Assessing the Reintroduction capability of the Japanese Crested Ibis (Nipponia nippon)

Japanese Crested Ibis (Nipponia nippon) 

Source: © Japan Experience

Partners:

Technical University of Munich Chair of Zoology (TUM)

Max Planck Institute for Ornithology (MPIO)

Ministry of the Environment (環境省)

Sado Japanese Crested Ibis Conservation Center (佐渡トキ保護センター)

Ornithological Society of Japan (日本鳥学会)

State Forestry Administration of the People’s Republic of China (国家林业和草原局)

Project Duration: 10 years

Project Funding Required: ~ €5.000.000 (± 12%)

Submission: June 26, 2023

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1. Current Situation and the Nature of the Problem

Japanese or Asian Crested Ibis, or “Toki” in the Japanese language, are birds of the Pelicaniform order known as Nipponia nippon in scientific nomenclature. They weigh between 1.5 and 2 kg and their bodies, covered in white feathers, measure about 75 cm. Their wings have a beautiful pale pink-orange hue and when spread reach more than 1 m. They are carnivorous, feeding on pond snails, crabs and frogs as well as insects such as worms, crickets and grasshoppers (Noto Region Crested Ibis Release Promotion Council, 2023).

According to the latest assessment by the IUCN Red List, it has been classified in the B1 ab (iii) category (IUCN, 2018). This means that it is considered an endangered taxon susceptible to extinction because the extent of occurrence in a geographic range falls below 5,000 km2, as a result of fragmentation and thus presents continuing decline both in extent and quality of habitat (IUCN, 2012).

Historically, this majestic bird was abundant across various regions of Japan, as well as neighbouring Korea, eastern Russia and China (where a population of wild native birds remains) (Sun et al., 2016). In Japan, their habitat consisted of “satoyama” landscapes, “a dynamic mosaic of socio-ecological systems comprising secondary woodlands, plantations, grasslands, paddy fields and wetlands'' which provided a suitable forage, shelter and nesting habitat (Yiu, 2017).

However, since the 19th century, anthropogenic factors, in particular overhunting and habitat destruction due to changing agricultural practices and use of chemicals led to a severe decline of the population pushing them to the brink of extinction by the beginning of the 20th century, with exception of a few individuals found in the Noto Peninsula (Ishikawa Prefecture) and Sado Island (Niigata Prefecture) (Yo, 2023). Even after being designated as a protected species in 1952, their decline continued. Consequently, in 1967, the Niigata prefectural government established a conservation facility in Sado Island (Nagata, 2012). 

Unfortunately, by 1981, all Crested Ibises had disappeared from the wild, and only 5 birds (1 male and 4 females) remained in captivity, making it hard to develop a breeding program (Kanto Regional Environmental Office, 2020). At about the same time, a fortuitous discovery happened in the mountains of Shaanxi Province, in Northwest China. Chinese scientists, ironically trying to prove their extinction, found a group of wild crested ibis (Sun et al., 2016). 

Following their rediscovery, the government of China protected the species by prohibiting tree cutting and pesticide use in the area, and created a successful breeding program (Sun et al., 2016). In 1999 as a gesture of friendship and international cooperation, China donated a mating couple to the Sado Japanese Crested Ibis Conservation Centre. You you (male) and Yan yan (female) became the parents of Yuu yuu, the first Crested Ibis hatched by artificial incubation at the centre (Ishikawa Prefecture, 2022). Then, in 2005, a genetic analysis was conducted to discern if the populations found in China are in fact the same species. Only 11 bases of 16,793 base pairs in the whole mtDNA were found to be different (approx. 0.065%), a level indicating individual variation (Nagata, 2014). Since then, a campaign to bring back the Crested Ibis to the skies started to take shape, combining breeding programmes and development of symbiotic relationships between humans and nature, with the aim to eventually release the birds back into the wild.

Sado Island has become a model for landscape restoration, and in 2011, it was included in the Food and Agriculture Organisation’s Globally Important Agricultural Heritage Systems (Yiu, 2017). This has been possible by the local farmers’ commitment to the “Toki-to-kurasu-sato” (Villages coexisting with the Crested Ibis) initiative, adopting specific practices that increase biodiversity in the paddies, securing the Japanese Crested Ibis feeding grounds. This included reducing the use of pesticides and chemical fertilisers by half, refraining from using herbicides on embankments between fields, conducting biodiversity surveys of paddies twice a year, and constructing irrigation canals. In return, rice producers meeting these requirements receive the “Crested Ibis Friendly'' certification (Yo, 2023).

Between 2008 to June 2022, there have been 26 releases with an average of two a year, and 446 artificially bred Crested Ibis set into the wild. Moreover, monitoring shows encouraging data regarding successful breeding in the wild, so that the population of wild-born Crested Ibises now exceeds the number of surviving birds that have been released (Kanto Regional Environmental Office, 2020).

2. Goals and Objectives

So far conservation translocation efforts for the Japanese Crested Ibis have been limited to Sado Island, overlooking their historical distribution across the rest of the country. Consequently, there are research gaps reading broader-scale reintroductions that include mainland Japan, in particular Honshu Island.

The goal of this project is to address these gaps and develop a population restoration proposal, considering reintroduction feasibility issues and potential impact and risk. The scope is simply to evaluate and design a plan but will not proceed towards implementation. The proposal will centre around four main objectives, analysing actions, timelines and resources required to carry them out. 

2.1 Objective

1. Habitat Suitability: Assess the suitability of potential habitats across various regions in Japan on the basis of various parameters (e.g. agricultural pesticide use, water availability, vegetation and land cover, connectivity, etc.).

2. Human Dimensions: Investigate the socio-economic factors and human-wildlife interaction in target regions to further refine potential reintroduction habitats.

3. Genetic Selection: Analyse genetic composition of the Japanese Crested Ibis population on Sado Island and identify individuals best fit for reintroduction with an emphasis on Major Histocompatibility Complex (MHC).

4. Monitoring and Behavioural Analysis: Implement a comprehensive monitoring and behavioural analysis programme to assess post-reintroduction dynamics (e.g. reproductive success, adaptive behaviours, etc.).

3. Materials and Methods

3.1 Study Area

The study area will centre around historically significant locations where the Japanese Crested Ibis once thrived. While the species was historically distributed across East Asia (including Korea, China and Russia), this research will specifically focus on Japanese territory to maintain a more targeted scope.

Figure 1 - Map showing historically significant sites of Japanese 

Crested Ibis in East Asia 

Source: Li et al., 2009

Figure 2 - Areas in which the Japanese Crested Ibis once live in Japan

(Sado in red circle as only area in which Japanese Crested Ibis are currently present)

Source: Kanto Regional Environmental Office, 2020

Habitat preferences of the Japanese Crested Ibis are characterised by a combination of shallow water wetlands for feeding, and forested areas for roosting and nesting, often observed at lower elevations (Ma et al., 2021). Notably, these birds show a particular affinity for areas impacted by human activities, benefiting from the optimal foraging conditions provided by rice paddies (Ma et al., 2021). However, the introduction of pesticides in rice cultivation as well as the alteration of paddy field practices during winter had significant consequences for the habitat of the species. This resulted in a shift towards higher elevation areas with reduced wetland availability, contributing to their gradual decline in the 1980s. Consequently, a comprehensive Habitat Suitability Analysis (further discussed in section 3.2), is essential, incorporating variables that consider human land-use patterns, disturbance and vegetation dynamics (Mochizuki et al., 2015) to assess whether historical points remain suitable habitats, particularly in light of changing environmental conditions. 

3.2 Experiment Design

3.2.1 Habitat Suitability

As mentioned, habitat suitability will be assessed with an emphasis on the Japanese territory. At present, the only habitat suitability on nesting sites has been conducted on Sado Island, therefore a knowledge gap remains. As a result, we expect to expand the output in Figure 3 to encompass all locations in mainland Japan where Japanese Crested Ibises could potentially thrive.

Figure 3 - Example of Sado Island Habitat Suitability for Nesting Sites of the Japanese Crested Ibis

Source: Mochizuki et. al., 2015

The present study starts by establishing a baseline approach for modelling suitable habitats, building upon the work of Mochizuki et al. (2015). Their model which focused on nesting suitability in Sado Island,  will serve as the foundation of our analysis. By extending this framework to a broader geographical scale, our aim is to obtain an initial estimation of potential suitable habitats for the Crested Ibis. In Table 1, we present the variables both necessary and tentative, that will be utilised to implement Mochizuki’s model. The table should be regarded as a template for variable selection, however not all will be used in the present analysis. 

 Nesting grounds are recognised as crucial contributors in reproductive success, as they provide optimal conditions for the upbringing of vulnerable and dependent offspring (Baden, 2019; Mainwaring et al., 2014). To achieve this, our methodology centres around a nearest neighbour approach based on similarities to the Mochizuki et al. study. This approach will enable us to leverage existing knowledge and extend it to new areas.

Table 1: Tentative Variable List for Habitat Suitability Analysis 

Source: Lantz & Kirsten, 2023

To create and assess the model, we will use R. We will apply the theory found in Habitat Suitability and Distribution Models: with Applications in R by Guisan et al., which not only accounts for GIS analysis, but also other interesting considerations such as the application on Machine Learning Approaches as well as evaluating and dealing with modelling errors (Guisan et al., 2017). To further assess the habitat suitability for reintroduction of Crested Ibises to the rest of Japan, we will need to add a human-dimensions factor to our model.  

3.2.2 Human Dimensions

Incorporating Human Dimensions in the next step of our baseline habitat suitability model is essential. This is because habitat suitability models face significant limitations in the lack of spatial understanding of human acceptance and attitudes towards the focal species (Behr et al., 2017). Our goal here is to distribute questionnaires across areas identified in the habitat suitability model and create a spatial acceptance model considering socio-ecological factors that might impact the reintroduction of the Japanese Crested Ibis. The main challenge resides in gaining trust, hence the need to establish cooperation agreements with local organisations, government agencies and people. 

We will randomly sample locations based on the output of our base-line habitat suitability model (see Section 3.2.1). We decide to opt for random sampling as opposed to density-based sampling due to a skew towards areas surrounding larger cities (e.g. Tokyo, Kyoto, Sapporo). To identify survey participants in these randomly selected locations of suitable habitat, we will employ a stratified sampling method. Similar to Mochizuki’s approach, we will divide each selected location into smaller subunits based on factors like urbanisation level, land-use patterns and proximity to forested areas (Mochizuki et al., 2015). Within each unit, we will randomly select households or individuals as survey respondents. The sample size will be determined based on statistics to ensure an appropriate representation of the target population.

To gather information on human acceptance and attitudes towards Crested Ibises, we will design a questionnaire. The questionnaire will cover various aspects including awareness and knowledge of our focal species, perception of its ecological importance, willingness to support conservation efforts, attitudes towards potential conflicts between conservation measures and human activities. Additionally, questions that assess preferences towards habitat restoration, community involvement and educational initiatives will be required.

Data collection will consist of online and mail-sent surveys, as in-person interviews require travelling around all of Japan. To ensure the reliability and validity of data, we will use standardised survey protocols and employ techniques like randomization of question order and inclusion of validation questions (Consorte-McCrea et al., 2022).

By incorporating the human dimensions aspect into our research, we aim to develop a comprehensive understanding of the socio-ecological factors that influence the suitability of areas across Japan for Crested Ibis reintroduction. This information will guide conservation planning and limit detrimental effects that could arise if habitat suitability were taken under consideration in isolation. 

3.2.3 Genetic Selection

Genetic selection is important in any reintroduction project as it allows to maximise the chance of population stabilisation following the identification of optimal locations (on the basis of both environmental and human impact variables). Therefore, we need to choose appropriate individuals who can provide adequate genetic diversity (IUCN, 2013).

In the case of Japanese Crested Ibis, understanding the role of the Major Histocompatibility Complex (MHC) proteins can serve to understand genetic fitness (Sommer, 2005). Although most studies on MHC have not included this species, Chen et al. (2015) provided valuable insights into the functioning and labelling of these proteins, which can now inform our selection process. Chen’s study concluded that the Crested Ibis has undergone a severe bottleneck and displays low genetic variation due to inbreeding (Chen et al., 2015; Wajiki et al, 2016; Sun et al., 2019).

Our research aims to sample both wild and captive bred Crested Ibis populations through non-invasive means on Sado Island. We then plan to identify unique genetic composition and compare MHC Allele Richness and Heterozygosity. For this we will follow MHC research conducted by Sun et al., (2019) on the Japanese Crested Ibis. The study assessed MHC-based mate preference and quantified the impacts on reproductive output (Sun et al., 2019), and concluded that females preferred MHC-heterozygous males which may be identified by darker nuptial plumage while males preferred DAB*d-free females, a genotype which correlated with larger body size and mass than the average  (Sun et al., 2019). As a result, we will follow the procedure of extracting genomic DNA using phenol-chloroform method using Polymerase Chain Reaction (PCR) amplification to measure MHC dissimilarity on the basis of polymorphic loci (Class I - UAA and Class II - DAB). We will forgo microsatellite testing as no conclusive evidence has been found on it affecting mate-selection. 

Table 2: Primers for polymorphic MHC loci in Crested Ibis with base pairs size and annealing temperature

Source: Sun et al., 2019

Figure 4: MHC type (difference between male heterozygous and female DAB*d carrying)

Source: Sun et al., 2019

MHC dissimilarity will be measured using the number of shared alleles (Sxy) accounting for multi-locus heterozygosity and the number of different Antigen-Binding Sites (ABS) between pairs (Dxy). We will also score heterozygosity and homozygosity in a single locus (UAA and DAB) by giving the former a value of 1 and the latter 0. Lastly, to account for multi-locus heterozygosity a proportion of the two regions (UAA and DAB) will be calculated. 

The exact number of birds to be released will be assessed after understanding the habitat size and human-dimensions aspects and therefore this proposal is unable to give such projections. We plan to account for genetic diversity to ensure the fittest and most stable population. After finding the most fit and diverse individuals we will quarantine and acclimate the birds in facilities similar to that established on Sado Island with simulation habitats (to aid in foraging, flight and interactions) (Richardson et al., 2013). Days in acclimatisation will depend, however ideally a time limit should be established throughout the project. 

3.2.4 Monitoring and Behavioural Analysis

The final element of our experiment design involves post-reintroduction monitoring and for this we will need to incorporate behavioural analysis. 

The first thing to consider are the tools to monitor the Crested Ibis. Following a study by Huo et al., (2014) on fledglings we plan to fit around 5 breeding-paired birds that are released with OrniTrack25 GPS-GSM solar-powered transmitters with the ability to capture the position of the bird every hour. These transmitters are only 1.25% of the average Crested Ibis body mass and total height is around 40 mm to ensure that no feathers block the solar panel.

To account for errors that may arise with the transmitters, we plan to confirm the survival status and locations of released Crested Ibises 3 times a week to start, and reduce the amount of days as the years go by (Li et al., 2022). Moreover, recording days will be split between early morning (05:00 - 09:00), morning-noon (09:00 - 13:00), after-noon (13:00 - 17:00) and evening (17:00 - 21:00)(Li et al., 2022) An individual's survival will be considered on a yearly basis with the first year after release being the critical window. 

Subsequent analysis will be carried out as each year progresses understanding the post-release dispersion within the habitat selected as well as survival, demographics and population dynamics metrics. To assess reintroduction efforts, we plan to use R again. To reduce complexity RangeShift R, an R package will be used. RangeShift R is a process-based model that can help assess population dynamics and dispersal behaviour as well as taking into account inter-individual variability (Ranger Shifter Platform, 2020).

Additionally throughout monitoring and behavioural analysis, we will discuss with stakeholders exit strategies to be sure that once the project comes to a close, the population of Crested Ibis remains. Additionally, long-term population development checks could prove to be useful to understand the general trend in reintroducing toki in mainland Japan without having to micromanage further nor go beyond the scope and estimated budget of the project. 

4. Plan of Activity

4.1 Key Partners and Stakeholders

Cooperation and partnerships with the following institutions and organisations are required to achieve the objectives set out in the present proposal.

1. Technical University of Munich Chair of Zoology (TUM)

2. Max Planck Institute for Ornithology (MPIO)

3. Ministry of the Environment of Japan (環境省)

4. Sado Japanese Crested Ibis Conservation Center (佐渡トキ保護センター)

5. Ornithological Society of Japan (日本鳥学会)

6. State Forestry Administration of the People’s Republic of China (国家林业和草原局)

4.2 Activities and Schedule

Table 2 depicts a visualised Work Breakdown Structure composed of Work Packages. The proposed time frame is 10 years, each year consisting of trimesters (4 month intervals). Below is a brief rationale for the tentative project management timeline.

• Package 1: All activities in Work Package 1 (WP) should be completed by the last trimester of Year 2. The reason being that we would like to provide ample time to tweak variables and minimise Type I and II errors. Therefore, allocating sufficient time for this section promotes accurate decision-making and increases the overall effectiveness of the research programme. 

• Package 2: Human-dimensions is an important consideration and we want to supply  ample time for individuals to respond to our questionnaire as well as to analyse the data  and make well-informed decisions for the reintroduction efforts.  Additionally, in order to ensure cooperation and trust we aim to  foster a participatory environment, providing stakeholders with accurate and timely information and making them feel as valued members of the project.  Additionally, an exit strategy is needed once the project comes to an end  to ensure that Crested Ibis populations remain stable. 

• Package 3: The main objective of this WP is to assess the MHC diversity in the population of Crested Ibises established on Sado Island and select individuals with desirable MHC alleles for reintroduction based on the Chen et al., established sequencing.

• Package 4: WP4 involves monitoring and though counterintuitive is the bulk of our project. We want to make sure that this project ends in success and without long-term monitoring controls we might miss subtle potential changes that may arise.

• Package 5: Continuous outreach and collaboration are crucial throughout the process, fostering transparency, trust, engagement and collaboration (Riley et al., 2018; Consorte-McCrea et al., 2022). Lack of such framework to consider stakeholders can lead to failure to advance wildlife management activities(Riley et al., 2002).

• Package 6: Lastly we have considered the need to create progress reports in the last trimester of each year. Additionally, we provide a timeframe in which we can publish our results so that  future projects can learn from this reintroduction research.

Table 3: Project Proposal Timeline separated into Work Packages and Activities

Source: Lantz & Kirsten, 2023 Please see link for better quality

5. Cost Calculation

Cost calculations for the project are estimated in Table 3. The cost projection is relatively steep, incorporating labour and supplies in Japan, which is considered among the most expensive countries. We have also considered a confidence interval in the cost analysis of approximately ±12%. Below we describe briefly each section and some rationale behind the cost projection:

• Personnel: Scientific Researchers and Data Scientists will be the driving force behind the project with Student Assistants hired to help with field data collection, data cleansing, and sampling etc. 

• Equipment: Transmitters will be essential for reintroduction efforts and more may be required. An acclimatisation facility will need to be built in the desired locations. Additionally, transportation of Crested Ibises from Sado to the projected location needs to be considered as well. Supply materials include all other equipment required such as gloves, storage units, computer repairs, bags, printing material, etc.

• Labs: Lab rental and equipment needed for genetic analysis is subject to change but is a necessary projection. Lab rental was calculated under the assumption that some equipment for DNA testing is already present as well as the ability to strike a deal with universities in the area.

• Miscellaneous: This includes car rental and travel expenses that are subject to changes depending on the year and season of the rental period. Car rentals are based on leasing projections within Japan for large vehicles. 

Table 4: Cost Projection for Japanese Crested Ibis Reintroduction on mainland Japan

Source: Lantz & Kirsten, 2023

6. Acknowledgements

We express our sincere gratitude to Prof. Dr. Ralph Kühn for his invaluable supervision and guidance throughout the development of this research proposal. We are also grateful to the Sado Japanese Crested Ibis Conservation Centre for sharing their expertise and insider knowledge on Japanese Crested Ibises, which greatly enriched our understanding of the subject. 

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