Molecular phylogeny of Dipterocarpaceae in Indonesia based on chloroplast DNA

In order to construct a molecular phylogeny of Indonesian Dipterocarpoideae (Dipterocarpaceae), PCR-RFLP of the chloroplast regions rbcL, petB, psbA, psaA, and trnL-F was performed with seven restriction enzymes in 129 samples including 58 species from nine genera. In the strict consensus tree with Monotes kerstingii as outgroup Indonesian Dipterocarpaceae were divided into two major clades. One clade (bootstrap value=71) consisted of Upuna, Cotylelobium, Anisoptera, Vatica, Dipterocarpus (tribe Dipterocarpeae, bootstrap value=83) and Dryobalanops (tribe Shoreae, bootstrap value=99) in a basal position. The second clade consisted of Hopea, Parashorea, and Shorea (tribe Shoreae) with 95% bootstrap support. Tribe Dipterocarpeae is monophyletic, tribe Shoreae is polyphyletic since Dryobalanops is sister to tribe Dipterocarpeae. In the neighbour-joining tree the sister group position of Dryobalanops to tribe Dipterocarpeae is not supported by the bootstrap analysis. Alternatively, we used Upuna borneensis as outgroup. The effect of outgroup selection on tree topology, taxonomic classification and the interpretation of character evolution is discussed.     

The utility of leaf flavonoids as taxonomic markers for some Malaysian species of the tribe Shoreae (Dipterocarpaceae)

A flavonoid survey was carried out on 45 taxa from the genera Shorea, Hopea, Parashorea, Neobalanocarpus, and Dryobalanops of the tribe Shoreae in the Dipterocarpaceae. The study showed significant chemotaxonomic differences in leaf flavonoid aglycone patterns and the presence of tannins in these taxa. The flavonoid patterns are useful in the delimitation of some taxa. For example, the genus Parashorea is distinguished by the universal presence of kaempferol 3‐methyl ether, and the monotypic genus Neobalanocarpus is unique in not producing ellagic and gallo tannins. The presence of chalcones and flavone C‐glycosides supports the separation of the genus Hopea into two sections, section Dryobalanoides and section Hopea in Ashton's classification, which is based on the type of venation. The flavonoid distributions in this study show that they can be very useful for differentiating between the Balau group in the genus Shorea and some scaly barked Hopea species, particularly H. helferi (lintah bukit), H. nutans (giam), and H. ferrea (malut). © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 755–762.     

Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes

Dipterocarpaceae is the dominant family of Southeast Asia's climax tropical rain forest region, and it contains the region's most important commercial timber species. A molecular phylogeny of the Dipterocarpaceae subfamily Dipterocapoideae was constructed using restriction fragment length polymorphisms of polymerase chain reaction-amplified specific genes in chloroplast DNA. A total of 141 site changes were detected among ten genera and 30 species in 11 different genes: rbcL, psbA, psbD, rpoB, rpoC, petB, atpH, 16S, psaA, petA and trnK. Phylogenetic trees constructed by Wanger parsimony and neighbor-joining methods, using Upuna as the outgroup, displayed five monophytelic groups that included Upuna: HopeaShorea-Parashorea-Neobalanocarpus; Dryobalanops; Dipterocarpus; Anisoptera-Vatica-Cotylelobium; and Upuna. The phylogenetic trees clearly separate species with two different base chromosome numbers: the first group is x=7, and the other is x=11. The x=7 group is thought to be in a synapomorphic character state. Parashorea lucida is a sister to most Shorea species. Neobalanocarpus heimii and Hopea from a clade of a sister to two Shorea species, and Cotylelobium and Vatica are closely related species. Our conclusions agree with a phylogeny derived from wood anatomy data analysis, and with Symington's and Ashton's taxonomic classifications.The raw data of the PCR-RFLP analysis can be obtained from the authors     

Detecting invisible growth rings of trees in seasonally dry forests in Thailand: isotopic and wood anatomical approaches

We measured radial variation of carbon isotope composition and vessel traits in tree species in seasonally dry forests of Northeast Thailand to explore a more reliable and amenable method of tropical dendrochronology for trees that lack visually detectable and consistent growth rings. Six Dipterocarpaceae species (3 Shorea, 2 Dipterocarpus, and 1 Hopea species) with indistinct or irregular growth rings and teak (Tectona grandis), a species which forms distinct growth rings, were examined. The δ¹³C value variations in all species showed annual cyclicity. Dipterocarpaceae species usually marked the lowest values of δ¹³C in the middle of the growing season, whereas teak had the lowest values at nearly the end of the growing season. Since the growing season of the species examined almost corresponds to the rainy season in the study area, the δ¹³C variation was likely caused by the change in moisture availability. The different variation pattern of teak was attributable to its stronger dependence on ¹³C-enriched reserved material early in the growing season. Changes in tree vessel traits for all species examined also showed annual cyclicity. Dipterocarpaceae species showed significant correlation between δ¹³C values and vessel measurements. Vessel lumen (mean area, tangential and radial diameter, and proportion of total area) had a negative correlation, whereas vessel frequency showed a positive correlation. The correlations indicated that changes in vessel traits were caused by the seasonal variation of moisture available to the trees. Thus, we concluded that methods using wood anatomy, as well as δ¹³C, have great potential for use as tools in tropical dendrochronology within the context of seasonal climate.     

Phylogenetic Analysis of Dipterocarps Using Random Amplified Polymorphic DNA Markers

The phylogenetic relationships among 12 species belonging tothree different genera (Shorea, HopeaandAnisoptera) of Dipterocarpaceaewere studied using random amplified polymorphic DNA (RAPD) markers.A modified CTAB DNA extraction protocol was used to obtain tannin-and polysaccharide-free genomic DNA from mature leaves. Clusteranalysis of data from six random primers placed the 12 speciesin three groups corresponding to their respective genera. Fourdistinct nodes ofShoreaspp. and two ofHopeaspp. could be identified.Anisopteramegistocarpaserved as an outgroup, and was unique when comparedto the other genera examined. RAPD profiles of five individualsofH. odoratawith six random primers were identical, suggestingthat there is little intraspecific variation in this species.The RAPD technique can thus be successfully applied for thestudy of phylogenetic relationships of this important groupof tropical timber trees.Copyright 1998 Annals of Botany Company Dipterocarpaceae,Anisopteraspp.,Hopeaspp.,Shoreaspp., RAPD markers, tropical timber trees.     

Amino acids,polyamines and proteins during seed germination of two species of Dipterocarpaceae

Summary Amino acid, polyamine and protein concentrations in seeds and their evolution during seed germination of two dipterocarp species, Hopea odorata and Dipterocarpus alatus, were determined with the help of a multianalytical system. Glutamic acid and glutamine were the major amino compounds present. Hopea seeds also contain high levels of aspartic acid/asparagine, serine, threonine, arginine and alanine, while those of Dipterocarpus contain high levels of alanine, arginine and threonine. These species were quite different in their germination behavior and thus in their protein and amine metabolism rates. In Hopea, polyamines increased during the first 3 days of germination and reached a maximum by the 3rd day, 1 day before maximum germination rate. In Dipterocarpus polyamines reached their maximum at the 6th day while maximum germination rate is observed by the 7th day. This suggests that polyamine compounds could play a role in the early part of the germination process in Hopea and Dipterocarpus seeds. The possibility that control of polyamine biosynthesis could be used for the establishment of biochemical methods to improve seed storage and to control germination of these recalcitrant seeds is discussed.     

Responses of pre‐dispersal seed predators to sequential flowering of Dipterocarps in Malaysia

Many species of Dipterocarpaceae and other plant families reproduce synchronously at irregular, multi‐year intervals in Southeast Asian forests. These community‐wide general flowering events are thought to facilitate seed survival through satiation of generalist seed predators. During a general flowering event, closely related Shorea species (Dipterocarpaceae) stagger their flowering times by several weeks, which may minimize cross pollination and interspecific competition for pollinators. Generalist, pre‐dispersal seed predators might also track flowering hosts and influence predator satiation. We addressed the question of whether pre‐dispersal seed predation differed between early and late flowering Shorea species by monitoring flowering, fruiting and seed predation intensity over two general flowering events at the Pasoh Research Forest, Malaysia. Pre‐dispersal insect seed predators killed up to 63 percent of developing seeds, with Nanophyes shoreae, a weevil that feeds on immature seeds being the most important predator for all Shorea species. This weevil caused significantly greater pre‐dispersal seed predation in earlier flowering species. Long larval development time precluded oviposition by adults that emerged from the earliest flowering Shorea on the final flowering Shorea. In contrast, larvae of weevils that feed on mature seeds before seed dispersal (Alcidodes spp.), appeared in seeds of all Shorea species almost simultaneously. We conclude that general flowering events have the potential to satiate post‐dispersal seed predators and pre‐dispersal seed predators of mature fruit, but are less effective at satiating pre‐dispersal predators of immature fruit attacking early flowering species.     

The effect of shade on leaf structure and physiology of tree seedlings from a mixed dipterocarp forest

This study builds upon past work investigating seedling leaf physiology and structure among tropical trees. We seek to explain how related and unrelated species and genera co‐occur in relation to varying amounts of shade. Seedlings of eight Sri Lankan rain forest tree species in three genera (Dipterocarpus, Mesua, Shorea section Doona) were grown for 2 years in four treatments that simulated a variety of shade environments across the understorey of a rain forest. All three genera comprise major canopy tree species of mixed dipterocarp forest, a widespread and important Asian tropical forest type. Compared with the other genera, Dipterocarpus spp. had the largest leaves, the thinnest leaf blades and relatively high rates of stomatal conductivity across all shade treatments, making them water‐loving species sensitive to droughty soils. Mesua spp. had intermediate sized leaves, with the thickest leaf blades and palisade mesophyll layers, the highest stomatal densities, the smallest aperture sizes and the lowest rates of stomatal conductance, making them the most water conservative. Shorea spp. were generally intermediate in blade and palisade mesophyll dimensions between Dipterocarpus spp. and Mesua spp., but they had the smallest leaves. Greater differences among genera than among species within genera were apparent, but species differences within genera were also apparent. Differences among genera and species conform to their known successional status and topographical affinities and provide a more comprehensive understanding of species site adaptation. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 332–343.     

How does light and phosphorus fertilisation affect the growth and ectomycorrhizal community of two contrasting dipterocarp species?

Phosphorus concentrations in many south-east Asian tropical rain forest soils are very low. To determine the growth responses of seedlings of a light-demanding (Shorea leprosula) and a more shade-tolerant (Hopea nervosa) dipterocarp species to increasing P, we carried out a nursery fertilisation experiment. Responses of symbiotic ectomycorrhizal (EcM) fungi to the treatments were also determined. Seedlings were grown under high light (13 mol m⁻² d⁻¹) or moderate light (4 mol m⁻² d⁻¹) in shade-chambers and were fertilised with a solution containing 0, 1, 10 or 100 mg L⁻¹ P. The growth of Hopea and Shorea showed different responses to the light and P fertilisation treatments with Hopea having greater growth under moderate light conditions and Shorea having greater growth under high light conditions. Shorea responded to P fertilisation by increasing its foliar P concentrations and growth rates, whereas Hopea did not take up additional P and did not improve its growth rates. There was no effect of either light or P fertilisation on total EcM colonisation or EcM diversity, but around half of the EcM morphotypes observed were affected by one of these two abiotic perturbations, most notably for Riessiella sp. which increased with P fertilisation suggesting it may not be a mutualistic fungus. These results show how niche partitioning in both dipterocarp seedlings and EcM fungi can be divided along contrasting axes.     

Morphological and molecular evidence of natural hybridization in Shorea (Dipterocarpaceae)

Shorea (Dipterocarpaceae) is a large genus in which many closely related species often grow together in Southeast Asian lowland tropical rain forests. Many Shorea species share common pollinators, and earlier studies suggested occurrence of interspecific hybridization and introgression. Here, we show morphological and molecular evidence of hybridization between Shorea species. In the census of all the trees of Shorea curtisii, Shorea leprosula, and Shorea parvifolia (>30 cm dbh) within the 164-ha area of Bukit Timah Nature Reserve in Singapore, we found 21 morphologically recognizable hybrid individuals. All of the putative hybrids could be distinguished obviously from the parental species on the basis of vegetative characters. Population genetic analysis of DNA sequences of two nuclear (GapC and PgiC) and chloroplast (trnL-trnF) regions demonstrated that each of the three species had several species-specific mutations. The nuclear sequences of the putative hybrids were heterozygote at all the species-specific sites between two parental species. Hybrid between S. curtisii and S. leprosula was found most, while S. curtisii × S. parvifolia and S. leprosula × S. parvifolia hybrids were also found. Almost no shared polymorphism between populations of the parental species suggests rarity of introgression. The study indicated that natural hybridization between sympatric Shorea species should not be uncommon, but all of the hybrid individuals were F₁, and the post-F₁ hybrids were considerably rare.     

Structure and dynamics in seasonal dry evergreen forest in northeastern Thailand

Abstract. Studies of tropical forest dynamics have often been based on one large-scale permanent plot, representative of a given forest type. Broad classifications of tropical forest types are expected to include a wide range of stand structures, dynamics patterns and species compositions – a range which cannot be represented in a single plot. To demonstrate this problem two 1-ha permanent plots, dominated by Hopea ferrea and Shorea henryana (both Dipterocarpaceae), respectively, were established in 1987 in seasonal dry evergreen forest at the Sakaerat Environmental Research Station in northeastern Thailand. In 1997 the plots were remeasured as to patterns of recruitment, mortality and growth. The Hopea plot was relatively static with low mortality, recruitment and growth. The Shorea plot was very dynamic with high rates of growth, mortality and recruitment. If the current trends continue, the plots are likely to further diverge. Even if the study of a large forest plot provides a good insight into tropical forest dynamics, it is necessary to consider the entire local pattern of variation.     

Sources of Canopy Chemical and Spectral Diversity in Lowland Bornean Forest

Sources of variation among the chemical and spectral properties of tropical forest canopies are poorly understood, yet chemical traits reveal potential ecosystem and phylogenetic controls, and spectral linkages to chemical traits are needed for remote sensing of functional and biological diversity. We analyzed 21 leaf traits in 395 fully sunlit canopies, representing 232 species and multiple growth forms, in a lowland mixed dipterocarp forest of Sarawak, Malaysia. Leaf traits related to light capture and growth (for example, photosynthetic pigments, nutrients) were up to 55% lower, and defense traits (for example, phenols, lignin) were 15–40% higher, in the dominant family Dipterocarpaceae and in its genus Shorea, as compared to all other canopy species. The chemical variation within Dipterocarpaceae and Shorea was equivalent to that of all other canopy species combined, highlighting the role that a single phylogenetic branch can play in creating canopy chemical diversity. Seventeen of 21 traits had more than 50% of their variation explained by taxonomic grouping, and at least 16 traits show a connection to remotely sensed spectroscopic signatures (RMSE < 15%). It is through these chemical-to-spectral linkages that studies of functional and biological diversity interactions become possible at larger spatial scales, thereby improving our understanding of the role of species in tropical forest ecosystem dynamics.     

Borneo Illipe,a fat product from differentShorea spp. (Dipterocarpaceae)

Fat extracted from kernels of Shorea spp. (Dipterocarpaceae) in the tropical rainforests of Borneo and Sumatra are traded under the name Borneo Illipe. The fat is used in chocolate formulations. The majority of kernels collected are fromShorea species in the sectionPachycarpae. Fat characteristics ofShorea species in this section show differences in fat quality in relation to its use as exotic sources in Cocoa Butter Equivalent (CBE) formulations. In order to comment on the future potential of the naturally occurring tree populations distribution maps of fiveShorea spp. involved in Borneo Illipe utilization are presented.     

Molecular phylogeny of the Cyathocotylidae (Digenea,Diplostomoidea) necessitates systematic changes and reveals a history of host and environment switches

The Cyathocotylidae is a globally distributed family of digeneans parasitic as adults in fish, reptiles, birds and mammals in both freshwater and marine environments. Molecular phylogenetic analysis of interrelationships among cyathocotylids is lacking with only a few species included in previous studies. We used sequences of the nuclear 28S rRNA gene to examine phylogenetic affinities of 11 newly sequenced taxa of cyathocotylids and the closely related family Brauninidae collected from fish, reptiles, birds and dolphins from Australia, Southeast Asia, Europe, North America and South America. This is the first study to provide sequence data from adult cyathocotylids parasitic in fish and reptiles. Our analyses demonstrated that the members of the genus Braunina (family Brauninidae) belong to the Cyathocotylidae, placing the Brauninidae into synonymy with the Cyathocotylidae. In addition, our DNA sequences supported the presence of a second species in the currently monotypic Braunina. Our phylogeny revealed that Cyathocotyle spp. from crocodilians belong to a separate genus (Suchocyathocotyle, previously proposed as a subgenus) and subfamily (Suchocyathocotylinae subfam. n.). Morphological study of Gogatea serpentum indicum supported its elevation to species as Gogatea mehri. The phylogeny did not support Holostephanoides within the subfamily Cyathocotylinae; instead, Holostephanoides formed a strongly supported clade with members of the subfamily Szidatiinae (Gogatea and Neogogatea). Therefore, we transfer Holostephanoides into the Szidatiinae. DNA sequence data revealed the potential presence of cryptic species reported under the name Mesostephanus microbursa. Our phylogeny indicated at least two major host switching events in the evolutionary history of the subfamily Szidatiinae which likely resulted in the transition of these parasites from birds to fish and snakes. Likewise, the transition to dolphins by Braunina represents another major host switching event among the Cyathocotylidae. In addition, our phylogeny revealed more than a single transition between freshwater and marine environments demonstrated in our dataset by Braunina and some Mesostephanus.     

Molecular phylogeny of Potamotrygonocotyle (Monogenea,Monocotylidae) challenges the validity of some of its species

Fehlauer‐Ale, K. H. & Littlewood, D. T. J. (2011). Molecular phylogeny of Potamotrygonocotyle (Monogenea, Monocotylidae) challenges the validity of some of its species. —Zoologica Scripta, 40, 638–658. The marine‐derived stingrays Potamotrygonidae are the only chondrichthyans landlocked to freshwaters of Central and South America. The family includes approximately 22 described species organized in four genera widely distributed across the main Atlantic and Caribbean continental drainages. Investigations into the parasite fauna of potamotrygonids have mainly focused on cestodes, with a few studies addressing the biodiversity of monogeneans. Potamotrygonocotyle (Monogenea, Monocotylidae) is composed of 12 species, exclusively found in the gills of species of Potamotrygonidae. This study presents molecular phylogenetic analyses of this group of monogeneans distributed throughout La Plata and Amazonas basins, with the purpose of readdressing the phylogeny of Monocotylidae based on 28S rDNA sequences and of unravelling the phylogeny of its species using data from mitochondrial gene cytochrome c oxidase subunit I and nuclear gene internal transcribed spacer 1. The phylogenetic status of the five tested monocotylid subfamilies and most of their internal relationships are concordant with the results of a previous study, and the monophyletic status of Potamotrygonocotyle based on molecular data is corroborated for the first time. However, the placement of the genus within Monocotylidae is not resolved, as its sister‐group relationship with Neoheterocotyle and Troglocephalus is uncertain. Investigations into the relationships within Potamotrygonocotyle support the monophyletic status of nine nominal species and suggest the existence of cryptic lineages for the remaining three. Molecular analyses reveal distinct sister‐groups relationships in comparison with a previously published phylogeny for the genus based on morphological data. Finally, the surveys of this study expand the known distribution range of some members of Potamotrygonocotyle.     

Survivorship and growth of seedlings of four dipterocarp species in a tropical rainforest of Sarawak,East Malaysia

Survivorship and growth of seedlings of four dipterocarp species (Dipterocarpus actangulus, D. globosus, Dryobalanops aromatica, Dryobalanops lanceolata) were studied for 2.5 years in a mixed dipterocarp forest in Sarawak, East Malaysia. Predispersal seed predation rates were larger forD. globosus (75%) thanD. lanceolata (27–34%) andD. aromatica (18–26%). Less than 20% of the twoDryobalanops seeds were damaged by vertebrates after seed dispersal. During the period from seed dispersal to the time when the seedlings had shed cotyledons, more dispersed seeds died in the twoDipterocarpus (ca 90%) than the twoDryobalanops (ca 60–70%). The major mortality factors during this period were uprooted and seed/seedling predation by insects or vertebrates. After the seedlings shed cotyledons, all species showed constant mortality rates of 34, 15–16, 17 and 6%/year forD. actangulus, D. lanceolata, D. aromatica andD. globosus, respectively, in the forest understorey. Mortality was lower in less shaded conditions than in more shaded ones forD. aromatica andD. actangulus, but not significantly different forD. lanceolata andD. globosus. A majority of dead seedlings were killed by fallen branches or were found standing with wilted leaves, probably due to water stress. No significant correlation was found between seed/seedling mortality and distance from mother trees or the initial density of seeds/seedings for all species. The mean leaf production was positively correlated with the estimated diffuse light factor of their habitats for each species.     

Molecular phylogeny of Central and South American slider turtles: implications for biogeography and systematics (Testudines: Emydidae: Trachemys)

We analyse phylogeny, systematics and biogeography of slider turtles (Trachemys spp.) using sequence data of four mitochondrial genes (3242 bp) and five nuclear loci (3396 bp) of most South American and southern Central American taxa and representatives of northern Central American, West Indian and North American slider species (16 species and subspecies) and allied North American species (genera Chrysemys, Deirochelys, Graptemys, Malaclemys, Pseudemys). By applying maximum likelihood, relaxed molecular clock and ancestral range analyses, we provide evidence for two successive colonizations of South America by slider turtles. In addition, we show that the current species delineation of Central and South American slider turtles is incorrect. Our data suggest that Trachemys grayi is a distinct polytypic species that embraces, besides the nominotypical subspecies, T. g. emolli and T. g. panamensis. Trachemys ornata is also polytypic with the subspecies T. o. ornata, T. o. callirostris, T. o. cataspila, T. o. chichiriviche and T. o. venusta. Moreover, T. adiutrix should be regarded as a subspecies of T. dorbigni. All studied Trachemys species are inferred to have originated in the Late Miocene to Early Pliocene. The ancestor of the two subspecies of T. dorbigni colonized South America most probably prior to the establishment of the land bridge connecting Central and South America, whereas the two South American subspecies of T. ornata represent a younger independent immigration wave from Central America.     

THE EVOLUTION OF DIAPAUSE IN THE KILLIFISH FAMILY RIVULIDAE (ATHERINOMORPHA,CYPRINODONTIFORMES): A MOLECULAR PHYLOGENETIC AND BIOGEOGRAPHIC PERSPECTIVE

Phylogenetic relationships within the family Rivulidae (order Cyprinodontiformes) are investigated using 1972 aligned base pairs of mitochondrial DNA (mtDNA) for samples representing 66 species. Genes analyzed include those encoding the 12S ribosomal RNA; transfer RNAs for valine, glutamine, methionine, tryptophan, alanine, asparagine, cysteine, and tyrosine; complete NADH dehydrogenase subunit II; and part of cytochrome oxidase I. Parsimony analysis of the aligned mtDNA sequences results in a single most parsimonious tree. The phylogeny reveals two independent origins of developmental diapause within the family Rivulidae. It is unlikely that diapause evolved de novo in each group, suggesting that the presence or absence of diapause is the result of developmental switches between alternative stabilized pathways. Phylogeny of the family Rivulidae shows high concordance with predictions derived from the geological history of South America and Central America. Basal lineages in the rivulid phylogeny are distributed primarily on geologically old areas, whereas more nested lineages occur in geologically younger areas. However, there is little concordance between the molecular phylogeny and currently available morphological hypotheses and existing taxonomies. Based on the mtDNA phylogeny, the genera Pterolebias, Rivulus, Pituna, and Plesiolebias are considered nonmonophyletic and warrant taxonomic reassessment.