13,000 Y chromosome single nucleotide variations (SNVs) by Hallast et al. (2015) revealed various previously-hidden aspects of worldwide Y chromosome diversity. This was quickly followed by an analysis by Poznik et al. (2016) that included more than 60,000 SNVs, 1,400 indels, 110 copy-number variations, and 3,200 short tandem repeats from more than 1,200 full-length chromosomes sequenced by the 1000 Genomes Project. These new studies provide important new insights into human genetic history, and the discovery process has just begun. The Y and mitochondrial chromosomes can be subdivided into distinct ‘haplogroups’ by the particular set of mutations each carries. Due to technological limitations, haplogroup identification was traditionally limited to a small set of specific discriminating alleles. For example, the first successful typing method for mitochondria involved restriction endonuclease digestion (Johnson et al. 1983). This allowed for the identification of the major clades (after much work and many revisions). Later, sequencing of the two hypervariable regions (HVRI and HVRII) allowed for improved