[Show abstract][Hide abstract] ABSTRACT: Tropical forest ecosystems are threatened by habitat conversion and other anthropogenic actions. Timber production forests can augment the conservation value of primary forest reserves, but studies of logging effects often yield contradictory findings and thus inhibit efforts to develop clear conservation strategies. We hypothesized that much of this variability reflects a common methodological flaw, simple pseudoreplication, that confounds logging effects with preexisting spatial variation. We reviewed recent studies of the effects of logging on biodiversity in tropical forests (n = 77) and found that 68% were definitively pseudoreplicated while only 7% were definitively free of pseudoreplication. The remaining proportion could not be clearly categorized. In addition, we collected compositional data on 7 taxa in 24 primary forest research plots and systematically analyzed subsets of these plots to calculate the probability that a pseudoreplicated comparison would incorrectly identify a treatment effect. Rates of false inference (i.e., the spurious detection of a treatment effect) were >0.5 for 2 taxa, 0.3-0.5 for 2 taxa, and <0.3 for 3 taxa. Our findings demonstrate that tropical conservation strategies are being informed by a body of literature that is rife with unwarranted inferences. Addressing pseudoreplication is essential for accurately assessing biodiversity in logged forests, identifying the relative merits of specific management practices and landscape configurations, and effectively balancing conservation with timber production in tropical forests.
Full-text · Article · Jan 2013 · Conservation Biology
[Show abstract][Hide abstract] ABSTRACT: Background/Question/Methods
In the past decade our capacity to assess the taxonomic, functional, and genetic dimensions of microbial biodiversity has exploded with the increasing availability of molecular data. Access to techniques such as environmental microarrays, metagenomics, transcriptomics, and proteomics has expanded the breadth of datasets from primarily taxonomic markers (e.g. 16S, 18S, ITS) to include information about the genetic and functional dimensions of biodiversity. As these methods become widely available and less expensive, massive amounts of data are being collected with far deeper sampling. We address how these new data can be used to quantitatively compare biodiversity patterns across the domains of life, between ecosystems, and among the taxonomic, genetic and functional dimensions of biodiversity.
The meta-analyses we present use diverse datasets previously generated by the authors and include bacterial, archaeal, fungal, and viral molecular data from a variety of ecosystems. Data were collected at various temporal and spatial scales from the terrestrial subsurface, cyanobacterial mats, a hypersaline lake, acid mine drainage, and surface soil using a range of molecular methods and study designs. We analyzed and compared the microbial diversity in these heterogeneous samples using a combination of traditional diversity indices, phylogenetic indices, diversity profiles and gene networks.
We have found that the use of metrics that incorporate multiple types of information (similarity, evolutionary history, abundance) are best suited for comparing disparate data and providing meaningful ecological information independent of the goals of particular studies. For example, incorporating similarity (e.g. molecular homology) to build gene networks and diversity profiles avoids the issue of which similarity threshold should be used to delineate species or other taxonomic levels, and facilitates the incorporation of evolutionary history into analyses. These methods have also provided a more informative view of how community composition and diversity changes with concurrent environmental changes or disturbance. Analyzing the topology of gene networks allows us to compare different dimensions of biodiversity to better elucidate the relationships between functional, genetic, and taxonomic diversity. Diversity profiles in particular, show promise for comparing biological entities across the domains of life, provided similarity is defined on relevant scales. Given that the amount of molecular data being submitted to open-access databases is increasing exponentially, our results will help guide efforts to synthesize these large and complex datasets.
[Show abstract][Hide abstract] ABSTRACT: Background/Question/Methods
Ecosystems worldwide are experiencing elevated extinction rates, and tropical forest species are especially threatened as a result of rapid and widespread habitat loss. Primary forests generally support the highest levels of biodiversity, but tropical timber production forests, which account for the majority of the remaining natural forest area protected from conversion, can augment the conservation value of primary forest reserves. However, studies of logging effects often yield contradictory findings, fostering vigorous debate and frustrating efforts to develop clear conservation strategies. Here, we assess the extent to which this variation may be due to simple pseudoreplication (i.e., the confounding of treatment effects with pre-existing differences between treated and untreated areas). First, we conducted a literature review to determine the proportion of recent peer-reviewed tropical logging-effects studies that suffer from this problem (N=78). Second, we asked: If one part of a primary forest had been logged, and if this treatment had no effect on species composition, what is the probability that a pseudoreplicated comparison of logged and unlogged areas would incorrectly infer logging effects? We addressed this question with field data for seven taxa (trees, ants, dung beetles, moths, stingless bees, bats, and birds), collected from a primary forest in Peninsular Malaysia.
We found that 54 papers (69%) were definitively guilty of simple pseudoreplication with regard to logging effects, 19 papers (24%) could not be definitively categorized, and only five studies (6%) were definitively free of simple pseudoreplication. Via our analyses of field data, we found that the probability of falsely inferring a treatment effect was > 0.2 for five taxa, > 0.3 for four taxa, > 0.4 for three taxa, and > 0.5 for two taxa. These results were consistent regardless of whether species composition was analyzed as presence-absence or abundance data. We also found that rates of false inference can exceed 0.40 when the correlation between physical distance and compositional distance is non-significant, and can exceed 0.25 even when there is an inverse correlation. Our findings demonstrate that tropical conservation strategies are being informed by a body of literature that is rife with unwarranted inferences, and suggest that tropical forest ecologists need to place greater emphasis on true replication. Confronting pseudoreplication is essential for accurately assessing biodiversity in logged forests, identifying the relative merits of specific management practices and landscape configurations, and effectively balancing conservation with timber production in tropical forest landscapes.
[Show abstract][Hide abstract] ABSTRACT: The diversity of stingless bees throughout Peninsular Malaysia is poorly documented. With regards to conservation efforts, this means that despite their known ecological value and sensitivity to disturbance, stingless bees cannot currently be used as indicators to compare the health of undisturbed forests to that of human-altered landscapes in Peninsular Malaysia. We undertook an extensive survey of stingless bee diversity in and around six lowland, hill, and upper hill dipterocarp forest reserves located in four different states in Peninsular Malaysia. Sugar-water baiting at 486 sampling stations resulted in the collection of stingless bees from 17 different species. We used an NMDS ordination to compare the communities found at the different sites. We also compared the species we collected to those recorded by previous studies carried out in nearby Borneo. Our fi ndings provide baseline data on stingless bee diversity in forests throughout Peninsular Malaysia.
Full-text · Article · Feb 2012 · The Raffles bulletin of zoology
[Show abstract][Hide abstract] ABSTRACT: Studies of ant diversity provide valuable insights into the health and functioning of forest ecosystems, but ants are surveyed infrequently in many tropical forest ecosystems. The majority of lowland forests in Peninsular Malaysia was cleared for land development in the 1970s and 1980s, leaving upper hill dipterocarp forests as almost all remaining contiguous, primary forests in Peninsular Malaysia. The ant communities of these forests have not previously been documented. Our extensive survey of a 200 ha upper hill dipterocarp forest site in Temengor Forest Reserve captured 10,307 individual ants, representing 211 species from 60 genera and nine subfamilies. Myrmicinae was the most common ant subfamily censused, with Pheidole recorded as the most speciose genera (40 species) followed by Polyrhachis (19 species) and Camponotus (13 species). Generalised Myrmicinae was the most diverse functional group, followed by Cryptic Species, Subordinate Camponotini and Tropical Climate Specialists. Seven undetermined specimens of possibly new species were recorded, suggesting that the upper hill dipterocarp forest of Temengor Forest Reserve is home to numerous ant species that have not been documented before. Our fi ndings can be utilised to better understand the ant community composition and function of primary upper hill dipterocarp forests in Peninsular Malaysia as compared to other dipterocarp forests. Our results can also serve as a baseline to understand post-disturbance changes to ant community composition and functional diversity.
Full-text · Article · Aug 2011 · The Raffles bulletin of zoology
[Show abstract][Hide abstract] ABSTRACT: Fused genes are important sources of data for studies of evolution and protein function. To date no service has been made available online to aid in the large-scale identification of fused genes in sequenced genomes. We have developed a program, Gene deFuser, that analyzes uploaded protein sequence files for characteristics of gene fusion events and presents the results in a convenient web interface.
To test the ability of this software to detect fusions on a genome-wide scale, we analyzed the 24,725 gene models predicted for the ciliated protozoan Tetrahymena thermophila. Gene deFuser detected members of eight of the nine families of gene fusions known or predicted in this species and identified nineteen new families of fused genes, each containing between one and twelve members. In addition to these genuine fusions, Gene deFuser also detected a particular type of gene misannotation, in which two independent genes were predicted as a single transcript by gene annotation tools. Twenty-nine of the artifacts detected by Gene deFuser in the initial annotation have been corrected in subsequent versions, with a total of 25 annotation artifacts (about 1/3 of the total fusions identified) remaining in the most recent annotation.
The newly identified Tetrahymena fusions belong to classes of genes involved in processes such as phospholipid synthesis, nuclear export, and surface antigen generation. These results highlight the potential of Gene deFuser to reveal a large number of novel fused genes in evolutionarily isolated organisms. Gene deFuser may also prove useful as an ancillary tool for detecting fusion artifacts during gene model annotation.
[Show abstract][Hide abstract] ABSTRACT: The methionine salvage pathway is responsible for regenerating methionine from its derivative, methylthioadenosine. The complete set of enzymes of the methionine pathway has been previously described in bacteria. Despite its importance, the pathway has only been fully described in one eukaryotic organism, yeast. Here we use a computational approach to identify the enzymes of the methionine salvage pathway in another eukaryote, Tetrahymena thermophila. In this organism, the pathway has two fused genes, MTNAK and MTNBD. Each of these fusions involves two different genes whose products catalyze two different single steps of the pathway in other organisms. One of the fusion proteins, mtnBD, is formed by enzymes that catalyze non-consecutive steps in the pathway, mtnB and mtnD. Interestingly the gene that codes for the intervening enzyme in the pathway, mtnC, is missing from the genome of Tetrahymena. We used complementation tests in yeast to show that the fusion of mtnB and mtnD from Tetrahymena is able to do in one step what yeast does in three, since it can rescue yeast knockouts of mtnB, mtnC, or mtnD. Fusion genes have proved to be very useful in aiding phylogenetic reconstructions and in the functional characterization of genes. Our results highlight another characteristic of fusion proteins, namely that these proteins can serve as biochemical shortcuts, allowing organisms to completely bypass steps in biochemical pathways.
[Show abstract][Hide abstract] ABSTRACT: We used the recently sequenced genomes of the ciliates Tetrahymena thermophila and Paramecium tetraurelia to analyze the codon usage patterns in both organisms; we have analyzed codon usage bias, Gln codon usage, GC content and the nucleotide contexts of initiation and termination codons in Tetrahymena and Paramecium. We also studied how these trends change along the length of the genes and in a subset of highly expressed genes. Our results corroborate some of the trends previously described in Tetrahymena, but also negate some specific observations. In both genomes we found a strong bias toward codons with low GC content; however, in highly expressed genes this bias is smaller and codons ending in GC tend to be more frequent. We also found that codon bias increases along gene segments and in highly expressed genes and that the context surrounding initiation and termination codons are always AT rich. Our results also suggest differences in the efficiency of translation of the reassigned stop codons between the two species and between the reassigned codons. Finally, we discuss some of the possible causes for such translational efficiency differences.
[Show abstract][Hide abstract] ABSTRACT: The genetic code is degenerate, i.e. some amino acids are coded for by more than one codon. Although coding for the same amino acid, synonymous codons are not equally used in different genomes, and even in a single genome the synonymous codon usage can vary widely among genes, or even along the gene sequences. With the recent advent of full genome sequences we are starting to unravel the reasons for these deviations. In this review we will cover some of the proposed factors that might cause different codon usage bias and the selective forces influencing it.
Preview · Article · Jan 2008 · Journal of the Brazilian Chemical Society