Population dynamics of Caladenia: Bayesian estimates of transition and extinction probabilities

Tremblay, Raymond L.; Hernández, María Eglée Pérez; Larcombe, Matthew J.; Brown, Andrew F.; Quarmby, Joe; Bickerton, Doug; French, G. W.; Bould, A.

doi:10.1071/bt08167

Cited by 6 publications

(5 citation statements)

References 25 publications

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“…For this species, most of the parameters estimated by modelling approaches are similar to those measured in the present study, except one, which is different (dormancy for C. graniticola was several years longer in the present study). It is worth noting that the population of C. graniticola where data for the Tremblay et al (2009b) were collected seemed to be relatively viable in the past (their quasi extinction rate for 50% of Vital statistics and core habitats of rare orchids Australian Journal of Botanypopulations was 24 years); however, no plants have been seen in the plot where these data were obtained for a decade (they are still growing nearby). This highlights a problem with estimates of long-term population viability produced by models, because they must assume that habitat conditions are relatively constant or change gradually and predictably.…”

Section: Drakaea Isolatamentioning

confidence: 99%

Using vital statistics and core-habitat maps to manage critically endangered orchids in the Western Australian wheatbelt

Brundrett¹

2016

Aust. J. Bot.

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Abstract. Vital-statistics data concerning population viability were gathered for four of the rarest orchids in Western Australia using surveys to define population sizes and habitat areas and annual measurements of plant demographics. These orchids were Caladenia melanema, C. graniticola, C. williamsiae and Drakaea isolata from the wheatbelt of Western Australia. This agricultural area has a Mediterranean climate with unreliable rainfall, and is >80% cleared of native vegetation. Surveys with 10-30 volunteers increased population-size estimates by up to 10 times and provided spatial data to define core habitat areas. These areas included most of the individuals of a species, but were only 2-10 ha in size. Within these areas, orchids were often highly aggregated in patches a few metres wide, potentially resulting in a high degree of intraspecific competition. Vital statistics were obtained using 4-m wide and 30-50-m-long transects to measure rates of emergence, flowering, grazing and seed-set for each orchid. Plants emerging at the same position in different years were considered to be the same individual, but most emerged in new positions. Many plants emerged just once in 4 years, and 2-3 years of dormancy was common. Emergence frequencies were used to provide estimates of population sizes that were two or three times larger than suggested by data from a single year. Seed production was typically very low. Grazing by kangaroos and rabbits was most severe for C. melanema, but was greatly reduced by fencing. Severe drought prevented flowering of C. graniticola in the driest year, whereas other species were more resilient. These orchids are likely to persist as long as there are some years where rainfall is sufficient for flowering and seed set followed by a year with adequate rain for seed germination. Populations of all these orchids were stable or increasing, but they are still at high risk of extinction because of the impacts of increasing soil salinity or fire on their habitats. These species are unlikely to spread elsewhere in the highly cleared and fragmented wheatbelt. Intervention by hand-pollination, grazing protection and translocation to new locations is required to mitigate these risks. Results were summarised in vital statistics report cards with thresholds set to inform conservation management for these species. Core habitat maps and vital-statistics report cards should also be valuable new tools for terrestrial-orchid conservation in other biomes.

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Section: Drakaea Isolatamentioning

confidence: 99%

Using vital statistics and core-habitat maps to manage critically endangered orchids in the Western Australian wheatbelt

Brundrett¹

2016

Aust. J. Bot.

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“…Reporting the distribution and associated parameters provide a measure of uncertainty from which to inform the construction of an MPM (Lubben, Tenhumberg, Tyre, & Rebarber, 2008;Tenhumberg, Louda, Eckberg, & Takahashi, 2008). Furthermore, the use of hierarchical models to estimate missing values and borrowing strength from other populations or species may improve parameter estimation (Tremblay et al, 2009a(Tremblay et al, , 2009bTremblay & McCarthy, 2014;Che-Castaldo, Che-Castaldo, & Neel, 2018;James, Salguero-Gómez, Jones, Childs, & Beckerman, 2021;Davis, 2022).…”

Section: Indirectly Calculating Vital Ratesmentioning

confidence: 99%

“…, Jenouvrier et al (2018), using the multi-event algorithm of Choquet et al (2009)). Omitting a cryptic life stage can reduce the biological realism of an MPM (Nguyen et al, 2019) and alter the number of stages in the MPM, which can further impact demographic outputs (Vandermeer, 1978; Tenhumberg et al, 2009; Tremblay et al, 2009a, 2009b; Salguero-Gómez & Plotkin, 2010). In some cases, cryptic life stages will only be identified via a multidisciplinary approach including field and laboratory methods, coupled with Bayesian frameworks to integrate data and prior knowledge ( e.g.…”

Section: Common Issues In Matrix Constructionmentioning

confidence: 99%

A standard protocol to report discrete stage-structured demographic information

Gascoigne

Rolph

Sankey

et al. 2023

Preprint

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Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology, and conservation science. Accordingly, MPMs now exist for over 3,000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n=60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility, and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardized protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare, and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology, and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

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“…This advantage of using a Bayesian inferred multinomial Dirichlet distribution for estimating the mean values is that the researchers can infer variance and skew of the posterior distributions to further inform MPM construction and demographic inference (e.g. Tremblay et al, 2009a, 2009b). And finally, since sample size can be a key driver of unrealistic stage‐specific survival, sample size and uncertainty (e.g.…”

Section: Common Issues In Matrix Constructionmentioning

confidence: 99%

A standard protocol to report discrete stage‐structured demographic information

et al. 2023

Self Cite

View full text Add to dashboard Cite

Stage‐based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open‐access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre‐db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open‐access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

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Population dynamics of Caladenia: Bayesian estimates of transition and extinction probabilities

Cited by 6 publications

References 25 publications

Using vital statistics and core-habitat maps to manage critically endangered orchids in the Western Australian wheatbelt

Using vital statistics and core-habitat maps to manage critically endangered orchids in the Western Australian wheatbelt

A standard protocol to report discrete stage-structured demographic information

A standard protocol to report discrete stage‐structured demographic information

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