The complete mitochondrial DNA sequence of the guanaco ( Lama guanicoe) : comparative analysis with the vicuña ( Vicugna vicugna) genome (original) (raw)
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Mitochondrial DNA structure and organization of the control region of South American camelids
Molecular Ecology Notes, 2004
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 tRN-APro 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.
Animal Genetics, 2013
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.
Mitochondrial DNA Variation and Systematics of the Guanaco (Lama guanicoe, Artiodactyla: Camelidae
Journal of Mammalogy, 2008
Guanacos (Lama guanicoe) are the most important native herbivorous species in the South American steppes and the dominant ungulate in a fauna rich in rodents but poor in large mammal species. Between 2 and 4 subspecies are usually recognized within Lama guanicoe, based on subtle morphological differences and geographic distribution. To evaluate whether molecular variation is consistent with the latter hypotheses, we analyzed the complete cytochrome-b and partial control region mitochondrial DNA sequences of L. guanicoe from 22 localities in Peru, Bolivia, Argentina, and Chile. Sequence analyses of both genes support the monophyly of the species but failed to distinguish the occurrence of subspecies along the geographic range. Despite that, the northernmost populations (Peru and northern Chile) showed some degree of genetic differentiation with respect to southern representatives from Argentina, Bolivia, and rest of Chile. Analysis of genetic diversity also showed a strong signal of past low population size and a recent population expansion. L. g. voglii . A recent review by González et al. (2006) provides extensive information on the morphology and biogeography of the 4 subspecies. Scattered, relict populations of the smallest guanaco, L. g. cacsilensis, are * Correspondent: jcmarin@ubiobio.cl
Mitochondria DNA variation and systematics of the guanaco (Lama guanicoe, Artiodactyla: Camelidae)
Journal of Mammalogy, 2008
Guanacos (Lama guanicoe) are the most important native herbivorous species in the South American steppes and the dominant ungulate in a fauna rich in rodents but poor in large mammal species. Between 2 and 4 subspecies are usually recognized within Lama guanicoe, based on subtle morphological differences and geographic distribution. To evaluate whether molecular variation is consistent with the latter hypotheses, we analyzed the complete cytochrome-b and partial control region mitochondrial DNA sequences of L. guanicoe from 22 localities in Peru, Bolivia, Argentina, and Chile. Sequence analyses of both genes support the monophyly of the species but failed to distinguish the occurrence of subspecies along the geographic range. Despite that, the northernmost populations (Peru and northern Chile) showed some degree of genetic differentiation with respect to southern representatives from Argentina, Bolivia, and rest of Chile. Analysis of genetic diversity also showed a strong signal of past low population size and a recent population expansion. L. g. voglii . A recent review by González et al. (2006) provides extensive information on the morphology and biogeography of the 4 subspecies. Scattered, relict populations of the smallest guanaco, L. g. cacsilensis, are * Correspondent: jcmarin@ubiobio.cl
Molecular Study of Energy Related Mitochondrial Genes in Arabian and Bactrian Camels
American Journal of Biochemistry and Biotechnology, 2013
The single-humped camel, Camelus dromedaries inhabiting Afro-Arabia and the double-humped camel, Camelus bactrianus inhabiting central Asia are the only species in their genus. The present study aimed to amplify and partially sequence the mitochondrial DNA genes encoding for NADH dehydrogenase subunit 1, cytochrome c oxidase subunit 1, ATP synthase subunit 6 (ATP6), cytochrome b and displacement region (d-loop) in the single-humped camel and compare it to their counterparts already sequenced for the doublehumped camel. These energy-related genes showed amino acid substitutions gradually increased according to their locations among macromolecular energy transducers. Both ATP synthase 6 in the central core and cytochrome b in the inner mitochondrial membrane acquired the greatest substitutions of 5 and 7 amino acids, respectively. Cytochrome c oxidase is the terminal complex of the electron transport chain of the inner mitochondrial membrane and it showed no substitutions. These substitutions seemed to be correlated with the energy metabolism in both camel phenotypes. The d-loop showed tandem repeats of six nucleotides at its 3` end with polymorphism between both species without any evidence relates such variation to energy production.
Journal of Molecular Evolution, 1996
The nucleotide sequence of the complete mitochondrial genome of the donkey, Equus asinus, was determined. The length of the molecule is 16,670 bp. The length, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of two types of repetitive motifs in the control region. The sequence of the repeats is (a) 5Ј-CACACCCA and (b) 5Ј-TGCGCGCA, respectively. The order of (a) and (b) can be expressed as {n[2(a)+(b)]+m(a)}. In 32 different clones analyzed the number of n and m ranged from 0 to 9 and 1 to 7. The two rRNA genes, the 13 peptide-coding genes, and the 22 tRNA genes of the donkey and the horse, Equus caballus, were compared in detail. Total nucleotide difference outside the control region was 6.9%. Nucleotide difference between peptide-coding genes ranged from 6.4% to 9.4% with a mean of 8.0%. In the inferred protein sequences of the 13 peptide-coding genes the amino acid difference was 0.2-8.8%, and the mean for the 13 concatenated amino acid sequences was 1.9%. In the 22 tRNA genes, the mean difference was 3.5%, and that in the two rRNA genes was 4.1%. The mtDNA differences between the donkey and the horse suggest that the evolutionary separation of the two species occurred ≈9 million years ago. Analyses of differences among the mtDNAs of three other species-pairs, harbor seal/grey seal, fin whale/blue whale, and Homo/ common chimpanzee, showed that the relative evolutionary rate of individual peptide-coding genes varies among different species-pairs and modes of comparison. The findings show that the superimposition of sequence data of one lineage for resolving and dating evolutionary divergences of other lineages should be performed with caution unless based on comprehensive data.
In South American societies, domesticated camelids were of great cultural importance and subject to trade and translocation. South American camelids were even found on remote and hard to reach islands, emphasizing their importance to historic and prehistoric South American populations. Isla Mocha, a volcanic island 35 km offshore of Central-South Chile, is an example of such an island. When Dutch and Spanish explorers reached the island in the early 17th century, they found that domesticated camelids called " chilihueque " played a major role in the island's society. The origin and taxonomy of these enigmatic camelids is unclear and controversial. This study aims to resolve this controversy through genetic analyses of Isla Mocha camelid remains dating from pre-Columbian to early historic times. A recent archaeological excavation of site P21-3 on Isla Mocha yielded a number of camelid remains. Three complete mitochondrial genomes were successfully recovered and analysed. Phylogenetic analyses suggest that " chilihueque " was a local term for a domesticated guanaco. Results from phylogeographic analyses are consistent with Isla Mocha camelids being sourced from Southern Chilean guanaco populations. Our data highlights the capability of ancient DNA to answer questions about extinct populations which includes species identity, potential translocation events and origins of founding individuals. The translocation of animals to islands has been an important human adaptive strategy even before the development of domestication 1. Live animals are transported for numerous reasons including as future food resources, for their by-products, which can include bones, teeth, fibre, or dung, or for their cultural/spiritual or ritual importance. Often sizable challenges and obstacles had to be overcome to transport larger animals across considerable water gaps, emphasizing the cultural importance of these translocated animals. The enigmatic camelids of Isla Mocha, an island located approximately 35 km off the coast in the Arauco region of South Central Chile, are an example of such a challenging translocation of animals. Isla Mocha has not been connected to the mainland since it rose above sea level during the Pleistocene, and it has no native large land mammals 2,3. The earliest human occupation of the island is dated to about 3500 years ago and evidence of permanent occupation dates from about 1500 years ago 4,5. Archaeological excavations on Isla Mocha have provided a large number of bone artifacts made of large mammal bones such as cetaceans, pinnipeds and camelids. Camelid bones make up the majority of the mammal remains in archaeological sites on the island.
In South American societies, domesticated camelids were of great cultural importance and subject to trade and translocation. South American camelids were even found on remote and hard to reach islands, emphasizing their importance to historic and prehistoric South American populations. Isla Mocha, a volcanic island 35 km offshore of Central-South Chile, is an example of such an island. When Dutch and Spanish explorers reached the island in the early 17th century, they found that domesticated camelids called " chilihueque " played a major role in the island's society. The origin and taxonomy of these enigmatic camelids is unclear and controversial. This study aims to resolve this controversy through genetic analyses of Isla Mocha camelid remains dating from pre-Columbian to early historic times. A recent archaeological excavation of site P21-3 on Isla Mocha yielded a number of camelid remains. Three complete mitochondrial genomes were successfully recovered and analysed. Phylogenetic analyses suggest that " chilihueque " was a local term for a domesticated guanaco. Results from phylogeographic analyses are consistent with Isla Mocha camelids being sourced from Southern Chilean guanaco populations. Our data highlights the capability of ancient DNA to answer questions about extinct populations which includes species identity, potential translocation events and origins of founding individuals. The translocation of animals to islands has been an important human adaptive strategy even before the development of domestication 1. Live animals are transported for numerous reasons including as future food resources, for their by-products, which can include bones, teeth, fibre, or dung, or for their cultural/spiritual or ritual importance. Often sizable challenges and obstacles had to be overcome to transport larger animals across considerable water gaps, emphasizing the cultural importance of these translocated animals. The enigmatic camelids of Isla Mocha, an island located approximately 35 km off the coast in the Arauco region of South Central Chile, are an example of such a challenging translocation of animals. Isla Mocha has not been connected to the mainland since it rose above sea level during the Pleistocene, and it has no native large land mammals 2,3. The earliest human occupation of the island is dated to about 3500 years ago and evidence of permanent occupation dates from about 1500 years ago 4,5. Archaeological excavations on Isla Mocha have provided a large number of bone artifacts made of large mammal bones such as cetaceans, pinnipeds and camelids. Camelid bones make up the majority of the mammal remains in archaeological sites on the island.
Animal Genetics, 2010
Hybridization between wild species and their domestic congeners often threatens the gene pool of the wild species. The last wild Bactrian camel (Camelus ferus) populations in Mongolia and China are examples of populations facing such a hybridization threat. To address this key issue in the conservation of wild camels, we analysed wild, hybrid and domestic Bactrian camels (Camelus bactrianus) originating from Mongolia, China and Austria. Through screening of an 804-base-pair mitochondrial fragment, we identified eight mitochondrial haplotypes and found high sequence divergence (1.9%) between C. ferus and C. bactrianus. On the basis of a mitochondrial DNA sequence fixed difference, we developed a diagnostic PCR restriction fragment length polymorphism (PCR-RFLP) assay to differentiate between wild and domestic camel samples. We applied the assay to 81 individuals and confirmed the origin of all samples including five hybrids with known maternal ancestry. The PCR-RFLP system was effective for both traditional (blood, skin) and non-invasive samples (faeces, hair), as well as for museum specimens. Our results demonstrate high levels of mitochondrial differentiation between wild and domestic Bactrian camels and that maternal hybridization can be detected by a rapid and reliable PCR-RFLP system.