Human breeding practices found to be likely reason for lack of paternal DNA diversity in modern horses

Práticas de reprodução humana são provavelmente a razão para a falta de diversidade de DNA paterno em cavalos modernos

April 19, 2018 by Bob Yirka, Phys.org report

Credit: CC0 Public Domain

A team of researchers from across Europe has found that human breeding practices, particularly during the Iron Age, are likely the cause of a lack of variability in paternally inherited DNA in modern horses. In their paper published on the open access site Science Advances, the group describes the DNA study they undertook to better understand the genetic history of the modern horse and what they found. 

It has been known for some time that modern horses are genetically diverse, maternally speaking, but have a distinct lack of variability on the paternal side. The prevailing theory regarding this state of affairs is that during the time when horses were first being domesticated there were many more mares than stallions. In this new effort, the researchers suggest a different reason—they believe it is due to selective breeding, particularly during the Iron Age. The group came to this conclusion after conducting an extensive DNA analysis of both modern and ancient horses.

The study consisted of gathering DNA samples from 350 horses covering the past 5,000 years and attempting to genotype them—in the end they were able to genotype just 86 of the samples, but that was enough to provide the team with a means for creating a timeline for four major haplotypes: Y-HT-1 through 4. Y-HT-1, the team notes, is dominant in modern horses. 

To create the timeline, the team divided the DNA samples into four time periods: earlier than 2,200 BC, between 2,200 BC and 900 BC, between 900 BC to 400 AD and from 400 AD till today. In looking at the haplotypes, the researchers found all but Y-HT-1 were heavily represented in the first period, but over time Y-HT-1 became increasingly prominent as the other three became less so.

The researchers note that Y-HT-1 began its progression to dominance during the Bronze Age, a time during which humans were migrating across Eurasia. But the Iron Age was when Y-HT-1 really began to assert itself, a period during which the Roman Empire was reaching across Europe and changing ideas about how horses should be bred by focusing on males instead of females. This, the researchers claim, suggests that the lack of paternal diversity is very likely due to human breeding practices.

Explore further: Most modern horses are descendants of recently imported oriental stallions

More information: Saskia Wutke et al. Decline of genetic diversity in ancient domestic stallions in Europe, Science Advances (2018). DOI: 10.1126/sciadv.aap9691

Abstract
 
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages.

Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection—initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.

Journal reference: Science Advances

Revisitando um antigo mistério não resolvido: o que determina os níveis de diversidade genética dentro das espécies

Revisitando um antigo mistério não resolvido: o que determina os níveis de diversidade genética dentro das espécies

quinta-feira, novembro 08, 2012

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

Ellen M. Leffler1*, Kevin Bullaughey2#, Daniel R. Matute1#, Wynn K. Meyer1#, Laure Ségurel1,3#, Aarti Venkat1#, Peter Andolfatto4, Molly Przeworski1,2,3*

1 Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America, 2 Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America, 3 Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America, 4 Department of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America

Abstract

Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.

Citation: Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, et al. (2012) Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species? PLoS Biol 10(9): e1001388. doi:10.1371/journal.pbio.1001388

Published: September 11, 2012

Copyright: © Leffler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: E.M.L. was partially supported by National Institutes of Health Grant T32 GM007197. M.P. is a Howard Hughes Early Career Scientist. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

* E-mail: emleffler@uchicago.edu (EML); mfp@uchicago.edu (MP)

# These authors contributed equally to this work.

What evolutionary forces maintain genetic diversity in natural populations? How do diversity levels relate to census population sizes (Box 1)? Do low levels of diversity limit adaptation to novel selective pressures? Efforts to address such questions spurred the rise of modern population genetics and contributed to the development of the neutral theory of molecular evolution—the null hypothesis for much of evolutionary genetics and comparative genomics [1]–[3]. Yet these questions remain wide open and, for close to two decades, have been neglected [4]. Most notably, little progress has been made to resolve a riddle first pointed out 40 years ago on the basis of allozyme data: the mysteriously narrow range of genetic diversity levels seen across taxa that vary markedly in their census population sizes [5]. This gap in our understanding is glaring, and may hamper efforts at conservation (e.g., [6]).

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Diversidade dos Africanos

X-tra Diversity for Africans

1. Ann Gibbons

Call it the X factor. Compared with Europeans and Asians, Africans have extra diversity on their X chromosomes, according to an invited lecture at the meeting by Cornell University geneticist Andrew Clark. The lack of diversity in non-Africans may be the legacy, handed down for thousands of generations, of fewer women than men in the bands of modern humans who first left Africa to colonize the rest of the world, Clark said.

His team used new data from the 1000 Genomes Project to resolve a recent debate about diversity on the X and to begin to explain why non-Africans have so little variation on this sex chromosome compared with the other chromosomes, or autosomes. “We're seeing a very consistent pattern of reduced X diversity out of Africa,” Clark said. “It shows a greater loss of variation than even in the autosomes out of Africa.” 

To evolutionary geneticists, the X chromosome has always been something of a riddle. Unlike its partner the Y, the X still has its full complement of genes. But because of the way it is inherited—men inherit only one copy from their mothers, whereas women inherit a copy from each parent—the X is less diverse than autosomes in populations. So the chromosome has been a low priority for sequencers interested in disease risk, and published sequences have been of poor quality. But interest was piqued 3 years ago when teams studying frequencies of different alleles on the X got different results: One group found the X was less diverse in non-Africans, but another group didn't.

Then last year, the 1000 Genomes Project (Science, 29 October 2010, p. 574) posted its pilot data, including sequences of the complete genomes of 69 women from Africa and Europe. These data provide a much sharper view of the X, including single-nucleotide polymorphisms (SNPs). “The 1000 Genomes data rides to the rescue,” Clark quipped.

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On the X trail.

The X chromosome is less diverse outside Africa (faded pink), whereas the Y chromosome's diversity (blue) does not change.

CREDIT: ADAPTED FROM A. KEINAN

 

Researchers have long known that Africans have more diverse genomes overall, presumably because the small bands of ancestors traveling out of Africa passed through a genetic bottleneck and lost many variants. Cornell's Alon Keinan, Clark, and their colleagues devised a clever method to compare the amount of variation in SNPs on the X with that on the autosomes and applied it to 36 Yoruba women from West Africa. They found the X had about 73% of the diversity of the autosomes, as expected. But when Keinan examined the genomes of 33 European women, he found that their X chromosomes had only about 61% of the diversity of their autosomes. Because the European genomes were already less diverse overall, this extra effect meant that the Africans' X chromosomes were twice as diverse as those of the Europeans.

Because of the X's pattern of inheritance, the reduction in diversity out of Africa is likely due to some sex-linked demographic process, Keinan says. One likely explanation is that more men than women were members of the bands who moved out of Africa, a gender imbalance also seen on the front line of some other migrations. 

Other researchers find the work convincing. “We are converging on an answer,” says computer scientist August Woerner, who works with geneticist Michael Hammer at the University of Arizona in Tucson. Hammer's lab was the one that saw more diversity on the X of non-Africans, but with whole genome sequences, they, too, have now found more diversity in Africans, resolving the debate. “The simplest explanation is waves of male migrations or a few males disproportionately passing on their X chromosomes” by having many children, says geneticist Joshua Akey of the University of Washington, Seattle.