Dormancy in Caladenia: a Bayesian approach to evaluating latency

Dormancy is common in many terrestrial orchids in southern Australia and other temperate environments. The difficulty for conservation and management when considering dormancy is ascertaining whether non-emergent plants are dormant or dead. Here we use a multi-state capture–recapture method, undertaken over several seasons, to determine the likelihood of a plant becoming dormant or dying following its annual emergent period and evaluate the frequency of the length of dormancy. We assess the transition probabilities from time series of varying lengths for the following nine terrestrial orchids in the genus Caladenia: C. amoena, C. argocalla, C. clavigera, C. elegans, C. graniticola, C. macroclavia, C. oenochila, C. rosella and C. valida from Victoria, South Australia and Western Australia. We used a Bayesian approach for estimating survivorship, dormancy and the likelihood of death from capture–recapture data. Considering all species together, the probability of surviving from one year to the next was ~86%, whereas the likelihood of observing an individual above ground in two consecutive years was ~74%. All species showed dormancy of predominantly 1 year, whereas dormancy of three or more years was extremely rare (<2%). The results have practical implications for conservation, in that (1) population sizes of Caladenia species are more easily estimated by being able to distinguish the likelihood of an unseen individual being dormant or dead, (2) population dynamics of individuals can be evaluated by using a 1–3-year dormancy period and (3) survey effort is not wasted on monitoring individuals that have not emerged for many years.

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Using visual encounter data to improve capture-recapture abundance estimates

10.1101/2020.01.22.915314 ◽

2020 ◽

Author(s):

Maxwell B. Joseph ◽

Roland A. Knapp

Keyword(s):

Population Size ◽

Lower Bounds ◽

Bayesian Approach ◽

Individual Identification ◽

Hierarchical Bayesian ◽

Sampling Occasion ◽

Demographic Rates ◽

Abundance Estimates ◽

Population Sizes ◽

Capture Recapture

AbstractCapture-recapture studies are widely used in ecology to estimate population sizes and demographic rates. In some capture-recapture studies, individuals may be visually encountered but not identified. For example, if individual identification is only possible upon capture and individuals escape capture, visual encounters can result in failed captures where individual identities are unknown. In such cases, the data consist of capture histories with known individual identities, and counts of failed captures for individuals with unknown identities. These failed captures are ignored in traditional capture-recapture analyses that require known individual identities. Here we show that if animals can be encountered at most once per sampling occasion, failed captures provide lower bounds on population size that can increase the precision of abundance estimates. Analytical results and simulations indicate that visual encounter data improve abundance estimates when capture probabilities are low, and when there are few repeat surveys. We present a hierarchical Bayesian approach for integrating failed captures and auxiliary encounter data in statistical capture-recapture models. This approach can be integrated with existing capture-recapture models, and may prove particularly useful for hard to capture species in data-limited settings.

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Preliminary investigations into the life cycle of Ventruia inaequalis (Cooke) WINT. in South Australia.

Australian Journal of Agricultural Research ◽

10.1071/ar9530415 ◽

1953 ◽

Vol 4 (4) ◽

pp. 415 ◽

Cited By ~ 2

Author(s):

MW Jeffery

Keyword(s):

Life Cycle ◽

Primary Infection ◽

South Australia ◽

Late Summer ◽

Relative Importance ◽

New Information ◽

One Year

Investigation into the possible sources of primary infection by the fungus Ventruia inaequalis (Cooke) Wint. in spring has been carried out. The results present new information on the life cycle of the pathogen under South Australian conditions. Sources of primary infection, such 'as lesions on one-year-old wood or overwintering superficial conidia on the trees, do not appear important. Bud-scale infection of dormant buds has been shown, and its relative importance is discussed. Ascospores are the most important source of primary infection. Their period of discharge extends to a later date than previously reported for South Australia and is considered in relation to leader shoot and late summer spot infection.

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The Initial Response of a Chenopod Shrubland Plant and Invertebrate Community to Two Pulses of Intensive Cattle Grazing.

The Rangeland Journal ◽

10.1071/rj9990169 ◽

1999 ◽

Vol 21 (2) ◽

pp. 169 ◽

Cited By ~ 13

Author(s):

JL Read

Keyword(s):

Water Distribution ◽

Marked Effect ◽

Plant Cover ◽

South Australia ◽

Initial Response ◽

Plant Species Richness ◽

Cattle Grazing ◽

Invertebrate Community ◽

Distribution Features ◽

One Year

The initial effect of two pulses of heavy cattle grazing on chenopod shrubland plants and invertebrates in northern South Australia was assessed in a two year trial. Both plant and invertebrate communities were structured by subhabitats which were defined by edaphic and water-distribution features. The cover of grasses and the dominant shrubs, Atriplex vesicaria and Maireana astrotricha, declined significantly following grazing but only total vegetation cover was significantly lower than controls one year after grazing. Plant species richness was not affected by the grazing pulses. Abundance of ants increased, but the responses of other invertebrates were inconsistent following grazing. Rainfall had a marked effect upon both plant cover and invertebrate abundance. Key words: chenopod shrublands, pulsed cattle grazing, Atriplex vesicaria, invertebrates, bioindicators

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Hybrid machine learning process improves operations in South Australian trial

Water e-Journal ◽

10.21139/wej.2020.027 ◽

2021 ◽

Vol 5 (4) ◽

pp. 1-16

Author(s):

Kalan Braun ◽

James Ireland ◽

Jonathan Klaric

Keyword(s):

Machine Learning ◽

Asset Management ◽

South Australia ◽

Cloud Data ◽

Engineering Teams ◽

Deterministic Modelling ◽

Full Production ◽

Machine Learning Applications ◽

Hybrid Machine ◽

One Year

TRILITY has developed a production cloud data management solution, KOIOS DatalytiX to provide hybrid machine learning applications and deterministic modelling tools to its operations, asset management, and engineering teams. Two optimiser applications for chemical coagulant prediction and filtration performance were deployed in the Riverland, South Australia at 10 conventional water treatment plants in 2018, to full production in 2019. One year later the impacts on the optimisation behaviour of operations teams, process performance and trihalomethane (THM) reduction outcomes are discussed.

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Model comparison and assessment for multi-state capture–recapture–recovery models

Journal of Ornithology ◽

10.1007/s10336-010-0611-z ◽

2010 ◽

Vol 152 (S2) ◽

pp. 293-303 ◽

Cited By ~ 5

Author(s):

Rachel S. McCrea ◽

Byron J. T. Morgan ◽

Thomas Bregnballe

Keyword(s):

Model Comparison ◽

State Capture ◽

Capture Recapture ◽

Recovery Models

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Abstract 29: Loss of Ideal Total Cholesterol Early in Life: The National Health and Nutrition Examination Survey (NHANES)

Circulation ◽

10.1161/circ.131.suppl_1.29 ◽

2015 ◽

Vol 131 (suppl_1) ◽

Author(s):

Joseph C Engeda ◽

Katelyn M Holliday ◽

Shakia T Hardy ◽

Sujatro Chakladar ◽

Gerardo Heiss ◽

...

Keyword(s):

American Heart ◽

Transition Probabilities ◽

Heart Association ◽

Blood Cholesterol ◽

Total Blood ◽

Cross Sectional ◽

Demographic Groups ◽

Health And Nutrition ◽

One Year ◽

Total Blood Cholesterol

Introduction: Ideal total blood cholesterol (TC) levels are associated with lower cardiovascular disease (CVD) morbidity and mortality. In the U.S. TC increases up to middle age, but declines at older ages. Few studies have characterized the transition from ideal to intermediate and poor TC levels in different life epochs and in minorities. Methods: Cross-sectional 2007-2012 NHANES data (N = 11,140) were used to estimate the age-, race-, and sex- specific prevalence of ideal (≥20 years: <200 mg/dL untreated, 16-19 years: <170 mg/dL), intermediate (≥20 years: 200-239 mg/dL or treated to goal, 16-19 years: 170-199 mg/dL), and poor (≥20 years: ≥240 mg/dL, 16-19 years: ≥200 mg/dL) TC, defined per American Heart Association criteria. We then used these data and novel Markov-type models to estimate net transition probabilities between ideal, intermediate and poor TC. Results: Between the ages of 16 and 18, the prevalence of ideal TC among European American (EA) and African American (AA) men was approximately 68%, notably higher than the prevalence in EA women (63%) and AA women (61%). Variation in the loss of ideal TC was also observed by race and sex. Between 16-50 years of age, the proportion of AA men, EA men and EA women with ideal levels of TC declined approximately 2.0% (95% CI: 1.8%, 2.2%) per year. In AA women by contrast, the age-specific decline in ideal TC was not uniform between 16-50 years of age. The proportion of AA women with ideal levels of TC declined 0.7% (95% CI: 0.2%, 1.2%) per year from 16-20 years of age but increased to 2.8% (95% CI: 2.4%, 3.3%) per year by age 50. Among populations with intermediate TC levels, estimated 1-year net transitions to poor TC peaked at age 16, the earliest age under investigation, for EA men, EA women, and AA men but remained stable for AA women through 70 years of age, where a net 0.6% (95% CI: 0.1%, 1.3%) of the population with intermediate TC levels transitioned to poor TC levels one year later. In all demographic groups and life epochs, greater proportions of the population transitioned from intermediate to poor TC than from poor to intermediate TC. Conclusions: Loss of ideal TC begins early in life and shows divergent patters by gender and race. Difficulties re-attaining ideal TC once classified as intermediate or poor support interventions that promote ideal TC levels in younger ages, especially among AA women.

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Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression

BMC Biology ◽

10.1186/s12915-020-00897-y ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Ulfar Bergthorsson ◽

Caroline J. Sheeba ◽

Anke Konrad ◽

Tony Belicard ◽

Toni Beltran ◽

...

Keyword(s):

Natural Selection ◽

Transcriptional Activation ◽

Small Rnas ◽

Active Regions ◽

Purifying Selection ◽

Ancestral Population ◽

Sequence Context ◽

C Elegans ◽

Population Sizes

Abstract Background Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Results Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Conclusions Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.

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