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Irion, D. N.; Schaffer, A. L.; Grant, Sherry; Wilton, Alan N.; Pedersen, Niels C

doi:10.1186/1471-2156-6-6

Cited by 35 publications

(22 citation statements)

References 20 publications

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“…This was consistent with a long-term isolation of the Bali dog population [18]. Additionally, 5 haplotypes (of 18 total) were found only on Bali.…”

Section: Resultssupporting

confidence: 87%

“…The time estimates, while necessarily imprecise, were qualitatively robust because they were based on calibration to known-age indigenous, insular dog populations of Bali and Australia. These Island populations were known to be founded on the order of 3,000–5,000 years BP, based on archaeological evidence [17], [18], [27] and confirmed with mtDNA both for Bali dogs (this study) and dingoes [28]. Thus, extant Middle Eastern and Southeast Asian village dog patrilines clearly reflect a deep divergence reaching at least as far back as 10,000–16,000 years.…”

Section: Discussionsupporting

confidence: 68%

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Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

et al. 2011

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Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.

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“…This was consistent with a long-term isolation of the Bali dog population [18]. Additionally, 5 haplotypes (of 18 total) were found only on Bali.…”

Section: Resultssupporting

confidence: 87%

Section: Discussionsupporting

confidence: 68%

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

et al. 2011

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“…This staining is consistent with a role for CnVam7 (CNAG_02676) in assisting endocytic transport from the membrane to the vacuole. Previous work characterizing this protein in S. cerevisiae , as well as homologous proteins in other fungi, have indicated additional roles for Vam7 in fungal cell wall stress and organization (Dou et al, 2011; Lesage et al, 2005; Wedlich-Söldner et al, 2000; Zhang et al, 2015). …”

Section: Resultsmentioning

confidence: 94%

Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans

Esher

Granek

Alspaugh

2015

Fungal Genetics and Biology

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Random insertional mutagenesis screens are important tools in microbial genetics studies. Investigators in fungal systems have used the plant pathogen Agrobacterium tumefaciens to create tagged, random mutations for genetic screens in their fungal species of interest through a unique process of trans-kingdom cellular transconjugation. However, identifying the locations of insertion has traditionally required tedious PCR-based methods, limiting the effective throughput of this system. We have developed an efficient genomic sequencing and analysis method (AIM-Seq) to facilitate identification of randomly generated genomic insertions in microorganisms. AIM-Seq combines batch sampling, whole genome sequencing, and a novel bioinformatics pipeline, AIM-HII, to rapidly identify sites of genomic insertion. We have specifically applied this technique to Agrobacterium-mediated transconjugation in the human fungal pathogen Cryptococcus neoformans. With this approach, we have screened a library of C. neoformans cell wall mutants, selecting twenty-seven mutants of interest for analysis by AIM-Seq. We identified thirty-five putative genomic insertions in known and previously unknown regulators of cell wall processes in this pathogenic fungus. We confirmed the relevance of a subset of these by creating independent mutant strains and analyzing resulting cell wall phenotypes. Through our sequence-based analysis of these mutations, we observed “typical” insertions of the Agrobacterium transfer DNA as well as atypical insertion events, including large deletions and chromosomal rearrangements. Initially applied to C. neoformans, this mutant analysis tool can be applied to a wide range of experimental systems and methods of mutagenesis, facilitating future microbial genetic screens.

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“…To test for correlation between genetic and geographic distance (km), we performed Mantel tests with 10,000 permutations59. Analyses were performed using the Φ ST , the Slatkin's [Φ ST /(1 − Φ ST )] and the D est values previously calculated.…”

Section: Methodsmentioning

confidence: 99%

High genetic diversity and absence of founder effects in a worldwide aquatic invader

Lejeusne

Saunier

Petit

et al. 2014

Sci Rep

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The introduced oriental shrimp Palaemon macrodactylus has recently become widespread in temperate estuaries worldwide. However, this recent worldwide spread outside of its native range arises after a previous introduction to the US Pacific coast, where it was restricted for more than 30 years. Using a phylogeographic approach, the present work investigates the genetic history of the invasion of this decapod worldwide. Japan acted as the main native source area for worldwide introduced populations, but other native areas (likely South Korea and China) may act as source populations as well. The recently introduced European and NW Atlantic populations result from colonization from both Japan and an unknown area of the native range, although colonization from the NE Pacific could not be ruled out. Most introduced populations had higher haplotypic diversity than most native populations. P. macrodactylus has a strong potential to become one of the most widespread introduced species and may become the dominant estuarine shrimp in Europe. The ecological and economic consequences of this invasion remain to be thoroughly evaluated.

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Untitled

Cited by 35 publications

References 20 publications

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans

High genetic diversity and absence of founder effects in a worldwide aquatic invader

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