Let K be a non-Archimedean valued field with valuation ring R. Let $C_\eta $ be a K-curve with compact-type reduction, so its Jacobian $J_\eta $ extends to an abelian R-scheme J. We prove that an Abel–Jacobi map $\iota \colon C_\eta \to J_\eta $ extends to a morphism $C\to J$, where C is a compact-type R-model of J, and we show this is a closed immersion when the special fiber of C has no rational components. To do so, we apply a rigid-analytic “fiberwise” criterion for a morphism to extend to integral models, and geometric results of Bosch and Lütkebohmert on the analytic structure of $J_\eta $.

Soils developed on Pleistocene andesitic lava flows and fluvial detritus in the Atlantic coastal plain of Costa Rica display a clay mineral assemblage that includes 10 Å and 7 Å halloysite and lesser amounts of kaolinite and dioctahedral vermiculite. Other secondary minerals include gibbsite, goethite, hematite, maghemite, allophane and amorphous Al hydroxides. Active floodplain soils are dominated by 10 Å halloysite and contain less allophane, while soil clays from Pleistocene terraces consist of a mixture of 10 Å and 7 Å halloysite as well as less dioctahedral vermiculite, kaolinite, and amorphous Al hydroxides. Residual soils formed on Pleistocene lava flows are dominated by 7 Å halloysite with less abundant kaolinite, dioctahedral vermiculite, 10 Å halloysite and amorphous Al hydroxides. This sequence suggests transformations of 10 Å halloysite to 7 Å halloysite and allophane to amorphous Al hydroxides with time. The presence of 10 Å halloysite in Pleistocene terrace soils implies slow reaction rates or metastability.

Quantitative X-ray diffraction (QXRD) analysis indicates a decrease in the amount of plagioclase feldspar from 34 wt.% in the 1–2 year floodplain to 0–1.6% in terrace and residual soils. Plagioclase weathering is paralleled by the formation of dioctahedral clay, allophane and Al hydroxides. Analysis by QXRD also indicates that crystalline minerals comprise 70–95% of the soil fraction, implying 5–30% X-ray-amorphous material. These data are verified by selective extraction using ammonium oxalate, which indicates 8–30% amorphous material. Chemical analysis of the extractant by inductively coupled plasmaatomic emission spectrometry indicates that allophane (Al:Si ratios of 0.92–3.82) occurs in floodplain and some terrace soils while amorphous Al hydroxides appear to coexist with allophane in Pleistocene terrace and residual soils with Al:Si ratios of 6.53–8.53. Retention of Mg to a greater extent than Na, Ca and K suggests Mg incorporation into hydroxide sheets in dioctahedral vermiculite as well as substitution into hydroxides.

Pedogenic smectite from a young (Holocene) tropical soil was reacted in Al-rich solution at 150ºC for a range of reaction times (3 to 120 days) in orderto study mechanisms and rates associated with the transformation of smectite to kaolinite via interstratified kaolinite-smectite (K-S). As has been observed in tropical soils, the overall reaction rate is logarithmic, with rapid initial transformation of smectite to K-S with ~50% smectite layers, followed by progressively slower transformation of intermediate K-S to kaolinite-rich K-S and eventually Fe-kaolinite. Sub-micron hexagonal non-Fe-bearing kaolinite forms in the final stage (after 120 days) as a minor mineral in an assemblage dominated by Fe-kaolinite. The pedogenic smectite used as starting material consisted of two end-members, Fe-beidellite and Al-smectite, enabling comparison of reaction pathways. Fe-beidellite transforms to K-S or Fe-kaolinite within 3 days, whereas Al-smectite transforms much more slowly, appearing to reach a maximum rate in intermediate stages. This difference is probably due to hydrolysis of relatively weak Mg-O and Fe-O bonds (relative to Al-O bonds) in Fe-beidellite octahedral sheets, which drives rapid reaction, whereas the driving force behind transformation of Al-smectite is more likely to be related to stripping of tetrahedral sheets which reaches its maximum rate at intermediate stages. Multiple analytical approaches have indicated that Al is rapidly fixed from solution into smectite interlayers within K-S, and that K-S and Fe-kaolinite inherit octahedral Fe and Mg from precursor smectite; as the reaction progresses, octahedral sheets become progressively more Al-rich and Fe and Mg are lost to solution. These results demonstrate that: (1) early-formed pedogenic smectite in tropical soils is expected to transform to kaolinite via interstratified K-S; (2) K-S has a strong potential to sequester plant-toxic Al in tropical soil; and (3) the presence in tropical soils of Fe-kaolinites with relatively large cation exchange capacities may be related to inheritance of octahedral sheets from precursor smectite and K-S.

Soils developed on Quaternary fluvial fill terraces in the humid tropics of Costa Rica display progressive changes in mineral assemblage, chemical composition and particle size with age. Clay minerals from B horizons of active floodplains are predominantly smectite with lesser amounts of disordered kaolinite. B horizons in 5 to 10 ka soils consist of sub-equal amounts of smectite and disordered kaolinite, and soils on 37–125 ka terraces consist of disordered kaolinite with only traces of smectite. The composition of the smectite, as determined by EDX scans of smectite-rich pore space, is [(Mg0.2,Ca0.1)(Fe0.6Al1.4)(Si3.6Al0.4)O10(OH)2], consistent with ferruginous beidellite.

Bulk mineral assemblage varies from a smectite-plagioclase-augite-quartz-magnetite assemblage in ⩽ 10 ka terrace soils to a disordered kaolinite-goethite-hematite-quartz-magnetite assemblage in ⩾37 ka terrace soils. Leaching results in rapid loss of soluble base cations and residual concentration of Ti and Zr indicates mass losses of ∼50% by chemical denudation by 125 ka. Plots of terrace age vs. various measures of clay mineralogy, chemical composition, and particle size produce parabolic curves consistent with rapid chemical weathering pre-37 ka and slower to imperceptible rates of change from 37 to 125 ka. For some pedogenic properties, particularly particle size and concentrations of base cations and Zr, soils appear to reach steady-state conditions within 37 ka.

These results were applied to interpretation of landscape evolution in this tectonically active region by: (1) facilitating identification of two Holocene (5 ka and 10 ka) terraces on the Esterillos Block 5–30 m above sea level (masl), and two Pleistocene terraces ⩾ 125 ka on the Parrita Block 30 masl, and, in turn, (2) documenting uplift rates as high as 4.4 m/ka between 37 and 10 ka on the Esterillos Block, and as low as 0.1 m/ka over the past 125 ka on the adjacent Parrita Block. These findings are consistent with previous work indicating that the subduction of anomalous bathymetric features at the Middle America Trench is having a significant impact on fore-arc dynamics and topography over relatively short geological time periods and spatial scales.

Tropical soils range from nutrient-depleted lateritic soils rich in halloysite or kaolinite to Inceptisols rich in interstratified kaolinite-smectite (K-S), smectite, or related 2:1 clays. Given the strong influence of clay minerals on tropical soil quality, better understanding of factors influencing their occurrence is important for modeling and managing tropical environments. This study examines the alteration of smectite to kaolinite by way of intermediate K-S and halloysite in a 120 ka moist tropical chronosequence. Iron-rich smectite (11.6 ± 2.2% Fe2O3) is the dominant mineral in Holocene soils (1–8 ka) originating from sediments rich in plagioclase and clinopyroxene. The cation exchange capacity (CEC) of smectite is 54–84 cmolc/kg and pH is 6.1 to 7.4. Within 50 ka, smectite fixes Al-hydroxy complexes into interlayers, K+ is retained preferentially over Ca2+, and 2:1 layers are stripped of tetrahedral sheets; the resulting K-S inherits flaky smectite crystal habit and the 2:1 layers — which only expand partially — include Al-hydroxy smectite and some illite-like layers. After 50 ka, the dominant mineral is K-S, the CEC is 18–28 cmolc/kg, and the pH is 5.3. Flaky Fe-kaolinite with ~10% residual smectite layers and halloysite (7.4% Fe2O3) also occur in 50 ka soil. The 120 ka soils are dominated by flaky Fe-kaolinite (<10% residual smectite layers) and halloysite (4.9% Fe2O3), and Fe-poor hexagonal kaolinite also occurs (5–10% of soil). The CEC is 11–16 cmolc/kg and the pH is 4.7–5.3.

Changes in crystal chemistry of the soil clays (decreasing Fe, Mg, Ca, and K; increasing Al) over time reflects two reaction mechanisms: (1) cell-preserved transformation of smectite layers to kaolinite layers that accompanies conversion of smectite to K-S and eventually kaolinite; this results in the formation of flaky Fe-rich kaolinites after 50 ka; and (2) dissolution of K-S followed by crystallization of halloysite. Neoformation of hexagonal kaolinite and/or halloysite with low Fe (<3% Fe2O3) follows dissolution of Fe-kaolinite or halloysite after 100 ka. This sequence is probably common in moist tropical soils and these findings may inform modeling of soil composition in tropical landscapes where tectonic, volcanic, or geomorphic activity periodically exposes unweathered parent material, producing a range of soil ages.

Studies on benthic foraminifera were conducted in the mangrove forests of Teluk Tempoyak, Pulau Betong and Kuala Sungai Pinang, Penang Island, Peninsular Malaysia to examine species composition and distribution patterns in different intertidal zones. Twenty-eight live benthic foraminiferal species were successfully identified at the study locations, predominantly species with agglutinated tests. Assemblages in Pulau Betong and Teluk Tempoyak were dominated by similar species such as Ammonia aoteana, Elphidium hispidulum, Elphidium neosimplex and Trochammina inflata, while Kuala Sungai Pinang comprises a high number of Trochammina inflata and Arenoparrella mexicana. Three species, Aubignyna perlucida, Elphidium neosimplex and Elphidium sandiegoense, were recorded for the first time in Malaysian mangrove forests. Principal component analysis showed that sediment type and organic matter content were the dominant parameters that explained the variation of environmental gradient. Canonical correspondence analysis of these parameters with benthic foraminiferal species indicated that sand particles influenced distribution of the hyaline tests. Species with agglutinated tests were abundant in sediment with rich organic matter in combination with high silt and clay content. Species with hyaline tests dominated lower intertidal zones, while those with agglutinated tests inhabited the area from the middle to upper intertidal zones. This distribution pattern of benthic foraminiferal species mirrored patterns found at other local and global mangrove locations.

The dengue virus type 3 (DENV-3) homotypic outbreak cycles reported in Klang Valley, Malaysia in 1992–1995 and 2002 demonstrated different epidemic magnitude and duration. These outbreak cycles were caused by two closely related strains of viruses within the DENV-3 genotype II (DENV-3/II). The role of viral genotypic diversity and factors that could have influenced this phenomenon were investigated. The serum neutralisation sensitivity of DEN3/II strains responsible for the DENV-3 outbreak cycles in 1992–1995 and 2002 were examined. Representative virus isolates from the respective outbreaks were subjected to virus neutralisation assay using identified sera of patients with homotypic (DENV-3) or heterotypic dengue infections (DENV-1 and DENV-2). Results from the study suggested that isolates representing DENV-3/II group E (DENV-3/II-E) from the 1992–1995 outbreak and DENV-3/II group F (DENV-3/II-F) from the 2002 outbreak were neutralised at similar capacity (intergenotypic differences <2-fold) by sera of patients infected with DENV-3, DENV-1 and DENV-2/Asian genotypes. Sera of the DENV-2/Cosmopolitan infection efficiently neutralised DENV-3/II-F (FRNT50 = 508.0) at a similar neutralisation capacity against its own homotypic serotype, DENV-2 (FRNT50 = 452.5), but not against DENV-3/II-E (FRNT50 = 100.8). The different neutralisation sensitivities of DENV-3/II strains towards the cross-reacting DENV-2 heterotypic immunity could play a role in shaping the DENV-3 recurring outbreaks pattern in Malaysia. Two genetic variations, E-132 (H/Y) and E-479 (A/V) were identified on the envelope protein of DENV-3/II-E and DENV-3/II-F, respectively. The E-132 variation was predicted to affect the protein stability. A more extensive study, however, on the implication of the naturally occurring genetic variations within closely related DENV genotypes on the neutralisation profile and protective immunity would be needed for a better understanding of the DENV spread pattern in a hyperendemic setting.

A new nematode species, Raphidascaris mundeswariensis n. sp. (Raphidascarididae), is described from male and female specimens found in the intestines of the mudskipper Apocryptes bato (Hamilton, 1822) (Gobiidae) from the Mundeswari River of West Bengal, India. This species is distinguished from its congeners by 214–255-μm-long spicules, 14 pairs of preanal papillae of two markedly different sizes, one pair of adanal papillae, six pairs of postanal papillae and the absence of lateral alae. Phylogenetic analyses using partial sequences of the 28S ribosomal RNA gene place the new species in a clade containing Raphidascaris gigi, Raphidascaris lophii, Raphidascaris longispicula and two species of Hysterothylacium. The molecular analyses also corroborate results of previous studies that have found Raphidascaris and Hysterothylacium to be paraphyletic. The finding of R. mundeswariensis in A. bato is the first Raphidascaris species described from a mudskipper anywhere.

The frequency and intensity of harmful algal bloom (HAB) events have been increasing in many places around the world. Heterosigma akashiwo is a marine raphidophyte species known to cause HABs in many places across tropical and temperate climates. Studies of temperate strains have identified that H. akashiwo blooms are driven by mass activation of cysts which, for this species, can only form at <15°C temperatures. Although these temperatures do not occur in the tropics, there have been no comparative studies for tropical H. akashiwo. This study aimed to investigate whether tropical H. akashiwo can form cysts under warm temperatures, therefore having different responses from temperate strains. Results showed that tropical H. akashiwo were similar with temperate strains and could only form round cyst-like structures at 5°C but not 25°C. We also observed novel response of a decline and recovery in cell densities at 25°C. The decline was interrupted when the cultures were diluted, implying a tendency for H. akashiwo to rapidly spread and accumulate within surrounding waters, thereby facilitating blooms. This behaviour presents unique bloom concerns. Close monitoring of H. akashiwo distribution patterns is needed for better assessment of the bloom threat posed within tropical waters.

A total of 5478 fishes were sampled between 2009 and 2020 to assess length–weight, length–length and weight–weight relationships in 39 marine species from 10 families caught in the Seychelles waters by the artisanal fishery. Two types of length (total length TL, fork length FL) and three types of weight (whole weight WT, gutted weight GW and gilled-gutted weight GGW) were measured. The parameters of the relationships were estimated using the log-transformed allometric model with bias correction. Our results include length–weight, length–length and weight–weight relationships for 39, 20 and 18 species, respectively. Our length–weight data and resulting relationships were compared against FishBase database for 36 species and were in the Bayesian 95% confidence interval of the relationships available for 33 species and above for Gnathanodon speciosus, Lutjanus gibbus and Variola louti. Finally, for five abundant and widely dispersed species we tested for spatial differences in morphometric relationships between the Mahé Plateau and three southern atoll groups. Significant differences were found for two species only, but their magnitude was small. We thus argue for the regression relationships based on pooled data to be used for most types of population and community analyses. The availability of these morphometric relationships will support the application of accurate size-based analyses for Seychelles fisheries survey data, and so enhance understanding of the ecology of the reef-associated fish component of marine ecosystems and food webs, and improve fisheries research management.

Litter breakdown is an important ecological process at the bottom of food webs in streams. Previous studies have been based only on a temporal interval of a single season, thus ignoring seasonal variation in litter input and community structure. We investigated organic matter input in a Brazilian savanna stream and the influence of its associated hyphomycetes on the invertebrate community. Organic matter input was sampled monthly and the leaves submitted to decomposition experiments. There were lower breakdown rates and higher invertebrate species richness and abundance during the dry season, which reached their maximum in July due to low stream discharge. Invertebrate composition was best explained by hyphomycetes (mainly by Flagellospora curvula and Anguillospora filiformis). Hyphomycetes have the capacity to degrade complex compounds of litter and to rapidly absorb nutrients by growing branched filaments, thus making the leaves more favourable for consumption by invertebrates. Shredder abundance was negatively related to litter richness, indicating possible species-specific relationships. We observed a sequential process with increased leaf litter input promoting an increase in hyphomycetes biomass, which in turn favoured invertebrate density.

Herbaceous plants are often under-studied in tropical forests, despite their high density and diversity, and little is known about the factors that influence their distribution at microscales. In a 25-ha plot in lowland Amazonian rain forest in Yasuní National Park, Ecuador, we censused six species of Heliconia (Heliconiaceae) in a stratified random manner across three topographic habitat types. We observed distribution patterns consistent with habitat filtering. Overall, more individuals occurred in the valley (N = 979) and slope (N = 847) compared with the ridge (N = 571) habitat. At the species level, Heliconia stricta (N = 1135), H. spathocircinata (N = 309) and H. ortotricha (N = 36) all had higher abundance in the valley and slope than ridge. Further, H. vellerigera (N = 20) was completely absent from the ridge. Conversely, H. velutina (N = 903) was most common in the drier ridge habitat. The two most common species (H. stricta and H. velutina) had a reciprocal or negative co-occurrence pattern and occurred preferentially in valley versus ridge habitats. These results suggest that taxa within this family have different adaptations to the wetter valley versus the drier ridge and that habitat partitioning contributes to coexistence.

Soil has been proposed as a driver explaining the development of monodominant forests in the tropics, for example, Gilbertiodendron dewevrei forests (GDF) in central Africa. The aim of this study was to compare the physical and chemical properties of soils under GDF with those under an adjacent mixed forest (AMF), while controlling for topography. To this end, we set up sixteen 0.25-ha plots according to forest type and topography (plateau vs. bottomland), in the Yoko forest reserve, Democratic Republic of Congo. In each plot, we measured litter thickness and collected a total of 80 soil samples at depths of 0–5, 5–10, 10–20, 20–40 and 120–150 cm, for standard physical and chemical analyses. When controlling for topography and soil texture, we found that most of the chemical properties of soils under GDF did not differ from those of soils under AMF, particularly acidity, cation concentration, total N and the C:N ratio. The litter layer was 2.3 times thicker under GDF than under AMF stands, and, for a given texture, soils under GDF had a slightly higher organic C concentration in the 0–5 cm soil layer. This study suggests that G. dewevrei stands modify organic matter dynamics, which may be important in maintaining its monodominance.

The lowland area of southern Vietnam contains a high diversity of corticolous, crustose lichens, particularly in the family Graphidaceae. Two species, Acanthothecis verrucosa S. Joshi, Upreti & Hur and Graphis exuta S. Joshi, Upreti & Hur, are described new to science. Acanthothecis verrucosa is characterized by a verrucose, olive green thallus containing irregular to shortly lirellate apothecia, hyaline to brownish proper exciple apically lined by robust periphysoids, muriform ascospores, 30–70 × 15–20 μm, and the presence of psoromic and subpsoromic acids. Graphis exuta is characterized by a smooth, greenish white thallus, simple lirellae lacking thalline margin, entire labia coarsely white pruinose towards slit, muriform ascospores, 20–35×10–13 μm, and norstictic acid in the thallus. A new name, Acanthothecis yokdonensis S. Joshi & Hur, is proposed here for the species Acanthothecis salazinica S. Joshi & Hur, a later homonym of A. salazinica van den Boom & Sipman. In addition, 34 species from Vietnam are newly reported. A world key to the group of Graphis species characterized by short, simple and sessile lirellae lacking or with basal thalline margins (nuda-morph) is presented.

High abundances of mangrove pollen have been associated with transgressive cycles on tropical margins, but the detailed relations between systems tracts and the taphonomy of the pollen are unclear. We report here the occurrence and high abundance of Rhizophora pollen, in association with taraxerol, a Rhizophora-sourced biomarker, from a high-resolution Congo fan core covering the last deglaciation. An age model based on 14C dates enables the temporal changes in taraxerol content and the percentage frequencies and flux (pollen grains (pg) cm–2 (103 yr)–1) of mangrove pollen to be compared quantitatively with the lateral rate of transgression across the flooding surface (derived from glacio-hydro-isostatic model output and the bathymetry of the margin). Rhizophora pollen concentrations and taraxerol content of the sediment are very strongly positively correlated with the lateral rate of transgression and indicate, independently of any sequence stratigraphic context, that mangrove pollen spikes are associated with the transgressive systems tract rather than the highstand systems tract or maximum flooding surface. Lower-resolution longer-term records from this margin indicate an association between taraxerol concentrations and transgressive rather than regressive phases. The flux of these materials to the Congo fan is interpreted as a function of the erosion of flooded mangrove swamp on the shelf and less importantly, changing extent of mangrove habitat, during sea-level rise. Congo River palaeoflood events also result in reworking of mangrove pollen and supply to the fan, but this mechanism is subdominant. Rhizophora pollen has been underestimated in many palynological studies undertaken on cores from the African margin because of inappropriate sieve mesh size used during laboratory preparation.

In the south-eastern Amazon, positive feedbacks between land use and severe weather events are increasing the frequency and intensity of fires, threatening local biodiversity. We sampled fruit-feeding butterflies in experimental plots in a south-eastern Amazon forest: one control plot, one plot burned every 3 y, one plot burned yearly. We also measured environmental parameters (canopy cover, temperature, humidity). Our results show no significant differences in overall species richness between plots (34, 37 and 33 species respectively), although richness was lower in burned plots during the dry season. We found significant differences in community composition and structure between control and burned plots, but not between burned treatments. In the control plot, forest-specialist species represented 64% of total abundance, decreasing to 50% in burned every 3 y and 54% in yearly burned plots. Savanna specialist species were absent in the control plot, but represented respectively 8% and 3% of total abundance in burned plots. The best predictor of the change in spatial community patterns and abundance of forest specialists was canopy cover. Although we found high resilience to forest burning in many species, our study suggests that fire disturbance can still be a threat to forest specialists due to changes in microclimate.