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\begin{document}

\title{Geographical contrasts of Y-chromosomal haplogroups from wild and
domestic goats reveal ancient migrations and recent introgressions}



\author[1]{Vargoats Consortium}%
\author[2]{Isaäc Nijman}%
\author[3]{Benjamin Rosen}%
\author[1]{Philippe Bardou}%
\author[1]{Thomas Faraut}%
\author[4]{Tristan Cumer}%
\author[5]{Kevin Daly}%
\author[6]{Zhuqing Zheng}%
\author[6]{Yudong Cai}%
\author[6]{Hojjat Asadollahpour}%
\author[6]{Bengi Cinar-Kul}%
\author[6]{Wei-Yi Zhang}%
\author[7]{guangxin e}%
\author[6]{A Ayin}%
\author[6]{Hayley Baird}%
\author[6]{Meirat Bakhtin}%
\author[6]{Valentin Balteanu}%
\author[6]{Diana Barfield}%
\author[6]{Beate Berger}%
\author[6]{Thor Blichfeldt}%
\author[6]{Geert Boink}%
\author[6]{Sri Rachma Bugiwati}%
\author[6]{Zexi Cai}%
\author[6]{Sean Carolan}%
\author[8]{Emily Clark}%
\author[9]{Vladka Cubrić Curik}%
\author[6]{Muhammad Dagong}%
\author[6]{Tashi Dorji}%
\author[6]{Louise Drew}%
\author[6]{Jiazhong Guo}%
\author[6]{Jón Hallsson}%
\author[6]{Simon Horvat}%
\author[10]{Juha Kantanen}%
\author[6]{Fuki Kawaguchi}%
\author[6]{Polat Kazymbet}%
\author[6]{Negar khayatzadeh}%
\author[6]{Namshin Kim}%
\author[6]{Manoj Kumar Shah}%
\author[6]{Yuying Liao}%
\author[11]{Amparo Martinez}%
\author[6]{Joseph Masangkay}%
\author[6]{Maho Masaoka}%
\author[12]{Raffaele Mazza}%
\author[13]{John McEwan}%
\author[6]{Marco Milanesi}%
\author[14]{Md Omar Faruque}%
\author[6]{Yuto Nomura}%
\author[6]{Nadjet-Amina  Ouchene-Khelifi}%
\author[15]{Filipe Pereira}%
\author[6]{Goutam Sahana}%
\author[6]{Mazdak Salavati}%
\author[6]{Shinji Sasazaki}%
\author[16]{Anne DA SILVA}%
\author[17]{Mojca  Simčič}%
\author[18]{Johann Soelkner}%
\author[6]{Alison Sutherland}%
\author[6]{Johannes Tigchelaar}%
\author[19]{Hongping Zhang}%
\author[6]{Econogene Consortium}%
\author[20]{Paolo Ajmone Marsan}%
\author[21]{Daniel Bradley}%
\author[22]{Licia Colli}%
\author[23]{Cord Drögemüller}%
\author[24]{Yu Jiang}%
\author[24]{chuzhao Lei}%
\author[25]{H Mannen}%
\author[26]{Francois Pompanon}%
\author[27]{GWENOLA TOSSER-KLOPP}%
\author[2]{Johannes A. Lenstra}%
\affil[1]{INRA}%
\affil[2]{Utrecht University}%
\affil[3]{Agriculture Research Service}%
\affil[4]{University of Lausanne}%
\affil[5]{Trinity College}%
\affil[6]{Affiliation not available}%
\affil[7]{Southwest University}%
\affil[8]{University of Edinburgh}%
\affil[9]{University of Zagreb}%
\affil[10]{Natural Resources Institute Finland Jokioinen}%
\affil[11]{University of Cordoba}%
\affil[12]{Associazione Italiana Allevatori}%
\affil[13]{AgResearch Invermay Agricultural Centre}%
\affil[14]{Bangladesh Agricultural University}%
\affil[15]{University of Porto - CIIMAR}%
\affil[16]{University de Limoges}%
\affil[17]{University of Ljubljana}%
\affil[18]{University of Natural Resources and Life Sciences}%
\affil[19]{Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province}%
\affil[20]{Universita Cattolica del Sacro Cuore}%
\affil[21]{Trinity College Dublin}%
\affil[22]{Universita' di Piacenza}%
\affil[23]{University of Bern}%
\affil[24]{Northwest A\&F University}%
\affil[25]{Kobe University}%
\affil[26]{University of Grenoble}%
\affil[27]{Institut National de Recherche pour lAgriculture, l'Alimentation, et l'Environnement Occitanie-Toulouse}%


\vspace{-1em}



  
  \date{May 21, 2024}


\begingroup
\let\center\flushleft
\let\endcenter\endflushleft
\maketitle
\endgroup





\selectlanguage{english}
\begin{abstract}
By their paternal transmission, Y-chromosomal haplotypes are sensitive
markers of population history and male-mediated introgression. Previous
studies identified biallelic single-nucleotide variants in the SRY, ZFY,
DDX3Y genes, which in domestic goats identified four major Y-chromosomal
haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning.
Here, we analyze whole-genome sequences of 386 domestic goats from 75
modern breeds and 7 wild goat species that were generated by the
VarGoats goat genome project. Phylogenetic analyses indicated domestic
haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A
is split into Y1AA and Y1AB. All five haplogroups were detected in 26
ancient DNA samples from southeast Europe or Asia. Haplotypes from
present-day bezoars are not shared with domestic goats and are attached
to deep nodes of the trees and networks. Haplogroup distributions for
180 domestic breeds indicate ancient paternal population bottlenecks and
expansions during the migrations into northern Europe, eastern and
southern Asia and Africa south of the Sahara. In addition, sharing of
haplogroups indicates male-mediated introgressions, most notably an
early gene flow from Asian goats into Madagascar and the crossbreeding
that in the 19th century resulted in the popular Boer and Anglo-Nubian
breeds. More recent introgressions are those from European goats into
the native Korean goat population and from Boer goat into Uganda, Kenya,
Tanzania, Malawi and Zimbabwe. This study illustrates the power of the
Y-chromosomal variants for reconstructing the history of domestic
species with a wide geographic range.%
\end{abstract}%



\sloppy


\textbf{Geographical contrasts of Y-chromosomal haplogroups from wild
and domestic goats reveal ancient migrations and recent introgressions}

Running title: Y-chromosomal variation in goats

VarGoats Consortium\textsuperscript{1}, Isa\selectlanguage{ngerman}äc J.
Nijman\textsuperscript{2,3}, Benjamin D. Rosen\textsuperscript{4},
Philippe Bardou\textsuperscript{5}, Thomas Faraut\textsuperscript{5},
Tristan Cumer\textsuperscript{6}, Kevin G. Daly\textsuperscript{7},
Zhuqing Zheng\textsuperscript{8}, Yudong Cai\textsuperscript{8}, Hojjat
Asadollahpour\textsuperscript{8}, Bengi Ç\selectlanguage{polish}ı\selectlanguage{english}nar Kul\textsuperscript{9},
Wei-Yi Zhang\textsuperscript{10}, Guangxin E\textsuperscript{10}, A
Ayin\textsuperscript{11}, Hayley Baird\textsuperscript{12}, Meirat
Bakhtin\textsuperscript{13}, Valentin A. B\selectlanguage{ngerman}âlteanu\textsuperscript{14},
Diana Barfield\textsuperscript{15}, Beate Berger\textsuperscript{16},
Thor Blichfeldt\textsuperscript{17}, Geert Boink\textsuperscript{18},
Sri R.A. Bugiwati\textsuperscript{19}, Zexi Cai\textsuperscript{20},
Sean Carolan\textsuperscript{21}, Emily Clark\textsuperscript{22} ,
Vlatka Cubric-Curik\textsuperscript{23}, Muhammad I.A.
Dagong\textsuperscript{19}, Tashi Dorji\textsuperscript{24}, Louise
Drew\textsuperscript{25}, Jiazhong Guo\textsuperscript{26}, Jón
Hallsson\textsuperscript{27}, Simon Horvat\textsuperscript{28}, Juha
Kantanen\textsuperscript{29}, Fuki Kawaguchi\textsuperscript{11}, Polat
Kazymbet\textsuperscript{13}, Negar Khayatzadeh\textsuperscript{16},
Namshin Kim\textsuperscript{30}, Manoj Kumar Shah\textsuperscript{31},
Yuying Liao\textsuperscript{32}, Amparo Martínez\textsuperscript{33},
Joseph S Masangkay\textsuperscript{34}, Maho
Masaoka\textsuperscript{11}, Raffaele Mazza\textsuperscript{35}, John
McEwan\textsuperscript{12}, Marco Milanesi\textsuperscript{36}, Faruque
Md. Omar\textsuperscript{37}, Yuto Nomura\textsuperscript{11},
Nadjet-Amina Ouchene-Khelifi\textsuperscript{38}, Filipe
Pereira\textsuperscript{39}, Goutam Sahana\textsuperscript{20}, Mazdak
Salavati\textsuperscript{22}, Shinji Sasazaki\textsuperscript{11}, Anne
Da Silva\textsuperscript{40}, Mojca Sim\selectlanguage{polish}č\selectlanguage{english}i\selectlanguage{polish}č\selectlanguage{english}\textsuperscript{28}, Johann
S\selectlanguage{ngerman}ölkner\textsuperscript{16}, Alison Sutherland\textsuperscript{41},
Johannes Tigchelaar\textsuperscript{18}, Hongpin
Zhang\textsuperscript{26}, Econogene Consortium\textsuperscript{42},
Paolo Ajmone-Marsan\textsuperscript{43,44}, Daniel G.
Bradley\textsuperscript{7}, Licia Colli\textsuperscript{43,45}, Cord
Drögemüller\textsuperscript{46}, Yu Jiang\textsuperscript{8}, Chuzhao
Lei\textsuperscript{8}, Hideyuki Mannen\textsuperscript{11}, François
Pompanon\textsuperscript{6}, Gwenola Tosser-Klopp\textsuperscript{5} and
Johannes A. Lenstra\textsuperscript{2\textbf{*}}

\textsuperscript{1} http://www.goatgenome.org/vargoats.html

\textsuperscript{2} Utrecht Univ., Netherlands

\textsuperscript{3} Univ. Medical Center Utrecht, Utrecht Univ., The
Netherlands

\textsuperscript{4} Agriculture Research Service, Beltsville, MD, United
States

\textsuperscript{5} GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet
Tolosan, France

\textsuperscript{6} Université Grenoble Alpes, Université Savoie Mont
Blanc, CNRS, LECA, Grenoble, France

\textsuperscript{7} Trinity College Dublin, Dublin, Ireland

\textsuperscript{8} College of Animal Science \& Technology,Northwest
A\&F Univ., Yangling, China

\textsuperscript{9} Faculty of Veterinary Medicine, Ankara Univ., Turkey

\textsuperscript{10} Southwest Univ., Chongqing, China

\textsuperscript{11} Kobe Univ., Kobe Japan

\textsuperscript{12} AgResearch, Invermay Agricultural Centre, Mosgiel,
New Zealand

\textsuperscript{13} Astana Medical Univ., Astana, Kazakhstan

\textsuperscript{14} Inst. of Life SciencesUniv. Agricultural Sciences
and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania

\textsuperscript{15} Pleystole, Queensland, Australia

\textsuperscript{16} Univ. Natural Resources and Life Sciences Vienna
(BOKU)

\textsuperscript{17} Norwegian Association of Sheep and Goat Breeders,
Aas, Norway

\textsuperscript{18} Stichting Zeldzame Huisdierrassen, Wageningen, The
Netherlands

\textsuperscript{19} Hasanuddin Univ., Makassar, Indonesia

\textsuperscript{20} Aarhus Univ., Tjele, Denmark

\textsuperscript{21} Old Irish Goat Society, Mulranny, Ireland

\textsuperscript{22} Univ. Edinburgh, Edinburgh, UK

\textsuperscript{23} Univ. Zagreb, Zagreb, Croatia

\textsuperscript{24} International Centre for Integrated Mountain
Development, Kathmandu, Nepal

\textsuperscript{25} Finch Hatton, Queensland, Australia

\textsuperscript{26} Sichuan Agricultural Univ., Chengdu, China

\textsuperscript{27} Agricultural Univ. Iceland, Reykjavik, Iceland

\textsuperscript{28} Biotechnical Faculty, Univ. Ljubljana, Ljubljana,
Slovenia

\textsuperscript{29} Natural Resources Inst. Finland (Luke), Helsinki,
Finland

\textsuperscript{30} Korea Research Institute of Bioscience and
Biotechnology (KRIBB), Daejeon, South Korea

\textsuperscript{31} National Animal Nutrition Research Centre,
Lalitpur, Nepal

\textsuperscript{32} Guangxi Key Laboratory of Livestock Genetic
Improvement, Guangxi, China

\textsuperscript{33} Universidad de Córdoba, Córdoba, Spain

\textsuperscript{34} Univ. of the Philippines, Los Banos, Philippines

\textsuperscript{35} Laboratorio Genetica e Servizi, Agrotis srl,
Cremona, Italy

\textsuperscript{36} Univ. degli studi della Tuscia, Viterbo, Italy

\textsuperscript{37} Bangladesh Agricultural Univ., Mymensingh,
Bangladesh

\textsuperscript{38} Science Veterinary Inst., University of Blida,
Blida, Algeria

\textsuperscript{39} IDENTIFICA Genetic Testing Maia \& Centre for
Functional Ecology, Porto, Portugal

\textsuperscript{40} E2LIM, Univ. Limoges, Limoges, France

\textsuperscript{41} New Zealand Arapawa Goat Association, New Zealand

\textsuperscript{42} See the list at the end of this paper

\textsuperscript{43} Univ. Cattolica del S. Cuore di Piacenza and BioDNA
Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy

\textsuperscript{44} UCSC PRONUTRIGEN Nutrigenomics Res. Centre,
Piacenza, Italy

\textsuperscript{45} UCSC BioDNA Biodiversity and Ancient DNA Res.
Centre, Piacenza, Italy

\textsuperscript{46} Univ. Bern, Bern, Switzerland.

\textsuperscript{\textbf{*}} \textbf{Correspondence:}

J.A. Lenstra

j.a.lenstra@uu.nl

Faculty of Veterinary Medicine, Utrecht University, IRAS, P.O. Box
80177,

3508 TD Utrecht, The Netherlands



\textbf{Abstract}

By their paternal transmission, Y-chromosomal haplotypes are sensitive
markers of population history and male-mediated introgression. Previous
studies identified biallelic single-nucleotide variants in the
\emph{SRY} , \emph{ZFY} , \emph{DDX3Y}genes, which in domestic goats
identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B
with a marked geographic partitioning. Here, we analyze whole-genome
sequences of 386 domestic goats from 75 modern breeds and 7 wild goat
species that were generated by the VarGoats goat genome project.
Phylogenetic analyses indicated domestic haplogroups corresponding to
Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB.
All five haplogroups were detected in 26 ancient DNA samples from
southeast Europe or Asia. Haplotypes from present-day bezoars are not
shared with domestic goats and are attached to deep nodes of the trees
and networks. Haplogroup distributions for 180 domestic breeds indicate
ancient paternal population bottlenecks and expansions during the
migrations into northern Europe, eastern and southern Asia and Africa
south of the Sahara. In addition, sharing of haplogroups indicates
male-mediated introgressions, most notably an early gene flow from Asian
goats into Madagascar and the crossbreeding that in the
19\textsuperscript{th} century resulted in the popular Boer and
Anglo-Nubian breeds. More recent introgressions are those from European
goats into the native Korean goat population and from Boer goat into
Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the
power of the Y-chromosomal variants for reconstructing the history of
domestic species with a wide geographic range.

\emph{Keywords~}\textbf{:}

goat, Y-chromosome, phylogeography, haplogroup, domestication,
migration, introgression



\textbf{Introduction}

Goat (\emph{Capra hircus} ), sheep (\emph{Ovis aries} ), cattle
(\emph{Bos taurus} ) and pigs (\emph{Sus scrofa} ) are four major
livestock species, which after their domestication in southwest Asia
about 10,000 BP (Larson \& Fuller, 2014; Stiner et al., 2022) spread to
all inhabited continents. Because of their relatively small size, sheep
and goats were the earliest domesticates, but have become less important
than cattle and pigs as suppliers of food. However, sheep and goat are
suitable for extensive management by smallholders or hobby breeders with
goats being favored in conditions of poverty (Peacock, 2005). Whereas
the high-quality goat cashmere wool and mohair fibres do not attain the
volume of sheep wool, the demand of goat milk and cheese has increased
considerably since the 1960s (Dubeuf, Morand-Fehr, \& Rubino, 2004;
Miller \& Lu, 2019). During the last four decades, this has doubled the
global number of goats to around 1 billion heads (Utaaker, 2021), which
now approaches the numbers for sheep and cattle (Hegde, 2019).

As for other livestock, genetic isolation, adaptation and selection have
created numerous local goat populations, whereas a restricted number of
high-performing breeds play a major role in the agricultural production.
The genetic diversity of goat breeds has been studied extensively
(Ajmone-Marsan et al., 2014; Amills et al., 2017; Deniskova et al.,
2021; Zheng et al., 2020). This demonstrated for autosomal DNA a
geographic partitioning of the diversity (Colli et al., 2018), which is
in sharp contrast to similar studies of sheep (Belabdi et al., 2019;
Ciani et al., 2020; Kijas et al., 2012), but has been confirmed by
similarities of ancient and modern DNA samples from the same regions
(Cai et al., 2020; Daly et al., 2018, 2021). However, the goat
Y-chromosome as a marker for the paternal lineages has not yet been
studied at a worldwide scale.

Because of its absence of recombination, the male-specific part of the
mammalian Y-chromosomes is by far the longest haplotype that is stably
transmitted across generations (Hughes et al., 2015). In many species,
males have a relatively small male effective population size, which
makes Y-chromosomal variants highly informative markers for paternal
origin that generally show a much stronger phylogeographic
differentiation than mitochondrial or autosomal variants. This is now
widely exploited in population-genetic studies of humans (Batini \&
Jobling, 2017; Jobling \& Tyler-Smith, 2017; Kivisild, 2017), cattle
(Edwards et al., 2011; Ganguly et al., 2020; Xia et al., 2019), horse
(Felkel et al., 2019; Wallner et al., 2017; Wutke et al., 2018), water
buffalo (Zhang et al., 2016), sheep (Deng et al., 2020; Meadows \&
Kijas, 2009; Zhang et al., 2014), camel (Felkel et al., 2019), llamas
and alpacas ((Marín et al., 2017) pigs (Choi et al., 2020; Guirao-Rico
et al., 2018) and dogs (Natanaelsson et al., 2006; Oetjens et al.,
2018).

A preliminary analysis of the Y-chromosomal diversity in European and
Turkish goats defined the three haplotypes Y1A, Y1B and Y2, which had a
strong geographic differentiation (Lenstra \& Econogene Consortium,
2005). The same haplotypes were found in goats from Portugal and
North-Africa (Pereira et al., 2009), Turkey (Çinar Kul et al., 2015),
eastern and southern Asia (Waki et al., 2015; Tabata et al., 2018, 2019)
and Switzerland and Spain (Vidal et al., 2017) with the additional
haplotypes Y2B in east Asia, Y2C in Turkish Hair and Kilis goats, and
Y1B2 as well Y1C mainly in Switzerland (Table S1). However, these
haplotypes are based on a low number of SNPs in or near \emph{DDX3Y,
SRY} and \emph{ZFY} and genotyping in a limited number of domestic goat
breeds. Thus, it is not clear if the haplotypes represent major
haplogroups or local variants or if other major haplogroups exist. Nor
does it inform us on the Y-chromosomal variants that existed in the
earlier domestic goats or in their wild ancestor, the bezoar
(\emph{Capra aegagrus} ) (Amills et al., 2017). Whole-genome sequences
(WGSs), however, has confirmed the differentiation of the Y1 and Y2
haplogroups (Xiao et al., 2021; Zheng et al., 2020).

In this study, we used WGS data for a large panel of goat breeds
(Denoyelle et al., 2021) to systematically characterize the SNP-level
variation in the single-copy male-specific part of the caprine
Y-chromosome. In addition, we determined the Y-chromosomal haplogroups
in goats originating from several European, Asian or African countries,
in ancient goat DNA samples and in the wild bezoar (Alberto et al.,
2018; Cai et al., 2020; Daly et al., 2018, 2021; M. Zhang et al., 2014;
Zheng et al., 2020). We sought to answer the following questions (1) How
are the WGS- based haplogroups related to the previously reported
haplotypes? (2) How are the domestic paternal lineages related to those
of bezoars from Iran and Anatolia, respectively? (3) How strong is the
phylogeographic structure of the caprine male lineages? (4) What does
the pattern of diversity tell us about Neolithic and later migrations?
(5) Can we also infer other gene flows between or within continents?
Answering these questions will contribute to our understanding of the
genetic background of the domestic goat, which is relevant for breed
management and conservation.

\textbf{Materials and Methods}

\emph{WGS data, filtering and phylogenetic analysis}

We selected as source of the SNPs four scaffolds that together cover
1,567,760 bp of the male-specific part of the caprine Y-chromosome.
These are unplaced in the ARS1 assembly but for a large part closely
match a recent Y-chromosomal contig of the Saanen\_v1 assembly (Table
S2)(Li et al., 2021) and contain the single-copy Y-chromosomal genes
\emph{SRY} , \emph{DDX3Y} ,\emph{ZFY} with the SNPs that define the
major haplotypes Y1A, Y1B, Y2A and Y2B (Çinar Kul et al., 2015; Lenstra
\& Econogene Consortium, 2005; Waki et al., 2015). The genes
\emph{USP9Y, UTY, DDX3Y} and \emph{ZFY}are proximate near one of the
ends of the male-specify Y-chromosomal region and well separated from
\emph{SRY} (Li et al., 2021). The selected contigs have a low overall
level of apparent heterozygosity, indicating a high frequency of
hemizygous markers (Table S2).

In a preliminary study
(https://www.biorxiv.org/content/biorxiv/early/2020/02/17/2020.02.17.952051.full.pdf),
we used WGS data from the Sequence Read Archive for 70 mainly Asian and
Moroccan male goats. We extracted the genotypes of 2350 SNPs without
female of male-heterozygous scores, \textless{}5\% missing scores/SNP
and a minor allele frequency (MAF) \textgreater{}0.02.

For a more comprehensive global coverage, we used the WGS datasets
generated by the VarGoats project (Denoyelle et al., 2021,
www.goatgenome.org/vargoats.html) or whole-genome sequences that have
been published previously or have been submitted to the Short-Read
Archive (Table S3). Four Y-chromosomal scaffolds were selected with a
low average frequency of heterozygous variants, which cannot belong to a
hemizygous Y-chromosomal SNP (Table S2). A VCF file for these scaffolds
was imported into Plink and contained 65556 variants, 54032 of which
were SNPs. From the 424 male samples, 34 were from wild goats, whereas
354 domestic goats had call rate of \textgreater{}5\%. After discarding
two domestic goats with unknown breed origin, we kept 386 wild or
domestic goats. SNPs were selected in four subsequent steps. (i) In 670
female goats with \textless{}1\% scores for the Y-chromosomal SNPs
(\emph{i.e.} free of male contamination) 36804 SNPs had a call rate of
zero and thus were considered male-specific. (ii) 29035 SNPs did not
show heterozygous score in the 424 males and were considered as being
hemizygous. (iii) 16495 had a call rate in the 388 male goats (354
domestic, 34 wild) of \textgreater{}1\%. (iv) 552 SNPs had a MAF in the
354 male domestic goats of \textgreater{}95\% and from the remaining
15943, 9977 SNPs had a at least one score in wild goats, summing up to a
total of 10529 SNPs representing male-specific Y-chromosomal variation
in domestic and/or wild goats.

Allele-sharing distances between individuals were calculated using Plink
or Mega (Tamura et al., 2011), and visualized in Neighbor-Joining trees
by using the programs Splitstree (Huson \& Bryant, 2006) and Mega.

For construction of a Median-Joining networks (Bandelt et al., 1999), we
selected 286 male goats and 27 bezoars, omitting transboundary breeds
outside their region of origin and balancing the breed representation by
analyzing \selectlanguage{english}[?]18 individuals per breed. With 1734 polymorphic SNPs, the
program Popart (Leigh \& Bryant, 2015) generated a network of 91
haplotypes (Table S4).

\emph{Haplogroups distribution in 180 goat breeds}

We differentiated the major Y-chromosomal haplogroups Y1AA, Y1AB, Y1B,
Y2A and Y2B for 2223 domestic goats from 180 breeds by combining data
from several sources as detailed per breed in Table S5:

\begin{enumerate}
\tightlist
\item
  From the goat panel collected for the Econogene project, DNA samples
  of 353 male goats from 38 European or southwestern Asian breeds were
  analyzed by PCR amplification and dideoxy-sequencing of \emph{DDX3Y}
  ,\emph{SRY} and \emph{ZFY} segments (Lenstra \& Econogene Consortium,
  2005) as described previously for bovine samples (Edwards et al.,
  2011; Nijman et al., 2008) and using the primers listed in Table S6.
\item
  We used published data from five Portuguese breeds or from Moroccan
  goats (Pereira et al., 2009), 12 Asian breeds or national populations
  (Waki et al., 2015, Tabata 2018, 2019, combined with unpublished
  data), for eight Turkish breeds (Cinar Kul et al., 2015) and for 26
  Spanish and Swiss breeds (Vidal et al., 2017).
\item
  Genotypes of 85 breeds in the VarGoats dataset were derived from their
  position in the phylogenetic trees (Fig. S1) and/or the alleles of the
  diagnostic SNPs (Table S1) without any conflicting assignments.
\item
  368 DNA samples from several sources, including the AdaptMap panel
  (Colli et al., 2018) were genotyped by the KASP assay (Kompetitive
  allele specific PCR assay), at the Van Haeringen Laboratory
  (Wageningen, Netherlands) and differentiated Y1 vs Y2 and Y1A vs Y1B.
\item
  For 31 breeds genotypes were obtained by Blast searching of the
  Short-Read Archive (SRA) or derived from the original WGS data. SRA
  data for pools of individuals were only used if this allowed an
  unambiguous identification of the haplogroup composition.
\end{enumerate}

For samples collected by Vidal \emph{et al.} (2017), a few samples
analyzed by Cinar-Kul \emph{et al.} (2015) and samples analyzed by KASP
before genomic data became available, Y1AA and Y1AB have been both
scored as Y1A haplotype. Several of these samples did not contain Y1A or
belonged to breeds for which additional data were available (Table S1).
However, for 17 breeds we only have the Y1A frequency. Likewise,
Vidal\emph{et al.} (2017) and the KASP assays did not differentiate Y2A
and Y2B. Since the VarGoats and Econogene panels with a comprehensive
coverage of Europe and Africa did not contain a single Y2B-carrying
goat, we assigned Y2 scores in other European and African goats to Y2A.

\emph{Haplotypes of ancient DNA samples}

Daly \emph{et al.} (2021) assigned ancient DNA samples from southwest
Asia and southeast Europe to the domestic Y-chromosomal haplogroups on
the basis of their positions in a phylogenetic tree. Cai \emph{et al.}
(2020) and Zheng \emph{et al.} (2020) described eight Chinese ancient
DNA samples and one medieval sample from the northern Caucasian region.
Sample YJL2G (coverage 13.4x) clustered with the Y1AB haplogroup, but
the low coverage of the others (from 0.013 to 0.118x) resulted in an
insufficient overlap with the 552 SNPs that are variable in domestic
goats and did not display female scores or male heterozygote scores (see
above). Therefore, we relaxed the latter requirements and allowed SNPs
scoring in 1\% of the females. After removal of two male samples, each
representing a unique haplotype, with a high proportion of heterozygote
scores, we excluded SNPs with male heterozygote scores only if this
occurred in a panel of 78 individuals representing different haplotypes.
This resulted in 5593 SNPs, 1018 of which were also scored in the
low-coverage aDNA samples. The combined phylogenetic signals (Table S7)
showed for sample GTM6G a high proportion of inconsistent scores,
presumably due to contamination, but allowed plausible haplogroup
assignment for samples KA1G, SMG11 and YJL2G and a tentative assignment
for GB3.

\textbf{Results}

\emph{Phylogeny of Y-chromosomal haplogroups}

A phylogenetic tree of the wild and domestic goats (Fig. 1A) shows an
intermingling of bezoars and the domestic goat. From the other wild goat
species, the markhor is the closest relative of the bezoar and the
domestic goat.

We found 107 different haplotypes in our panel of 352 domestic goats and
27 bezoars with markhor as outgroup. A phylogenetic tree (Fig. 1B) shows
haplogroups that correspond to the haplotypes Y1B, Y2A (Lenstra \&
Econogene Consortium, 2005) and Y2B (Waki et al., 2015) whereas the Y1A
haplotypes are split in haplogroups Y1AA and Y1AB. This is confirmed in
a dataset of mainly Asian and Moroccan goats (Fig. S1). All domestic
haplotypes differ from the Iranian or Anatolian bezoar haplotypes, which
also differ from each other. The bezoar haplotypes are associated with
the domestic Y1AA or Y2B clusters (CaY1AA and CaY2B, respectively), are
linked to the Y1 or Y2 roots (CaY1 and CaY2) or are outside the domestic
cluster (Y0).

Fig. S2 shows subtrees containing all 352 domestic goats. This figure
also indicates goats with the previously proposed local haplotypes
(Vidal et al., 2017; this study, Table S2): Y1AB2 (this study), Y1B2 and
Y1C. Y1B2 is represented by Swiss, French and Dutch goats. Our goat
panel does not contain goats with the Y2C diagnostic allele (Cinar Kul
et al., 2015).

The phylogenetic relationships of domestic and bezoar haplotypes are
confirmed by a Median-Joining Network (MJN, Fig. 2). Both the NJ tree
and the MJN network allow a few interesting observations to be made: (i)
a close relationship of Y1B sequences from Switzerland and Korean Native
goats, suggesting a recent crossbreeding; (ii) likewise, a close
relationship of Y1AA sequences from Central as well as South Asia, from
South-African Boer goats and from other Y1AA goats in southern and
eastern Africa and iii) a clear divergence of the Malagasy Y2A
haplotypes from the African continental haplotypes.

\emph{Geographic distribution of haplogroups}

Figs. 2 and 3 show the haplogroup distributions in 80 breeds from
Europe, Asia and Africa. Remarkably, there is clear difference between
the ancient and modern DNA samples. All five haplogroups were detected
in ancient goat samples from Southeast Europe and southwest Asia (Fig.
3A). In contrast, we observe a strong geographic differentiation of
domestic goats:

\begin{enumerate}
\tightlist
\item
  Haplogroup Y1B is predominant in central and northern Europe, but
  outside Europe and North Africa it has only been found in one Ugandan
  Karamonja goat, in the Korean native breed and in exported Saanen
  populations.
\item
  In northern and central Europe Y2A is only found in a single French
  des Fosses sample and together with Y1AA in the crossbred
  Anglo-Nubian. It is the predominant haplogroup in Spain, Anatolia and
  Africa south of the Sahara, but it is not found in China and Southeast
  Asia except in about 20\% of the goats in the Philippines and
  Sulawesi. Remarkably, most Y2A haplotypes on Madagascar are more
  related to Asian than to continental-African Y2A haplotypes.
\item
  Y2B is absent in Europe, continental Africa and west Asia, but is a
  major haplotype in east and southeast Asia. It is also observed in one
  Malagasy Diana sheep.
\item
  Y1AA is in Europe only represented by three haplotypes in the local
  Ciocara breed and the island Montecristo population (Somenzi et al.,
  2022). The Italian haplotypes are outside the cluster of closely
  related south-Asian and southeast-African Y1AA haplotypes (Figs. 2,
  S2).
\item
  The available data suggest a contrast of Y1AB dominating in northern
  China and Y1AA with Y2B in the south.
\end{enumerate}

\textbf{Discussion}

One of the benefits of the current availability of WGS datasets is the
access to an abundance of sequence variants, which allow a comparison of
individuals or populations for several purposes. This is especially
useful for the analysis of Y-chromosomal diversity, which used to be
restricted by the availability of Y-chromosomal markers. The
male-specific part of the Y-chromosome constitutes the longest haplotype
in the mammalian genome and may serve as marker for mammalian paternal
lineages. Here, we combined the dataset of the VarGoats project with
published data and genotyped diagnostic SNPs in male goat samples from
several sources.

The Y-chromosomal phylogeny of wild and domestic goats is in agreement
with the Y-chromosomal tree on the basis of \emph{AMELY} and
\emph{ZFY}gene fragments (Pidancier \emph{et al.} 2006) and with a
phylogeny of WGS sequences (Grossen et al., 2020; Cai et al.,
unpublished). MtDNA trees confirm the close relationship of markhor
(\emph{Capra falconeri} ) with bezoar and domestic goat, but do not show
the separation of these species and the other wild goats. In addition,
mitochondrial DNA (mtDNA) sequences of some, but not all East-Caucasian
turs (\emph{Capra cylindricornis} ) cluster with the mtDNAs of markhor,
bezoar and domestic goat, illustrating a separate history of maternal
and paternal lineages in cross-fertile species (Chen et al., 2018; Marin
et al., 2017; O'Connell et al., 2014; Zhang et al., 2020; Zhang et al.,
2016).

On the basis of WGS data, Zheng \emph{et al.} (2020) and Xiao \emph{et
al.} (2021) reproduced the divergence of the domestic Y1 and Y2
haplogroup previously found on the basis of SNPs within or near
Y-chromosomal genes (Lenstra et al., 2005). Here we report a further
differentiation of haplogroups, resulting in a phylogeny supported by a
largely independent preliminary dataset (Fig. S1) and two phylogenetic
algorithms. We found that the major haplogroups corresponds with
haplotypes defined by SNPs (Cinar Kul et al., 2015; Lenstra \& Econogene
Consortium, 2005; Pereira et al., 2009; Tabata et al., 2018, 2019; Vidal
et al., 2017; Waki et al., 2015), but Y1A haplotypes belong to either
haplogroup Y1AA or haplogroups Y1AB.

The phylogeny also indicates that these haplogroups diverged after the
split of the markhor and the cluster of the wild bezoar and the domestic
goats. The domestic goats and the two bezoar populations from Anatolia
and Iran do not share haplotypes, whereas the bezoar haplotypes are
attached to deep nodes in the tree of domestic haplotypes. This suggests
an absence of male gene flow between the bezoar populations and between
the bezoar and domestic goats from the same region. Thus, domestic
goats, which possibly were derived from bezoar populations not sampled
in this study, maintained their paternal lineages during the migration
from the Fertile Crescent via Anatolia to Europe, this in spite of
indications of management of wild goats in central Anatolia (Stiner et
al., 2022).

Geographic plots of domestic haplogroup frequencies show a considerable
spatial differentiation, which resonates with the strong phylogeography
displayed by autosomal SNPs (Colli et al., 2018), but is in clear
contrast with the weak phylogenetic structure displayed by the major
mtDNA haplogroups (Luikart et al., 2001; Naderi et al., 2007, 2008; Zhao
et al., 2014b, 2014a, Colli et al., 2015). Remarkably, Y-chromosomal
haplotypes from all five haplogroups have been found in ancient DNA
samples from Southwest Asia or Southeast Europe. The locations of
ancient Y1AA, Y1B and Y2B samples are well outside the range of the
corresponding domestic haplogroups (Fig. 3). This indicates that during
the Neolithic and later worldwide migrations a series of bottlenecks and
expansions in the domestic male lineage created a strong geographic
differentiation of the haplogroup distribution (Fig. 4):

\begin{enumerate}
\tightlist
\item
  The dominance of haplogroup Y1B in central and northern Europa may
  very well reflect population bottlenecks during the Neolithic
  introduction of agriculture via the Danube route (Cymbron et al.,
  2005; Rivollat et al., 2015; Tresset \& Vigne, 2007)
\item
  Y2A and Y1AA are almost the only haplogroups in Africa south of the
  Sahara. The two African Y1AA haplotypes are related to those of Asian,
  indicating that only Y2A expanded during the first introduction of
  domesticated goats in central and southern Africa
\item
  Y2B has been found in two Neolithic Iranian samples whereas related
  CaYB2 haplotypes are present in Iranian and Anatolian bezoars.
  However, by population bottlenecks during the global spreading of
  domestic goats Y2b now only occurs in Asia east of the Indus River and
  in one goat from Madagascar (see below).
\item
  Y1AA was found in Neolithic samples in southeast Europe, but now has a
  low frequency in Europe. In Asia it expanded together with Y2B and
  later came to South Africa when Asian goats were used to breed the
  Boer goat (see below).
\item
  Y1AB is the most frequent haplogroup in north China. The distributions
  of Y1AB and Y1AA/ Y2B in East Asia correspond to ranges of the
  north-Chinese cashmere goats and the small Southeast Asian `katjang'
  type, respectively (Porter et al., 2016). This obviously reflects the
  large difference of climate between northern and southern China, which
  determined a similar distribution of taurine and indicine cattle.
  These two types of cattle are supposed to have entered China via a
  northern and southern migration route, respectively (Chen et al.,
  2018; K. Zhang et al., 2020), which support the separate eastern
  expansions of the Y1AB and Y1AA/Y2B goats, respectively.
\end{enumerate}

Exceptions to these geographic patterns follow from close relationships
between haplotype from different continents, which are most likely
explained by later major introgressions. Interestingly, in the
phylogenetic trees and networks (Figs. 2 and S2) the Y2A haplotypes on
Madagascar are closely related to Asian haplotypes and one Diana goat
from northern Madagascar even has an eastern-Asian Y2B haplotype.
However, autosomal DNA shows that the Malagasy goats are more related to
the southern and eastern African continental goats (Colli et al., 2018;
Denoyelle et al., 2021). This parallels a recent finding that Malagasy
cattle combines Indian and admixed African zebu ancestry (Magnier et
al., 2022). The Malagasy language has an Austronesian origin, which
testifies the colonization of Madagascar by immigrants from southeastern
Asia about 500 CE. Thus, it is likely that these immigrants brought
Austronesian goats, cattle and possibly also other livestock from their
region of origin to Madagascar.

Other introgressions are more recent. The exceptional Y1AA and Y2A in
the English Anglo-Nubian is explained by the documented import during
the 19\textsuperscript{th} century of Indian and African goats to
England. These served on the ships as source of milk and meat, but
surviving males were crossed with English goats, which resulted in the
emergence of a popular transboundary breed.

The worldwide popular Boer goat also is of mixed origin (Porter et al.,
2016; Vidal et al., 2017) and carries exclusively Y1AA haplotypes. This
breed is supposed to be a crossbred of local African and Indian goats,
possibly mediated by incrossing of Anglo-Nubian males (Porter et al.,
2016). The crossbred origin is consistent with the results of
Colli\emph{et al.} (2018): a separate phylogenetic position of the Boer
relative the other African and Asian goats and the K=3 pattern of
model-based clustering showing African and west-Asian ancestry. The
Indian ancestry is entirely in agreement with a close clustering of the
Boer and Pakistani Y1AA haplotypes (Figs. 1B and 2).

Subsequently, the Boer became itself a source of introgression. The same
Y1AA haplotypes are closely related to Y1AA haplotypes in local breeds
in Uganda, Malawi, Mozambique and Zimbabwe. In these countries
crossbreeding with Boer goats from Africa is popular because of its
excellent meat production (Banda et al., 1993; Garrine, 2007; Lu, 2011;
Onzima et al., 2018). Therefore, it is most likely that the Y1AA in
eastern and southern African goats originates from the Boer.

There were three out-of-range findings of Y1B, in the Ugandan Karamonja,
in the Korean native goat and in the indigenous goats kept on the
Chongmin Island in Shanghai. Because of the popularity of Swiss dairy
goats in both Uganda (NAADS, 2005) and Korea (Kim et al., 2019),
crossbreeding again is the most likely explanation. There are no data on
European admixture in the Chongmin goats (Gao et al., 2020). Thus,
exotic occurrence of Y chromosomal variants are direct and sensitive
indicators of admixture events, but are to be complemented with
quantitative admixture tests, such as model-based clustering,
the\emph{f} \textsubscript{3} and \emph{f} \textsubscript{4} test or,
ideally, identification of introgressed segments across the genome.

The latter approach may also lead to clues on the phenotypic
consequences of the introgression via the identification of the admixed
genes (Chen et al., 2018; Lv et al., 2014; Wang et al., 2015; Zheng et
al., 2020). A more direct link with the Y-chromosomal variation would be
provided if this can be linked to male phenotypic traits, but even in
human genetics this has scarcely be investigated (Matsunaga et al.,
2021; Yang et al., 2018; X. Zhang et al., 2021). Breeds in which
different Y-chromosomal haplogroups occur may allow to study an
association of haplogroups with typically male traits such as male
fertility and dominance behavior. It would be interesting if
Y-chromosomal variants can be related to the climate or other
environmental features, because this would imply that the geographic
differentiation of the Y-chromosomal variation is driven by regional
adaptation.

Most introgressions described in this study contribute to the expansion
of popular breeds at the expense of the original local breeds. On the
one hand, depending on the extent of the gene flow this may decrease the
diversity of the genetic resources; on the other hand, it does not
necessarily disrupt the environmental adaptation, arguably one of the
most consequential components of the phenotypic repertoire. If properly
managed, admixture of productive breeds may also contribute to the
sustainable conservation of local populations and illustrates that
genetic diversity has never been a static phenomenon.

We conclude that the Y-chromosomal variation of goats reveals
bottlenecks, expansions and introgressions, illustrating the power of
Y-chromosomal markers for inferring the genetic origin of mammalian
populations.

\textbf{Ethics Approval}

Blood samples were collected according to the regulations of
veterinarian

practice in the country where the sampling was carried out.

\textbf{Conflict Of Interest}

The authors declare that the research was conducted in the absence of
any commercial or financial relationships that could be construed as a
potential conflict of interest.

\textbf{Acknowledgements}

The VarGoats project sequencing effort has been funded mainly by France
Genomique ``Call for high impact projects'' (ANR\selectlanguage{english}-10\selectlanguage{english}-INBS\selectlanguage{english}-09\selectlanguage{english}-08) and by
the BBSRC Global Challenges Research Fund Data and Resources Grant
BBS/OS/GC/000012F awarded to the Roslin Institute for Reference genome
and population sequencing of African goats. Detailed funding sources of
the VarGoats project are described in Denoyelle et al, 2021). This study
was supported by the Croatian Science Foundation (Project
ANAGRAMS-IP-2018-01-8708 ``Application of NGS in assessment of genomic
variability in ruminants'' and by the European Union (projects ECONOGENE
QLK5--CT2001--02461). We are grateful to Dr E. Cuppen (Utrecht Medical
Centre) for access to dideoxy sequencing facilities.

\textbf{VarGoats Consortium}

\textbf{Australia} : James Kijas, CSIRO; \textbf{Denmark} : Bernt
Guldbrandtsen, Aarhus University; \textbf{Finland} : Juha Kantanen,
Luke;\textbf{France} : Gwenola Tosser\selectlanguage{english}-Klopp, Philippe Bardou, Laure
Denoyelle, Thomas Faraut, Julien Sarry, Estel le Talouarn, GenPhySE,
Castanet\selectlanguage{english}-Tolosan; Adriana Alberti, Celine Orvain , Stefan Engelen,
Universite Paris-Saclay, Evry; Dylan Duby, Museum National d'Histoire
Naturelle; Pierre Martin, Capgenes; Coralie Danchin, Delphine Duclos,
Institut de l'Elevage; Daniel Allain, Remy Arquet, Nathalie Mandonnet,
Michel Naves, Isabelle Palhiere, Rachel Rupp, INRAE, and CABRICOOP
breeders; Francois Pompanon, LECA; \textbf{Iran} : Hamid R. Rezaei,
Gorgan University of Agricultural Sciences and Natural
Resources;\textbf{Ireland} : Sean Carolan and Maeve Foran, Old Irish
Goats Society;\textbf{Italy} : Alessandra Stella, IBBA-CNR; Paolo
Ajmone-Marsan, Licia Colli, Marcello Del Corvo, Universita Cattolica del
Sacro Cuore; Alessandra Crisa, Council for Agricultural Research and
Economics (CREA); Donata Marletta, University of Catania, Italian Goat
Consortium; Paola Crepaldi, University of Milan, Italian Goat
Consortium; Michele Ottino, Parco Nazionale del Gran Paradiso; Ettore
Randi, ISPRA Istituto Superiore per la Protezione e la Ricerca
Ambientale; \textbf{Kenya} : Denis Fidalis Mujibi, International
Livestock Research Institute (ILRI), Nairobi; Malawi: Timothy Gondwe,
Department of Animal Science, Lilongwe University of Agriculture and
Natural Resources; \textbf{Morocco} : Badr Benjelloun, INRA Maroc;
\textbf{Mozambique} : Maria Da Gloria Taela, Animal Production
Institute, Ministry of Agriculture, Maputo;\textbf{Netherlands} :
Johannes A, Lenstra, Utrecht University;\textbf{Nigeria} : Oyekan Nash,
National Biotechnology Development Agency; \textbf{Pakistan} : Muhammad
Moaeen-ud-Din, PMAS-Arid Agriculture University; \textbf{South Africa} :
Carina Visser, Faculty of Natural and Agricultural Sciences;
\textbf{Spain} : Felix Goyache, Isabel Alvarez, Area de Genetica y
Reproduccion Animal del Serida, Villaviciosa; Marcel Amills and Armand
Sanchez, Centre for Research in Agricultural Genomics (CRAG); Juan
Capote, Instituto Canario de Investigaciones Agrarias (ICIA); Jordi
Jordana, Universitat Autonoma de Barcelona; Agueda Pons, Serveis de
Millora Agraria i Pesquera (SEMILLA), Illes Balears; Amparo Martinez and
Antonio Molina, University of Cordoba;\textbf{Switzerland} : Cord
Drogemuller, University of Bern;\textbf{Tanzania} : Hassan Ally Mruttu,
Ministry of Livestock and Fisheries Development; \textbf{Uganda} : Clet
Wandui Masiga, Tropical Institute of Development Innovations (TRIDI);
\textbf{UK} : Emily Clark, Mazdak Salavati, University of Edinburgh,
Edinburgh; \textbf{USA} : Benjamin Rosen, Curtis P. Van Tassell,
USDA/ARS; Jim Reecy, Iowa State University, Ames; Gordon Luikart,
Montana Conservation Genomics lab (MCGL), Division of Biological
Sciences, University of Montana, Missoula; \textbf{Zimbabwe} : Joseph
Sikosana, Department of Research and Specialist Services, Division of
Livestock Research.

\textbf{Econogene Consortium}

\textbf{Albania:} Hoda Anila, Dobi Petrit, Fac. Agriculture,
Tirana;\textbf{Austria:} Baumung Roswitha, Univ. Natural Resources
Applied Life Sciences, Vienna; \textbf{Belgium:} Baret Philippe,
Fadlaoui Aziz, Univ. Cath. Louvain, Louvain-la-Neuve; \textbf{Cyprus:}
Papachristoforou Christos, Agricult. Research Instit., Nicosia;
\textbf{Egypt:} El-Barody M.A.A., Minia Univ.; \textbf{France:} Taberlet
Pierre, England Phillip, Luikart Gordon, Beja-Pereira Albano, Zundel
Stephanie, Univ. Joseph Fourier, Grenoble; Trommetter Michel, Inst.
Recherche Agronomique, Grenoble; \textbf{Germany:} Erhardt Georg, Brandt
Horst, Ibeagha-Awemu Eveline, Luhken, Gesine, Daniela Krugmann,
Prinzenberg Eva-Maria, Lipsky Shirin, Gutscher Katja, Peter Christina,
Justus-Liebig Univ. Giessen; Roosen Jutta, Bertaglia Marco, Univ. Kiel;
\textbf{Greece:} Georgoudis Andreas, Al Tarrayrah, Jamil, Kliambas
Georgios, Kutita Olga, Karetsou Katerina, Aristotle Univ. Thessaloniki,
Thessaloniki; Ligda Christina, National Agric. Research Foundation,
Thessaloniki; \textbf{Hungary:}Istvan Anton, Fesus Lazlo, Research Inst.
Animal Breeding Nutrition, Herceghalom; \textbf{Italy:} Ajmone-Marsan
Paolo, Canali Gabriele, Milanesi Elisabetta, Pellecchia Marco,
Universita Cattolica S. Cuore, Piacenza; Carta Antonello, Sechi Tiziana,
Ist. Zootecnico Caseario Sardegna, Sassari; Cicogna Mario, Fornarelli
Francesca, Giovenzana Stefano, Marilli Marta, Univ. Studi di Milano;
Marletta Donata, Bordonaro S., D'Urso Giuseppe, Univ. Studi Catania;
Pilla Fabio, D'Andrea Mariasilvia, Univ. Molise, Campobasso; Valentini
Alessio, Cappuccio Irene, Pariset Lorraine, Univ. Tuscia,
Viterbo;\textbf{Jordan:} Abo-Shehada Mahamoud, Jordan Univ. Science
Technology;\textbf{Netherlands:} Lenstra Johannes A., Nijman, Isaac J.,
Van Cann, Lisette M., Utrecht Univ.; \textbf{Poland:} Niznikowski Roman,
Dominik Popielarczyk, Strzelec Ewa, Warsaw Agricultural Univ.;
\textbf{Romania:}Vlaic Augustin, Univ. Cluj-Napoca; \textbf{Spain:}
Dunner Susana, Canon Javier, Cortes Oscar, Garcia David, Univ.
Complutense Madrid;\textbf{Switzerland:} Caloz Regis, EPFL, Lausanne;
Obexer-Ruff Gabriela, Marie-Louise Glowatzki, Universitat Bern;
\textbf{Turkey:} Ertugrul Okan, Ankara Univ.; Togan Inci, Koban Evren,
Middle East Technical Univ., Ankara; \textbf{UK:} Bruford Mike, Perez
Trinidad, Juma Gabriela, Cardiff Univ.; Hewitt Godfrey, Dalamitra
Stella, Wiskin Louise, Taylor Martin, Univ. East Anglia, Norwich; Jones
Sam, The Sheep Trust; Scarpa Riccardo, Univ. York.



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\textbf{Data Availability}

The novel whole-genome sequences from European, Pakistan and African
goats analyzed in this study were obtained from the VarGoats project
(www.goatgenome.org/vargoats.html) (Denoyelle et al., 2021).

\textbf{Authors' Contributions}

\par\null

IJN, PAM and JAL designed the study; GT-K and LC coordinated the
VarGoats project; IJN and BÇK carried out the ABI sequencing; BDR, PB,
TF, ZZ, YJ, YC, ZC, MMi and GS analyzed the WGS data; TC, FPo and CD
supplied the bezoar genotypes; KGD, DGB, YC and YJ supplied the aDNA
data; HM, FK, SS, MMa, YN, AA, JSM, IAD, SRAB, FMD, TD, MKS, MB and PK
provided genotypes for south Asian goats; BDR supplied most of the
African samples for KASP genotyping; VAB, DB, BB, TB, SC, VC-C, LD, JG,
JH, JK, NKh, NK, AM, RM, JMc, NAOC, FPe, AdS, MS, JS, AS, JT and HZ
collected material and/or data for other breeds; JAL and IJN performed
the downstream analysis; JAL wrote the first draft; and KGD, AM, FPe,
BÇK, JMc, MM, MS, PAM, LC, CD and GTK contributed to the text\textbf{.}



\textbf{Fig. 1A}

\textbf{Hosted file}

\verb`image1.emf`  available at \url{https://authorea.com/users/465598/articles/560169-geographical-contrasts-of-y-chromosomal-haplogroups-from-wild-and-domestic-goats-reveal-ancient-migrations-and-recent-introgressions}



\textbf{Hosted file}

\verb`image2.emf`  available at \url{https://authorea.com/users/465598/articles/560169-geographical-contrasts-of-y-chromosomal-haplogroups-from-wild-and-domestic-goats-reveal-ancient-migrations-and-recent-introgressions}

\textbf{Fig. 1B}

Fig. 1. Neighbor-joining tree of allele-sharing distances calculated on
the basis of 10529 hemizygous male-specific SNPs extracted from the
VarGoats WGSs. \textbf{A.} Fourteen wild goats and five domestic goats
with indicated haplogroup. \textbf{B.} 101 different haplotypes in 352
male domestic goats and 27 male bezoars and (not shown) markhor as
outgroup. Individual codes consist of \textbf{(\emph{i})} Country codes,
first two letters: AZ, Azerbaijan; BD, Bangladesh; CH, Switzerland; CN,
China, DK, Denmark; ET, Ethiopia; FI, Finland; FR, France; IE, Ireland;
IL, Israel; IR, Iran; IS, Iceland; IT, Italy; KE, Kenya; KO, Korea; MG,
Madagascar; ML, Mali; MO, Morocco; MZ, Mozambique; NL, Netherlands; NZ,
New Zealand; PK, Pakistan; RU, Russia; SD, Sudan, TR, Turkey; TJ,
Tadjikistan; TZ, Tanzania; UZ, Uzbekistan; ZA, South Africa; ZW,
Zimbabwe); \textbf{(\emph{ii})} Species code,
3\textsuperscript{rd}-4\textsuperscript{th} letter: CA (\emph{Capra
aegagrus} ), bezoar; CC (\emph{Capra caucasica} , \emph{Capra
cylindricornis} ), West- and East-Caucasian tur, respectively; CF
(\emph{Capra falconeri} ), markhor; CH (\emph{Capra hircus} ), domestic
goat; CI (\emph{Capra ibex} ) Alpine ibex; CN (\emph{Capra nubiana} ),
Nubian ibex; CS (\emph{Capra sibirica} ), Siberian
ibex.\textbf{(\emph{iii})} Codes for domestic breeds (three letters), or
bezoar populations (four letters): see Figure 3.
\textbf{(\emph{iv})}Sample number. Numbers near the nodes indicate
bootstrapping values (\%) after carrying out 100 bootstrap replicates.
Y0, CaY1, CaY1AA, CaY2 and CaY2B indicate bezoar haplotypes.

\textbf{Hosted file}

\verb`image3.emf`  available at \url{https://authorea.com/users/465598/articles/560169-geographical-contrasts-of-y-chromosomal-haplogroups-from-wild-and-domestic-goats-reveal-ancient-migrations-and-recent-introgressions}

Fig. 2. Median-Joining Network of 286 male domestic goats and 27
bezoars, omitting transboundaries breeds outside their region of origin
and balancing the breed representation by reducing the sample size of
ALP and SAA to 18 individuals. This panel has 1734 SNPs with MAF
\textgreater{} 0.01, and 91 different haplotypes (Table S3)

Fig. 3a

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Fig.
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Fig.
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Fig.
3d

Fig. 3. Haplogroup distributions for 171breeds (2210 goats). (a) Ancient
DNA samples and bezoars; (b) European breeds; (c) Asian breeds; (d)
African breeds; Breed or bezoar population codes: ABA, Abaza; ABR,
Abergelle; ALG, Algarve; ALP, Alpine; ANB, Anglo-Nubian; AND, Androy;
ANK, Angora; APP, Appenzell; ARA, Arabia; ARG, Argentata dell'Etna; ARR,
Arran; ARW, Arapawa; BAG, Bagot; BAL, Balearic; BBL, Black Bengal; BCM,
British Composite Dairy; BEE, Beetal Black Pakistan; BEY, Bermeya;
Bhutan; BIO, Bionda dell'Amadello; BLA, Blanca Andaluzza; BLB, Bilbery;
BLO, Blobe; BOE, Boer; BRI, Barbari (Bari) ; BRV, Bravia; BUK, Polish
Fawn Colored; BZAl, Algorz bezoar; BAAz, Azerbaijan bezoar; BZFa, Fars
bezoar; BZMa; Markazi bezoar; BZTr, Anatolian bezoar; BZZa, Zagros
bezoar; CAG, Capra Grigia; CAM, Cambodjan; CAP, Capore; CCG, Ciociara;
CDB, Chengdu Brown; CDM, Chaidamu Qinhai; CHQ, Charnequeira; CHV,
Cheviot; COR, Corsican; CPC, Changtangi Pashmira Cashmere; CRO, Croatian
Spotted; CRP, Carpathian; DAM, Damani; DIA, Diana; DJA, Djallonke; DKL,
Danish Landrace; DPG, Dutch Pied Goat; DRZ, Dreznica; DSA, Dutch Saanen;
DUA, Du'an; DUK, Dukati; DUL, Dutch Nordic Goat; ESF, Esfahan; ETH,
Ethiopian; FIN, Finnish; FLR, Florida; FSS, de Fossés; FUE,
Fuenteventura; GAL, Galla; GAR, Garganica; GDR, Guadarrama; GGT,
Girgentata; GMO, Grigia Molisana; GRG, Greek; GRS, Grisons Striped; GUA,
Guadeloupe Creole; GUE, Guéra; GUR, Gurcu; HAI, Hair (Anatolian Black);
HAS, Hasi; HNM, Honamli; IND, Indian; IRA, Iran; IRQ, Iraq; IST,
Istrian; JBL, Jintang Black; JPA, Shjiba; JSA, Saanen; KCC, Kacchan;
KHA, Khazakhstani; KHU, Khurasani; KIG, Kigezi; KLS, Kilis; KMO,
Karamonja; KMR, Kamorr; KNG, Korean Native; KSA, Korean Saanen; LAO,
Laos; LBA, Lori-Bakhtiari; lCL, Icelandic; LGL, Longlin; LIQ, Liqenasi;
LOR, Lorraine; MAK, Makatia; MAT, Mati; MAU, Maure; MEN, Menabe; MGL,
Mongolian; MLG, Malagueña; MLI, Mali; MLT, Maltese; MLW, Malawi; MLY,
Malya; MNT, Montecristo; MOR, Moroccan; MSH, Mashona; MTB, Matebele;
MUB, Mubende; MUG, Murciano Granadina; MUL, Mulranny; MUZ, Muzhake; MYA,
Myanmar; MZ, Mozambique; MZA, M'Zabite; NAC, Nacki; NCG, Norwegian
Coastal; NDG, Norwegian Dairy; NDZ, Norduz; NEP, Nepalese; NGD, Nganda;
NKA, Naine de Kabylie; ORO, Orobica; PCG, Peacock; PAT, Pateri; PER,
Percy Island; PEU, Peulh; PHI, Pilippine; PIZ, Pinzgauer; PRW,
Pare-White; PTV, Poitevin; PVC, Provencale; PYR, Pyrenean; PYY, Payoya;
QIN, Qin; QHI, Qinhai; RAN, Rangeland; RAO, Henan Raoshan White; RAS,
Rasquera; ROV, Rove; RSK, Nigerian Maradi (Red Sokoto); SAA, Saanen;
SAR, Sarda; SAV, Savoye; SCA, Shaanbei Cashmere; SDN, Sudan; SEA, Small
East African; SEB, Sebei; SER, Serrana; SGB, St Gallen Booted; SHL,
Shahel; SHN, Nigerian Sahel; SKO, Skopelos; SNJ, Sanja; SOF, Sofia; SOU,
Southwest; SRP, Serpentina; SSG, Steirische Schecken; SSU, South
Sulawesi; TAS, Tauernschecken; TED, Teddi; TER, Teramo; THA, Thari; TIB,
Tibetan; TNF, Tinerfena; TOG, Toggenburg ; TWZ, Thuringian Forest; TZ,
Tanzania; VAG, Valais Blackneck; VAG, Valais Blackneck; VAL, Valdostana;
VIE, Vietnamese; VRT, Verata; VZC, Verzasca; WAD, West African Dwarf;
XJI, Xinjiang; YBL, Youzhou Black Skin; YIM, Shandong Yimeng White; ZAR,
Zaraiba.



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Fig. 4. Bottlenecks, migrations and introgressions of domestic goat.
Fill block arrows indicate the approximated place where
population-bottlenecks that have altered regional haplogroup
distributions. Open block arrows indicate subsequent migrations. Dashed
arrows indicate later introgressions. This figure does not indicate
export of transboundary breeds.



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\textbf{Supplemental Figures}

Fig. S1. Neighbor-joining tree of allele-sharing distances calculated on
the basis of 2350 hemizygous male-specific SNPs extracted from WGS of 70
male goats (Table S1) and the markhor sequence as an outgroup. BDCH-BEE,
Beetal Black; CNCH-QHI, Qinghai; CNCH-RAO, Henan Raoshan white;
CNCH-YIM, Shandong Yimeng Black; CNCH-TIB, Tibetan; CNCH-XJI, Xinjiang;
CNCH-YIM, Chinese Shandong Yimeng White FRCH-ALP, French Alpine;
FRCH-PTV, Poitevine; IRCH-IRA, Iran; KRCH-KNG, Korea native; KRCH-KSA,
Korean Saanen; MOCH-MOR, Morocco; NLCH-LNR, Dutch Landrace; NLCH-SAAA,
Dutch Saanen; PKCH-BEE, Pakistan Beetal Black. SDCH-SDN, Sudan; SNPs
with missing values were omitted. Figure near the nodes indicate
bootstrapping values (\%).

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Fig. S2. Neighbor-joining tree of allele-sharing distances for
haplogroups Y1AA and Y1AB (left), Y1B (middle) and Y2A and Y2B (right).



\textbf{Supplemental Tables (see separate file)}

Table S1. Diagnostic SNPs used in this and previous studies. Mutations
are relative to the goat reference sequence, which has haplotype Y1AB.
Haplotype assignments are consistent with their position on the
phylogenetic trees.

Table S2. Selection of Y-chromosomal scaffolds in the ARS1 assembly with
the lowest frequency of heterozygote SNP scores in male goats. Scaffolds
used as source of SNPs are printed in bold.

Table S3. Individual codes (see Figs. 1 and 3) and SRA accession numbers
of WGS data used retrieved from the Sequence Read Archive and used for
phylogenetic analysis. Other SRA accession codes are in Table S5.

Table S4. Y-chromosomal haplotypes in domestic goats (A) and bezoars (B)
used for Figs. 1b and 2. See Fig. 1 for the individual codes. Horizontal
lines separate animals with the same haplotype. Haplotypes for the
Neighbor-joining tree in Fig. 1b are based on allele-sharing distances.
For the Median-Joining Network in Figure 2 trees, transboundary goats
outside their countries have been omitted and \selectlanguage{english}[?]18 goats per breed were
considered. Eight haplotypes for Fig. 1b were fused to other haplotypes
by the default settings of the program Popart used for the construction
of the Median-Joining Network.

Table S5. Haplogroup distributions in breeds or populations, in ancient
DNA and in the bezoar. Kasp, (Kompetitive allele-specific PCR assay);
ddSeq, dideoxy sequencing. Codes starting with ERX or SRX indicate Short
Reads Archive accessions.

Table S6. Primers for amplification and dideoxy sequencing
of\emph{DDX3Y} , \emph{SRY} and \emph{ZFY} fragments and genomic
coordinates of sequence covered by the sequence reads excluding the most
upstream and most downstream primer sequences.

Table S7. Identification of haplogroups for ancient DNA samples. Minor
allele frequencies are based on a panel of 354 male goats with call
rates \textgreater{}5\%.

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