Y‐chromosome and mtDNA variation confirms independent domestications and directional hybridization in South American camelids

Investigations of genetic diversity and domestication in South American camelids (SAC) have relied on autosomal microsatellite and maternally‐inherited mitochondrial data. We present the first integrated analysis of domestic and wild SAC combining male and female sex‐specific markers (male specific Y‐chromosome and female‐specific mtDNA sequence variation) to assess: (i) hypotheses about the origin of domestic camelids, (ii) directionality of introgression among domestic and/or wild taxa as evidence of hybridization and (iii) currently recognized subspecies patterns. Three male‐specific Y‐chromosome markers and control region sequences of mitochondrial DNA are studied here. Although no sequence variation was found in SRY and ZFY, there were seven variable sites in DBY generating five haplotypes on the Y‐chromosome. The haplotype network showed clear separation between haplogroups of guanaco–llama and vicuña–alpaca, indicating two genetically distinct patrilineages with near absence of shared haplotypes between guanacos and vicuñas. Although we document some examples of directional hybridization, the patterns strongly support the hypothesis that llama (Lama glama) is derived from guanaco (Lama guanicoe) and the alpaca (Vicugna pacos) from vicuña (Vicugna vicugna). Within male guanacos we identified a haplogroup formed by three haplotypes with different geographical distributions, the northernmost of which (Peru and northern Chile) was also observed in llamas, supporting the commonly held hypothesis that llamas were domesticated from the northernmost populations of guanacos (L. g. cacilensis). Southern guanacos shared the other two haplotypes. A second haplogroup, consisting of two haplotypes, was mostly present in vicuñas and alpacas. However, Y‐chromosome variation did not distinguish the two subspecies of vicuñas.     

The complete mitochondrial DNA sequence of the guanaco (<Emphasis Type="Italic">Lama guanicoe)</Emphasis>: comparative analysis with the vicuña (<Emphasis Type="Italic">Vicugna vicugna)</Emphasis> genome

South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), which are wild species, and the domestic llama (Lama glama) and alpaca (Lama pacos). This paper presents the first complete mitochondrial (mt) genome of the guanaco and the mt coding sequence of the vicuña. The guanaco mtDNA is 16,649 nt long and its composition and organization are similar to the mitochondrial genome of other mammals. Excluding the control region, comparison of the complete guanaco and vicuña mtDNA showed 4.4% sequence divergence. Nucleotide differences in peptide coding genes varied from 1.9% in ATP6 to 6.4% in Cyt b. These values are compatible with the close relatedness of both species identified by other authors. Based on the differences between the control region sequence here reported and that previously described, we also discuss the occurrence of NUMTs in the genome of South American camelids.     

DNA composition in South American camelids I. Characterization and in situ hybridization of satellite DNA fractions

The DNA composition and the in situ hybridization of satellite fractions were analysed in the New World camelids llama, alpaca, guanaco and vicuña. In the four camelid forms, it was possible to identify a similar main band DNA and five satellite fractions (I–V) with G+C base contents ranging from 32% to 66%. Satellites II–V from llama were in situ reannealed on chromosomes from the four camelid forms. The results obtained were: (a) the four satellites hybridized with regions of C-banding (centromeric regions of all chromosomes and short arms of some autosomes); (b) in general, homologous hybridizations (llama DNA versus llama chromosomes) were more efficient than heterologous reassociations; there were however three exceptions to this rule (vicuña and alpaca satellite fraction II, chromosome group B; vicuña fraction V, chromosome groups A and B); (c) X chromosomes from the four camelids had satellites III–V but lacked satellite II, (d) no satellite fraction was detected on chromosome Y. The analysis of the in situ hybridization patterns allowed to conclude that most or all C-banded chromosome regions comprise several satellite DNA fractions. It is, moreover, proposed that there is an ample interspecies variation in the number of chromosomes that cross-react with a given satellite fraction. Our data give further support to the close genomic kinship of New World camelids.     

Ag-NOR staining and in situ hybridization of rDNA in the chromosomes of the South American camelids

The location and frequency of Ag-stained NORs and sites of rDNA hybridization were studied in the chromosomes of the South American camelids. In the four camelids these regions occur distally on chromosomes 18, 21, and 27 and the smallest biarmed elements. Quantitative analysis of NOR distribution showed variations between both cells and species. In llama, guanaco and alpaca the NORs number averaged 6 per cell, this being higher than in vicuña where the average was 3. Relative frequencies of NOR-bearing chromosomes in the four camelids were similar. Yet, in vicuña the virtual absence of NOR sites on one of the smallest biarmed pairs was observed. The rDNA sites assessed in llama and vicuña by in situ hybridization with cloned 18S DNA were coincident with the NOR locations and with the frequencies characteristics for each species. Moreover, varying the exposure time of the autoradiographs, labeling patterns specific for each camelid were observed. Grain counts on individual chromosomes indicated that under our conditions one month exposure is enough to demonstrate all the rDNA sites available in the complement of llama. Conversely, at least two months are necessary to show the total sites existing in vicuña. Most probably this finding reflects the presence of variations in the amount of copies of the ribosomal genes per chromosome.     

Evolution and present situation of the South American Camelidae

This paper provides a review of South American camelid evolution, classification and present status. Particular attention is paid to the debate concerning origins of the domestic alpaca and llama and the contribution of research on faunal remains from Andean archaeological sites towards resolving this issue. Changes in incisor morphology during the domestication process suggest that the alpaca may be descended from the vicuna, while a comparison of fibre production characteristics in preconquest and extant llama and alpaca breeds indicates that extensive hybridization between the two species is likely to have occurred since European contact. The potential role of hybridization in the formation of extant South American camelid populations has not been studied, and may be the root cause of taxonomic disputes.     

Genetic identification of hybrid camelids

North American zoos in 1984 had the first opportunity in many years to obtain South American camelids after a long embargo on imports. The Rio Grande Zoo in Albuquerque, New Mexico, purchased two alpacas and one presumptive llama during this period. The llama, however, appeared to be phenotypically intermediate between a llama and an alpaca. In an attempt to ascertain the identity of this animal, it and purebred individuals of llama and alpaca were compared at 22 presumptive genic loci using starch-gel electrophoresis. Genic differences between llama and alpaca suggest this animal to be a hybrid. If further tests prove consistent with the findings of this study, this technique will provide a simple assay using easily obtained blood for identifying llama and alpaca. The use of genetic management techniques such as this in zoos holds great potential for helping to preserve pure breeding lines of closely related interfertile animals.     

Recovery of Trichuris tenuis Chandler, 1930, from camelids (Lama glama and Vicugna vicugna) in Argentina

A survey of whipworms was conducted in llamas and vicu?as in northwestern Argentina. Fecal examinations of a group of 14 llamas (April 1995-March 1996) and 69 vicu?as (November 1996) indicated a high prevalence (usually >50%) of Trichuris sp. in these hosts. Prevalence was highest during July-November 1995 that also coincided with the highest mean fecal egg count. During postmortem examinations of 1 llama and 1 vicu?a, specimens of Trichuris tenuis were recovered from the cecum/large intestine of each camelid. This is the first report of T. tenuis in South America, and the first report in the vicu?a. It is suggested that T. tenuis is the typical whipworm of aboriginal camelids.     

Mitochondrial DNA structure and organization of the control region of South American camelids

This work presents the mitochondrial DNA molecular organization of the control region (CR) of South American camelids. Sequencing of five individuals each of guanaco, llama, alpaca and vicuna species showed that this region spans 1060 bp including three conserved sequence blocks (CSB I–III) adjacent to the tRNAPhe gene, a conserved central domain and one extended termination‐associated sequence in the 3′ domain of the CR close to the tRNAPro gene. A repeated array formed by three units of 26 bp was detected between CSB I and II. Alignment of the CR sequences from the four species shows a 337‐bp segment that includes most of the nucleotide variability with 10 polymorphic sites. We suggest the use of this segment as a molecular marker to infer data on camelid genetic relationships and population diversity studies.     

Analysis of mitochondrial DNA in Bolivian llama,alpaca and vicuna populations: a contribution to the phylogeny of the South American camelids

The objectives of this work were to assess the mtDNA diversity of Bolivian South American camelid (SAC) populations and to shed light on the evolutionary relationships between the Bolivian camelids and other populations of SACs. We have analysed two different mtDNA regions: the complete coding region of the MT‐CYB gene and 513 bp of the D‐loop region. The populations sampled included Bolivian llamas, alpacas and vicunas, and Chilean guanacos. High levels of genetic diversity were observed in the studied populations. In general, MT‐CYB was more variable than D‐loop. On a species level, the vicunas showed the lowest genetic variability, followed by the guanacos, alpacas and llamas. Phylogenetic analyses performed by including additional available mtDNA sequences from the studied species confirmed the existence of the two monophyletic clades previously described by other authors for guanacos (G) and vicunas (V). Significant levels of mtDNA hybridization were found in the domestic species. Our sequence analyses revealed significant sequence divergence within clade G, and some of the Bolivian llamas grouped with the majority of the southern guanacos. This finding supports the existence of more than the one llama domestication centre in South America previously suggested on the basis of archaeozoological evidence. Additionally, analysis of D‐loop sequences revealed two new matrilineal lineages that are distinct from the previously reported G and V clades. The results presented here represent the first report on the population structure and genetic variability of Bolivian camelids and may help to elucidate the complex and dynamic domestication process of SAC populations.     

Interaction of allosteric effectors with alpha-globin chains and high altitude respiration of mammals. The primary structure of two tylopoda hemoglobins with high oxygen affinity: vicuna (Lama vicugna) and alpaca (Lama pacos)

Polyacrylamide gel electrophoresis and ion-exchange chromatography revealed one hemoglobin component for vicuna (Lama vicugna) and alpaca (Lama pacos). Following chain separation by chromatography on carboxymethyl-cellulose, the amino-acid sequences were elucidated for the alpha- and beta-chains of both hemoglobins using automatic Edman degradation of the chains and the tryptic peptides. Vicuna and alpaca have identical beta-chains showing no substitutions to llama (Lama glama) either. In the alpha-chains alpaca differs from llama by the exchange of one amino-acid residue: alpha 122(H5)Asp----His. The same substitution is present in vicuna too, but in addition we found two more exchanges: alpha 10(A8)Ile----Val and alpha 130(H13)Ala----Thr. The close relationship between llama and alpaca suggests that they both originate from the wild guanaco, and there is no domesticated form of vicuna. The sequence data show that the higher oxygen affinity in vicuna compared to llama and alpaca must be due to the alpha-chains as the beta-chains are identical. The significance of the substitutions in alpha 122(H5), an alpha 1/beta 1-contact, and alpha 130(H13) is discussed.     

Maintaining genetic integrity of coexisting wild and domestic populations: Genetic differentiation between wild and domestic Rangifer with long traditions of intentional interbreeding

This study investigates the genetic effect of an indigenous tradition of deliberate and controlled interbreeding between wild and domestic Rangifer . The results are interpreted in the context of conservation concerns and debates on the origin of domestic animals. The study is located in Northeastern Zaba?kal'e, Russia at approximately 57 degrees North latitude. Blood and skin samples, collected from wild and domestic Rangifer , are analyzed for their mtDNA and microsatellite signatures. Local husbandry traditions are documented ethnographically. The genetic data are analyzed with special reference to indigenous understandings of the distinctions between local domestic types and wild Rangifer . The genetic results demonstrate a strong differentiation between wild and domestic populations. Notably low levels of mtDNA haplotype sharing between wild and domestic reindeer, suggest mainly male‐mediated gene flow between the two gene pools. The nuclear microsatellite results also point to distinct differences between regional domestic clusters. Our results indicate that the Evenki herders have an effective breeding technique which, while mixing pedigrees in the short term, guards against wholesale introgression between wild and domestic populations over the long term. They support a model of domestication where wild males and domestic females are selectively interbred, without hybridizing the two populations. Our conclusions inform a debate on the origins of domestication by documenting a situation where both wild and domestic types are in constant interaction. The study further informs a debate in conservation biology by demonstrating that certain types of controlled introgression between wild and domestic types need not reduce genetic diversity.     

Restriction site patterns in the ribosomal DNA of Camelidae

The restriction map of rDNA from South American camelids and the Bactrian camel was analyzed by digestion of high-molecular-weight DNA with endonucleases EcoRI, BamHI and the two combined followed by Southern blot hybridization with probes for the 18S and 28S rDNA sequences. We scored a total of 17 restriction sites, six of which were mapped conserved in all the species. The other eleven corresponded to spacer regions and revealed variations between these taxa. The study showed that the two groups differ in the length of the internal transcribed spacer. Also they showed the existence of two regions of fast evolution on the opposite termini of the external spacer. A restriction site present at low frequency in the non-transcribed spacer of guanaco and llama was the only difference encountered within the South American group.     

Hair follicle characteristics and fibre production in South American camelids

Hair follicle and fibre characteristics of Peruvian alpaca and llama and Bolivian llama were analysed in three experimental studies. The first experiment was designed to determine the age at which all the secondary follicles reach maturity, as well as to compare the skin follicular structure and activity among these different types of Peruvian camelids. It is concluded that the South American camelids investigated in this study gained a complete and mature skin follicle apparatus at an early age, and hence producers should practise an early first shearing. A second Peruvian experiment investigated comparative fibre cuticular structure on twenty Peruvian domestic camelids comprising huacaya, suri and llama (woolly) 'chacos' genotypes. The results showed that the number of cuticular scales per 100 μm fibre length proved to be strongly affected by both the fleece type and the fibre diameter. The suri fleece was clearly differentiated from those of both huacaya and llama by possessing the highest percentage of fibres with a number of scales less than eight, the lowest percentage of fibres with more than nine scales, along with the lowest percentage of fibres with a diameter of more than 35 μm. It is concluded that, with the exception of the scale height, the cuticular parameters investigated in this study can be utilised in textile fibre analyses for distinguishing among these three types of fleece, as well as in selection projects designed to produce homogeneous fibres from Peruvian domestic camelids. A further study was conducted to determine the age at which the hair follicles in Bolivian llamas reach maturity as well as for comparing the skin follicular structure and activity between the two distinct genotypes. Thirty-one llama kids were chosen. They were born between January and April 1998 and were of different sex and of 'Q'aras' (or Carguera) or 'T'amphullis' type. Skin biopsies were taken from the right mid-costal region at 2, 4, 6, 8,10,12 and 14 months of age in order to monitor four follicular parameters. In this experiment, secondary to primary (S/P) data show that the Bolivian llama population analysed possessed a complete and mature skin follicle apparatus at birth that remained essentially constant throughout the investigation period. Due to the variation of these traits inside the same genetic population, the present results showed that T and Q types could only be subjective on the basis of S/P ratio.     

Isolation and characterization of 10 polymorphic dinucleotide microsatellite markers for llama and guanaco

We isolated and characterized five polymorphic dinucleotide microsatellite markers from llama (Lama glama) and five from guanaco (Lama guanicoe). All loci were assayed on wild llamas and guanacos from Argentina, as all of the primers were able to amplify in both species.     

Prediction of gestational age by ultrasonic fetometry in llamas (Lama glama) and alpacas (Lama pacos)

Fetal biparietal diameter (BPD) and thorax height (TH) were measured by ultrasound during intrauterine growth in pregnant llamas (Lama glama) and alpacas (Lama pacos). The goal was to establish representative curves that allows estimation of gestational age (GA) from real-time ultrasonic measurements of these fetal structures at any stage of gestation. Llamas and alpacas were mated under controlled conditions. Ultrasound exams were conducted to determine pregnancy status 1 month later. Measurements of fetal BPD and TH were conducted from the second month of pregnancy until term. Observation and assessment of fetal TH was difficult during the last 3 months of pregnancy, specially in llamas. Regression curves were calculated from the data as a function of GA, with the best fit represented by the following equations: llama GA=(BPD-0.002399)43.02293,r=0.98,P<0.001; llama GA=(TH-0.07137)46.94485, r=0.95,P<0.001; alpaca GA=(BPD-0.11376)47.23287, r=0.98,P<0.001; alpaca GA=(TH-0.36436)52.87663, r=0.96,P<0.001, where GA was measured in days and BPD and TH in centimeters. Results indicate that ultrasonic measurement of these fetal biometric variables constitute a valuable tool to estimate GA at any stage of pregnancy in these domestic South American camelids.     

New polymorphic microsatellite loci for different camel species

New microsatellite loci were screened and sequenced from the genomic DNA of male Camelus bactrianus. Among 32 loci, 23 were amplified in bactrian and dromedary species, 19 in llama and 20 in alpaca. The different species had similar fragment lengths per locus, with more striking similarities between bactrian and dromedary and between llama and alpaca, respectively. Seven loci had more than 10 alleles each, nine were monomorphic in all species, and one was monomorphic in Old World and polymorphic in New World camels. The results show that the informative microsatellite loci can be widely applied to several species.     

The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America

A comprehensive study of the phylogeography and population genetics of the largest wild artiodactyl in the arid and cold‐temperate South American environments, the guanaco (Lama guanicoe) was conducted. Patterns of molecular genetic structure were described using 514 bp of mtDNA sequence and 14 biparentally inherited microsatellite markers from 314 samples. These individuals originated from 17 localities throughout the current distribution across Peru, Bolivia, Argentina and Chile. This confirmed well‐defined genetic differentiation and subspecies designation of populations geographically separated to the northwest (L. g. cacsilensis) and southeast (L. g. guanicoe) of the central Andes plateau. However, these populations are not completely isolated, as shown by admixture prevalent throughout a limited contact zone, and a strong signal of expansion from north to south in the beginning of the Holocene. Microsatellite analyses differentiated three northwestern and 4–5 southeastern populations, suggesting patterns of genetic contact among these populations. Possible genetic refuges were identified, as were source‐sink patterns of gene flow at historical and recent time scales. Conservation and management of guanaco should be implemented with an understanding of these local population dynamics while also considering the preservation of broader adaptive variation and evolutionary processes.     

Traditional livestock activities modify the spatial behavior of small wildcats in the high Andes

Human activities lead to declines in species’ abundance and diversity, as well as loss of habitat quality from overexploitation. The effects of livestock grazing increase on small felids are poorly understood, primarily due to the low detectability of these species. The grazing of domestic camelids, such as the llama (Lama glama) and the alpaca (Vicugna pacos), is the main traditional source of income for the inhabitants of the Andes, where the Andean cat (Leopardus jacobita) and Pampas cat (L. colocolo) are also present. In this study, we employ camera trap data to evaluate the association of llama and alpaca grazing with occupancy by the Andean and Pampas cat in Sajama National Park. In each of 36 sampling stations, we installed a camera trap, a grid of traps for rodents and two habitat transects along a gradient of intensity of livestock grazing. Occupancy models showed that negative effect of camelid abundance was stronger for the Andean cat than the Pampas cat. For both species, occupancy was also associated positively to the abundance of prey, proximity to water bodies, and vegetation. Given that livestock activity is a way of life for human populations in the Andes, we suggest that mechanisms should be implemented to compensate for the negative effects of livestock on Andean and Pampas cat populations.     

Simple sequence repeats for genetic studies of alpaca

Trace sequences from the 2X alpaca genome sequencing effort were examined to identify simple sequence repeats (microsatellites) for genetic studies. A total of 6,685 repeat-containing sequences were downloaded from GenBank, processed, and assembled into contigs representing an estimated 4,278 distinct sequences. This sequence set contained 2,290 sequences of length > 100 nucleotides that contained microsatellites of length > or = 14 dinucleotide or 10 trinucleotide repeats with purity equal to 100%. An additional 13 sequences contained a GC microsatellite of length > or = 12 repeats (purity = 100%) were also obtained. Primer pairs for amplification of 1,516 putative loci are presented. Amplification of genomic DNA from alpaca and llama by PCR was demonstrated for 14 primer sets including one from each of the microsatellite repeat types. Comparative chromosomal location for the alpaca markers was predicted in the bovine genome by BLAT searches against assembly 4.0 of the bovine whole genome sequence. A total of 634 markers (41.8%) returned BLAT hits with score > 100 and Identity > 85%, with the majority assignable to unique locations. We show that microsatellites are abundant and easily identified within the alpaca genome sequence. These markers will provide a valuable resource for further genetic studies of the alpaca and related species.