Patterns of homozygosity in insular and continental goat breeds

Ca dosoe al. Gene Sel E ol (2018) 50:56 h ps://doi.o g/10.1186/s12711-018-0425-7 RESEARCH ARTICLE Pa e ns o homozygosi y ininsula andcon inen al goa b eeds Taina F. Ca doso1,2†, Ma cel Amills1,3*† , F ancesca Be olini4, Max Ro hschild4, Gab iele Ma as5, Gee Boink6, Jo di Jo dana3, Juan Capo e7, Sean Ca olan8, Jón H. Hallsson9, Juha Kan anen10, Agueda Pons11, Johannes A. Lens a12* and The Adap Map Conso ium Abs ac Backg ound: Gene ic isola ion o b eeds may esul in a signi ican loss o di e si y and ha e consequences on heal h and pe o mance. In his s udy, we examined he e ec o geog aphic isola ion on cap ine gene ic di e si y pa e ns by geno yping 480 indi iduals om 25 Eu opean and A ican b eeds wi h he Goa SNP50 BeadChip and compa ing pa e ns o homozygosi y o insula and nea by con inen al b eeds. Resul s: Among he b eeds analysed, numbe and o al leng h o ROH a ied conside ably and depending on b eeds, ROH could co e a subs an ial ac ion o he genome (up o 1.6 Gb in Icelandic goa s). When compa ed wi h hei con inen al coun e pa s, goa s om Iceland, Madagasca , La Palma and I eland (Bilbe y and A an) displayed a signi ican inc ease in ROH co e age, ROH numbe and FROH alues (P alue < 0.05). Goa s om Medi e anean islands ep esen a mo e complex case because ce ain popula ions displayed a signi ican ly inc eased le el o homozygo‑ si y (e.g. Gi gen ana) and o he s did no (e.g. Co se and Sa da). Co ela ions o numbe and o al leng h o ROH o insula goa popula ions wi h he dis ance be ween islands and he nea es con inen al loca ions e ealed an e ec o ex emely long dis ances on he pa e ns o homozygosi y. Conclusions: These esul s indica e ha he e ec s o insula iza ion on he pa e ns o homozygosi y a e a iable. Goa s aised in Madagasca , Iceland, I eland (Bilbe y and A an) and La Palma, show high le els o homozygosi y, whe eas hose b ed in Medi e anean islands display pa e ns o homozygosi y ha a e simila o hose ound in con inen al popula ions. These esul s indica e ha he di e si y o insula goa popula ions is modula ed by mul iple ac o s such as geog aphic dis ibu ion, popula ion size, demog aphic his o y, ading and b eed managemen . © The Au ho (s) 2018. This a icle is dis ibu ed unde he e ms o he C ea i e Commons A ibu ion 4.0 In e na ional License (h p://c ea i eco mmons .o g/licen ses/by/4.0/), which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided you gi e app op ia e c edi o he o iginal au ho (s) and he sou ce, p o ide a link o he C ea i e Commons license, and indica e i changes we e made. The C ea i e Commons Public Domain Dedica ion wai e (h p://c ea i eco mmons .o g/ publi cdoma in/ze o/1.0/) applies o he da a made a ailable in his a icle, unless o he wise s a ed. Backg ound The ad en o nex -gene a ion sequencing and high h oughpu geno yping echniques has made i possible o iden i y, in he genomes o mul iple species, con inu- ous homozygous s e ches o sequence, which a e named uns o homozygosi y (ROH) [1]. The genomic dis i- bu ion, abundance, and leng h o ROH a e modula ed by mul iple ac o s including local ecombina ion a e, guanine-cy osine con en , posi i e selec ion and demog- aphy [2, 3]. A high equency o long ROH is o en caused by ecen inb eeding, whe eas a high equency o sho ROH can be explained by he occu ence o an ancien ounde e ec o popula ion bo leneck. A e he i s pionee ing s udy o Fe enčako ić e al. [4], he pa e ns o ROH ha e been cha ac e ized o mul iple domes ic species and b eeds wi h he goal o making in e ences abou hei his o y and demog aphy as well as o iden i ying he genomic oo p in o na u al and a i i- cial selec ion [5]. Geog aphic isola ion o popula ions may lead o a conside able loss o di e si y, an inc ease in inb eeding and ulne abili y o s ochas ic e en s [6]. Fo ins ance, human popula ions wi h a his o y o p olonged Open Access G ene ics S elec ion E olu ion *Co espondence: ma cel[email p o ec ed]; j[email p o ec ed] †Taina F. Ca doso and Ma cel Amills sha e he i s au ho ship 1 Depa men o Animal Gene ics, Cen e o Resea ch in Ag icul u al Genomics (CRAG), CSIC‑IRTA‑UAB‑UB, Campus de la Uni e si a Au ònoma de Ba celona, 08193 Bella e a, Ba celona, Spain 12 Facul y o Ve e ina y Medicine, U ech Uni e si y, U ech , The Ne he lands Full lis o au ho in o ma ion is a ailable a he end o he a icle Page 2 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 isola ion on he O kney o Dalma ian Islands o in Sa - dinia ha e longe ROH han con inen al popula ions, which indica es an ele a ed ela edness [7, 8]. A high equency o ROH can ha e de imen al e ec s on bio- logical i ness and ep oduc i e success because ROH a e o en en iched in dele e ious mu a ions [9]. Indeed, mi ochond ial encephalomyopa hy is ela i ely e- quen in people om he Fa oe Islands due o homozy- gosi y o he SUCLA2 gene [10]. In ca le, Zhang e al. [11] epo ed ha dele e ious a ia ions a e o e ep- esen ed in ROH egions, pa icula ly in hose longe han 3 Mbp. Howe e , geog aphically isola ed popu- la ions may ha e e ained ancien alleles o a ian s ha a e no ound in o he popula ions [12, 13], which e lec s adap a ion o ha sh en i onmen s and/o a p ac ice o b eed managemen ha a e no common o mainland popula ions [13–15]. Recen ly, genome-wide single nucleo ide polymo - phism (SNP) da a o a comp ehensi e panel o goa s b eeds has become a ailable [16]. Fo he same panel o b eeds, signa u es o selec ion [17] and he e ec s o popula ion size, b eed managemen and c ossb eeding on he pa e ns o ROH as well as ch omosomal ROH ho spo s ha e been epo ed [18]. The aim o ou s udy was o in es iga e i goa b eeds ha a e aised in islands ha e highe le els o homozygosi y han hei con inen al coun e pa s. In o de o achie e his goal, we compa ed he numbe and genomic co e age o ROH in 25 cap ine b eeds om 16 Eu opean and A ican islands wi h hose o nine con inen al popula ions. Me hods Goa sampling andgeno yping Goa s we e sampled and geno yped as pa o he Adap - Map p ojec [19] and see Table1. The geog aphic dis- ibu ion o he b eeds in es iga ed in his s udy is illus a ed in Figu eS1 (see Addi ional ile1: Figu eS1). Genomic DNA was ex ac ed wi h s anda d p o o- cols and goa s we e geno yped wi h he Illumina Goa SNP50 BeadChip [20] by ollowing he manu ac u e ’s ins uc ions. Monomo phic and unmapped SNPs in he whole da ase , and SNPs wi h a call a e lowe han 98% we e elimina ed. Indi iduals wi h a geno ype call a e lowe han 96% we e emo ed. Quali y con ol was pe o med by using he PLINK p og am [21]. The inal da ase included 46,654 SNPs and 480 goa s wi h 260 and 220 indi iduals om insula and con inen al popu- la ions, espec i ely (Table1) and (see Addi ional ile1: Figu eS1). In o de o calcula e allele-sha ing dis ances (ASD), linkage disequilib ium-p uning o SNPs was implemen ed (plink op ion—indep-pai wise 50 5 0.03) [21], which e ained 19,879 SNPs. Da a analysis The Zana di so wa e [22] was used o iden i y ROH. Runs o homozygosi y we e de ined as homozygous genomic s e ches ha a e a leas 1Mb long and ha con ain a min- imum numbe o 15 SNPs. We allowed one he e ozygous SNP pe ROH o accoun o geno yping e o s. Coo di- na es o p incipal componen analysis (PCA) and allele- sha ing dis ances (ASD) we e calcula ed wi h he PLINK p og am [21]. A neighbo -joining ee was buil and isual- ized wi h he Spli s ee p og am [23]. Genomic inb eeding de i ed om ROH co e age (FROH) was calcula ed by di iding o al ROH leng h pe indi- idual by o al genome leng h ac oss all 29 au osomes (2456.50Mb). Inb eeding coe icien s i.e. Fhe , Fha 1, Fha 2, and Fha 3 we e calcula ed wi h he PLINK so wa e [21] o popula ions wi h a leas 20 indi iduals. On he one hand, he—he command o PLINK [21] was used o compu e obse ed and expec ed au osomal homozygous geno ype coun s (Fhe ) and on he o he hand, we used he—ibc com- mand o PLINK [21] o calcula e Fha , Fha 2 and Fha 3 pa am- e e s. Obse ed he e ozygosi y (Ho) and e ec i e size (Ne) pa ame e s we e e ie ed om es ima es p o ided by Colli and cowo ke s [16]. S a is ical analyses we e pe o med by using he R so - wa e .2.15.3 [24]. The alues and s a is ical signi icances o Spea man’s ank co ela ions (ρ) o FROH wi h Ho and Ne we e compu ed. We also calcula ed Spea man’s ank co - ela ions (ρ) o numbe and o al leng h o ROH o insula goa popula ions wi h he dis ance be ween each island and he nea es con inen al loca ion. We used a gene alized leas squa es model implemen ed in he nlme package (R so wa e .2.15.3, [24]) o in e whe he FROH and o al ROH leng h and numbe di e ed signi ican ly be ween con inen al and insula popula- ions. We conside ed six g oups o b eeds and pe o med s a is ical compa isons be ween he b eeds con ained wi hin each g oup (all b eeds agains each o he wi hin each g oup). We did no pe o m s a is ical compa isons be ween g oups o be ween b eeds belonging o di e - en g oups. The ollowing g oups o b eeds we e aken in o conside a ion: (1) Icelandic goa s, Danish, Du ch and Finnish Land ace; (2) A an, Bilbe y, Mul anny, and Fos- ses; (3) A gen a a, Asp omon ana, Ciocia a G igia, Co se, Gi gen ana, Mal ese Sa da and Sa da; (4) Mallo quina and Blanca de Rasque a; (5) Mo occan goa and Palme a; and (6) And oy, Diana, Menabe, Ma ebele, So ia and SudOues . On he basis o explo a o y analyses o he da a ( esul s no shown), we used a model which assumes inequali y o he a iances (he e oscedas ici y) ha a e associa ed wi h each o he h ee pa ame e s aken in o conside a ion (FROH and o al ROH leng h and numbe ) and each popula ion: Y i=Xiβ+εi,εi∼N  0, σ2i  and i=1, ...,m , Page 3 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 whe e β is a ec o o he ixed e ec “b eed” (m le els), Xi is an incidence ma ix ela ing Yi o β , and i is a pos- i i e-de ini e ma ix o he a iances and co a iances o he wi hin-g oup e o s. Fo ull de ails on he me hodol- ogy, see Pinhei o and Ba es [25]. The leas squa e means o each pa ame e and popula ion we e con as ed on a pai wise basis wi h a Wald uni a ia e es o signi icance [26] and mul iple es ing was adjus ed wi h he Bon e - oni co ec ion. Resul s Ou panel o goa b eeds included insula b eeds om di e en egions (see Addi ional ile1: Figu eS1): Ice- land (N = 11) and I eland (N = 31) in no he n Eu ope; Co sica (N = 29), Sa dinia (N = 39), Sicily (N = 48) and Mallo ca (N = 18) in Sou he n Eu ope; and La Palma (N = 15) and Madagasca (N = 69) in A ica. Each o hese was compa ed o he nea es con inen al popu- la ions. Among he con inen al popula ions, he Finn- ish, Danish and Du ch goa s belong o he No dic ype and a e also subjec o gene ic isola ion ei he because hey a e b ed on a peninsula (Finland, Denma k) o managed unde he scope o a s ic ly closed he dbook (Ne he lands). The PCA i s ac o ial map is shown in Fig.1a. The i s wo coo dina es PC1 and PC2 high- ligh he sepa a ion be ween Malagasy and Icelandic goa s, espec i ely. These wo b eeds and he goa pop- ula ions om La Palma and Iceland, also ha e ex eme posi ions on he PC1-PC3 and PC1-PC4 plo s (see Addi ional ile2: Figu e S2), bu his was no obse ed Table 1 ROH numbe , ROH leng h andFROH mean, minimum (min) andmaximum (max) alues calcula ed o  he25 goa popula ions used in his s udy (SE = s anda d e o ) B eed code B eed name Coun y Numbe o animals ROH leng h ROH numbe FROH Mean ± SE Min/max Mean ± SE Min/max Mean ± SE Min/max AND And oy Madagasca 6 478.44 ± 19.43 423.28/559.05 259.67 ± 7.88 235/289 0.19 ± 0.01 0.17/0.23 ARG A gen a a I aly (Sicily) 24 47.01 ± 9.21 16.78/248.58 21.79 ± 1.15 13/35 0.02 ± 0.00 0.01/0.10 ARR A an I eland 8 733.63 ± 47.82 513.01/938.65 178.00 ± 7.05 147/209 0.30 ± 0.02 0.21/0.38 ASP Asp omon ana I aly 23 135.05 ± 30.77 20.77/599.81 35.61 ± 4.40 15/102 0.05 ± 0.01 0.01/0.24 BLB Bilbe y I eland 10 533.28 ± 44.00 88.00/780.21 67.00 ± 5.33 23/114 0.22 ± 0.02 0.04/0.32 CCG Ciocia a G igia I aly 16 155.39 ± 29.90 7.83/362.79 30.63 ± 4.12 7/60 0.06 ± 0.01 0.00/0.15 CRS Co se F ance (Co ‑ sica) 29 93.72 ± 14.29 23.55/295.13 34.86 ± 1.68 18/65 0.04 ± 0.01 0.01/0.12 DIA Diana Madagasca 14 636.87 ± 60.53 481.75/1279.29 265.79 ± 4.88 229/292 0.26 ± 0.02 0.20/0.52 DKL Danish Lan‑ d ace Denma k 50 401.18 ± 28.00 490.30/714.81 67.06 ± 1.94 111/141 0.16 ± 0.01 0.20/0.29 DUL Du ch Lan‑ d ace Ne he lands 15 622.60 ± 15.80 133.11/889.28 125.27 ± 1.96 41/102 0.25 ± 0.01 0.05/0.36 FIN Finnish Lan‑ d ace Finland 20 225.46 ± 32.00 118.47/686.10 80.75 ± 2.77 65/122 0.09 ± 0.01 0.05/0.28 FSS Fosses F ance 24 218.30 ± 42.49 25.07/665.76 47.46 ± 3.69 15/79 0.09 ± 0.02 0.01/0.27 GGT Gi gen ana I aly (Sicily) 24 363.58 ± 37.61 161.21/863.58 93.71 ± 2.60 73/122 0.15 ± 0.02 0.07/0.35 ICL Icelandic goa s Iceland 11 1625.59 ± 57.30 1263.82/1979.66 366.45 ± 12.60 324/455 0.66 ± 0.02 0.51/0.81 MAL Mallo quina Spain (Mal‑ lo ca) 18 334.68 ± 63.06 49.57/938.51 74.39 ± 4.61 29/102 0.14 ± 0.03 0.02/0.38 MEN Menabe Madagasca 19 797.36 ± 21.95 673.26/1156.91 392.63 ± 4.70 345/425 0.32 ± 0.01 0.27/0.47 MLS Mal ese Sa da I aly (Sa dinia) 12 287.56 ± 36.34 24.37/486.45 73.42 ± 6.71 18/102 0.12 ± 0.01 0.01/0.20 MOR Mo occan goa Mo occo 30 151.03 ± 40.45 15.76/1025.09 32.43 ± 2.94 13/74 0.06 ± 0.02 0.01/0.42 MTB Ma ebele Zimbabwe 22 146.35 ± 14.97 110.73/451.20 84.55 ± 1.37 71/96 0.06 ± 0.01 0.05/0.18 MUL Mul anny I eland 13 323.02 ± 33.76 59.55/604.71 74.50 ± 5.42 36/111 0.13 ± 0.01 0.02/0.25 PAL Palme a Spain (La Palma) 15 571.80 ± 14.11 471.68/641.05 276.13 ± 4.86 234/314 0.23 ± 0.01 0.19/0.26 RAS Blanca de Rasque a Spain 20 246.55 ± 37.98 20.01/588.65 56.45 ± 5.33 17/103 0.10 ± 0.02 0.01/0.24 SAR Sa da I aly (Sa dinia) 27 97.19 ± 17.14 21.52/376.47 34.81 ± 2.35 14/55 0.04 ± 0.01 0.01/0.15 SOF So ia Madagasca 22 854.77 ± 30.68 672.20/1251.19 363.95 ± 4.65 310/391 0.35 ± 0.01 0.27/0.51 SOU SudOues Madagasca 8 564.73 ± 16.40 488.34/637.01 300.63 ± 7.40 263/325 0.23 ± 0.01 0.20/0.26 Page 4 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 o goa s om Sou he n Eu opean islands (Mallo ca, Co sica, Sa dinia and Sicily). A neighbo -joining ee o ASD dis ances (Fig. 1b) shows a clea clus e ing o goa s om he same b eed, excep o wo Mal ese Sa da goa s ha clus e wi h he Sa da and ice e sa. Gi gen ana, Palme a and So ia a e nes ed wi hin he Asp omon ana, Mo occo and Diana popula ions, espec i ely, while bo h Menabe and Sud- Oues popula ions a e wi hin he And oy popula ion. Mos b eeds appea o be homogeneous, excep o Dan- ish Land ace, Mallo quina and Asp omon ana, which show some he e ogenei y. Fo Icelandic, I ish, Palme a and Malagasy goa s, we obse ed a dec ease in gene ic dis ances be ween indi iduals om he same b eed (Fig.1b) bu no o goa s om Medi e anean islands. Apa om he ex emely inb ed Icelandic goa s [12], gene ic isola ion was mos in ense o he I ish A an, Du ch, Palme an (Cana y Islands) and Malagasy (And oy, So ia, Diana, Menabe and Sud-Oues ) popula ions. As shown in Figu e S3 (see Addi ional ile3: Figu eS3), he wi hin-b eed ASD dis ances co ela e closely wi h Ho, which indica es ha a ee as ha shown in Fig.1b ai h- ully illus a es he di e si y pa e ns and a he same ime ep oduces he egional clus e ing o b eeds [16]. The numbe o ROH and he o al ROH co e age a e displayed in Fig.2 and he means and s anda d e o s o hese wo pa ame e s a e in Fig.3 and Table1. Signi ican di e ences in ROH co e age, ROH numbe and FROH (Padj- alue < 0.05) we e obse ed be ween goa s om Iceland, Madagasca , La Palma and I eland (Bilbe y and A an) and hei con inen al coun e pa s (Fig.3). Goa s om Medi e anean islands ep esen a mo e complex case because ce ain popula ions display a signi ican ly inc eased le el o homozygosi y (e.g. Gi gen ana) while o he s do no (e.g. Co se and A gen a a). Genomic ROH co e age is di ec ly p opo ional o he ROH-based inb eeding coe icien s [27] ha a e shown in Fig.4 and Table1. In he Icelandic, A an (I eland), Malagasy and Palme an goa popula ions, he numbe o ROH and hei o al leng h ange om 147 o 455 and om 423.28 o 1979.66Mb (Fig.4 and Table1), espec- i ely, which co espond o ex emely high inb eeding coe icien s in Icelandic (FROH = 0.66), and Malagasy goa s (FROH = 0.19–0.35). The gene ic isola ion o he Du ch goa s [14] is e idenced by a high ROH co e age anging om 133.11 o 889.28Mb (FROH = 0.25) a he han by he numbe o ROH (41–102). Inb eeding coe - icien s a e also high o he Palme an (FROH = 0.23), Bil- be y (FROH = 0.22) and A an (FROH = 0.30) popula ions (Fig.4 and Table1). In con as , Medi e anean insula goa s ha e a mos 122 ROH wi h a mean o al leng h o 47.1–363.6Mb (Fig.2 and Table1), hese alues being simila o hose obse ed o nea by con inen al goa popula ions (Fig.3). A o al leng h o ROH g ea e han 500Mb was obse ed only o a ew Gi gen ana and Mal- lo quina goa s. Fig. 1 a PCA plo o indi iduals om 25 insula o con inen al popula ions. Red and da k blue indica e insula and con inen al b eeds, espec i ely, wi h a high le el o homozygosi y. Pink and ligh blue indica e insula and con inen al b eeds, espec i ely, wi h a low o mode a e le el o homozygosi y. b Neighbo ‑joining ee based on allele‑sha ing dis ances ep esen ing he gene ic ela ionships among insula and con inen al goa popula ions Page 5 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 Fig. 2 Numbe and o al leng h o ROH in A ican, Eu opean and Medi e anean insula and con inen al goa popula ions. Red and da k blue indica e insula and con inen al b eeds, espec i ely, wi h a high le el o homozygosi y. Pink and ligh blue indica e insula and con inen al b eeds, espec i ely, wi h a low o mode a e le el o homozygosi y. The numbe o ROH ound o each indi idual genome (y‑axis) is plo ed agains o al ROH size (i.e. numbe o Mb co e ed by ROH in each genome, x‑axis). The ollowing codes a e used (insula popula ions in bold): AND, And oy (Madagasca ); ARG, A gen a a (Sicily); ARR, A an (I eland); ASP, Asp omon ana; BLB, Bilbe y (I eland); CCG, Ciocia a G igia; CRS, Co se (Co sica); DIA, Diana (Madagasca ); DKL, Danish Land ace; DUL, Du ch Land ace; FIN, Finnish Land ace; FSS, Fosses; GGT, Gi gen ana (Sicily); ICL, Icelandic goa s (Iceland); MAL, Mallo quina (Mallo ca); MEN, Menabe (Madagasca ); MLS, Mal ese Sa da (Sa dinia); MOR, Mo occan goa ; MTB, Ma ebele; MUL, Mul anny (I eland); PAL, Palme a (La Palma); RAS, Blanca de Rasque a; SAR, Sa da (Sa dinia); SOF, So ia (Madagasca ); SOU, SudOues (Madagasca ) Fig. 3 S a is ical analysis o he mean ROH numbe s, ROH co e age and FROH. Red and da k blue indica e insula and con inen al b eeds, espec i ely, wi h high homozygosi y. Pink and ligh blue indica e insula and con inen al b eeds, espec i ely, wi h low o modes homozygosi y. Di e en le e s indica e s a is ically signi ican di e ences be ween g oups (mean ± s anda d e o , linea models wi h he e oscedas ic wi hin g oup‑e o s, Padj‑ alue < 0.05). The ollowing codes a e used (insula popula ions in bold): AND, And oy (Madagasca ); ARG, A gen a a (Sicily); ARR, A an (I eland); ASP, Asp omon ana; BLB, Bilbe y (I eland); CCG, Ciocia a G igia; CRS, Co se (Co sica); DIA, Diana (Madagasca ); DKL, Danish Land ace; DUL, Du ch Land ace; FIN, Finnish Land ace; FSS, Fosses; GGT, Gi gen ana (Sicily); ICL, Icelandic goa s (Iceland); MAL, Mallo quina (Mallo ca); MEN, Menabe (Madagasca ); MLS, Mal ese Sa da (Sa dinia); MOR, Mo occan goa ; MTB, Ma ebele; MUL, Mul anny (I eland); PAL, Palme a (La Palma); RAS, Blanca de Rasque a; SAR, Sa da (Sa dinia); SOF, So ia (Madagasca ); SOU, SudOues (Madagasca ) (See igu e on nex page.) Page 6 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 Page 7 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 In mos b eeds, we ound an in e se ela ionship be ween ROH size and equency (Fig.5). Howe e , ROH longe han 1–5Mb a e ela i ely equen in he genome o Icelandic, I ish, Du ch, Danish and Mallo quina goa s. Fo he ex emely inb ed Iceland goa , an a e age o 366 ROH we e de ec ed, 286 o which we e longe han 1 o5Mb. We also in es iga ed he ela ionship be ween FROH and se e al popula ion pa ame e s including (Ho, Ne and he inb eeding coe icien s Fhe , Fha 1, Fha 2 and Fha 3 calcula ed wi h PLINK [21] i.e. (see Addi ional ile4: TableS1 and Addi ional ile5: TableS2). On he one hand, Spea man co ela ions coe icien s be ween FROH and Ne and Ho we e nega i e (ρ < − 0.87) and sig- ni ican (P alue < 0.002), which e lec s ha popula ions wi h smalle Ne unde go mo e gene ic d i han la ge popula ions [27] and, in consequence, hey end o be mo e homozygous. On he o he hand, Spea man co e- la ions coe icien s be ween FROH and he ou inb eed- ing coe icien s calcula ed wi h PLINK [21] we e posi i e (ρ < 0.64–0.88) and signi ican (P alue < 0.01) o e y sig- ni ican (P alue < 0.0001). P e ious s udies ha e epo ed simila ends o co ela ions be ween FROH and a wide ange o inb eeding coe icien s [27–29]. We also calcula ed Spea man co ela ions coe icien s o ROH leng h and numbe wi h he dis ance o insu- la goa popula ions o he nea es con inen al coas al si e. Fo goa s aised in dis an islands, such as Ice- land (1277km om No way) o Madagasca (1051km Fig. 4 Plo o he ac ion o he genome co e ed by ROH (FROH) in insula ( ed) and con inen al (blue) goa popula ions. The ollowing codes a e used (insula popula ions in bold): AND, And oy (Madagasca ); ARG, A gen a a (Sicily); ARR, A an (I eland); ASP, Asp omon ana; BLB, Bilbe y (I eland); CCG, Ciocia a G igia; CRS, Co se (Co sica); DIA, Diana (Madagasca ); DKL, Danish Land ace; DUL, Du ch Land ace; FIN, Finnish Land ace; FSS, Fosses; GGT, Gi gen ana (Sicily); ICL, Icelandic goa s (Iceland); MAL, Mallo quina (Mallo ca); MEN, Menabe (Madagasca ); MLS, Mal ese Sa da (Sa dinia); MOR, Mo occan goa ; MTB, Ma ebele; MUL, Mul anny (I eland); PAL, Palme a (La Palma); RAS, Blanca de Rasque a; SAR, Sa da (Sa dinia); SOF, So ia (Madagasca ); SOU, SudOues (Madagasca ) Page 8 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 om Mozambique), ROH numbe and o al leng h had he la ges alues. Spea man co ela ion coe icien s o he dis ances wi h ROH numbe (ρ = 0.54 and, P alue = 0.023) and o al leng h (ρ = 0.63 and, P alue = 0.007) we e posi i e and signi ican . Discussion In insula and o he isola ed popula ions, homozygosi y is o en inc eased by ounde e ec s and geog aphic iso- la ion. In ou s udy, he la ge numbe s and longe o al leng hs o ROH and highe FROH in goa s om Iceland, I eland, La Palma and Madagasca han in hei con i- nen al coun e pa s illus a e his inc ease in he le el o homozygosi y (Table1 and Figs.2, 3 and 4). In con- as , Medi e anean insula and con inen al popula- ions o m a igh clus e . Al hough goa popula ions ha a e aised in emo e islands end o ha e highe le els o homozygosi y, o he ac o s a e also in ol ed, such as b eed managemen , his o y and demog aphy, which could ha e s ong e ec s on b eed di e si y. We we e no able o analyse he impac o some o hese ac o s because o lack o in o ma ion (his o ic and demog aphic eco ds a e sca ce o comple ely absen o mos o he b eeds unde analysis). The analysis illus a ed in Fig. 1a e eals a s ong sepa a ion be ween Malagasy and Ma ebele (Zimba- bwe) and be ween Icelandic and No dic Land ace goa popula ions and, o a lesse ex en , be ween Palme an and Mo occan goa s. This esul p obably e lec s he ex eme geog aphic isola ion o hese h ee insula pop- ula ions. Indeed, we ound ha ROH numbe and o al leng h we e co ela ed posi i ely wi h dis ance be ween each island and he nea es con inen al loca ion. E ec s o insula iza ion and/o small e ec i e popula ions sizes Fig. 5 Dis ibu ion o ROH acco ding o hei size in A ican, Eu opean and Medi e anean insula and con inen al goa popula ions. The ollowing codes a e used (insula popula ions in bold): AND, And oy (Madagasca ); ARG, A gen a a; ARR, A an (I eland); ASP, Asp omon ana; BLB, Bilbe y (I eland); CCG, Ciocia a G igia; CRS, Co se (Co sica); DIA, Diana (Madagasca ); DKL, Danish Land ace; DUL, Du ch Land ace; FIN, Finnish Land ace; FSS, Fosses; GGT, Gi gen ana (Sicily); ICL, Icelandic goa s (Iceland); MAL, Mallo quina (Mallo ca); MEN, Menabe (Madagasca ); MLS, Mal ese Sa da (Sa dinia); MOR, Mo occan goa ; MTB, Ma ebele; MUL, Mul anny (I eland); PAL, Palme a (La Palma); RAS, Blanca de Rasque a; SAR, Sa da (Sa dinia); SOF, So ia (Madagasca ); SOU, SudOues (Madagasca ) Page 9 o 11 Ca dosoe al. Gene Sel E ol (2018) 50:56 we e p e iously epo ed in a compa ison be ween Japa- nese wild boa s and Asian mainland pigs [2], and o se - e al insula and/o inb ed ca le popula ions [28]. We obse ed he mos ex eme combined e ec s o ounde e en s, geog aphic isola ion and small popu- la ion size o he Icelandic goa s wi h 324 o455 ROH ha co e be ween 1263 and 1979Mb, a high equency o e y long ROH (> 30 Mb) and a e y high FROH o 0.66 (Table1 and Figs.3, 4, 5). Icelandic goa s ha e a No h-Eu opean (mos likely No wegian) o igin and we e impo ed du ing he coloniza ion o Iceland o e 1100yea s ago [12, 29]. The lack o e idence o subse- quen goa impo a ions sugges s a scena io o s ong geog aphic isola ion. Mo eo e , he e we e less han 100 Icelandic goa s a he end o he nine een h cen u y and again in 1960, bu , in 1994, he es ima ed census was equal o 348 heads dis ibu ed o e 48 locks [29]. Small popula ion size combined wi h a agmen ed dis ibu- ion p obably a ou ed he main enance o high le els o inb eeding in his goa popula ion. Old I ish goa s, mos no ably hose om A an and Bilbe y, also show inc eased ROH co e age, bu no as ex eme as ha obse ed in Icelandic goa s (Figs.3, 4, 5). The ex emely small popula ion (27 in 2006, [30]) o Bilbe y goa s has led o he eme gence o ela i ely long ROH (Figs.3, 5), which indica es ecen consanguini y. Old I ish goa s ha e been subjec ed o casual hun ing and indisc imina e culling o e al he ds, which has led his popula ion o he e ge o ex inc ion [31]. Inc eased homozygosi y was also obse ed in goa popula ions ha ha e la ge popula ion sizes bu , as o he Icelandic and I ish goa s, ha e endu ed a p o- longed geog aphic isola ion. Fo bo h Palme a and Malagasy goa s, a ela i ely la ge numbe o ROH, high ROH co e age (Fig.2) and ele a ed FROH (0.19–0.35, Table1) we e ound, bu sho ROH (1–5Mb) we e p edominan (Fig.5). This is p obably he consequence o an ancien ounde e ec and geog aphic isola- ion, whe eas hei la ge popula ion size (1.2 million in Madagasca and mo e han 6000 in La Palma) p e- en s consanguini y and he gene a ion o long ROH. Madagasca , he ou h la ges island in he wo ld, was se led by Aus onesians, who a i ed om Bo neo du ing he i h o se en h cen u ies, and subsequen ly by Ban u people [32], bu i is clea ha Malagasy goa s a e o A ican o igin (Fig. 1). The pa e ns o ROH obse ed in ou s udy sugges ha , a e an ini ial ounde e ec , Malagasy goa s we e subjec o a his o y o p olonged geog aphic isola ion, wi h he dis ance o 1000km be ween Madagasca and he A ican land- mass cons i u ing an e ec i e ba ie o gene low. La Palma, in he Cana ian a chipelago, was se led 2500 YBP by colonis s wi h p obably a Be be ances y and emained isola ed om he main ma i ime ou es un il i s coloniza ion by he Spanish in he i een h cen u y [33]. This No h A ican ances y o Palme an goa s is e lec ed in he neighbo -joining ee shown in Fig.1, wi h Palme an goa s displaying a close ela ionship wi h Mo occan goa s. In he La Palma island, a limi ed numbe o ounde s in combina ion wi h geog aphic isola ion esul ed in a low le el o di e si y o cap ine m DNA [34] and a high ROH co e age. The abo e esul s a e in s ong con as wi h he majo - i y o he Medi e anean insula goa b eeds showing ROH pa e ns and FROH alues ha a e simila o hose obse ed in nea by con inen al popula ions (Table1 and Figs.2, 3, 4, 5). Mallo ca, Co sica, Sicily and Sa dinia a e ela i ely close (5–300km) o con inen al Eu ope and a e loca ed along ma i ime ou es ha we e used in ensi ely by he Phoenicians, Ca haginians, G eeks, Romans, A abs and many o he sea a ing ci iliza ions [35]. This si ua ion p obably a ou ed he ecu en admix u e o goa popula ions wi h di e en gene ic backg ounds, hus coun e ac ing he dec ease in gene ic a ia ion p o- duced by he ini ial ounde e ec . This is also illus a ed by he seg ega ion o he m DNA G haplog oup in Mal- lo quina goa s, which so a has only been iden i ied in goa s om Egyp , I an and Tu key [34]. Fu he mo e, a mixed ances y wi h a majo in luence o Mal ese goa s has been men ioned o Sa da goa [36]. Howe e , Mal- lo quina and Gi gen ana goa s a e excep ions wi h a high equency o long ROH (> 30Mb, Fig.5) and FROH alues o 0.14 and 0.15, espec i ely. The highly endan- ge ed Mallo quina goa s ha e su e ed s ong popula ion bo lenecks (cu en census = 150 indi iduals) [34]. The Gi gen ana b eed has also expe ienced a s ong demo- g aphic ecession om 30,000 indi iduals in 1983 o 461 in 1993 [37]. Thus, o bo h hese b eeds, long ROH (> 30Mb) a e explained by popula ion bo lenecks and ecen inb eeding. As illus a ed by he Finnish, Danish and Du ch Lan- d ace b eeds, gene ic isola ion may also occu in con i- nen al popula ions ha a e aised in emo e loca ions om Finland and Denma k o subjec o a s ic b eed- ing managemen and selec ion in combina ion wi h he occu ence o ounde e ec s (Ne he lands). The Du ch goa popula ion has been e i ed since 1958: i s a ed wi h wo emaining indi iduals, in ol ed undocumen ed c ossb eeding and esul ed in he cu en popula ion o ca. 2000 animals [14]. Gene ic dis ances show a ela ed- ness o he Danish and Finnish Land ace popula ions, which was no de ec ed by a panel o 26 mic osa elli es [14]. Rema kably, he numbe s and leng h dis ibu- ions o ROH o hese popula ions a e simila o hose epo ed o B i ish ca le b eeds Angus, He e o d, Je sey and Gue nsey [28], and la ge han hose epo ed o