A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

Biodiversity and ecosystem functions depend on environmental conditions and resources rather than the geodiversity of a tropical biodiversity hotspot

Biodiversity and ecosystem functions are highly threatened by global change. It has been proposed that geodiversity can be used as an easy-to-measure surrogate of biodiversity to guide conservation management. However, so far, there is mixed evidence to what extent geodiversity can predict biodiversity and ecosystem functions at the regional scale relevant for conservation planning. Here, we analyse how geodiversity computed as a compound index is suited to predict the diversity of four taxa and associated ecosystem functions in a tropical mountain hotspot of biodiversity and compare the results with the predictive power of environmental conditions and resources (climate, habitat, soil). We show that combinations of these environmental variables better explain species diversity and ecosystem functions than a geodiversity index and identified climate variables as more important predictors than habitat and soil variables, although the best predictors differ between taxa and functions. We conclude that a compound geodiversity index cannot be used as a single surrogate predictor for species diversity and ecosystem functions in tropical mountain rain forest ecosystems and is thus little suited to facilitate conservation management at the regional scale. Instead, both the selection and the combination of environmental variables are essential to guide conservation efforts to safeguard biodiversity and ecosystem functions.

Tropical bee species abundance differs within a narrow elevational gradient

Insect pollination is among the most essential ecosystem services for humanity. Globally, bees are the most effective pollinators, and tropical bees are also important for maintaining tropical biodiversity. Despite their invaluable pollination service, basic distributional patterns of tropical bees along elevation gradients are globally scarce. Here, we surveyed bees at 100 m elevation intervals from 800 to 1100 m elevation in Costa Rica to test if bee abundance, community composition and crop visitor assemblages differed by elevation. We found that 18 of 24 bee species spanning three tribes that represented the most abundantly collected bee species showed abundance differences by elevation, even within this narrow elevational gradient. Bee assemblages at the two crop species tested, avocado and squash, showed community dissimilarity between high and low elevations, and elevation was a significant factor in explaining bee community composition along the gradient. Stingless bees (Tribe Meliponini) were important visitors to both crop species, but there was a more diverse assemblage of bees visiting avocado compared to squash. Our findings suggest that successful conservation of tropical montane bee communities and pollination services will require knowledge of which elevations support the highest numbers of each species, rather than species full altitudinal ranges.

GENEALOGY OF CONSERVATION NGOs ON THE ESTABLISHMENT OF THE AMBEL-MA'YA TRIBE CONSERVATION AREA IN RAJA AMPAT

This article aims to reveal the genealogy of the International Conservation NGO towards the establishment of the Ambel-Ma'ya tribal conservation area so that the Ma'yalibit Bay conservation area in Raja Ampat is formed as well as a departure station for the establishment of other conservation areas in Raja Ampat. The research approach uses a Cultural Studies approach with descriptive qualitative research methods and slices of theory used, namely, the genealogy of practice and power from Michel Foucault.The results showed that before international conservation NGOs operated in Raja Ampat, they recruited actors and agents who were recruited from intellectuals of the Ma'ya indigenous peoples' institutions and religious and traditional leaders. Conservation NGOs act as captains as well as organic intellectuals and traditional intellectuals for the Ambel-Ma'ya tribe in the Ma'yalibit Bay of Raja Ampat acting as sea commanders in the boat of conservation ideology. Conservation NGOs are hiding behind the discourse of knowledge about high marine tropical biodiversity and the threat of its degradation as a result of the fishing behavior of fishermen who are not environmentally friendly, becoming the basis for discourse on knowledge, articulation and practice of language texts and capital of power to carry out discursive practices in the formation of conservation areas on tribal waters stage. Abel-Ma'ya. Keywords: Genealogy, NGO, Conservation, Ambel-Ma'ya, Raja Ampat

Preface

It is a great honor for us, Faculty of Forestry of Hasanuddin University, to host the 2nd Biennial Conference of Tropical Biodiversity 2021 (BCTB) 2021 on August 4th - 5th, 2021, in Makassar City of South Sulawesi Province, Indonesia. This conference is a series of international scientific seminars held by the Faculty of Agriculture, Universitas Hasanuddin, Makassar, Indonesia, held biennially since 2018. In addition, The proceedings of BCTB have been published in the IOP conference series: Earth and Environmental Science (EES). Biodiversity is evenly distributed and varies widely across the world and within regions, the diversity of which is highly dependent on environmental factors such as temperature, rainfall, altitude, soil geography, and the presence of other species. Biodiversity is also essential in supporting ecosystem services, including air quality, climate, carbon dioxide absorption, water purification, pollination, and erosion prevention. Rapid environmental changes have led to many mass extinctions of species. Therefore, protecting its existence has become one of the most significant challenges humanity has to face. The Biennial Conference of Tropical Biodiversity is a scientific forum to enhance science and technology, together with researchers, scientists, practitioners, and scholars to anticipate the impacts of climate change in biodiversity. This is also conducted to promote Sustainable Development Goals (SDGs). Hence, this conference chose an SDGs-related theme, namely “Managing Challenges in Biodiversity Conservation During The Pandemic to Achieve Sustainable Development Goals for Better Environment” with six sub-themes: 1. Assessment of global biodiversity: the impact of a pandemic to biodiversity. 2. The existence of genetic diversity to maintain biodiversity. 3. Community partnership for biodiversity conservation. 4. Biodiversity and utilization. 5. The conservation of tropical biodiversity: current challenges for the management. 6. Ecological risk and natural disaster. The Biennial Conference of Tropical Biodiversity will be held every two years. The first was in 2018, and the second should be in 2019. Due to the Covid-19 outbreak, the conference was postponed to be this year (2021). Hence, the conference model has performed with a virtual conference instead of a live meeting. This conference presents keynote speakers from 5 countries, namely Prof. Enrico Bonello from Ohio State University, USA, Dr. Doan Nainggolan from Aarhus University-Denmark, Prof. Erin P. Riley from San Diego State University-USA, Dr. Ida Ayu Pradnya Resosudarmo from Australian National University-Australia, and Prof. Supratman from Hasanuddin University-Indonesia. The plenary session and discussion for all speakers were for 3 hours. Participant presentations (oral and video presentations) were held in 3 sessions, and each session was divided into ten rooms. The number of participants per room was 15-20 participants with an allocation of presentations for 5 minutes/participant conducted in parallel as many as three parallel sessions. Discussions sessions were held in parallel in each parallel session with an allocation of 3 minutes per participant. The Virtual BCTB conference implementation applied the zoom meeting application provided by the Faculty of Forestry, Universitas Hasanuddin. List of Conference Committee & Reviewer BCTB 2021 are available in this pdf.

Deconstruction of the ultimum remedium basic concept on protection and management tropical biodiversity

The biological potential in Indonesia is no longer managed and protected. So far Indonesia has had biologically related laws and regulations, but its implementation is still weak and less effective. Therefore, Law No. 32 of 2009 on Environmental Protection and Management or called UUPPLH mentioned the management and protection of biodiversity based UUPPLH namely two principles in law of criminal provision, the principle of remedium ultimum which is an effort, and the principle of premium remedium that takes care of the law. So far many mistakes in interpreting the application of the principle of remedium ultimum which is said to make it difficult for law enforcement to enforce environmental criminal laws and can shackle law enforcements in carrying out task of environmental law enforcement. In addition, it is also said that the principle of remedium ultimum can also harm the environment due to violations of waste water quality standards, emissions, and disturbances that take precedence is the administration of administrative sanctions, meaning that there is no deterrent effect on perpetrators. Therefore, it is necessary to deconstruct the principle of remedium ultimum in the proper enforcement of environmental criminal law including structuring and enforcement (compliance) which can also be a view of criminal law that can be used as an instrument in the framework of protection and management of tropical biodiversity, especially the environment and can bring consequences for the intertwining of criminal law with administrative law. The results of the research are based on UUPPLH that can protect biodiversity by Indonesia and reconstruct the principle of ultimum remedium in environmental law. Research methods using normative legal research on philosophical.

Blood variation implicates respiratory limits on elevational ranges of Andean birds

The extent to which species ranges reflect intrinsic physiological tolerances is a major, unsolved question in evolutionary ecology. To date, consensus has been hindered by the limited tractability of experimental approaches across most of the tree of life. Here, we apply a macrophysiological approach to understand how hematological traits related to oxygen transport shape elevational ranges in a tropical biodiversity hotspot. Along Andean elevational gradients, we measured traits that affect blood oxygen-carrying capacity—total and cellular hemoglobin concentration and hematocrit—for 2,355 individuals of 136 bird species. We used these data to evaluate the influence of hematological traits on elevational ranges. First, we asked whether hematological plasticity is predictive of elevational range breadth. Second, we asked whether variance in hematological traits changed as a function of distance from the midpoint of the elevational range. We found that the correlation between hematological plasticity and elevational range breadth was slightly positive, consistent with a facilitative role for plasticity in elevational range expansion. We further found reduced local variation in hematological traits near elevational range limits and at high elevations, patterns consistent with intensified natural selection, reduced effective population size, or compensatory changes in other cardiohematological traits with increasing distance from species-specific optima for oxygen availability. Our findings suggest that constraints on hematological plasticity and local genetic adaptation to oxygen availability promote the evolution of the narrow elevational ranges that underpin tropical montane biodiversity.

Seasonal Activity of Fruit Bats in a Monoculture Rubber and Oil Palm Plantation in the Southern Philippines

The increasing expansion of monoculture plantations poses a major threat to Asian tropical biodiversity. Yet, in many countries such as the Philippines, the ability of species to persist within plantations has never been explored. We studied the seasonal activity and response of fruit bats in two types of monocultural plantations (rubber and oil palm) in the Southern Philippines from 2016–17 for 12 months. Our mist-netting and monitoring data showed that both plantations can support cosmopolitan species of fruit bats (Cynopterus brachyotis, Eonycteris spelaea, Macroglossus minimus, Ptenochirus jagori, and Rousettus amplexicaudatus), yet a significant variation in the abundance and guild distribution between plantations was observed. Rubber hosted a higher bat abundance than oil palm, which may be influenced by better habitat structure of the matrix (e.g., presence of orchard and fruit plantations) and practices occurring in the rubber plantation. We find that, among seasonal climatic variables, temperature showed significant negative effects on fruit bat abundance. Our results suggest that although monoculture plantations host low diversity (i.e., richness and endemism) they still support generalists which are still ecologically important species. Furthermore, wildlife-friendly commercial plantation practices could both enhance economic growth and biodiversity conservation in the Philippines. Our data both provide the potential for long-term monitoring in the Philippines and highlight the need for more comprehensive monitoring of other bat functional groups and their ability to transverse plantations to provide a more in-depth understanding of the roles and impacts of plantations and other land-use changes.