Italian Journal of Animal Science ISSN: (Print) 1828-051X (Online) Journal homepage: https://www.tandfonline.com/loi/tjas20 Analysis of genetic distance between Peruvian Alpaca (Vicugna Pacos) showing two distinct fleece phenotypes, Suri and Huacaya, by means of microsatellite markers Vincenzo La Manna, Antonietta La Terza, Silvia Ghezzi, Siva Saravanaperumal, Norberto Apaza, Teodosio Huanca, Riccardo Bozzi & Carlo Renieri To cite this article: Vincenzo La Manna, Antonietta La Terza, Silvia Ghezzi, Siva Saravanaperumal, Norberto Apaza, Teodosio Huanca, Riccardo Bozzi & Carlo Renieri (2011) Analysis of genetic distance between Peruvian Alpaca (Vicugna￿Pacos) showing two distinct fleece phenotypes, Suri and Huacaya, by means of microsatellite markers, Italian Journal of Animal Science, 10:4, e60, DOI: 10.4081/ijas.2011.e60 To link to this article: https://doi.org/10.4081/ijas.2011.e60 ©Copyright V. La Manna et al., 2011 Published online: 19 Feb 2016. Submit your article to this journal Article views: 648 View related articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tjas20 Italian Journal of Animal Science 2011; volume 10:e60 PAPER Analysis of genetic distance from previous studies. Measures of geneticdistance were 0.06 for Nei’s and 0.03 for Corresponding author: Dr .Vincenzo La Manna, between Peruvian Alpaca Cavalli-Sforza’s. The analysis of molecular Scuola di Scienze Ambientali, Università di (Vicugna Pacos) showing variance reported no existing variance Camerino, via Gentile III da Varano, 62032Camerino (MC), Italy. two distinct fleece pheno- between populations.Considering the origin of the animals, their Tel. +39.0737.403451 - Fax: +39.0737.403446. types, Suri and Huacaya, by post domestication evolution and the repro- E-mail: vincenzo.lamanna@unicam.it means of microsatellite ductive practices in place, the results do not markers show genetic differentiation between the two Key words: Alpaca, Vicugna Pacos, Microsatellite, Genetic distance, Genetic diversity. populations for the studied loci. Acknowledgment: the authors would like to thank Vincenzo La Manna,1 the LGS laboratories for carrying out the multi- Antonietta La Terza,1 Silvia Ghezzi,2 plex amplifications and band scoring. Siva Saravanaperumal,1 Norberto Apaza,3 Introduction Teodosio Huanca,3 Riccardo Bozzi,2 Received for publication: 5 April 2011. 1 Revision received: 12 July 2011.Carlo Renieri Two coat phenotypes exist in Alpaca, Accepted for publication: 7 October 2011. 1Scuola di Scienze Ambientali, Università Huacaya and Suri. They differ phenotypically di Camerino, Italy in terms of fleece structure. The first is a clas- This work is licensed under a Creative Commons 2Dipartimento di Biotecnologie Agrarie, sically built fleece: compact, bulky and with Attribution NonCommercial 3.0 License (CC BY- NC 3.0). Università di Firenze, Italy high fibre crimp, similar to a merino fleece. 3 The second is a fleece with longer and lustrousEstación Experimental Agraria Illpa, ©Copyright V. La Manna et al., 2011fibre organized in defined, hanging locks, more Instituto Nacional de Innovaciòn Agraria, Licensee PAGEPress, Italysimilar to a Lincoln or an Angora type of fleece. Italian Journal of Animal Science 2011; 10:e60 Puno, Peru These two phenotypes also differ with doi:10.4081/ijas.2011.e60 regard to fibre structure and characteristics (Antonini et al., 2001; Renieri et al., 2004; Post domestication evolution and Frank et al., 2006). In terms of demography, in Abstract the Peruvian population there is a predomi- secondary breed structure nance of the Huacaya type which represents Wheeler et al. (2006) recently confirmed the 90% of the alpaca fleece processed in Peru unanimous agreement that alpacas were Two coat phenotypes exist in Alpaca, (Hoffman and Fowler, 1995). This occurs domesticated from vicuñas (Vicugna vicugna Huacaya and Suri. The two coats show differ- despite the fact that the Suri trait seems to mensalis) but the species’ post domestication ent fleece structure, textile characteristics and segregate in a way closely similar to a single evolution has been strongly affected by histori- prices on the market. Although present scien- dominant gene or a haplotype (Ponzoni et al., cal events. In fact, its evolution is divided into tific knowledge suggests a simple genetic 1997). three main periods: i) pre-Conquest (from the model of inheritance, there is a tendency to A different distribution of phenotypes can be domestication to the arrival of the conquerors); manage and consider the two phenotypes as observed in North America, Europe and ii) the great Conquest crisis (lasting only a few two different breeds. A 13 microsatellite panel Australia, where growing interest of both the decades, but with devastating consequences); was used in this study to assess genetic dis- textile industry and breeder associations for and iii) the subsequent development (new tance between Suri and Huacaya alpacas in a the Suri fibre has led to increasing expansion of domesticated camelids to the pres- sample of non-related animals from two phe- Suri/Huacaya ratios and often to a paid premi- ent day). The potential existence of breeds in notypically pure flocks at the Illpa-Puno exper- um for Suri fibre in the same fineness range the first period is difficult to study and remains imental station in Quimsachata, Peru. The as Huacaya (McGregor, 2006). Over the years unknown; however, it is important to stress that animals are part of a germplasm established this trend has generated two different schools the Conquest caused a drastic decline in popu- approximately 20 years ago and have been bred of thought about the way the two phenotypes lation size (90% according to Flores Ochoa, separately according to their coat type since should be bred, classified and genetically man- 1982), the geographic marginalization of the then. Genetic variability parameters were also aged. This is mainly true at the level of farming animals and the loss of any reproductive barrier. calculated. The data were statistically analyzed and breeder associations in North America and The complete disruption of the breeding system using the software Genalex 6.3, Phylip 3.69 and in Australia who often recommend considering led to the mixing of species because four Fstat 2.9.3.2. The sample was tested for Hardy- and managing the two phenotypes as two sep- species co-existed within the same area: llamas, Weinberg equilibrium (HWE) and after strict arate breeds in order to keep the Suri line pure alpacas, vicuna and guanaco. The genetic con- Bonferroni correction only one locus (LCA37) (Holt, 2005; Walker, 2006; Baychelier, 2002). sequences of these events were drastic and per- showed deviation from equilibrium (P<0.05). This is not supported by present scientific manently changed the animals in comparison to Linkage disequilibrium (LD) was also tested knowledge, which suggests that the phenotype the preceding specialization of pre-Conquest and 9 loci associations showed significant dis- fleece type is a qualitative trait determined by 1 times. In this context, natural selection equilibrium. Observed heterozygosis (Ho= or 2 loci (Ponzoni et al., 1997; Renieri et al., regained a dominant role over artificial selec- 0.766; SE=0.044), expected heterozygosis 2009b; Presciuttini et al., 2010). tion and the specialization that had been estab- (He=0.769; SE=0.033), number of alleles lished was lost. Since the Conquest, there has (Na=9.667, SE=0.772) and Fixation index been a steady and slow demographic increase. (F=0.004; SE=0.036) are comparable to data At present, the demographic structure of the [Ital J Anim Sci vol.10:e60, 2011] [page 271] La Manna et al. Andean alpaca population seems to be based on all the available males (n=15) and a subset of primary populations, also called primitive Materials and methods females (n=50): in total 32 Huacaya (7 males breeds, in which natural selection is favored and 25 females) and 33 Suri (8 males and 25 over artificial selection. The mating system is Material collection and sample females). panmictic and the phenotypic variation inside structure For convenience and due to the lack of basic the flocks is high (Mason 1973; Denis 1982). Alpaca blood samples were collected in facilities, blood was collected by spotting a total For the moment, secondary standardized breeds spring 2008 within a larger sampling program of 100 µL of blood on Whatman FTA Nucleic do not seem to exist, apart from some experi- including skin biopsies and fibre. Animals Acid Collection cards (# WB120205). Possibly ences on very large private farms (Pacomarca, were kept and managed in the Illpa-Puno due to the non-sterile and difficult conditions Mallkini). Nevertheless, the Andean alpaca pop- Experimental Station in Quimsachata (Puno of facilities on the Peruvian plateau, not all ulation is subject to substantial genetic erosion province, Peru) at an altitude of approximately samples allowed a sufficient quality/quantity of through the diffusion of the full white pheno- 4200 m a.s.l. The animals belonged to two geo- DNA to be amplified for all microsatellites, and type. Suri is considered a phenotype with graphically separate and phenotypically pure in order to minimize the number of missing reduced fitness; for this reason, it is generally flocks (one Suri and one Huacaya) that have data, the dataset was rearranged to obtain a reared separately from Huacaya (Renieri et al., been managed and bred separately since the final number of 49 individuals: 10 males (5 2009a). alpaca germplasm was created at the experi- Huacaya and 5 Suri) and 39 females (19 mental station 20 years ago. It is important to Huacaya and 20 Suri), and 13 microsatellites; Population genetics by means of emphasize that common breeding practices in LCA 19 was not included in the analysis. microsatellite analysis local Peruvian communities involve rearing A 10 microsatellite markers panel has been Suri and Huacaya animals separately. Microsatellite amplification details used by the ARI (Alpaca Registry Inc.) since Blood samples were taken from a subset of All samples were processed in Italy and 1998, mainly for parentage verification, and has 65 non-related animals selected for the genomic amplification was carried out by LGS found other applications throughout the years in microsatellite analysis. The sample was struc- genetic laboratories (Cremona, Italy). The other fields such as genome mapping, popula- tured in order to include an equal number of markers, dyes utilized, primer sequences, mul- tion structure and comparable genome analysis, Suri and Huacaya individuals and to respect tiplex associations and allele sizes for the 14 as reviewed by Munyard et al. (2009). The con- the sex ratio as much as possible. It included microsatellites are shown in Table 1. The panel tinuous and ongoing effort in sequencing the alpaca genome will rapidly lead to a much larger set of markers, as demonstrated by a number of Table 1. Markers and multiplex reaction data. studies published in the past decade (Obreque et al., 1999; Penedo et al., 1999; McPartlan et al., Marker Fragment length Alleles Dye 5’-3’ Primer pair sequences 1998). Reed and Chaves (2008) report an addi- tional 1516 potential loci by blasting bos taurus LCA 19 80-122 17 Vic taagtccagccccacactca SSRs and Munyard et al. (2009) have recently ggtgaaggggcttgatcttcLCA 94 187-213 9 Pet gtccattcatccagcacagg found a set of 9 tetranucleotide markers. Some acatttggcaatctctggagaa of these markers have already been used to cal- YWLL 44 84-136 18 Ned ctcaacaatgctagaccttgg culate genetic distances among different species gagaacacaggctggtgaata of South American Camelids (Wheeler et al., YWLL 36 136-176 17 Vic agtcttggtgtggtggtagaa 2006; Bustamante et al., 2002). Since Goldstein tgccaggatactgacagtgat et al. (1995) evaluated their use for the calcula- YWLL 43 128-164 10 Pet Atacctctcttgctctctctc tion of genetic distances, they have been used in cctctacaaccatgttagcca an increasingly large number of species. YWLL 29 210-232 9 Fam gaaggcaggagaaaaggtag Given the unusual post domestication evolu- cagaggcttaataacttgcagLCA 37 124-174 19 Fam Aaacctaattacctccccca tionary history of the species and the increas- ccatgtagttgcaggacacg ing interest in Suri fibre, the aim of this study LCA 5 178-218 13 Vic Gtggtttttgcccaagctc was, therefore, to use a microsatellite panel to acctccagtctggggatttc study the genetic distance between Suri and LCA 8 211-261 14 Pet gctgaaccacaatgcaaaga Huacaya alpacas and to assess the amplitude aatgcagatgtgcctcagtt of genetic variability in the Peruvian alpaca LCA 65 159-193 14 Fam Tttttcccctgtggttgaat population. The studied population belongs to aactcagctgttgtcagggg a germplasm established approximately 20 LCA 66 216-266 24 Ned gtgcagcgtccaaatagtca years ago in Quimsachata (Puno province, ccagcatcgtccagtattcaYWLL 40 176-190 7 Ned cacatgaccatgtccccttat Peru) and has been bred separately according ccagtgacagtgtgactaaga to their coat type since then. LCA 99 263-297 11 Vic caggtatcaggagacgggct agcatttatcaaggaacaccagc YWLL 46 87-115 5 Fam aagcagagtgatttaaccgtg ggatgactaagactgctctga List of markers, allele fragment lengths, number of alleles, dyes used and respective primer pairs in the multiplex reactions. [page 272] [Ital J Anim Sci vol.10:e60, 2011] Genetic distance between Peruvian Alpaca has been optimized to be amplified in two mul- 1% table wide level was significant. ence in results when the sample was split into tiplex reactions of 7 primer pairs each. Cavalli-Sforza’s chord distance and two different populations. Amplifications were carried out in 20 µL Reynolds-Weir Cockerham distance were cal- The test for genotypic disequilibrium reactions with final concentrations of 0.2 µM culated using Gendist, an application of the between pairs of loci showed 9 loci associa- of each primer, 1X Ampli-Taq Gold Buffer, 1.5 software package Phylip version 3.69 tions out of 65 to be in some degree of linkage mM MgCl2, 200 µM of each dNTP and a total of (Felsenstein, 1989). The first measure is disequilibrium. The loci LCA8, LCA66 and 2 units of Ampli-Taq Gold (#4398833, Applied assuming a stepwise mutation model in an LCA65 appear in 8 of the 9 associations show- Biosystems, Monza, italy). After a first denatu- infinite allele model with equilibrium between ing linkage disequilibrium. ration step at 94°C for 10 min, reactions were mutation and genetic drift, whereas the sec- cycled 30 times (45 s at 94°C; 30 s at 58°C; 30 ond and the third measures are dimensional Heterozygosis, polymorphism s at 72°C) with a final 10 min elongation step models assuming only genetic drift. information content and fixation at 72°C. Finally, the genetic structure of the sample was investigated with the Structure 2.3.3 soft- index Software and statistical analysis ware (Pritchard, 2000) and the indentification When the dataset was considered as a single of the most likely number of clusters (K) was population, the average Ho for the 12 markersAll microsatellite data were first checked was high (Ho=0.766; SE=0.044), extremely with the software micro-checker (Oosterhout made by the Evanno method (Evanno, 2005) close to the average He (He=0.769; SE=0.033), et al., 2004) in order to spot null alleles and using the online version of Structure Harvester (Earl, 2011). The burning period was set to and the unbiased expected heterozygosiswrong size detections. The statistical analysis of the microsatellite data for the genetic vari- 50,000 and repetitions of the MCMC chain to (UHe=0.778; SE=0.033), with an overall aver- 106; the ancestry model chosen was the admix- age fixation index of 0.004 (SE 0.036). Theability measures, including the analysis of ture model. Four replicates for each tested high mean number of alleles (Na=9.667;molecular variance (AMOVA) and the principal value of K (1-6) were performed. SE=0.77), effective alleles (Ne=4.89; SE=0.39)coordinate analysis (PCA), was performed and the low fixation indices (F) confirm such using the latest version of the software high values of heterozygosis and genetic vari- Genalex 6.3 (Peakall and Smouse, 2006), while ability. The polymorphism information content the Excel Microsatellite Toolkit (Park 2001) (PIC) for each locus is in line with previous was used for calculating the polymorphism Results findings and ranges from 0.411 for locus information content (PIC) for each allele. YWLL46 to 0.826 for locus YWLL44. Table 2 A series of indices and parameters were cal- Hardy-Weinberg equilibrium and shows Ho, He, UHe, PIC and F for each locus culated, such as allele frequencies and number linkage disequilibrium and as a mean for all loci with the relative of alleles, number of effective alleles, private A number of indices have been calculated standard errors. alleles, expected and observed heterozygosis only on 12 microsatellites, excluding YWLL43, There was no significant difference in and fixation indices. The Fixation index which is linked to the X sexual chromosome. results when the sample was analyzed as two (Wright’s inbreeding coefficient) was calculat- Only one locus (LCA37) was found not to be in separate populations (Huacaya and Suri). The ed using the software Genalex as (He - Ho)/He. Hardy-Weinberg equilibrium after strict null hypothesis was tested for Ho (P=0.69), He Arcos-Burgos and Muenke (2002) gives an Bonferroni correction, showing excess of (P=0.61), F (P=0.95), Ne (P=0.69), PIC exhaustive review of this measure which, homozygosis (P<0.05). There was no differ- (P=0.61) and Na (P=0.37). Genetic variability when applied to microsatellite data, describes the probability that a given locus becomes fixed. Populations showing high levels of homozygosity will have a Fixation index signif- icantly different from zero. Table 2. Population genetic parameters for a single population. All these parameters were calculated for the Locus N Na Ne Ho He UHe F PIC whole dataset and for the two populations: Suri YWLL46 45 6 (5) 1.75 0.44 0.43 0.43 -0.03 0.41 and Huacaya. In order to assess if there were LCA65 44 13 (14) 5.50 0.90 0.81 0.82 -0.11 0.79 statistically significant differences between YWLL40 46 6 (7) 4.80 0.82 0.79 0.80 -0.04 0.75 these results, the null hypothesis was tested by LCA5 49 7 (13) 3.90 0.83 0.74 0.75 -0.12 0.70 means of one way analysis of variance LCA66 48 13 (24) 6.10 0.89 0.83 0.84 -0.07 0.81 (ANOVA) for observed heterozygosis (Ho), LCA8 49 9 (14) 6.18 0.83 0.83 0.84 0.01 0.81 expected heterozygosis (He), Fixation index LCA99 48 11 (11) 4.03 0.64 0.75 0.76 0.14 0.72 (F), number of effective alleles (Ne) and PIC YWLL44 49 11(18) 6.41 0.77 0.84 0.85 0.08 0.82 and by means of a non-parametric Mann- LCA37 47 13 (19) 4.49 0.55 0.77 0.78 0.28 0.76 Whitney Test for number of alleles (Na). LCA94 47 7 (9) 4.09 0.68 0.75 0.76 0.10 0.72 The statistical population genetics package YWLL36 49 10 (17) 6.16 0.91 0.83 0.84 -0.09 0.81 Fstat 2.9.3.2 (Goudet, 1995) was used to calcu- YWLL29 48 10 (9) 5.21 0.87 0.80 0.81 -0.08 0.78 YWLL43° 46 6 (10) 2.60 - - - - 0.56 late deviation from Hardy-Weinberg equilibri- Mean 47.41 9.667 4.89 0.76 0.76 0.77 0.01 0.74 um (HWE) and genotypic disequilibrium SE 0.48 0.77 0.39 0.04 0.03 0.03 0.03 0.03 among loci applying a strict Bonferroni correc- tion for multiple comparisons. The test for N, number of individuals; Na, number of different alleles, in brackets values from previous studies (Obreque et al., 1999; Penedo etal., 1999; McPartlan et al., 1998); Ne, number of effective alleles; Ho, observed heterozygosity; He, expected heterozygosity; UHe, HWE and the test for linkage disequilibrium unbiased expected heterozygosity = [2N / (2N-1)] * He; F, fixation index; PIC, polymorphism information content; °Ho, He, UHe and were carried out using 1300 randomizations: F not shown for X-linked YWLL43 locus. [Ital J Anim Sci vol.10:e60, 2011] [page 273] La Manna et al. parameters for the two populations are listed Table 3. Population genetic parameters for the two populations. in Table 3. A number of private alleles were Population Locus N Na Ne Ho He UHe F detected between the two phenotypes and a summary is given in Table 4 according to loci Huacaya YWLL46 21 5 1.42 0.33 0.29 0.30 -0.12 and phenotypes. LCA65 21 9 4.34 0.95 0.77 0.78 -0.23 YWLL40 21 6 4.47 0.85 0.77 0.79 -0.10 Genetic distance, AMOVA, PCA LCA5 24 6 4.08 0.91 0.75 0.77 -0.21LCA66 23 11 5.68 0.91 0.82 0.84 -0.10 and genetic structure LCA8 24 8 6.36 0.83 0.84 0.86 0.01 Genetic distance calculated by Pairwise LCA99 23 10 4.14 0.65 0.75 0.77 0.14 Population Matrix of Nei’s Genetic Distance YWLL44 24 9 5.78 0.70 0.82 0.84 0.14 and Unbiased Nei’s Genetic Distance (Nei, LCA37 24 9 4.15 0.50 0.76 0.77 0.34 1978) were 0.062 and <0.0001, respectively. LCA94 24 6 3.61 0.62 0.72 0.73 0.13YWLL36 24 9 6.29 0.91 0.84 0.85 -0.09 When calculated as the Cavalli-Sforza’s chord YWLL29 23 9 5.23 0.82 0.80 0.82 -0.02 distance (Cavalli-Sforza and Edwards, 1967) YWLL43§ 22 5 2.28 - - - - results showed 0.03. Reynolds-Weir Suri YWLL46 24 5 2.11 0.54 0.52 0.53 -0.02 Cockerham distance (Reynolds et al., 1983), LCA65 23 11 5.71 0.87 0.82 0.84 -0.05 suggested to be more precise in the calculation YWLL40 25 6 4.92 0.80 0.79 0.81 -0.01 of genetic distances between closely related LCA5 25 6 3.37 0.76 0.70 0.71 -0.08 species and breeds (Laval et al., 2002), was LCA66 25 9 6.28 0.88 0.84 0.85 -0.04 0.04. LCA8 25 9 5.68 0.84 0.82 0.84 -0.01 The PCA calculated on the distance matrix LCA99 25 8 3.85 0.64 0.74 0.75 0.13 among the individuals in Figure 1 graphically YWLL44 25 10 6.06 0.84 0.83 0.85 -0.01 LCA37 23 13 4.76 0.60 0.79 0.80 0.23 shows how samples from the Suri and Huacaya LCA94 23 7 4.40 0.73 0.77 0.79 0.04 datasets overlap and do not segregate into dif- YWLL36 25 8 5.98 0.92 0.83 0.85 -0.10 ferent groups. The first 3 dimensions of the YWLL29 25 10 5.04 0.92 0.80 0.81 -0.14 PCA explain 64.64% of the total variance. All YWLL43° 24 5 2.75 - - - - the variance observed in the two populations N Na Ne Ho He UHe F with the AMOVA test, calculated both by Fst Huacaya Mean 23 8.08 4.63 0.75 0.74 0.76 -0.01 and Rst values, was due to variation within SE 0.36 0.54 0.39 0.05 0.04 0.04 0.05 populations (100%) and not to variation Suri Mean 24.41 8.50 4.85 0.78 0.77 0.79 -0.01 between populations (0%). The software SE 0.26 0.66 0.36 0.03 0.02 0.02 0.03 Structure rendered a maximum likelihood for N, number of individuals; Na, number of different alleles; Ne, number of effective alleles; Ho, observed heterozygosity; He, expected K=2 both with the classic method by Pritchard heterozygosity; UHe, unbiased expected heterozygosity; F, fixation index; °Ho, He, UHe and F not shown for X-linked YWLL43 locus. (2000) and with that by Evanno (2005), there- fore suggesting a possible dual ancestry for the analyzed sample. However, individuals from both phenotypes were assigned in equal pro- portions to the two clusters without a clear-cut comparison with the data collected and ana- Table 4. List of private alleles in each pop- distinction between the two groups, as shown lyzed by the ARI since 1998 and by several ulation. in Figure 2. other authors, the sample in this study shows Population Locus Alleles the presence of a high number of alleles, matching the whole allelic range described in Huacaya YWLL46 95LCA65 175, 179 previous publications (Obreque et al., 1999; Discussion LCA5 190Penedo et al., 1999; McPartlan et al., 1998). LCA66 220, 244, 252, 256 Values for the polymorphic information con- LCA99 278, 290, 294 In terms of genetic variability within the tent (PIC=0.746, SE=0.033) were also in line YWLL44 108 Peruvian alpaca sample analyzed, all parame- with previous findings. Only one locus YWLL43 148 ters and findings, such as number of alleles (YWLL46) showed a PIC value less than 0.7 YWLL36 168, 172 (Na=9.667; SE=0.772), number of effective (PIC=0.411), which reflects the lower than Suri YWLL46 111 alleles (Ne=4.89; SE=0.388), observed and average Na and Ne found for this specific locus LCA65 165, 177, 185, 189 expected heterozygosis (Ho=0.766, SE=0.044; (Na=6; Ne=1.753) in previous studies. LCA5 192 He=0.769, SE= 0.033), show that the Peruvian Nevertheless, this value is higher than that LCA66 240, 260 LCA8 245 population is still conserving high genetic vari- from previous bibliographic data (Lang et al., LCA99 268 ability and does not show any sign of artificial 1996). YWLL44 116, 134 selection pressure for the studied loci. The low There was no significant difference YWLL43 162 fixation indices for these loci confirm this between the two phenotypic groups when LCA37 130, 138, 148, 170 interpretation of the data (F=0.004; SE=0.036) these parameters were evaluated separately. LCA94 197 and suggest that the microsatellite panel used In terms of genetic distance and differentia- YWLL36 170 is suitable for genetic diversity studies. In tion between the two phenotypes the PCA YWLL29 238 [page 274] [Ital J Anim Sci vol.10:e60, 2011] Genetic distance between Peruvian Alpaca Furthermore, the two phenotypes have similar genetic parameters in terms of allelic frequen- cies and genetic variability, showing high val- ues both in terms of allelic richness and het- erozygosis. References Antonini, M., Perdomici, F., Catalano, S., Frank, E.N., Gonzales, M., Hick, M.V.H., Castrignanò, F., 2001. Cuticular cell mean scale frequency in different types of fleece of domestic South American camelids (SAC). EAAP Publ. 105:110-116. Arcos-Burgos, M., Muenke, M., 2002. Genetics of population isolates. Clin. Genet. 61:233- 247. Figure 1. Principal coordinates analysis of Suri and Huacaya based on the distance matrix Baychelier, P., 2002. What is a pure Suri? from molecular data. Red, Huacaya; green, Suri. Alpacas Australia 39:30-33. Bustamante, A.V., Zambelli, A., De Lamo, D.A., von Thungen, J., Vidal-Rioja, L., 2002. Genetic variability of guanaco and llama populations in Argentina. Small Ruminant Res. 44:97-101. Cavalli-Sforza, L.L., Edwards, A.W., 1967. Phylogenetic analysis. Models and estima- tion procedures. Am. J. Hum. Genet. 19: 233-257. Denis, B., 1982. Consequences génétiques de Figure 2. Bar plot for cluster assignment. 1, Huacaya; 2, Suri. Colored bars indicate the l'evolution des races. INRA Publ. 20:12-18. probability of assignment to either cluster 1 (green) or cluster 2 (red). Earl, D.A., 2011. Structure Harvester v0.6.6. Available from: http://users.soe.ucsc.edu/~ dearl/software/structureHarvester/ analysis shows no separate segregation or for the sole purpose of conserving the genetic Evanno, G., Regnaut, S., Goudet, J., 2005. grouping of Suri and Huacaya individuals. diversity of the species. Secondly, although Suri Detecting the number of clusters of indi- To our knowledge, no previous studies have and Huacaya alpacas at the experimental sta- viduals using the software STRUCTURE: a investigated genetic distance between Suri tion have been bred and managed separately simulation study. Mol. Ecol. 14:2611-2620. and Huacaya alpaca by means of codominant since the creation of the germplasm, the time Felsenstein, J., 1989. Notices; PHYLIP markers, although microsatellite markers have interval of 20 years is unlikely to generate Phylogeny Inference Package (ver. 3.2). been used in the past to investigate the phy- genetic differentiation between the two pheno- Cladistics 5:164-166. logeny of a wider group of South American types, especially considering the absence of Flores Ochoa, J.A., 1982. Causas que origi- Camelids (Wheeler et al., 2006, Bustamante et selection, the reproductive physiology of the naron la actual distribución espacial de las al., 2002). species and its generation time (Mason, 1973). Alpacas y Llama. Universidad de San When ANOVA was carried out considering Antonio Abad, Cusco, Peru, Revista del the two phenotypes as two separate popula- Museo e Instituto de Arqueología 23:223- tions, it clearly identified the source of all vari- 250. ance in the component within populations, Conclusions Frank, E.N., Hick, M.V.H., Gauna, C.D., Lamas, excluding any source of variance to be found H.E., Renieri, C., Antonini, M., 2006. between populations. This result is supported by Given these considerations, if a secondary Phenotypic and genetic description of Nei’s index of genetic distance, Cavalli-Sforza’s breed structure had been present within the fibre traits in South American domestic chord distance and Reynolds-Weir Cockerham species at the time of the creation of the camelids (llamas and alpacas). Small distance, which also show no differentiation germplasm, it would have been preserved by Ruminant Res. 61:113-129. between the two populations. There are two the breeding practices in place at the experi- Goldstein, D.B., Linares, A.R., Cavalli-Sforza, important factors to be taken into consideration mental station. Nevertheless, the data L.L., Feldman, M.W., 1995. An Evaluation of while interpreting these results. Firstly, the obtained from the 13 loci suggest no genetic Genetic Distances for Use With germplasm established 20 years ago at the divergence between the two phenotypes and do Microsatellite Loci. Genetics 139:463-471. experimental station of Quimsachata is not not support the idea of two distinct populations Goudet, J., 1995. FSTAT, ver. 1.2: A Computer subjected to genetic selection and was created of Peruvian Suri and Huacaya alpacas. Program to Calculate F-Statistics. J. Hered. [Ital J Anim Sci vol.10:e60, 2011] [page 275] La Manna et al. 86:485-486. Obreque, V., Mancilla, R., Garcia-Huidobro, J., Pritchard, J.K., Stephens, M., Donnelly, P., Hoffman, E., Fowler, M.E., 1995. 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