Taiwan Island Research Articles

Complete Genome Sequence Resource of Pectobacterium colocasium Strain F1-1 that Causes Soft Rot Disease of Taro.

Pectobacterium colocasium is a recently named, narrow-host-range phytopathogenic bacterium causing soft rot of taro (Colocasium esculenta). It is found on the Chinese mainland and the island of Taiwan. Taro is a domesticated crop with a long history of cultivation in Taiwan and the Pacific islands. However, not much was known about Pectobacterium spp. from taro, especially from the islands in the Pacific. Herein, we report a high-quality, completely annotated genome sequence of P. colosacium strain F1-1. The 4,816,345 bp genome, which was assembled with Illumina and Nanopore reads with 217× and 311× coverage, respectively, consists of one chromosome and no plasmid. This completely circularized genome will aid future studies in comparative genomics, evolution, and pathogenicity of P. colocasium. This genome resource will also be helpful for developing strategies to control P. colocasium in taro.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Formation process of Pliocene cold seep carbonates from the southern Western Foothills, Southwestern Taiwan: A synthetical rare earth element and C–O–Sr–Nd isotope study

In this work, the Pliocene dolomitic carbonate concretions and pipes from Chiahsien of the Western Foothills, southwestern Taiwan were studied. We conducted a synthetical analysis of stable carbon and oxygen isotopes, rare earth element (REE) contents, and Sr and Nd isotopes, to trace the compositions and sources of pore fluids from which carbonates have precipitated and reconstruct the carbonate formation processes. The carbonates with low δ13C values (as low as −48.6‰) are promoted by the anaerobic oxidation of biogenic methane. The 87Sr/86Sr ratios of samples reflect the mixing of coeval bottom seawater and seep fluid enriched in 87Sr. The Nd isotopic signatures of studied carbonates indicate multiple Nd sources, including detrital components, Fe–Mn oxyhydroxides, organic matter, and seawater. The MREE-bulge patterns in samples are typical of anoxic conditions, which are supported by Ce anomalies. Our results demonstrate that the seepage intensity played a key role in the formation processes of concretions and pipes by controlling the depth of the sulfate-methane transition zone (SMTZ). The concretions characterized by the lowest δ13C values formed at a deeper depth in sediments under low methane flux, which suffered no/less influence of seawater. The representative pipe with obvious concentric lamination grew in a rim-to-core pattern. In the early stage, the variable flux of highly channelized seepage caused the fluctuation of carbon and oxygen isotopes. During the later stage, the modification of isotopic compositions in the core part were resulted from meteoric alteration. Our work provides insights into the formation process related to seepage evolution in ancient cold seeps on Taiwan Island.

The Complete Chloroplast Genomes of Blepharoglossum elegans and B. grossum and Comparative Analysis with Related Species (Orchidaceae, Malaxideae).

Blepharoglossum is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of Blepharoglossum has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two Blepharoglossum species, Blepharoglossum elegans (Lindl.) L. Li and Blepharoglossum grossum (Rchb.f.) L. Li. These cp genomes of Blepharoglossum share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with ycf1, clpP, and trnK-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely rps16-trnQ-UUG, trnS-GCU-trnG-GCC, rpoB-trnC-GCA, trnE-UUC-trnT-GGU, trnF-GAA-trnV-UAC, atpB-rbcL, petA-psbJ, psbE-petL, psbB-psbT, trnN-GUU-rpl32, trnV-GAC-rps7, and rps7-trnL-CAA, and five coding regions, including matK, and rpoC2, ycf1, and two ycf2 genes. Phylogenetic analysis indicated that Blepharoglossum and Oberonia form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades.

A new record of Squalus montalbani (Chondrichthyes: Squaliformes: Squalidae) from the Nansha (Spratly) Islands, South China Sea

The Indonesian greeneye spurdog (or a dogfish shark), Squalus montalbani Whitley, 1931, is widely distributed in the warm temperate to tropical waters of Indonesia, Philippines, the island of Taiwan, and Australia. Previous studies suggested that the distribution of dogfish shark species in the South China Sea is composed of two species, Squalus mitsukurii Jordan et Snyder, 1903 and Squalus brevirostris Tanaka, 1917. In March 2020 a dogfish shark specimen was collected from the Nansha (Spratly) Islands, South China Sea. We identified it as S. montalbani based on morphology and mitochondrial DNA barcoding. Our results confirmed the presence of S. montalbani in the South China Sea, leading us to conclude that it represents a new species record of the genus Squalus in the region. Furthermore, our findings demonstrate that the combined approach is highly effective in identifying Squalus species that share similar morphological characteristics.

Record of short-lived “orogen” on Eurasian continental margin by South China Sea obduction preserved in Taiwan collision

The Taiwan mountain belt is the result of an arc-continent collision following the total subduction of the South China Sea and subsequent closure of the Luzon forearc, a process important in the accretionary growth of continents. Due to the oblique convergence, the southern tip of Taiwan Island is experiencing incipient collision, which is key to observing the oceanic-continental subduction transition. Within the monotonous turbidite extensively exposed on the Hengchun Peninsula as an uplifted Manila Trench accretionary wedge, the Shihmen Conglomerate, as a few intercalated lenses of coarse mafic pebbles, represents a dramatic change in sediment provenance and the causal tectonic event. New zircon U-Pb and amphibole 40Ar/39Ar ages are obtained from sediments, including sands and mafic pebbles that are either gabbro or foliated amphibolite. The 22–24 Ma zircon crystallization ages confirm the South China Sea origin of the mafic clasts, while the much younger 13 ± 2 Ma amphibole 40Ar/39Ar isochron ages from foliated amphibolites suggest a later thermal-tectonic event other than seafloor metamorphism. The amphibole 40Ar/39Ar ages overlap with the biostratigraphic age (∼11–14 Ma), indicating that the mafic source rocks were exhumed and eroded in a high-relief topography immediately after metamorphism. Detrital zircon U-Pb ages from a sandy layer within the conglomerate are also mostly identical to those from the mafic pebbles. Since the paleocurrent of the Shihmen Conglomerate was similar to that of the neighboring turbidites, which were derived from major rivers draining the southeastern Chinese continent, the provenance of the mafic pebbles and sands was best explained as an isolated subaerial mountain on the Eurasian continental margin with a very limited temporal and spatial extent, as the detrital products are poorly distributed. The most likely cause of the ephemeral mountain was the obduction of the South China Sea onto the Eurasian continental margin when the latter first impinged on the Philippine Sea Plate at the Manila Trench, where the gabbroic oceanic crust was uplifted and exhumed, followed by dynamic metamorphism along the basal thrust.

Health-promoting lifestyle and its predictors among health-related and non-health-related university students in Taiwan: a cross-sectional quantitative study

BackgroundUniversity students majoring in different disciplines are believed to have different personality traits, courses exposure, and future roles, which may further affect their health behaviors and health status. The purpose of this study was to investigate the differences in health-promoting lifestyle (HPL) and its predictors among health-related and non-health-related students.MethodsThe research participants were university students in the main island of Taiwan, and a two-stage sampling approach was adopted to obtain the samples from November 2020 to March 2021. First, 37 universities were randomly selected based on the ratio of public and private universities in each region of Taiwan. Then, based on the ratio of health-related and non-health-related majors of selected university, 25–30 students were randomly drawn from each university according to the student ID number to complete self-administered questionnaires, which included items for personal factors, perceived health status (PHS), health conception (HC), and health-promoting lifestyle profile (HPLP). A total of 1062 valid questionnaires were recovered, including 458 from health-related students and 604 from non-health-related students. Chi-squared test, independent samples t-test, one-way ANOVA, Pearson product-moment correlation analysis, and multiple regression analysis were performed.ResultsThe results showed that gender (p < 0.001), residential status (p = 0.023), body mass index (p = 0.016), and daily sleep duration (p = 0.034) of the students majoring in different disciplines were different. Health-related students having better HC (p = 0.002) and HPLP (p = 0.040) than non-health-related students. In addition, for both majors, females, low PHS scores, and low scores for functional/role, clinical, and eudaimonistic dimensions of HC were important indicators of a relatively negative HPLP, while health-related students who exercised 75 min or less per week and non-health-related students with a monthly disposable income of 15,000 TWD or less or who dined out 15 times or more per week also required attention in the promotion of HPL (health-related majors: adjusted R2 = 0.481, p < 0.001; non-health-related majors: adjusted R2 = 0.443, p < 0.001).ConclusionsStudents majoring in each discipline who had poor HPLP which is mentioned above should be prioritized in the provision of appropriate exercise or nutritional support programs on campus to promote their awareness and ability to pay attention to their health.

A relay of anticyclonic eddies transferring North Pacific subtropical mode water into the South China Sea

North Pacific subtropical mode waters (STMWs), which are subducted with air-sea interaction signals and characterized by low potential vorticity (PV), play an important role in climate change issues. STMW (PV&lt;2×10−10 m−1· s−1) can be advected westward by large-scale ocean circulation and mesoscale eddies. However, whether and how the STMW intrudes into the South China Sea (SCS) remains unclear. Low PV signals that originate from the STMW and intruding into the SCS are investigated by comparing observations and ocean general circulation models during 2003-2017. These signals mostly move across the Luzon Strait (LS) into the SCS during the 2008-2009 and 2014-2016 periods. The results of case studies selected from these two periods indicate that the low PV signals can move to the LS and are trapped by anticyclonic eddies (AEs). When the velocity vorticity is negative southwest of Taiwan Island, vertical stratification becomes weaker west of the coming AE (AE1), and low PV signals can consequently be transported along the STMW layer (25.0 σθ- 25.5 σθ isopycnal layer). Thus, an AE (AE2) forms east of AE1 and isolates the low PV signal from AE1, and then AE2 transports the low PV water southwestward in the SCS. In contrast, the low PV signal has difficulty migrating eastward when the velocity vorticity is positive west of AE1, as vertical stratification strengthens and then weakens that signal. The results suggest that only AEs can relay low PV signals from east of the LS and carry them over long distances in the SCS.

A Statistical Analysis of Tropical Cyclone-Induced Low-Level Winds near Taiwan Island

Using ERA5 reanalysis data and the tropical cyclone (TC) best track datasets from the China Meteorological Administration and Joint Typhoon Warning Center (from 1979 to 2021), TC-induced low-level winds near Taiwan Island are statistically analyzed. This study mainly concerns TC activity, low-level wind fields around Taiwan Island under TCs, and the detailed characteristics of TC wind structure. Results show that on average, 8.3 TCs enter the study region near Taiwan Island every year mainly from May to November, with more frequent and stronger TCs on the eastern and southern sides of Taiwan Island. For TC centers located at different positions around Taiwan Island, positive and negative vertical vorticity belts alternate between Taiwan Island and the TC center. Moreover, stronger and more frequent TC-induced winds mainly occur on the eastern side of Taiwan Island and the north of Taiwan Strait. TCs to the east of Taiwan Island have stronger maximum sustained wind than those on the western side of the island. Radii of the maximum wind (RMW) for TCs around Taiwan Island range from 5 to 90 nautical mile (nm, 9.3 to 116.7 km) with a mean value of 24.7 nm (44.4 km). Moreover, the RMWs of TCs are the largest (smallest) when the TC centers are located to the southwest (east) of the island. In addition, the outer sizes of TC winds vary from 52 to 360 nm (17.2 to 666.7 km) in the study region, with 187.4 nm (347.1 km) on average, and smaller values for TCs on the western side of the island. The average radii of severe winds, including R34, R50, and R64, are largest in the northeast quadrant and smallest in the southwest quadrant of the TC. The higher the specific wind speed is, the smaller the TC radius and the more symmetric its wind circle. These statistical results may provide references for TC gale forecasting and wind-resistant design for offshore engineering to mitigate TC-induced wind hazards.

Two distinct types of turbidity currents observed in the Manila Trench, South China Sea

Sediment gravity flows are the most direct and efficient transport mechanisms for moving terrestrial sediments into deep oceans. Scarcity of firsthand measurements, however, has hindered the quantitative, even qualitative characterization of such flows. Here we present a unique year-long data record from ~4000 m depth in the Manila Trench that captured two very different gravity flows in terms of their hydraulic and sedimentary properties. The first flow was of slow speed (~40 cm s−1) and long duration (~150 h), thus nicknamed ‘Tortoises’, and carried very fine sediment with low concentration (~0.01%). The fast (~150 cm s−1) but short-lived (~40 h) flow, nicknamed ‘Hares’, carried much coarser sediment with higher concentration (~1.2%). Clay mineral compositions suggest that the ‘Tortoises’ originated from upstream canyon wall slumping, whereas the ‘Hares’ was likely submarine canyons southwest of Taiwan Island due to typhoon. Grain size is a key factor in determining evolution of turbidity currents.

Changjiang coastal mud‐belt deposits in Taiwan Strait: Controls on its distribution and facies

ABSTRACTCoastal mud belts, which lie parallel to the coast just seaward of the shoreface, are one of the most important settings where shallow‐marine muddy deposits accumulate. However, sedimentary processes and facies distributions of coastal mud belts remain largely uninvestigated. This study uses process‐oriented sedimentology, coupled with provenance analysis and organic geochemistry of sedimentary records at the northern entrance to the Taiwan Strait, to investigate one of the largest such systems in the world, the Changjiang coastal mud belt. Carbon‐14 dates indicate that deposition has been intermittent throughout Marine Isotope Stages 1, 2 and 3, with several cryptic gaps in the muddy succession as a result of exposure or transgressive erosion during periods of lower or rising sea level, respectively. The palaeowater depth of each depositional unit was roughly estimated based on a global sea‐level curve and the elevation and age of the depositional units. Integrated provenance and sedimentology studies suggest that an incised valley most likely cut by the Minjiang, a nearby river draining the Chinese mainland, probably during Marine Isotope Stage 6, was filled with shelf mud during Marine Isotope Stage 3. These results demonstrate that deposition of mud on the Changjiang coastal mud belt was influenced by sea‐level changes that controlled water depth and flow patterns through Taiwan Strait. The Changjiang coastal mud belt migrates landward when sea level rises and moves seaward when sea level drops. In addition, changes in oceanic circulation associated with opening and closing of Taiwan Strait due to sea‐level changes causes significant changes in the source of the mud, with an alternation between sediment contributions from the Changjiang in the north, the nearby Minjiang, and the island of Taiwan to the south‐east. This study also reveals that the Changjiang coastal mud belt deposits are composed of both shallower‐water and deeper‐water facies. The shallower‐water facies predominantly comprises abundant fluid‐mud beds generated by waves and tidal currents. The deeper‐water facies contains shell‐rich mud and bioturbated mud, which were likely deposited by the Chinese coastal current and Taiwan Warm current. The bed types and interpretation of sedimentary processes of the Changjiang coastal mud belt are useful for recognition of ancient deposits of coastal mud belts elsewhere.

Evaluating the Urban-Rural Differences in the Environmental Factors Affecting Amphibian Roadkill

Roads have major impacts on wildlife, and the most direct negative effect is through deadly collisions with vehicles, i.e., roadkill. Amphibians are the most frequently road-killed animal group. Due to the significant differences between urban and rural environments, the potential urban-rural differences in factors driving amphibian roadkill risks should be incorporated into the planning of mitigation measures. Drawing on a citizen-collected roadkill dataset from Taiwan island, we present a MaxEnt based modelling analysis to examine potential urban-rural differences in landscape features and environmental factors associated with amphibian road mortality. By incorporating with the Global Human Settlement Layer Settlement Model—an ancillary human settlement dataset divided by built-up area and population density—amphibian roadkill data were divided into urban and rural data sets, and then used to create separate models for urban and rural areas. Model diagnostics suggested good performance (all AUCs &gt; 0.8) of both urban and rural models. Multiple variable importance evaluations revealed significant differences between urban and rural areas. The importance of environmental variables was evaluated based on percent contribution, permutation importance and the Jackknife test. According to the overall results, road density was found to be important in explaining the amphibian roadkill in rural areas, whilst precipitation of warmest quarter was found to best explain the amphibian roadkill in the urban context. The method and outputs illustrated in this study can be useful tools to better understand amphibian road mortality in urban and rural environments and to inform mitigation assessment and conservation planning.

Seismic evidence for slab detachment beneath the Taiwan Orogen

To clarify the deep structure of the Taiwan Orogen formed by the collision between the Eurasian and the Philippine Sea plates, we determine a robust 3-D shear-wave velocity (Vs) model of the crust and upper mantle beneath the Taiwan Island and its surrounding regions by applying a novel joint inversion method to local and teleseismic P and S wave travel times, Rayleigh-wave phase velocities and S-wave receiver functions. A notable new feature revealed by our model is the morphologic variation of the subducting Eurasian slab along the orogen belt. Beneath South Taiwan, the subducting Eurasian slab is imaged as a continuous high-Vs zone down to ∼400 km depth with an obvious dip angle change at ∼70 km depth. Beneath Central Taiwan, the Eurasian slab is imaged as intermittent high-Vs anomalies in the upper mantle, whereas the Eurasian slab exhibits as a sheet-like high-Vs zone with a low dip angle down to only ∼100 km depth beneath North Taiwan. These results suggest that parts of the subducting Eurasian slab have been detached beneath the Philippine Sea east off the Taiwan Island, which may result in the remnant slab rebounding to underplate the upper plate and so promote mountain building on the Taiwan Island.

Key factors promoting the niche establishment of black-winged kite Elanus caeruleus in farmland ecosystems

Human disturbance has modified the ecosystem’s structure and function, reducing the availability of wildlife habitat, while environmental change has driven the migratory behavior birds. Black-winged Kites (Elanus caeruleus, BWK) have changed their migratory behavior to become residents in Taiwan since 2001, with the expansion of their population on the island in the following years. However, there is limited knowledge about the factors that impact the dispersal population of BWK and the areas suitable for this species’ habitat in Taiwan. Here, we aimed to identify important factors promoting the niche establishment of BWK in Taiwan. Our study integrated a fuzzy expert-based approach with empirical data to assess habitat suitability in farmland ecosystems. The results show that the model has high accuracy and that distance to grasslands and landscape ecological integrity are important factors related to BWK habitat. In addition, suitable habitat for BWK accounts for 206,734.91 ha (28.19%) of farmland area, primarily in eastern and southeastern areas of the Taiwan Island. Our findings are likely applicable to support conservation policies, prioritizing resources effectively to protect BWK habitat.

Phylogenetic divergence associated with climate oscillations and topology illustrates the dispersal history of Formosan sambar deer (Rusa unicolor swinhoii) in Taiwan

The island of Taiwan represents an ideal context for studying the effects of climatic oscillations and topographic variation on large herbivores due to its varied tropical to sub-tropical climate zones at different elevational ranges. We explored the phylogenetics of Formosan sambar deer (Rusa unicolor swinhoii) using the control region of the mitochondrial genome. We detected 18 haplotypes among 454 sequences across the island and grouped them into six regions based on SAMOVA, with 68.78% variance among regions. A Bayesian phylogenetic dendrogram revealed two spatially segregated genetic clades. Neutrality tests and Bayesian skyline plots uncovered different demographic expansion histories for the two clades. We further tested divergence times and chronology to propose potential phylogenetic scenarios, which were examined using approximate Bayesian computation. Finally, we present a credible hypothesis for a glacial refugium in the northern part of the Central Mountain Range. Subsequent secondary contact between the two clades during interglacial periods has led to the extant genetic structure of Formosan sambar deer.

The Observation-Based Index to Investigate the Role of the Lee Vortex in Enhancing Air Pollution over Northwestern Taiwan

Abstract This study quantifies the potential effect of the lee vortex on the fine particulate matter (PM2.5) pollution deterioration under the complex topography in Taiwan using observational data. We select the lee-vortex days that favor the development of the lee vortices in northwestern Taiwan under the southeasterly synoptic winds. We then define the enhancement index that discerns the areas with the high occurrence frequencies of the PM2.5 enhancement under the flow regime relative to the seasonal background concentrations. Under the lee-vortex days, the center of western Taiwan exhibits enhancement indices higher than 0.65. In addition, during the consecutive lee-vortex days, the index characterizes a northward shift in the PM2.5-enhanced areas under the subtle transition of the background wind directions. The areas with indices higher than 0.65 expand on the second day in northwestern Taiwan; the number of stations exhibiting indices higher than 0.8 increases by threefold from the first to the second day. The idealized numerical simulations using the Taiwan vector vorticity equation cloud-resolving model (TaiwanVVM) explicitly resolve the structures of leeside circulations and the associated pollutant transport, and their evolutions are highly sensitive to the background winds. Significance Statement Our study investigates the challenging question of local circulation patterns affected by mountain orography and the associated pollutant transport. We analyzed long-term balloon sounding and ground station observations to select the weather regime favoring the formation of lee vortices on Taiwan island. We then quantified the areas with a frequent enhancement of particulate pollutants. The long-term trend of the lee-vortex days exhibited a significant increase in the past decades. The pollution enhancement areas are highly consistent with the regions dominated by leeside local circulation. Together with the idealized high-resolution simulations, we identified that the detailed evolution of the lee vortices is highly sensitive to the subtle changes in background wind direction and hence the redistribution of local pollution.

Assessing the Prospect of Joint Exploitations of Offshore Wind, Wave, and Tidal Stream Energy in the Adjacent Waters of China

The exploitation of marine renewable energy sources, such as offshore wind (OW), wave (WA), and tidal stream (TS) energy, is essential to reducing carbon emissions in China. Here, we demonstrate that a well-designed deployment of OW-WA-TS joint exploitation would be better than OW alone in improving performance in terms of the total amount and temporal stability of integrated power output in the northern Bohai Sea/Strait, the Subei Shoal, and the surrounding areas of Taiwan and Hainan Island. The design principles for an efficient joint energy deployment can be summarized as follows: first, a small ratio of WA output favors a temporally stable performance, except for areas around Taiwan Island and southwest of Hainan Island. Second, more TS turbines will contribute to steadier integrated outputs. Meanwhile, in the coastal waters of Guangdong and Zhejiang, the potential of WA to increase the total amount of power output is very high due to its minor impact on temporal stability. Finally, joint exploitation significantly reduces diurnal power fluctuations compared with OW alone, which is crucial for the steady operation of power grids, power sufficiency, and controllability in periods with low or no wind.

Provenance and dispersal patterns of sediments on the continental shelf of northern South China Sea: Evidence from detrital zircon geochronology

The northern shelf of South China Sea is an important passageway for the transportation of sediments from the terrigenous source to the oceanic sink, but the provenance and dispersal patterns of sediments remain largely unclear. Here we report the results of zircon grain-size analysis and U-Pb geochronology to investigate the sediment provenance and illustrate the transport and dispersal patterns of sediments on the continental shelf of the northern South China Sea. The results show that detrital zircon U-Pb ages within sediments are characterized by a major peak at ca. 150 Ma, as well as three minor age populations at ca. 240 Ma, 400–500 Ma, and 900–1000 Ma. A detailed provenance study suggests that these sediments were primarily derived from both the Pearl River catchment and the drainage systems in Taiwan Island. Our study confirms that the transportation and dispersion of sediments were largely controlled by both topography and hydrodynamics of sea. The sediments in the inner continental shelf were transported from the Pearl River drainage system and subject to the Guangdong Coastal Current, whereas the sediments in the middle and outer continental shelf were markedly influenced by the South China Sea warm current. This study elucidates the transport and dispersal patterns of detrital sediments in the marginal sea by comprehensive analyses of detrital zircon grains.

Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird.

Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.

Origin and diversification of pheretimoid megascolecid earthworms in the Japanese Archipelago as revealed by mitogenomic phylogenetics

Megascolecid earthworms of the pheretimoid group are dominant detritivores of soil ecosystems in the Japanese Archipelago and East Asia. However, their diversity and phylogenetic relationships are poorly understood. We assembled whole mitogenome sequences for 197 megascolecid earthworms collected throughout Japan to study the phylogenetic relationships, phylogeography, divergence times, and diversification of important morphological characteristics among pheretimoid earthworms. Using 197 mitogenome sequences and 24 published mitogenome sequences from the East Asian mainland (221 sequences in total), we constructed a maximum likelihood tree and found that the pheretimoid earthworms currently assigned to Amynthas, Metaphire, Duplodicodrilus, and Manus are involved in the most senior genus Amynthas; thus, Amynthas can be treated as the sole genus encompassing all of the above genera. Within the Amynthas group, we identified three major lineages that led to four groups of endemic species in Japan. These lineages originated from different lineages on the East Asian mainland and Taiwan Island, indicating multiple colonization events from the East Asian mainland by different ancestral lineages, possibly after the Miocene. We also assembled nuclear ribosomal DNA sequences encompassing the 18S to 28S rRNA genes. The nuclear gene tree showed major groups consistent with the mitogenome tree except for different (and not well-resolved) relationships among major clades. Our molecular data covered 115–158 native and 7 non-native Amynthas group species in Japan in terms of DNA-based species delimitation. Our findings provide a basis for understanding the evolutionary relationships among diversified megascolecid earthworms in the Amynthas group in Japan and adjacent regions.

The diversity of cultivable endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan.

Ipomoeapes-caprae is a plant of sand coasts and it can tolerate stresses, such as high salinity, strong wind and sand movements and lack of nutrients. It plays an important role in coast protection and preventing erosion. Fungal endophytes show high biodiversity and have a strong influence on the survival of plants under different stress factors. Although this plant is important for sand coast ecosystems, little is known about the associated fungi. In this study, we isolated and identified endophytic fungi of Ipomoeapes-caprae, a dominant plant along the shore of Taiwan. The dataset contains 896 records, which correspond to 177 species. The geographical scope of the dataset covers the northern subtropical area of the main island of Taiwan, with its sand coasts in New Taipei, Taoyuan, Hsinchu and Taichung and two botanical gardens in Taipei and Taichung. The detailed original data of fungal diversity are rarely publicly shared under strictly formalised and, thus, reusable standards. As an example for such an approach, the complete occurrence dataset was made available in the Darwin Core Archive format via the Global Biodiversity Information Facility (GBIF) under Version 1.13, Taiwan Biodiversity Information Facility (TaiBIF) https://doi.org/10.15468/9h9rcg. In this first data paper on endophytic fungi, the scientific name and associated DNA sequence in the dataset were directly linked to other free online resource (Index Fungorum, GenBank), which shows the potential of GBIF for linking together different online data repositories. We describe a dataset, in which the diversity of endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan was investigated.