Fragmentation genetics in tropical ecosystems: from fragmentation genetics to fragmentation genomics

Tropical regions are experiencing unprecedented economic and population growth. This goes hand in hand with increase habitat fragmentation of tropical ecosystems. Understanding the genetic consequences of these spatial and temporal changes across landscapes is critical to conservation of the vast majority of global biodiversity. This virtual issue of Conservation Genetics, presents six empirical and one review paper showcasing fascinating and important findings with regard to how habitat fragmentation impacts on genetic diversity in rare or endangered tropical species. The message from these papers is clear, fragmentation has a number of serious genetic consequences, which can contribute to undermining the viability of species in fragmented landscapes. Conservation genetics provides a powerful tool to inform both conservation and management of species and genetic resources. But, careful consideration is needed to ensure studies apply appropriate sampling designs and genetic analysis to better test hypothesis. Next generation genomics offers great opportunities to provide even more answers and greater resolution of the consequences for adaptive genetic variation, to ensure future tropical landscapes are resilient.     

Evaluating contemporary pollen dispersal in two common grassland species Ranunculus bulbosus L. (Ranunculaceae) and Trifolium montanum L. (Fabaceae) using an experimental approach

Pollen flow is a key biological process that connects plant populations, preventing genetic impoverishment and inbreeding. Pollen‐mediated long‐distance dispersal (LDD) events are especially important for plant species in increasingly fragmented landscapes. Patterns of pollen dispersal were directly estimated and dispersal kernels modelled in an experimental population of Ranunculus bulbosus and Trifolium montanum to determine the potential for LDD. Eight and 11 microsatellite markers were used for R. bulbosus and T. montanum, respectively, to run a likelihood‐based paternity analysis on randomly chosen offspring (N_total = 180 per species) from five maternal plants. High rates of selfing were found in R. bulbosus (average 45.7%), while no selfing was observed in T. montanum. The majority (60%) of mating events occurred at very short distances: the median of the observed dispersal distances was 0.8 m in both species, and the average distances were 15.9 and 10.3 m in R. bulbosus and T. montanum, respectively. Modelling the pollen dispersal kernel with four different distribution functions (exponential‐power, geometric, 2Dt and Weibull) indicated that the best fit for both species was given by a Weibull function. Yet, the tail of the T. montanum pollen dispersal kernel was thinner than in R. bulbosus, suggesting that the probability for LDD is higher in the latter species. Even though the majority of pollen dispersal occurred across short distances, the detection of several mating events up to 362 m (R. bulbosus) and 324 m (T. montanum) suggests that pollen flow may be sufficient to ensure population connectivity in these herb species across fragmented grasslands in Swiss agricultural landscapes.     

Spatial phylogenetics of the native woody plant species in Hainan,China

To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.     

A network-based approach to classify the three domains of life

Background

Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements.

Results

We analyzed 7080 genes (five groups of 1416 orthologs each) from Rhizobiales species (S. meliloti, R. etli, and M. loti, plant symbionts; A. tumefaciens, a plant pathogen; and B. melitensis, an animal pathogen). We evaluated their phylogenetic relationships and observed three main topologies. The first, with closer association of R. etli to A. tumefaciens; the second with R. etli closer to S. meliloti; and the third with A. tumefaciens and S. meliloti as the closest pair. This was not unusual, given the close relatedness of these three species. We calculated the synonymous (dS) and nonsynonymous (dN) substitution rates of these orthologs, and found that informational and metabolic functions showed relatively low dN rates; in contrast, genes from hypothetical functions and cellular processes showed high dN rates. An alternative measure of sequence variability, percentage of changes by species, was used to evaluate the most specific proportion of amino acid residues from alignments. When dN was compared with that measure a high correlation was obtained, revealing that much of evolutive information was extracted with the percentage of changes by species at the amino acid level. By analyzing the sequence variability of orthologs with a set of five properties (polarity, electrostatic charge, formation of secondary structures, molecular volume, and amino acid composition), we found that physico-chemical characteristics of proteins correlated with specific functional roles, and association of species did not follow their typical phylogeny, probably reflecting more adaptation to their life styles and niche preferences. In addition, orthologs with low dN rates had residues with more positive values of polarity, volume and electrostatic charge.

Conclusions

These findings revealed that even when orthologs perform the same function in each genomic background, their sequences reveal important evolutionary tendencies and differences related to adaptation. This article was reviewed by: Dr. Purificación López-García, Prof. Jeffrey Townsend (nominated by Dr. J. Peter Gogarten), and Ms. Olga Kamneva.     

Hochstetter's frog (Leiopelma hochstetteri) egg,mobile larvae and froglet development

Egg strings and larvae of Hochstetter's frog (Leiopelma hochstetteri) were located at three widely separated North Island sites: in seeps at Brynderwyns in December 2004, in an open pool at Wharerino in March 2009, and in an underground pool near the Kaipawa Track, Coromandel, in late May 2009. Ten egg strings were also laid by captive frogs in water courses at Hamilton Zoo in April 2009. All egg strings held from 11 to 13 eggs. The egg strings laid in the Brynderwyns were regularly observed until metamorphosis was completed in March 2005. Twenty-four swimming larvae emerged from 25 capsules at c. 40 days after discovery, and at least 14 froglets were produced at c. 90 days. All of them developed in darkness, in a 120 ml pool <30 mm deep. The emerged froglets ranged from 9.8 to 10.8 mm snout-vent length. The detection of eggs, larvae and <11 mm froglets indicates that the egg laying period is at least from late September to May.     

BOOK REVIEWS

Psychoacoustic laboratory studies with live dolphins require considerable resources and are essential for assessing the validity of our models. Computerized numerical modelling methods are a reasonable approach to simulate the vibroacoustic functions of the dolphin biosonar apparatus. In order to validate this approach, we chose a vibroacoustic finite element model to simulate sound production and sound beam formation in the bottlenose dolphin (Tursiops truncatus), based on computed tomography scans from live and postmortem dolphins. The right and left dorsal bursae were assumed to be potential sound sources. The simulations confirm several hypotheses: (1) the shape of the skull plays a role in the formation of the sound transmission beam; (2) the melon appears to concentrate the acoustic energy by a factor of four in the transmitted beam; (3) focusing the sound beam apparently occurs in a series of stages that include contributions from the skull, nasal diverticula, melon and connective tissue structures. An unexpected result is that adjustments to the focus and direction of the sound beam can result from small (millimetre scale) changes in the relative position of the anterior and posterior bursae within each sound generation complex. Comparing our results with those from dolphin psychoacoustic experiments establishes validation of our vibroacoustic model. The potential for varied effects from anthropogenic sound also emphasizes the importance of developing vibroacoustic modelling. These numerical modelling tools complement experimental data for determining exposure thresholds and may allow us to simulate exposure levels, from moderate to extreme, without impacting live animals.     

Inhibitors of the tyrosine kinase EphB4. Part 4: Discovery and optimization of a benzylic alcohol series

Optimization of our bis-anilino-pyrimidine series of EphB4 kinase inhibitors led to the discovery of compound 12 which incorporates a key m-hydroxymethylene group on the C4 aniline. 12 displays a good kinase selectivity profile, good physical properties and pharmacokinetic parameters, suggesting it is a suitable candidate to investigate the therapeutic potential of EphB4 kinase inhibitors.     

Urate as a physiological substrate for myeloperoxidase: implications for hyperuricemia and inflammation

Urate and myeloperoxidase (MPO) are associated with adverse outcomes in cardiovascular disease. In this study, we assessed whether urate is a likely physiological substrate for MPO and if the products of their interaction have the potential to exacerbate inflammation. Urate was readily oxidized by MPO and hydrogen peroxide to 5-hydroxyisourate, which decayed to predominantly allantoin. The redox intermediates of MPO were reduced by urate with rate constants of 4.6 × 10(5) M(-1) s(-1) for compound I and 1.7 × 10(4) M(-1) s(-1) for compound II. Urate competed with chloride for oxidation by MPO and at hyperuricemic levels is expected to be a substantive substrate for the enzyme. Oxidation of urate promoted super-stoichiometric consumption of glutathione, which indicates that it is converted to a free radical intermediate. In combination with superoxide and hydrogen peroxide, MPO oxidized urate to a reactive hydroperoxide. This would form by addition of superoxide to the urate radical. Urate also enhanced MPO-dependent consumption of nitric oxide. In human plasma, stimulated neutrophils produced allantoin in a reaction dependent on the NADPH oxidase, MPO and superoxide. We propose that urate is a physiological substrate for MPO that is oxidized to the urate radical. The reactions of this radical with superoxide and nitric oxide provide a plausible link between urate and MPO in cardiovascular disease.