Rethinking tropical phenology: insights from long‐term monitoring and novel analytical methods

Here, we introduce the Special Section (SS) on long‐term monitoring and new analytical methods in tropical phenology. The SS puts together nine original papers plus a synthesis, bringing significant advances and new insights into our understanding of tropical phenology across Africa and tropical America. The papers address environmental cues, methodological shortcomings, and provide innovative analytical approaches, opening new pathways, perspective and applications of tropical phenology for forest management and environmental monitoring. The SS is a substantial step toward a more comprehensive overview of trends in tropical phenology, as seven of nine studies evaluate >10‐yr data sets applying new methods of analysis such as hierarchical Bayesian models, generalized additive models, and Fourier analysis. We argue that it is essential to maintain ongoing monitoring programs and build a tropical phenology network at least for long‐term (>10 yr) study sites, providing the means for national and international financial support. Cross‐continental comparisons are now a primary goal, as we work toward a global vision of trends and shifts in tropical phenology in the Anthropocene.     

High Bird Species Diversity in Structurally Heterogeneous Farmland in Western Kenya

Tropical ecosystems are globally important for bird diversity. In many tropical regions, land‐use intensification has caused conversion of natural forests into human‐modified habitats, such as secondary forests and heterogeneous agricultural landscapes. Despite previous research, the distribution of bird communities in these forest‐farmland mosaics is not well understood. To achieve a comprehensive understanding of bird diversity and community turnover in a human‐modified Kenyan landscape, we recorded bird communities at 20 sites covering the complete habitat gradient from forest (near natural forest, secondary forest) to farmland (subsistence farmland, sugarcane plantation) using point counts and distance sampling. Bird density and species richness were on average higher in farmland than in forest habitats. Within forest and farmland, bird density and species richness increased with vegetation structural diversity, i.e., were higher in near natural than in secondary forest and in subsistence farmland than in sugarcane plantations. Bird communities in forest and farmland habitats were very distinct and very few forest specialists occurred in farmland habitats. Moreover, insectivorous bird species declined in farmland habitats whereas carnivores and herbivores increased. Our study confirms that tropical farmlands can hardly accommodate forest specialist species. Contrary to most previous studies, our findings show that structurally rich tropical farmlands hold a surprisingly rich and distinct bird community that is threatened by conversion of subsistence farmland into sugarcane plantations. We conclude that conservation strategies in the tropics must go beyond rain forest protection and should integrate structurally heterogeneous agroecosystems into conservation plans that aim at maintaining the diverse bird communities of tropical forest‐farmland mosaics.     

Observations on the plankton of some Costa Rican lakes

We sampled 30 lakes in Costa Rica in the wet season (July–August) of 1991 for phytoplankton (with integrated and whole water samples), and 17 for zooplankton (with net tows). Taxa of plankton and community richness were poorly related to geography, morphology, chemistry, and other biota. Neither the zooplankton nor the phytoplankton appeared to influence the composition of the other, and neither were apparently influenced by the presence of fish.Phytoplankton richness reflected primarily sampling method, but also tended to decrease with elevation and with Secchi disk depth, and tended to increase with pH and alkalinity. Chlorophytes were the most abundant division in 14 lakes; these lakes tended to be unstratified, turbid, and located at higher elevation. Diatoms were common in 4 of the 7 lakes with elevated silica (over 30 ppm). Each lake showed at least a 3 : 1 dominance by copepods, cladocera, or insect larvae. Copepods dominated 7 of the 17 lakes, most of which were shallow, turbid, and had low alkalinity. Cladocera dominated 7 lakes that were typically deeper and located at low-to mid-elevations. Insect larvae dominated two small, turbid lakes.     

Immediate impact of a hurricane on the structure of a tropical butterfly community

More intense and frequent hurricanes may lead to long‐lasting effects to tropical ecosystems. Here, we describe the immediate impact on the butterfly community of a lowland forest in Belize, following Hurricane Earl. Species richness and abundance increased posthurricane, likely driven by convergence of the organization between the canopy and understory communities.     

Understanding sitatunga (Tragelaphus spekii) habitats through diet analysis in Rushebeya‐Kanyabaha wetland,Uganda

Between January and December 2008, we assessed the diet and habitat selection of sitatunga, a highly endangered tropical wetland antelope threatened by habitat loss in Rushebeya‐Kanyabaha wetland. Microhistological faecal analysis and vegetative sampling methods were used to assess plant forms, species and seasonal changes in the sitatunga diet. Habitat use was indirectly determined by assessing feeding patterns, distribution of dung and trails within the wetland. Sitatunga fed mainly on herbs, sedges, grasses and shrubs. A total of 34 plant species were recorded as eaten by sitatunga. The most eaten plant species was Cyperus papyrus L. (22%). Malenthera scandens Schum. & Thonn., Polygonum senegalense Meisu (12%) and Polygonum pulchrum Blume (5%) were the most eaten herbs. Zea mays L. was the most eaten agricultural crop (58% of domestic crops), mainly during the wet season. Sitatunga feeding was mainly concentrated on the wetland edge habitat (46%) where most of its food (53%) was located. The other preferred habitat was the tall closed papyrus. We conclude that the long‐term survival of sitatunga requires a management plan focussing on the conservation of the most preferred plant species and habitats.     

Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene,followed by secondary contact,polyploidization and local extinction in the Pleistocene

High tropical mountains harbour remarkable and fragmented biodiversity thought to a large degree to have been shaped by multiple dispersals of cold‐adapted lineages from remote areas. Few dated phylogenetic/phylogeographic analyses are however available. Here, we address the hypotheses that the sub‐Saharan African sweet vernal grasses have a dual colonization history and that lineages of independent origins have established secondary contact. We carried out rangewide sampling across the eastern African high mountains, inferred dated phylogenies from nuclear ribosomal and plastid DNA using Bayesian methods, and performed flow cytometry and AFLP (amplified fragment length polymorphism) analyses. We inferred a single Late Pliocene western Eurasian origin of the eastern African taxa, whose high‐ploid populations in one mountain group formed a distinct phylogeographic group and carried plastids that diverged from those of the currently allopatric southern African lineage in the Mid‐ to Late Pleistocene. We show that Anthoxanthum has an intriguing history in sub‐Saharan Africa, including Late Pliocene colonization from southeast and north, followed by secondary contact, hybridization, allopolyploidization and local extinction during one of the last glacial cycles. Our results add to a growing body of evidence showing that isolated tropical high mountain habitats have a dynamic recent history involving niche conservatism and recruitment from remote sources, repeated dispersals, diversification, hybridization and local extinction.     

Clinical and bacteriological profiles of patients with typhoid fever treated during 1975-1998 in the Tokyo Metropolitan Komagome Hospital

Patients with typhoid fever presenting to the Tokyo Metropolitan Komagome Hospital during the period 1975-1998 were retrospectively investigated. All cases were diagnosed by a positive culture for Salmonella typhi in either of their clinical specimens. Of the total number of 130 patients, 57% contracted the disease abroad; this population increased in later years as the total numbers of cases decreased. The period from disease onset to diagnosis averaged 14 days with 20% of the cases requiring over three weeks to establish a diagnosis. As for symptomatology relative bradycardia was seen in less than half of the cases, and rose spots or splenomegaly in less than one third. A positive blood culture was the most frequent test establishing the diagnosis followed by a positive stool culture. Intestinal bleeding was recognized in as many as 35 cases (27%) and even intestinal perforation occurred in two cases (1.5%). Chloramphenicol was most commonly employed during the early study period, however, during the late period it was replaced by fluoroquinolones. The clinical cure rate was 98% with regimens that include fluoroquinolones/quinolone; however it was 87% with the other antimicrobial regimens. Bacteriological relapse occurred in 25% of the non-fluoroquinolone group while only in 2.0% in the fluoroquinolone/quinolone group. Four strains of Salmonella typhi that were multi-resistant to chloramphenicol, ampicillin and cotrimoxazole were isolated in travelers from Asia. Early diagnosis by appropriate bacteriological examination regardless of classical symptomatology should be stressed and the use of fluoroquinolones is warranted in the treatment of typhoid fever.     

Niche expansion and temperature sensitivity of tropical African montane forests

Aim Climate and land‐use change will have a dramatic impact on future ecosystems through alterations to species ranges and community composition. When forming conservation strategies, correlative species distribution models are often created to assess risks for individual species. These models are based on the assumption of climatic equilibrium, such that the modern range is representative of the full range of conditions under which species could thrive. However, the palaeo‐ecological record illustrates examples of disequilibrium in species today, and recent studies suggest that many species could occur in much broader climatic settings than previously thought. Montane ecosystems are thought to be at disproportionate risk due to temperature sensitivity and restricted geographical ranges. However, in the Afrotropics the palaeo‐ecological record shows that montane forest taxa expanded into the lowlands numerous times, suggesting a possible tolerance to warm temperatures. Location Africa. Methods We integrate palaeo‐ecological and palaeo‐climatic data in order to compare climate conditions in which species are currently found with those in the past. We use species distribution models to construct potential modern ranges for Afromontane species based on modern distributions and distributions in the palaeo‐ecological record in order to evaluate the equilibrium of species ranges. Results We show that many Afromontane trees have occupied warmer climates in the past, which suggests that the current low‐elevation boundaries are not set by climate. Interestingly, the species with the largest disequilibrium between palaeo‐ and modern distributions are those whose modern distributions show the least temperature sensitivity. Mapping of species potential ranges based on modern and palaeo‐ distributions clearly shows that suitable climate conditions exist today in the lowlands for less temperature‐sensitive species. Main conclusions These results imply that the current range of these forest trees does not necessarily inform risk from climatic change, and that human land use may be the major pressure for many species in the future.     

Isolation and characterization of 11 new microsatellite markers for Macaranga (Euphorbiaceae)

We provide primer sequences for 11 new polymorphic microsatellite markers developed in the tropical ant-plant genus Macaranga (Euphorbiaceae), after enrichment cloning of Macaranga tanarius and Macaranga hypoleuca. Allele numbers per locus ranged from two to 16 among 20 accessions of M. tanarius, and from three to 10 among 22 accessions of M. hypoleuca. Observed and expected heterozygosities ranged from 0.150 to 0.900 and from 0.375 to 0.894 in M. tanarius, and from 0.545 to 1.000 and from 0.434 to 0.870 in M. hypoleuca, respectively. Six of the 11 primer pairs successfully cross-amplified polymorphic polymerase chain reaction products in Macaranga winkleri.     

Hydraulic variability of tropical forests is largely independent of water availability

Tropical rainforest woody plants have been thought to have uniformly low resistance to hydraulic failure and to function near the edge of their hydraulic safety margin (HSM), making these ecosystems vulnerable to drought; however, this may not be the case. Using data collected at 30 tropical forest sites for three key traits associated with drought tolerance, we show that site-level hydraulic diversity of leaf turgor loss point, resistance to embolism (P₅₀), and HSMs is high across tropical forests and largely independent of water availability. Species with high HSMs (>1 MPa) and low P₅₀ values (< −2 MPa) are common across the wet and dry tropics. This high site-level hydraulic diversity, largely decoupled from water stress, could influence which species are favoured and become dominant under a drying climate. High hydraulic diversity could also make these ecosystems more resilient to variable rainfall regimes.     

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high‐copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost‐effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under‐studied groups.     

Tropical rain forest conservation and the twin challenges of diversity and rarity

Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.     

Characterization of phytoplankton assemblages in a tropical coastal environment using Kohonen self‐organizing map

This study was aimed at understanding the main abiotic environmental factors controlling the distribution patterns of abundance and composition of phytoplankton (size less than 10 μm) assemblages in the coastal waters of south‐eastern Côte d'Ivoire. Data were collected during two cruises, in January (low‐water period) and October (high‐water period) of 2014. A total of 67 species were identified and assigned to Bacillariophyceae (49%), Cyanophyceae (21%), Chlorophyceae (13%), Euglenophyceae (10%), Dinophyceae (4%) and Chrysophyceae (3%). Three biotic zones (I, IIA and IIB) were distinguishable on a Kohonen self‐organizing map after an unsupervised learning process. The diatom genera Eunotia sp., Navicula sp. and Actinoptychus senarius are significantly associated with I, IIA and IIB biotic zones, respectively. A clear seasonal cum salinity trend was apparent in phytoplankton distribution patterns. Turbidity and nitrate levels were the main abiotic factors controlling phytoplankton distribution in I, the upland tidal regions of the lagoon. In regions along the lagoon–sea continuum, phosphate and turbidity exert the most control during the low‐water season (IIA), while total dissolved solids control phytoplankton distribution during the high‐water season (IIB). These are climate‐sensitive parameters whose concentrations depend on prevailing hydroclimatic processes. Therefore, seasonality can have important consequences on phytoplankton community and inadvertently the productivity of these systems.     

A preliminary assessment of large mammal and bird use of different habitats in Bwindi Impenetrable National Park

Understanding species distributions, habitat requirements, and population trends is helpful for implementing effective conservation. But expense often prevents such evaluations. Here, we present a preliminary assessment for a low‐cost method – road‐side observations – to see how effective it can be. The bamboo zone of Bwindi Impenetrable National Park is restricted, covering 0.3% of park area yet is poorly known. Our study evaluates the use of the bamboo zone and surrounding forest by species of large mammals and large ground birds. Data were collected while driving a road section running through this zone. During 416 trips, seven species of mammal and one bird were recorded. Distributions for most species were significantly nonrandom in both space (P < 0.02) and time (Hour of day: P < 0.040; Month: P < 0.0001) for all species but black‐fronted duikers and blue monkeys for which 0.085 > P > 0.050 for month. Of the species observed, francolins were more frequently seen in the zone of visible bamboo than the nonbamboo zone (P = 0.002). Black‐and‐white colobus, L’Hoest’s monkey, and jackals were more common in nonbamboo forest (P ≤ 0.05). Road sightings have potential for low‐cost habitat use assessments and monitoring.     

Zooplankton abundance and transport in a tropical white-water river

Zooplankton abundance and transport were studied in the Apure River of western Venuzuela over a 15-month period. Much of the lower portion of the drainage basin, which is an extensive savanna of low relief, is subject to seasonal flooding. Although more than 50 zooplankton species were recorded during the study, nine rotifer species accounted for more than 90% of total density (mean, 138 individuals · L^-1). Copepods were represented primarily by Mesocyclops decipiens. Most cladocerans were planktonic, but cladocerans were not abundant. Crustaceans comprised 46% of annual mean zooplankton biomass (1.9 gC·L^-1) but only 2% of zooplankton numbers. The annual transport of zooplankton biomass from the watershed was 29 300 kgC. Zooplankton abundance showed a strong, inverse relationship to discharge. Secondary branches (caños) of the braided channel appeared to be the primary source areas, but populations of some species also reproduced in the main channel at low water. As the river began to rise, caños were flushed and thus abruptly ceased to serve as source areas. Zooplankton transport fell sharply and remained low until the river inundated the floodplain. Secondary production in the floodplain was exported to the river as long as a connection existed. After drainage ceased from the floodplain, transport fell to very low levels until caños again became suitable habitat. Seasonal fluctuations in river level regulate the development of source areas suitable for zooplankton growth and control the export of plankton from the source areas. Plankton in the running waters reproduce only at low water.     

Disparity in Onset Timing and Frequency of Flowering and Fruiting Events in Two Bornean Peat‐Swamp Forests

The timing and frequency of flowering and fruiting events are key tropical forest characteristics that have substantial influence on fauna. Although our understanding of geographic variation in habitat‐wide timing and frequency of flowering and fruiting is advancing, corresponding information for individual tree species is limited. Thus, we compared climate and reproductive phenology of 16 tree species over 70 mo at two Bornean tropical peat‐swamp forest sites. We found significant inter‐site correlations in rainfall and temperature, and only small absolute temperature differences. In both sites, most species exhibited within‐site synchrony in flowering and fruiting onset. Broad‐scale flowering and fruiting onset frequency classifications showed high congruence between sites. Significant correlations in flowering and fruiting onset timing between sites were found for only 19 and 17 percent of the species, respectively. This remained the case when applying 1‐ and 2‐month lag periods for both sites, with neither site consistently lagging behind. Significant differences in the exact frequency of new flowering and fruiting events were detected for 44 and 58 percent of species, respectively, and no significant relationships between the onset timing synchrony and exact frequency of new reproductive events were found for either flowers or fruit. We conclude that inter‐site climatic and ecological similarities do not necessarily lead to high inter‐site synchrony in either onset timing or exact frequency of tree reproductive events. Potential reasons for this are discussed, as are the implications for understanding tropical forest ecology and improving forest restoration project seed collections.     

The ecology of Bactrocera tryoni (Diptera: Tephritidae): what do we know to assist pest management?

The distribution, systematics and ecology of Bactrocera tryoni, the Queensland fruit fly, are reviewed. Bactrocera tryoni is a member of the B. tryoni complex of species, which currently includes four named species, viz. B. tryoni ssp., B. neohumeralis, B. melas and B. aquilonis. The species status of B. melas and B. aquilonis is unclear (they may be junior synonyms of B. tryoni) and their validity, or otherwise, needs to be confirmed as a matter of urgency. While Queensland fruit fly is regarded as a tropical species, it cannot be assumed that its distribution will spread further south under climate change scenarios. Increasing aridity and hot dry summers, as well as more complex, indirect interactions resulting from elevated CO₂, make predicting the future distribution and abundance of B. tryoni difficult. The ecology of B. tryoni is reviewed with respect to current control approaches (with the exception of sterile insect technique (SIT) which is covered in a companion paper). We conclude that there are major gaps in the knowledge required to implement most noninsecticide‐based management approaches. Priority areas for future research include host–plant interactions, protein and cue‐lure foraging and use, spatial dynamics, development of new monitoring tools, investigating the use of natural enemies and better integration of fruit flies into general horticultural IPM systems.     

Reproductive biology of the smooth butterfly ray Gymnura micrura

This study provides the first detailed information on the reproductive biology of the smooth butterfly ray Gymnura micrura. A total of 905 individuals were sampled, 377 of which were used for the reproductive study. Juveniles accounted for 75% of the sample, but all life cycle stages were present in the study area. The disc width at which 50% were mature (W(D50) )was estimated at 269 and 405 mm for males and females, respectively. The W(D50V) (based on the onset of vitellogenesis) was estimated at 359 mm. Uterine fecundity (mean ±s.d. = 3·8 ± 1·3; range: 1-6) was positively correlated with female size. A 3564% gain in mean wet mass was observed from egg to full-term embryo in utero. Size at birth ranged from 135 to 175 mm W(D) (19·5 to 55·0 g), with a mean of 165·1 mm W(D) (43·3 g). The embryo sex ratio was not significantly different from 1:1. The ovaries of pregnant females were undergoing vitellogenesis during gestation, with females ready to ovulate soon after parturition. Gymnura micrura may have an asynchronous reproductive cycle, with females reproducing continuously throughout the year.     

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

Amazonian understory antbirds are thought to be relatively sedentary and to have limited dispersal ability; they avoid crossing forest gaps, and even narrow roads through a forest may limit their territories. However, most evidence for sedentariness in antbirds comes from field observations and plot‐based recapture of adult individuals, which do not provide evidence for lack of genetic dispersal, as this often occurs through juveniles. In this study, we used microsatellite markers and mitochondrial control‐region sequences to investigate contemporary and infer historical patterns of genetic diversity and structure of the Rufous‐throated Antbird (Gymnopithys rufigula) within and between two large reserves in central Amazonia. Analyses based on microsatellites suggested two genetically distinct populations and asymmetrical gene flow between them. Within a population, we found a lack of genetic spatial autocorrelation, suggesting that genotypes are randomly distributed and that G. rufigula may disperse longer distances than expected for antbirds. Analyses based on mitochondrial sequences did not recover two clear genetic clusters corresponding to the two reserves and indicated the whole population of the Rufous‐throated Antbird in the region has been expanding over the last 50,000 years. Historical migration rates were low and symmetrical between the two reserves, but we found evidence for a recent unilateral increase in gene flow. Recent differentiation between individuals of the two reserves and a unilateral increase in gene flow suggest that recent urban expansion and habitat loss may be driving changes and threatening populations of Rufous‐throated Antbird in central Amazonia. As ecological traits and behavioral characteristics affect patterns of gene flow, comparative studies of other species with different behavior and ecological requirements will be necessary to better understand patterns of genetic dispersal and effects of urban expansion on Amazonian understory antbirds.