Reintroducing endangered raptors: A case study of supplementary feeding and removal of nestlings from wild populations

AbstractGenomic prediction, the technique whereby an individual’s genetic component of their phenotype is estimated from its genome, has revolutionised animal and plant breeding and medical genetics. However, despite being first introduced nearly two decades ago, it has hardly been adopted by the evolutionary genetics community studying wild organisms. Here, genomic prediction is performed on eight traits in a wild population of Soay sheep. The population has been the focus of a >30 year evolutionary ecology study and there is already considerable understanding of the genetic architecture of the focal Mendelian and quantitative traits. We show that the accuracy of genomic prediction is high for all traits, but especially those with loci of large effect segregating. Five different methods are compared, and the two methods that can accommodate zero-effect and large-effect loci in the same model tend to perform best. If the accuracy of genomic prediction is similar in other wild populations, then there is a real opportunity for pedigree-free molecular quantitative genetics research to be enabled in many more wild populations; currently the literature is dominated by studies that have required decades of field data collection to generate sufficiently deep pedigrees. Finally, some of the potential applications of genomic prediction in wild populations are discussed.

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Parasite management in translocations: lessons from a threatened New Zealand bird

Oryx ◽

10.1017/s0030605311001281 ◽

2012 ◽

Vol 46 (3) ◽

pp. 446-456 ◽

Cited By ~ 14

Author(s):

John G. Ewen ◽

Doug P. Armstrong ◽

Raewyn Empson ◽

Sandra Jack ◽

Troy Makan ◽

...

Keyword(s):

Risk Assessment ◽

New Zealand ◽

Current Practice ◽

Disease Risk ◽

Passerine Bird ◽

Assessment Process ◽

Wild Populations ◽

Partial Overlap ◽

Review Current

AbstractAwareness of parasite risks in translocations has prompted the development of parasite management protocols, including parasite risk assessment, parasite screening and treatments. However, although the importance of such measures seems obvious it is difficult to know whether the measures taken are effective, especially when working with wild populations. We review current methods in one extensively researched case study, the endemic New Zealand passerine bird, the hihi Notiomystis cincta. Our review is structured around four of the 10 questions proposed by Armstrong & Seddon (Trends in Ecology & Evolution, 2008: 23, 20–25) for reintroduction biology. These four questions can be related directly to parasites and parasite management and we recommend using this framework to help select and justify parasite management. Our retrospective study of recent disease and health screening in hihi reveals only partial overlap with these questions. Current practice does not focus on, or aim to reduce, the uncertainty in most steps of the risk assessment process or on evaluating whether the measures are effective. We encourage targeted parasite management that builds more clearly on available disease risk assessment methodologies and integrates these tools within a complete reintroduction plan.

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Effects of levonorgestrel-quinestrol (EP-1) treatment on Mongolian gerbil wild populations: a case study

Integrative Zoology ◽

10.1111/1749-4877.12018 ◽

2013 ◽

Vol 8 (3) ◽

pp. 277-284 ◽

Cited By ~ 14

Author(s):

Heping FU ◽

Jinwei ZHANG ◽

Dazhao SHI ◽

Xiaodong WU

Keyword(s):

Mongolian Gerbil ◽

Wild Populations

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Genetic evaluation of the unknown contribution of stocked fish in angler catches: a case study using Mulloway Argyrosomus japonicus

Bulletin of Marine Science ◽

10.5343/bms.2020.0050 ◽

2021 ◽

Author(s):

Matthew D Taylor ◽

HKA Premachandra ◽

David A Hurwood ◽

Sudath T Dammannagoda ◽

King Hang Chan ◽

...

Keyword(s):

Microsatellite Loci ◽

Monitoring Program ◽

Stock Enhancement ◽

Genetic Evaluation ◽

Wild Populations ◽

Sampling Program ◽

Mixed Populations ◽

And Migration

Stock enhancement involves the augmentation of wild populations with hatchery-reared recruits. Stock enhancement generally also includes a postrelease monitoring program which tracks stocked individuals within the fishery, and this relies on having a means to identify the likely origin of recaptured fish (e.g., physical, otolith, or genetic tags). This study reports the application of sibship analysis to retrospectively infer the origin of Mulloway (Argyrosomus japonicus) within stocked estuaries, when other means of identification were not available. Eight cohorts of Mulloway were stocked into two estuaries, across a seven-year period, but only some of the fish released during the program were physically marked with chemical otolith stains. Fish were sampled from stocked estuaries (mostly through an angler-based sampling program) and genotyped for six microsatellite loci, alongside 129 fish sampled from nonstocked estuaries. The presence of multiple sibs within the mixed populations in stocked estuaries was used to infer the origin of captured fish, against a background of sibship for known-origin individuals (verified by otolith marks) and sibship levels within unstocked estuaries. The analysis suggested hatchery-reared fish could have contributed 9% of individuals sampled from the augmented populations (7% when corrected for background sibship). The proportion of fish inferred to be of hatchery origin decreased with size (likely due to mortality and migration), and the expected contribution rates for hatchery-reared fish differed among cohorts. The results highlight that sibship analysis may be useful for retrospective genetic evaluation of stocked estuaries.

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Re-identification of individuals from images using spot constellations: a case study in Arctic charr ( Salvelinus alpinus )

Royal Society Open Science ◽

10.1098/rsos.201768 ◽

2021 ◽

Vol 8 (7) ◽

pp. 201768

Author(s):

Ignacy T. De¸bicki ◽

Elizabeth A. Mittell ◽

Bjarni K. Kristjánsson ◽

Camille A. Leblanc ◽

Michael B. Morrissey ◽

...

Keyword(s):

Salvelinus Alpinus ◽

Arctic Charr ◽

Wild Populations ◽

Learning Techniques ◽

Small Set ◽

Set Up ◽

The Individual ◽

Classical Computer ◽

Better Than

The ability to re-identify individuals is fundamental to the individual-based studies that are required to estimate many important ecological and evolutionary parameters in wild populations. Traditional methods of marking individuals and tracking them through time can be invasive and imperfect, which can affect these estimates and create uncertainties for population management. Here we present a photographic re-identification method that uses spot constellations in images to match specimens through time. Photographs of Arctic charr ( Salvelinus alpinus ) were used as a case study. Classical computer vision techniques were compared with new deep-learning techniques for masks and spot extraction. We found that a U-Net approach trained on a small set of human-annotated photographs performed substantially better than a baseline feature engineering approach. For matching the spot constellations, two algorithms were adapted, and, depending on whether a fully or semi-automated set-up is preferred, we show how either one or a combination of these algorithms can be implemented. Within our case study, our pipeline both successfully identified unmarked individuals from photographs alone and re-identified individuals that had lost tags, resulting in an approximately 4% increase in our estimate of survival rate. Overall, our multi-step pipeline involves little human supervision and could be applied to many organisms.

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