Determination of a complete lemur mitochondrial genome from feces

Matsui, Atsushi; Rakotondraparany, Felix; Hasegawa, Masami; Horai, Satoshi

doi:10.3106/1348-6160(2007)32[7:doaclm]2.0.co;2

Cited by 22 publications

(22 citation statements)

References 47 publications

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“…In addition to the 15 published primates sequences containing Propithecus verreauxi coquereli data determined from feces sample by us (Matsui et al, 2007), complete mtDNA sequences of 40 nonprimate mammalian species were retrieved from DDBJ/EMBL/ GenBank (Table 1).…”

Section: Alignmentmentioning

confidence: 99%

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs

Matsui

Rakotondraparany

Munechika³

et al. 2009

Gene

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111

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Prosimians (tarsiers and strepsirrhini) represent the basal lineages in primates and have a close bearing on the origin of primates. Although major lineages among anthropoidea (humans, apes and monkeys) are well represented by complete mitochondrial DNA (mtDNA) sequence data, only one complete mtDNA sequence from a representative of each of the infraorders in prosimians has been described until quite recently, and therefore we newly determined complete mtDNA sequences from 5 lemurs, 4 lorises, one tarsier and one platyrrhini. These sequences were provided to phylogenetic analyses in combination with the sequences from the 15 primates species reported to the database. The position of tarsiers among primates could not be resolved by the maximum likelihood (ML) and neighbor-joining (NJ) analyses with several data sets. As to the position of tarsiers, any of the three alternative topologies (monophyly of haplorhini, monophyly of prosimians, and tarsiers being basal in primates) was not rejected at the significance level of 5%, neither at the nucleotide nor at the amino acid level. In addition, the significant variations of C and T compositions were observed across primates species. Furthermore, we used AGY data sets for phylogenetic analyses in order to remove the effect of different C/T composition bias across species. The analyses of AGY data sets provided a medium support for the monophyly of haplorhini, which might have been screened by the variation in base composition of mtDNA across species. To estimates the speciation dates within primates, we analyzed the amino acid sequences of mt-proteins with a Bayesian method of Thorne and Kishino. Divergence dates were estimated as follows for the crown groups: about 35.4 million years ago (mya) for lorisiformes, 55.3 mya for lemuriformes, 64.5 mya for strepsirrhini, 70.1 mya for haplorhini and 76.0 mya for primates. Furthermore, we reexamined the biogeographic scenarios which have been proposed for the origin of strepsirrhini (lemuriformes and lorisiformes) and for the dispersal of the lemuriformes and lorisiformes.

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Section: Alignmentmentioning

confidence: 99%

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs

Matsui

Rakotondraparany

Munechika³

et al. 2009

Gene

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111

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“…Recently, several methods were developed for DNA extraction from faeces, including a collection method, sample preservation, and PCR amplification (Brinkman et al 2009;Goossens et al 2000;Nsubuga et al 2004;Piggott et al 2004;Zhang et al 2006). Although problems with non-amplification, false alleles, and allelic dropout in microsatellites remain (Brinkman et al 2009;Murphy et al 2007), faecal DNA analysis has become popular for inferring phylogeny or intraspecific hybridization and for analyzing population genetics (Adams et al 2003;Ernest et al 2000;Matsui et al 2007). …”

Section: Introductionmentioning

confidence: 99%

Species identification based on the faecal DNA samples of the Japanese serow (Capricornis crispus)

Yamashiro

Baba

et al. 2010

Conservation Genet Resour

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The Japanese serow (Capricornis crispus) is endemic to mountain regions in Japan. Due to the difficulty of directly observing Japanese serows, traces such as faeces have been utilized to study their distribution and estimate their population size. However, the recent population increase of sika deer (Cervus nippon) often leads misidentification of sika deer faecal pellets as those of Japanese serows. Therefore, we developed species identification methods to differentiate between the Japanese serow and sika deer based on mtDNA cytchrome b gene sequences, and applied the method to faecal samples collected for a survey program on the Japanese serow. In 67 field-collected faecal samples examined, we could amplify mtDNA at relatively high PCR succession rates (86.6%). Species identification based on PCR-RFLPs using the cytochrome b gene revealed that 41.4% of faecal pellets of sika deer were misidentified as being from Japanese serow. This suggests that the present population size of the Japanese serow may be overestimated. This species identification method eliminates such misidentifications and should become a powerful tool for studying Japanese serow, including their distribution, precise population size, and estimations of density.

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“…Non-invasive sampling methods for DNA isolation provide an attractive alternative to methods that required the use of blood and tissue samples (Matsui et al 2007). A wide range of samples collected non-invasively have been used for genetic analysis, with the use of faecal samples probably being the most popular.…”

Section: Introductionmentioning

confidence: 99%

The effect of sample age and storage method on DNA yield and microsatellite amplification from baboon (Papio ursinus) faecal samples

et al. 2010

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Sampling methods that allow DNA collection without the physical handling of animals are popular in conservation genetics, but DNA isolated from faecal samples may be degraded, potentially leading to erroneous microsatellite genotyping results. We collected baboon faecal samples from fresh to 1-week post-defecation in a controlled sampling environment and preserved these using three storage techniques. After DNA isolation and quantification, the samples were genotyped at eight microsatellite loci. Quantitatively, DNA yield was highest when using silica as storage medium. However, microsatellite amplification from samples stored in 95% ETOH were most successful, with 100% success for fresh samples and dropping only marginally to 87.5% of loci for samples collected after 1 week. This disparity between quantitative and qualitative results suggests that total DNA concentrations do not necessarily provide a reliable indication of the amount of target DNA present in a DNA isolate. Our results nevertheless confirm that microsatellite fragments can successfully be amplified from faecal samples up to 1 week post-defecation, with careful selection of storage protocols and loci.

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Determination of a complete lemur mitochondrial genome from feces

Cited by 22 publications

References 47 publications

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs

Species identification based on the faecal DNA samples of the Japanese serow (Capricornis crispus)

The effect of sample age and storage method on DNA yield and microsatellite amplification from baboon (Papio ursinus) faecal samples

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