Hybrid Solutions for the Modelling of Complex Environmental Systems

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Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago

The Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species. mtDNA analysis was conducted with 142 DNA remote samples, mostly from faeces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure. Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population. We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among the archipelago's populations. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure

Roosting ecology of endangered plant‐roosting bats on Okinawa Island: Implications for bat‐friendly forestry practices

Roosting information is crucial to guiding bat conservation and bat-friendly forestry practices. The Ryukyu tube-nosed bat Murina ryukyuana (Endangered) and Yanbaru whiskered bat Myotis yanbarensis (Critically Endangered) are forest-dwelling bats endemic to the central Ryukyu Archipelago, Japan. Despite their threatened status, little is known about the roosting ecology of these species and the characteristics of natural maternity roosts are unknown. To inform sustainable forestry practices and conservation management, we radio-tracked day roosts of both species in the subtropical forests of Okinawa's Kunigami Village District. We compared roost and roost site characteristics statistically between M. ryukyuana nonmaternity roosts (males or nonreproductive females), maternity roosts, and all M. yanbarensis roosts. Generalized linear models were used to investigate roost site selection by M. ryukyuana irrespective of sex and age class. Lastly, we compiled data on phenology from this and prior studies. Nonreproductive M. ryukyuana roosted alone and primarily in understory foliage. Murina ryukyuana maternity roosts were limited to stands >50 years old, and ~60% were in foliage. Myotis yanbarensis roosted almost entirely in cavities along gulch bottoms and only in stands >70 years old (~1/3 of Kunigami's total forest area). Murina ryukyuana maternity roosts were higher (4.3 ± 0.6 m) than conspecific nonmaternity roosts (2.3 ± 0.5 m; p <.001) and M. yanbarensis roosts (2.7 ± 0.5 m; not significant). Model results were inconclusive. Both species appear to be obligate plant roosters throughout their life cycle, but the less flexible roosting preferences of M. yanbarensis may explain its striking rarity. To conserve these threatened bats, we recommend the following forestry practices: (a) reduce clearing of understory vegetation, (b) refrain from removing trees along streams, (c) promote greater tree cavity densities by protecting old-growth forests and retaining snags, and (d) refrain from removing trees or understory between April and July, while bats are pupping.コウモリのねぐらに関する生態学的な情報はコウモリの保全とそれを考慮する森林の施業のために重要である。リュウキュウテングコウモリMurina ryukyuana（絶滅危惧）とヤンバルホオヒゲコウモリMyotis yanbarensis（絶滅寸前）は森林性コウモリで、日本の琉球列島中部における固有種である。絶滅の恐れがある種にもかかわらず、これらの種のねぐらに関する生態については情報が不足しており、自然条件下における母子集団のねぐらの特徴は明らかになっていない。持続可能な森林施業と保全に関わる情報を提供するために、沖縄島国頭村における亜熱帯林で両種の昼間のねぐらの場所や特徴を、ラジオテレメトリー法によって個体を追跡することによって調査した。リュウキュウテングコウモリの非母子集団ねぐら（雄または非繁殖雌）、母子集団ねぐら、及び全てのヤンバルホオヒゲコウモリのねぐらの間で、ねぐらとねぐらの場所の特徴を統計的に比較した。一般化線形モデルを用いて、性別や年齢階級を考慮しない条件でリュウキュウテングコウモリによるねぐら場所の選好性を調査した。最後に、本研究と先行研究から、ねぐらに関わるフェノロジーに関するデータを収集・整理した。非生殖のリュウキュウテングコウモリは単独で、主に下層植生の葉をねぐらとして利用した。リュウキュウテングコウモリの母子集団のねぐらとしての利用は林齢50年以上の林分に限定され、約60％が葉であった。ヤンバルホオヒゲコウモリはほぼ完全に谷底の樹洞をねぐらとして利用し、ねぐらの形成は林齢70年以上の林分に限られていた（国頭村における森林面積の約1／3）。リュウキュウテングコウモリの母子集団ねぐらは同種の非母子集団ねぐら（2.3 ± 0.5 m; p < .001）とヤンバルホオヒゲコウモリのねぐら（2.7 ± 0.5 m; not significant）より高い位置にあった（4.3 ± 0.6 m）。モデルによる推定結果は決定的ではなかった。両種はライフサイクルの間ずっと偏性的な植物性コウモリであるようだが、ヤンバルホオヒゲコウモリの選好は柔軟性が低く、このことが本種の際だった希少性を説明する可能性がある。これらの絶滅危惧種であるコウモリを保全するためには、以下の森林施業が提案できる：（a）下層植生の除去を少なくすること、（b）渓流沿いの樹木の伐採を控えること、（c）高林齢の森林を保存し、枯死木も除去せず、樹洞の密度を確保すること、（d）コウモリが子育てしている時期である4月〜7月の間に、樹木と下層植生の除去を控えることである

Data from: How new concepts become universal scientific approaches – insights from citation network analysis of agent-based complex systems science

Progress in understanding and managing complex systems comprised of decision-making agents, such as cells, organisms, ecosystems, or societies, is—like many scientific endeavors—limited by disciplinary boundaries. These boundaries, however, are moving and can actively be made porous or even disappear. To study this process, we advanced an original bibliometric approach based on network analysis to track and understand the development of the model-based science of agent-based complex systems (ACS). We analyzed research citations between the two communities devoted to ACS research, namely agent-based (ABM) and individual-based modeling (IBM). Both terms refer to the same approach, yet the former is preferred in engineering and social sciences, while the latter prevails in natural sciences. This situation provided a unique case study for grasping how a new concept evolves distinctly across scientific domains and how to foster convergence into a universal scientific approach. The present analysis based on novel hetero-citation metrics revealed the historical development of ABM and IBM, confirmed their past disjointedness, and detected their progressive merger. The separation between these synonymous disciplines had silently opposed the free flow of knowledge among ACS practitioners and has thereby hindered the transfer of methodological advances and the emergence of general systems theories. A surprisingly small number of key publications sparked the ongoing fusion between ABM and IBM research. Beside reviews raising awareness of broad-spectrum issues, generic protocols for model formulation and boundary-transcending inference strategies were critical means of science integration. From the modeling viewpoint, the discovery of the unification of ABM and IBM demonstrates that a wide variety of systems substantiate the premise of ACS research that microscale behaviors of agents and system-level dynamics are inseparably bound

Historical evolution of ACS literature

Genesis and evolution of the science of agent-based complex systems seen from the perspective of its citation network from 1990 to January 2016. The dynamic graph shows the temporal dynamics of the agent-based modeling (blue vertices) and individual-based modeling (red vertices) corpora. Vertices are positioned based on the ForceAtlas2 layout algorithm without vertex overlapping. The video uploaded here is a high-resolution version of the one provided alongside the manuscript

Supplementary Data from How new concepts become universal scientific approaches: insights from citation network analysis of agent-based complex systems science

Supplementary Data (Figures S1 to S5, Tables S1 to S3, and Extended Methodology

Bibliographic Dataset

Bibliographic dataset compiling all Scopus records relevant to Agent-based Complex Systems (ACS) science (i.e. the fields of agent-based and individual-based modelling). This dataset was post-processed and used to create a citation graph using the Diderot R package (https://cran.r-project.org/package=Diderot)

Supplementary Video from How new concepts become universal scientific approaches: insights from citation network analysis of agent-based complex systems science

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Hybrid Solutions for the Modelling of Complex Environmental Systems

Systems studied in environmental science, due to their structure and the heterogeneity of the entities composing them, often exhibit complex dynamics that can only be captured by hybrid modeling approaches. While several concurrent definitions of “hybrid modeling” can be found in the literature, it is defined here broadly as the approach consisting in coupling existing modelling paradigms to achieve a more accurate or efficient representation of systems. The need for hybrid models generally arises from the necessity to overcome the limitation of a single modeling technique in terms of structural flexibility, capabilities, or computational efficiency. This book brings together experts in the field of hybrid modelling to demonstrate how this approach can address the challenge of representing the complexity of natural systems. Chapters cover applied examples as well as modeling methodology.Systems studied in environmental science, due to their structure and the heterogeneity of the entities composing them, often exhibit complex dynamics that can only be captured by hybrid modeling approaches. While several concurrent definitions of “hybrid modeling” can be found in the literature, it is defined here broadly as the approach consisting in coupling existing modelling paradigms to achieve a more accurate or efficient representation of systems. The need for hybrid models generally arises from the necessity to overcome the limitation of a single modeling technique in terms of structural flexibility, capabilities, or computational efficiency. This book brings together experts in the field of hybrid modelling to demonstrate how this approach can address the challenge of representing the complexity of natural systems. Chapters cover applied examples as well as modeling methodology

The Ryukyu flying fox (Pteropus dasymallus)—A review of conservation threats and call for reassessment

The conservation status of the Ryukyu flying fox (Pteropus dasymallus), a solitary island fruit bat inhabiting the Ryukyu archipelago in Japan, Green Island and Turtle Island in Taiwan, and some islands of the Batanes and Babuyan chain in the Philippines, was last assessed by the IUCN in 2008, when it was upgraded from Endangered (EN) to Near Threatened (NT). We review here the current status of P. dasymallus through a description of the perceived demographic trends of its different subspecies as well as the current threat factors that it faces. Important amendments to the initial assessment are advanced, such as a less pronounced consideration of the Philippine population, whose size seems much smaller than once expected. Coupled with new elements that were only recently reported (i.e. natural risks, such as typhoons and volcanic activity, as well as direct anthropogenic threats in the form of ongoing culling by farmers in Japan), these lead us to call for a prompt relisting of P. dasymallus to a higher threat level