Biodiversity Research Center, Academia Sinica

Mesopelagic ecosystems are vital to the ocean’s health yet face unprecedented threats due to accelerating climate change. Lanternfish (family Myctophidae) are key sentinels of midwater ecosystem health because they dominate mesopelagic fish biomass and mediate energy, nutrient, and carbon transfer across ocean layers. Despite their ecological importance, very little is known about their potential response to climate change stressors due to logistical challenges when studying mesopelagic ecosystems. We use thousands of fossil fish otoliths (calcium carbonate ear stones) recovered from marine surface sediments to reconstruct lanternfish growth, body size and energetic investment across contrasting oceanographic regimes. We compare assemblages from the highly productive, but oxygen-poor Tropical Eastern Pacific (TEP) and the oligotrophic, well-ventilated Caribbean, to test how oxygen availability and food supply shape mesopelagic fish energetics across the Isthmus of Panama. Otoliths from marine sediments serve as a cost-efficient, powerful archive to overcome methodological barriers and allow us to reconstruct long-term changes in lanternfish dynamics. We quantify energetic changes in lanternfish assemblages by reconstructing lanternfish body size estimates and mean per-capita biomass from otolith measurements and growth trajectories derived from increment biochronologies. Our results reveal anomalously small lanternfish in the TEP today, despite the region’s tendency to host larger fishes relative to the Caribbean, providing the first indication that mesopelagic fish size is potentially related to oxygen limitation. We then extend this approach to fossil otoliths to explore changes before the closure of the Isthmus of Panama using the Late Miocene/Pliocene as an analog system for warmer than modern conditions to test how mesopelagic ecosystems might respond to future climate change. We find that lanternfish dominated Panama’s ancient fish assemblages in the Caribbean but declined in relative abundance toward the Isthmus closure, while their mean per-capita biomass remained stable over the past 8 Ma. These results imply higher lanternfish biomass during periods of prolonged warming and lower biomass under less productive, better-oxygenated Caribbean conditions created by the Isthmus uplift. Yet in contrast to Panama’s geological past, our results suggest that oxygen availability exerts a dominant control on lanternfish energetics and production in the modern TEP. By integrating otolith archives from deep time to the recent past, we mapped shifts in lanternfish energetics in response to major environmental changes, revealing their sensitivity to oxygen availability and indicating that projected ocean deoxygenation might constrain the energetic capacity of the mesopelagic zone in a future ocean.

Fossil records of porcupines ( Hystrix ) from island environments in East Asia have never been reported, leaving their Pleistocene dispersal and biogeographic history poorly understood. This study describes fossil remains of Hystrix subcristata from the Chochen–Tsailiao locality, south-western Taiwan. The locality, part of the Chiting Formation in Tainan, is dated to the Middle Pleistocene. The collection includes a well-preserved upper molar (M1/2), a lower last premolar (p4), a fragmentary lower molar (m1/2) and three fragmentary incisors. Biometric analysis indicates that the Chochen–Tsailiao specimens are smaller than H. refossa , but larger than H. lagrelii and H. vinogradovi and closely comparable in size to H. subcristata . Morphological features further corroborate this identification. This discovery is the first record of H. subcristata from Taiwan, representing both its easternmost known occurrence and the first island evidence for the genus, contrasting with all prior records which consisted only of mainland forms.

ABSTRACTOrchids are traded globally, where wild populations can be threatened by overharvesting, habitat loss, and climate change. Many orchid species lack ex situ protection, such as botanical gardens, making in situ genetic studies of wild populations critical to inform conservation plans. Taiwan is a center for orchid diversity and has witnessed declines in wild orchids. Holcoglossum pumilum, an island endemic epiphytic species, is popular among citizen scientists and shows potential for public engagement in biodiversity conservation. This study aims to evaluate the genetic diversity, population structure, and adaptive potential of wild Holcoglossum pumilum in Taiwan, not only to serve as an example for public outreach but also to inform conservation policy. We collected 64 plants from 18 sites across Taiwan and used ddRADseq to generate genome‐wide SNP data. We found higher genetic diversity in southern populations than in northern ones. While evidence for genetic clustering and isolation by distance was limited, we detected significant genotype–environment associations, especially with annual precipitation. Demographic reconstructions suggested a pre‐LGM expansion followed by a plateau. Contemporary Ne estimates varied by data filtering strategies but were mostly below 500. Our study demonstrates the critical role of genomic data not only in revealing the evolutionary origin of genetic diversity but also in guiding conservation plans. Specifically, we argued that the seasonal monsoon and the mountainous landscape of Taiwan may have shaped a latitudinal gradient of genetic diversity in H. pumilum. As a result, southern populations exhibit greater genetic diversity, which makes them priorities for conservation management.

Background Acanthamoeba spp. are opportunistic protozoa that produce highly resistant cysts, complicating the treatment of ocular infections.MethodsWe assessed the anti-Acanthamoeba activity and cytotoxicity of chitosan nanoparticles loaded with propolis extracts from three stingless bee species, individually or combined with chlorhexidine (CHX). Encapsulation efficiency (EE), drug release kinetics, pH sensitivity, and anti-Acanthamoeba activity against trophozoite and cyst stages of four Acanthamoeba strains were evaluated. Additionally, cytotoxicity against Vero cells was examined.ResultsThe formulations demonstrated excellent EE (81–92%), with the combinations of Propolis 2, Propolis 3, and chlorhexidine achieving maximum drug entrapment and sustained release (>80%). It also exhibited the most effective cysticidal activity (minimal inhibitory cystic concentration (MICC) 1.25%) against A. polyphaga and the lowest toxicity (Minimal Cytotoxicity Concentration 2.5%) toward normal mammalian cells. Drug release conformed to non-Fickian (Case II) diffusion behavior and was enhanced in acidic pH conditions, which are relevant to disease. Scanning electron microscopy revealed morphological damage to the cyst walls.ConclusionThese results highlight that propolis–CHX-loaded chitosan nanoparticles (CS-NPs) show promise as a targeted, biocompatible therapy against drug-resistant Acanthamoeba cysts.

Variation in life history strategies is among the most striking features of animal diversity. Simultaneously, the microbes an animal interacts with are a critical and dynamic aspect of the host environment that can have profound impacts on their life history traits. As microbial environments diverge across animal lineages, life histories and their responses to such microbial contexts are expected to evolve as a consequence. Caenorhabditis nematodes are bacterivores that exhibit a diversity of life history strategies and fill diverse ecological niches. C. elegans thrives on rotting plants and grows rapidly with high fecundity; C. inopinata thrives in fresh figs and grows more slowly with lower fecundity. To understand how hosts with divergent life histories and ecologies respond to the microbes they interact with, we isolated over forty bacterial species from the natural fig environment of C. inopinata. This microbial survey revealed an isolate, Klebsiella sp. WOUb2, that doubles the population growth rate of C. inopinata. While this isolate also increases the population growth rate of C. elegans, Klebsiella sp. WOUb2 increases individual fecundity and developmental rate in C. elegans, whereas it only increases developmental rate of C. inopinata. Thus, fitness is modulated by variable life history mechanisms in the two species. Comparisons with nucleotide databases reveal Klebsiella sp. WOUb2 is closely related to other Klebsiella isolates known to influence Caenorhabditis nematode fitness. Additionally, the similarity of Klebsiella sp. WOUb2 to microbes associated with fig wasps and figs suggests C. inopinata frequently encounters this microbe in its natural context. Taken together, this shows that different physiological responses can underlie conserved, beneficial interspecific interactions.

The genus Peronella Gray, 1855 is a widespread group of sand dollars native to the Indo-Pacific region. However, compared to adjacent areas, their presence in Taiwan is extremely limited, with only two recorded species, including one only represented by a single denuded test. Here, we report new Peronella specimens from northern Taiwan. Based on petal outline, lateral outline, apical system, periproct position, and oral plating pattern, these specimens are identified as Peronella pellucida Döderlein, 1885. Their morphological variations during growth as well as individual differences are described. We found notable intraspecific variations in the gonopore size and periproct, suggesting that some previous diagnostic features for this genus may not be reliable. In contrast, hydropore distribution and periproct position emerge as the most reliable diagnosis. Additioanlly, except for the juvenile and deformed specimens, all other specimens exhibit four gonopores, consistent with the previous key diagnosis of Peronella. Our neighbor-joining tree based on mitochondrial COI sequences of four available Peronella species reveals strong monophyletic supports for each species and that P. pellucida is phylogenetically closer to P. rubra Döderlein, 1885. Our morphological measurements, combined with molecular evidence, provide valuable data for a better understanding of this underexplored group.

Studies of Taiwanese mammals reveal varied patterns of population divergence. Low-mobility species such as mole-shrews and Formosan wood mice exhibit strong north–south splits. Surprisingly, similar patterns also occur in mobile taxa like Formosan serow and sambar deer. In contrast, other mobile species, including flying squirrels, and Reeves’s muntjac, show weak or no population structure. This recurring north–south divergence across taxa with diverse ecologies suggests that shared environmental and geographic gradients, in addition to historical isolation, may underlie these patterns. If so, species occupying similar habitats may exhibit comparable genetic breaks regardless of life history traits. Prior studies based solely on mitochondrial DNA may have missed fine-scale structure in species like muntjac; high-resolution SNP data now offer improved resolution. Here, we analyzed genome-wide SNPs from 71 Taiwanese Reeves’s muntjac and comparative Chinese samples. We detected deep divergence from Chinese muntjac (~0.24 MYA), and further north–south subdivision within Taiwan (~0.06 MYA). Demographic modeling revealed a complex history involving glacial isolation and asymmetric gene flow, mainly from north to south. Within Taiwan, genetic differentiation was shaped by both geography and climate, especially temperature annual range (Bio7), with niche models showing environmental separation. Selection scans identified PLA2-associated genes, potentially linked to thermal adaptation. This is the first study to demonstrate that both geographic and environmental heterogeneity jointly contribute to mammalian divergence in Taiwan. The repeated north–south split across ecologically diverse species highlights shared climatic and topographic factors driving parallel population structure in Taiwan’s montane ecosystems.

Secondary growth is a key characteristic evolved from seed plants and generates secondary xylem-the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.

Marine fossils from the Upper Miocene Chagres Formation in northern Panama offer critical insights into the paleoenvironmental conditions and ecological responses prior to the separation of the Atlantic from the Pacific by the formation of the Isthmus of Panama. Here we present a systematic study based on more than 6,200 otoliths collected from a coastal exposure near the town of Piña, Colón. This assemblage is remarkable for the extraordinary dominance of the family Myctophidae, constituting over 96% of specimens. The otolith density in the sediments is among the richest known globally (278.80 ± 135.59 otoliths/kg). The taxonomic composition is represented by 31 taxa across 12 families, including four new species: namely Chiloconger aflorens sp. nov., Dasyscopelus inopinatus sp. nov., Hoplostethus boyae sp. nov., and Malakichthys schwarzhansi sp. nov. Taphonomic evidence, combined with abundant predatory marine vertebrate fossils and extensive burrow ichnofossils, indicates a dynamic and highly productive nearshore ecosystem. The dominance of myctophids and multiple lines of evidence support the existence of a Late Miocene coastal upwelling system in the region, highlighted by efficient trophic transfer channeled from high primary production to apex predators. These findings provide a nuanced understanding of Neogene marine ecosystems prior to the final emergence of the Isthmus of Panama.