Cooperative Research Centre

About: Cooperative Research Centre is a based out in . It is known for research contribution in the topics: Population & Sea ice. The organization has 7633 authors who have published 8607 publications receiving 429721 citations.

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Abstract: Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi‐quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa‐specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low‐level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population‐level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

Dna methylation in plants

Abstract: Methylation of cytosine residues in DNA provides a mechanism of gene control. There are two classes of methyltransferase in Arabidopsis; one has a carboxy-terminal methyltransferase domain fused to an amino-terminal regulatory domain and is similar to mammalian methyltransferases. The second class apparently lacks an amino-terminal domain and is less well conserved. Methylcytosine can occur at any cytosine residue, but it is likely that clonal transmission of methylation patterns only occurs for cytosines in strand-symmetrical sequences CpG and CpNpG. In plants, as in mammals, DNA methylation has dual roles in defense against invading DNA and transposable elements and in gene regulation. Although originally reported as having no phenotypic consequence, reduced DNA methylation disrupts normal plant development.

Observed 20th century desert dust variability: impact on climate and biogeochemistry

Abstract: Desert dust perturbs climate by directly and in- directly interacting with incoming solar and outgoing long wave radiation, thereby changing precipitation and tempera- ture, in addition to modifying ocean and land biogeochem- istry. While we know that desert dust is sensitive to pertur- bations in climate and human land use, previous studies have been unable to determine whether humans were increasing or decreasing desert dust in the global average. Here we present observational estimates of desert dust based on pa- leodata proxies showing a doubling of desert dust during the 20th century over much, but not all the globe. Large uncertainties remain in estimates of desert dust variability over 20th century due to limited data. Using these ob- servational estimates of desert dust change in combination with ocean, atmosphere and land models, we calculate the net radiative effect of these observed changes (top of at- mosphere) over the 20th century to be 0.14± 0.11 W/m 2 (1990-1999 vs. 1905-1914). The estimated radiative change

Tolerance of riverine plants to flooding and exposure indicated by water regime

Abstract: Selected water regime indices are used to describe the tolerances to flooding and exposure of littoral and floodplain plants of the River Murray, South Australia. The cover and abundance of 26 perennial species were surveyed at 12 sites along a reach where water levels were influenced by weir operations. Six indices were measured: days when water depths were ≥0, 0–20, 20–60 and ≥200 cm; days when plants were exposed to ≥100 cm of water; and days of longest exposure to water. Ordinations of plant abundances were correlated with the frequency of flooding to 0–20 and 20–60 cm, and exposure to ≥100 cm. Five species clusters were apparent, these being common floodplain species (e.g. Muehlenbeckia florulenta), uncommon floodplain species (e.g. Eleocharis acuta), species from the infrequently flooded littoral (e.g. Bolboschoenus caldwellii), species from the permanently flooded littoral (e.g. Vallisneria americana) and widespread, common species tolerant to flooding and exposure (11 species, including Phragmites australis, Cyperus gymnocaulos and Bolboschoenus medianus). Half of the 26 species occurred in at least four of seven regimes suggested by cluster analysis of water regime indices, thus indicating a broad tolerance to flooding and exposure. Preferred water regimes are summarised using minimum and maximum values and quartiles for the six indices, and similarities between preferences are illustrated by a model based on minimum spanning tree techniques. Copyright © 1999 John Wiley & Sons, Ltd.