Recent Progress on Methods for Estimating and Updating Large Phylogenies

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.

Baris Memedi Dance in Jatiluwih Village Tabanan Bali: A Strategy to Preserve Traditional Arts

The Baris Memedi dance depicts a group of ‘ghosts’ who live in haunted places such as graves, cliffs, and in large trees. It is danced by 7-15 male dancers. This dance is performed in Ngaben (cremation) ceremony called Pitra Yadnya, using the Baleganjur gamelan accompaniment. The objective of this study is to analyze the form of existence of the Baris Memedi dance in implementing the Pitra Yadnya ceremony. Another objective is to understand the strategy for its preservation as a traditional art so that this dance can live and be long-lasting until today. The additional objective is to find the uniqueness of the dance that it needs preservation. The method used was a qualitative method that considers the issues of cultural context, ideology, interests, power in the culture, and meaning which refers to the culturalistic-humanistic paradigm, namely civilizing humans and humanizing humans. Based on observation, Baris Memedi dance has four stages in its presentation form. The preservation strategy is the active role of supporting the community, the role of Jatiluwih Village apparatus, Jatiluwih artists’ participation, and the government’s support. The most important aspect of Baris Memedi it is inseparable from its community. The proponents of traditional arts should continue to pursue these preservation efforts so that the arts have cultural resilience through Ajeg Bali.

Tree Biomass Estimation in Karst Forest of West Papua, Indonesia

Indonesia is estimated to have 14,5 million hectares of karst areas. The characteristic of karst vegetation is specific, one of which is the dominance of small trees. With all of the potency, their vegetation acts as a significant carbon sequester and store it in biomass. This study aims to estimate and discuss biomass estimation in the karst forest within the Nature Recreational Park of Beriat, a protected area in South Sorong, West Papua. A total of 28 plots were made in the forest using the purposive random sampling method. Tree biomass (DBH ≥10 cm) was estimated using five different allometric equations. The results showed that the biomass was estimated at ca. 264 Mg ha-1 (95 % CI: 135-454 Mg ha-1). While small trees (DBH 10 – 30 cm) only contribute 30 % of the total biomass, about 38 % of the biomass is the contribution of large trees (DBH >50 cm), where Pometia pinnata contributes ca. 39 % of the biomass at plot-level. The use of various allometric equations results in different biomass estimates and biases with deviations ranged from -14.78 % to +17.02 % compared to the reference equation. Therefore, the selection of allometric equations used must be considered carefully to reduce uncertainties in biomass estimation.

The Urban Image Conservation and Development of Nakhon Si Thammarat’s Old Town Community in Thailand

Nakhon Si Thammarat Old Town Community dated a thousand years old from four eras of settlement development. The community is located on an ancient beach ridge that stands until the present day. It also has an image of a community that is unique to any city. Today the community is rapidly expanding, so the importance of the old town’s various elements has been diminished. The research objectives are to analyze Nakhon Si Thammarat Old Town Community’s image and landscape and provide suggestions to preserve and develop the community’s image. The methodology is theoretical concepts of the image of the city, urban landscape, historic urban landscape, and urban conservation, including field surveys to identify problems and the community’s awareness. Visual assessments and mapping were also undertaken. Based on the study, the urban conceptual framework emphasizes the five elements of physical perception, whereas the cultural landscape concept focuses on the physical perception of the community’s core components and sub-elements that express specificity of the district, including traditional custom, which is intangible culture and a landscape element as well. The analysis of urban image reveals that Nakhon Si Thammarat Old Town Community consists of the path in the area with Ratchadamnoen Road, Karom Road and Pattanakarn Khukwang Road as the main routes, the edge of the community divided by natural boundaries, which are various rivers and by man-made boundaries, which are canals and the old city’s embankments, and the unique district, such as Tha Wang Community, Khaek Market Community, and Nakhon Si Thammarat Old Town. The node or activity center is, for example, business activities in Tha Wang Community, Khaek Market Community and Hua It Market Community, and the tourism activities in the old community area around Phra Mahathat Woramahawihan Temple. The prominent landmark from the past to the present is Phra Borommathat Stupda. In addition, the unique physical elements in the old town are groups of large trees. Suggestions on conservation and development are to create awareness of secondary routes to reduce congestion of the main roads and connect to other attractions; to develop the old town’s border from four eras for clearer perception; to promote the main activities within each district; and to have measures to control the height, billboards, old buildings’ styles, and new buildings representing each district’s uniqueness that will not obscure the perception of the community’s landmarks.

Tenggar Cave, Tulungagung: preliminary study and its paleontological potentials

Goa Tenggar or Tenggar Cave is situated in the karstic physiography of southern Tulungagung, East Java that made up of prehistoric caves. These include the Wajak complex (minimum age of 37.4 to 28.5 thousand years ago) and the Song Gentong (around 7000 BP). The formation of Tenggar Cave is influenced by the subterranean river that penetrates the limestone unit. This cave has a front width of ± 10 m and a roof height of ± 8 m. The east side of the cave floor is a layer of soil, and the western side is the river. The inside of the cave composed by very compact conglomerate deposits and paleosoil that contains faunal remains, including Cervus sp., Bos sp., Bubalus sp., and Bibos sp., which may have occurred during the Pleistocene. The fossilized faunal remains from Tenggar Cave show that there was a relatively open environment during that time, such as a savannah with large trees and flowing rivers around the cave. The paleoenvironment indicates late Pleistocene to early Holocene period, similar to paleoenvironment in the Sewu Mountains that stretch along the southern part Java from central to the eastern tip of the island includes the coastal towns of Gunung Kidul, Pacitan and Tulungagung. The situation is certainly a point of interest when associating the findings with the surrounding sites, starting from Wajak, Song Gentong, Pacitan, Ponorogo, and Gunung Kidul. However, absolute dating test is necessary to be more certain of the lifetime of the fossilized fauna. If the fossils were from the Late Pleistocene, it could be an important information for the fields of paleontology, paleoanthropology, and prehistoric archaeology given that the occurrence of sites with such antiquity are limited in Southeast Asia. It is essential to conduct intensive research in Tenggar Cave in the future.

Network science inspires novel tree shape statistics

The shape of phylogenetic trees can be used to gain evolutionary insights. A tree’s shape specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic distance between branching events; well-known measures of tree shape include the Colless and Sackin imbalance, which describe the asymmetry of a tree. In other contexts, network science has become an important paradigm for describing structural features of networks and using them to understand complex systems, ranging from protein interactions to social systems. Network science is thus a potential source of many novel ways to characterize tree shape, as trees are also networks. Here, we tailor tools from network science, including diameter, average path length, and betweenness, closeness, and eigenvector centrality, to summarize phylogenetic tree shapes. We thereby propose tree shape summaries that are complementary to both asymmetry and the frequencies of small configurations. These new statistics can be computed in linear time and scale well to describe the shapes of large trees. We apply these statistics, alongside some conventional tree statistics, to phylogenetic trees from three very different viruses (HIV, dengue fever and measles), from the same virus in different epidemiological scenarios (influenza A and HIV) and from simulation models known to produce trees with different shapes. Using mutual information and supervised learning algorithms, we find that the statistics adapted from network science perform as well as or better than conventional statistics. We describe their distributions and prove some basic results about their extreme values in a tree. We conclude that network science-based tree shape summaries are a promising addition to the toolkit of tree shape features. All our shape summaries, as well as functions to select the most discriminating ones for two sets of trees, are freely available as an R package at http://github.com/Leonardini/treeCentrality.

Sex-Biased Habitat Use by Phyllostomid Bats on Riparian Corridors in a Human Dominated Tropical Landscape

Some animal species exhibit sex-specific patterns as an adaptation to their habitats, however, adaptability to a human-dominated landscape is commonly explored without considering intraspecific sexual differences. Differences between males and females lead to a sexual segregation in habitat use. In southern Mexico, we explored sex-specific responses to landscape modification of six common species of phyllostomid bats: Artibeus jamaicensis, A. lituratus, Sturnira lilium, Carollia perspicillata, Glossophaga soricina, and Platyrrhinus helleri using riparian corridors within continuous forest and cattle pastures. Furthermore, we explored sex related responses to vegetation attributes (i.e., tree height and basal area) and seasonality (i.e., wet and dry seasons). Overall, capture rates were significantly skewed toward females and riparian corridors in pastures. Females of G. soricina exhibited a strong positive relationship with greater tree height and basal area. Seasonality was important for A. lituratus and S. lilium females, only. The results indicate a sexual driven response of bats to habitat modification. The high energetic demands of females associated to reproduction could lead to foraging into riparian corridors in pastures. The presence of large trees along riparian corridors in pastures may help maintaining a diverse and dynamic bat community in modified tropical landscapes.

Live Crown Ratio as an Indicator for Tree Vigor and Stability of Turkey Oak (Quercus cerris L.): A Case Study

Stability of forests represents a significant objective for climate change mitigation. As stand stability is influenced by the stability of individual trees, promoting stable trees is vital for a sustainable forest management. However, inside stands, trees experience intense competition. As a result, the crown recedes and diameter growth is affected, the trees becoming slender and more susceptible to biotic and abiotic disturbances. Finding effective indicators for tree vigor and stability is therefore important. This study aimed to assess the performance of the live crown ratio as an indicator in deciding the timing of tending operations for obtaining and maintaining vigorous Turkey oak trees. Live crown ratio (LCR) and height to diameter ratio (HDR) were determined for 80 sampled Turkey oak trees. A threshold of 100 for HDR was chosen to classify trees as slender or not slender. Next, conditional inference tree and logistic regression were used to determine the LCR threshold value where trees become slender. As the sample included small trees, using breast height to measure diameter may have affected the results. Therefore, small and large trees were also analyzed separately. For the entire dataset, the methods reached quite different results (LCR threshold of 0.371 for conditional inference tree and of 0.434 for the logistic regression), and relatively high values compared to the literature. For tall trees (height > 12.5 m), the methods reached similar results: 0.386 for the conditional inference tree and 0.382 for the logistic regression. For small trees (height < 12.5 m), the conditional inference tree method could not calculate any LCR threshold estimate, while the one from the logistic regression was unrealistically large (0.628). This confirms that using DBH for small trees to compute slenderness brings systematic errors. The live crown ratio was a good indicator of growth vigor for Turkey oak trees. Therefore, for stable trees (HDR < 100), a LCR of 0.36–0.39 must be maintained and could be used to decide the timing for thinning in Turkey oak stands.

Native Forests Show Resilience to Selective Timber Harvesting in Southeast Queensland, Australia

There is little published information on effects of management on the structure of mixed species forests in Queensland, Australia. We used long-term growth, abundance and dimension data from permanent plots to test the hypothesis that harvesting would reduce numbers of large trees and growth increments, while increasing recruitment. This hypothesis is key to policy and management decisions for forests covering about 9.5 million hectares. Inclusion of data on changes in forest structure (e.g., tree diameter, stem density) helps in assessment of forest suitability as habitat for a range of species. Growth rate (basal area) varied widely among forest types. Growth of each of four key species (i.e., Eucalyptus pilularis, Corymbia citriodora ssp. variegata, Callitris glaucophylla, and Eucalyptus crebra) reflected variation in rainfall across the study region. Callitris glaucophylla, a native conifer, is dominant when rainfall is &lt; 600 mm per year. Corymbia citriodora ssp. variegata grows across much wider ranges in rainfall (600–1,200 mm year–1) at rates similar to Callitris glaucophylla. Historic harvesting increased recruitment and also increased the symmetry of diameter distributions. Harvesting has not reduced the current density of larger trees (diameter at breast height, DBH ≥ 60 cm) at a regional scale. Stand growth was unaffected by management principally owing to an increase in the density of trees of smaller diameter (10–20 cm DBH). Self-thinning limits potential stocking and we tested 3 methods for predicting self-thinning across forest types. We found that the slope of self-thinning lines under drier conditions is mostly &lt; –2, suggesting highly dynamic self-thinning. Using a species-boundary line approach, growth is predicted to slow when basal areas reach around 66.1 m2 ha–1 in E. pilularis, 19.0 m2 ha–1 in C. citriodora ssp. variegata, 16.5 m2 ha–1 in Callitris glaucophylla, and 14.2 m2 ha–1 in E. crebra. The slope of the self-thinning line for E. pilularis was –1.662, similar to Reineke’s Stand Density Index (slope –1.605). To date, there is little evidence that selective harvesting and thinning have had negative impacts on rates of growth, on timber production, carbon sequestration or on aspects of forest structure regarded as important for biodiversity.