Genetic Diversity and Societally Important Disparities

Rosenberg, Noah A.; Kang, Jonathan T. L.

doi:10.1534/genetics.115.176750

Cited by 40 publications

(29 citation statements)

References 57 publications

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“…Expected heterozygosity is an important and commonly used measure of within population genetic diversity (Rosenberg & Kang, ). Expected heterozygosity of A. stenophylla subpopulations in this study ranged from 0.392 to 0.480.…”

Section: Discussionmentioning

confidence: 99%

Gene flow and genetic structure in Acacia stenophylla (Fabaceae): Effects of hydrological connectivity

Murray

Reid

Capon

et al. 2019

Journal of Biogeography

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Aim Riparian ecosystems are regarded as vulnerable to the effects of climate change. Because of their reliance on passive dispersal to migrate from areas where conditions have become unfavourable, plants are particularly susceptible. On dryland river floodplains, the species diversity of herbaceous annuals is often high while that of structurally dominant woody perennials is low. We examined gene flow genetic structure and dispersal in Acacia stenophylla, a small perennial tree widely distributed throughout river systems of inland Australia. The role of the river corridor in shaping patterns of gene flow and genetic structure is also investigated. Location Murray‐Darling Basin, south eastern Australia Methods A total of 127 individuals, from 12 subpopulations located on seven rivers were genotyped at 13 microsatellite loci. Several population and landscape genetic tools were applied to the microsatellite data to evaluate spatial patterns of gene flow and genetic structure and make inferences regarding possible modes of dispersal. Results High gene flow and weak genetic structure was identified for the 12 subpopulations of A. stenophylla sampled, a surprising result given large distances between subpopulations. Pairwise genetic distance between subpopulations was low to moderate and could largely be explained (R2 = 0.68) by two variables: distance along the river and the proportion of no flow days. structure analysis revealed two genetic clusters. Subpopulations located on the Darling and Lower Balonne rivers were dominated by cluster one while subpopulations from the Warrego and Paroo rivers showed largely mixed ancestry with individuals descending from both clusters one and two. Main Conclusions These results indicate that the river corridor facilitates extensive gene flow between subpopulations of A. stenophylla in this system. Hydrochory appears to be the dominant process; however, upstream movements of propagules most probably via animal movement are sufficient to negate effects expected under unidirectional dispersal.

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Section: Discussionmentioning

confidence: 99%

Gene flow and genetic structure in Acacia stenophylla (Fabaceae): Effects of hydrological connectivity

Murray

Reid

Capon

et al. 2019

Journal of Biogeography

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“…Genetic patterns vary across different populations, such as the allele frequencies of SNPs and LD by haplotype structures . Therefore, SNPs, haplotypes and gene–gene interactions could provide broad aspects of genetic diversity in multiple dimensions.…”

Section: Discussionmentioning

confidence: 99%

“…Genetic patterns vary across different populations, such as the allele frequencies of SNPs and LD by haplotype structures. 46 Therefore, SNPs, haplotypes and gene-gene interactions could provide broad aspects of genetic diversity in multiple dimensions. In this study, we have shown that the number of common SNPs in stemness-related genes was greater in African descendants than in non-Hispanic whites.…”

Section: Discussionmentioning

confidence: 99%

Associations between RNA splicing regulatory variants of stemness‐related genes and racial disparities in susceptibility to prostate cancer

Wang

Freedman

Liu

et al. 2017

Intl Journal of Cancer

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Evidence suggests that cells with a stemness phenotype play a pivotal role in oncogenesis, and prostate cells exhibiting this phenotype have been identified. We used two genome-wide association study (GWAS) datasets of African descendants, from the Multiethnic/Minority Cohort Study of Diet and Cancer (MEC) and the Ghana Prostate Study, as well as two GWAS datasets of non-Hispanic whites, from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and the Breast and Prostate Cancer Cohort Consortium (BPC3), to analyze the associations between genetic variants of stemness-related genes and racial disparities in susceptibility to prostate cancer. We evaluated associations of single nucleotide polymorphisms (SNPs) in 25 stemness-related genes with prostate cancer risk in 1,609 cases and 2,550 controls of non-Hispanic whites (4,934 SNPs) and 1,144 cases and 1,116 controls of African descendants (5,448 SNPs) with correction by false discovery rate ≤ 0.2. We identified 32 SNPs in five genes (TP63, ALDH1A1, WNT1, MET and EGFR) that were significantly associated with prostate cancer risk, of which six SNPs in three genes (TP63, ALDH1A1 and WNT1) and eight EGFR SNPs showed heterogeneity in susceptibility between these two racial groups. In addition, 13 SNPs in MET and one in ALDH1A1 were found only in African descendants. The in silico bioinformatics analyses revealed that EGFR rs2072454 and SNPs in linkage with the identified SNPs in MET and ALDH1A1 (r2 > 0.6) were predicted to regulate RNA splicing. These variants may serve as novel biomarkers for racial disparities in prostate cancer risk.

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“…Overall levels of within‐ and among‐subpopulation genetic diversity in this study were low, and patterns of downstream increase in genetic diversity were not evident. Expected heterozygosity provides a valuable and regularly used measure of genetic diversity (Rosenberg & Kang, ). Expected heterozygosity levels (0.343 to 0.556) in this study were lower than expected for long‐lived perennial, widespread, and outcrossing plant species (~0.65) (Nybom, ) as well as other Australian riparian shrub (0.69) (Hevroy, Moody, & Krauss, ) and tree species (~0.8) (Butcher, McDonald, & Bell, ).…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis suggests extensive gene flow within and between catchments in a common and ecologically significant dryland river shrub species; Duma florulenta (Polygonaceae)

Murray

Reid

Capon

et al. 2019

Ecology and Evolution

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Aim The conservation of plant species biodiversity has been identified as a crucial factor for the resilience of dryland ecosystems in the face of climate change and desertification. Duma florulenta (lignum) is a keystone species that facilitates biodiversity in the floodplains and wetlands of Australia's dryland river systems. This paper explores spatial genetic structure of lignum and investigates factors influencing dispersal and gene flow within and among river catchments of the northern Murray–Darling Basin. Location Northern Murray–Darling Basin, eastern Australia. Methods A total of 122 individual plants from subpopulations located on rivers in four adjacent catchments were genotyped using 10 microsatellite markers. Microsatellite data were then analyzed using population genetic techniques to evaluate levels of gene flow and genetic structure and identify factors influencing dispersal. Results Results suggest high levels of gene flow between lignum subpopulations of the northern Murray–Darling Basin. AMOVA revealed small but significant differences between subpopulations, and STRUCTURE analysis did not detect meaningful structure when sampling information was not provided. However, when sampling information was supplied using the LOCPRIOR model, three genetic clusters were identified. All Lower Balonne subpopulations were assigned to cluster 1 while a number of the other subpopulations showed mixed ancestry. Weak relationships were identified between pairwise genetic distance and geographic as well as river distance, although the R 2 value of the former was only half that of the latter. Main conclusions Patterns of genetic variation suggest frequent long‐distance overland gene flow largely as a result of the movement of seeds via floodwater. Therefore, maintenance of natural variability in flow regime is key both to maintain conditions favorable to recruitment and to promote dispersal and gene flow across the landscape. However, given future climate change projections persistence may be more reliant on the species ability to endure long periods of drought between flood events.

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Genetic Diversity and Societally Important Disparities

Cited by 40 publications

References 57 publications

Gene flow and genetic structure in Acacia stenophylla (Fabaceae): Effects of hydrological connectivity

Gene flow and genetic structure in Acacia stenophylla (Fabaceae): Effects of hydrological connectivity

Associations between RNA splicing regulatory variants of stemness‐related genes and racial disparities in susceptibility to prostate cancer

Genetic analysis suggests extensive gene flow within and between catchments in a common and ecologically significant dryland river shrub species; Duma florulenta (Polygonaceae)

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