Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers’ tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha.

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution

Remote Estimation of Mangrove Aboveground Carbon Stock at the Species Level Using a Low-Cost Unmanned Aerial Vehicle System

There is ongoing interest in developing remote sensing technology to map and monitor the spatial distribution and carbon stock of mangrove forests. Previous research has demonstrated that the relationship between remote sensing derived parameters and aboveground carbon (AGC) stock varies for different species types. However, the coarse spatial resolution of satellite images has restricted the estimated AGC accuracy, especially at the individual species level. Recently, the availability of unmanned aerial vehicles (UAVs) has provided an operationally efficient approach to map the distribution of species and accurately estimate AGC stock at a fine scale in mangrove areas. In this study, we estimated mangrove AGC in the core area of northern Shenzhen Bay, South China, using four kinds of variables, including species type, canopy height metrics, vegetation indices, and texture features, derived from a low-cost UAV system. Three machine-learning algorithm models, including Random Forest (RF), Support Vector Regression (SVR), and Artificial Neural Network (ANN), were compared in this study, where a 10-fold cross-validation was used to evaluate each model’s effectiveness. The results showed that a model that used all four type of variables, which were based on the RF algorithm, provided better AGC estimates (R2 = 0.81, relative RMSE (rRMSE) = 0.20, relative MAE (rMAE) = 0.14). The average predicted AGC from this model was 93.0 ± 24.3 Mg C ha−1, and the total estimated AGC was 7903.2 Mg for the mangrove forests. The species-based model had better performance than the considered canopy-height-based model for AGC estimation, and mangrove species was the most important variable among all the considered input variables; the mean height (Hmean) the second most important variable. Additionally, the RF algorithms showed better performance in terms of mangrove AGC estimation than the SVR and ANN algorithms. Overall, a low-cost UAV system with a digital camera has the potential to enable satisfactory predictions of AGC in areas of homogenous mangrove forests

Litter dynamics and forest structure of the introduced Sonneratia caseolaris mangrove forest in Shenzhen, China

For the purpose of mangrove restoration in China, Sonneratia caseolaris has been introduced and planted in Guangdong Province outside and north of its native habitat, Hainan Province. We monitored the litter fall and forest structure of this S. caseolaris forest in Shenzhen City, Guangdong Province, China. from 1996 to 2005. The annual fluctuation in litter fall increased with increases in air temperature from spring to early summer, and reached a maximum in autumn when the fruits matured. The total litter fall was significantly affected by air temperature, day length, and evaporation, rainfall in the previous month and by typhoons. In 1998, the sixth year after cultivation, the total litter production of the mature S. caseolaris forest significantly increased. The mean annual total litter production during 1998-2005 was 15.1 t ha(-1) yr(-1), among which, leaves and reproductive materials contributed more than 80% of the total. During the ten years of study, the DBH (diameter at 1.30 m from ground level) and tree height of S. caseolaris increased from 5.2 cm to 18.3 cm, and from 4.5 m to 13.4 m, respectively. The litter fall production was strongly correlated with forest structure parameters, such as DBH, tree height, and crown area. The R value (the ratio of the maximum total litter fall to the minimum in the same community during the investigation periods) of S. caseolaris in the present study was 1.98, indicating a low annual variation of litter fall during these ten years. (C) 2009 Elsevier Ltd. All rights reserved.National Natural Science Foundation of China [30700092]; Natural Science Foundation of Fujian Province of China [2009J05085]; Shenzhen Bureau of Science Technology and Information of China [2004B-111

Bayesian assignment proportions for <i>K</i> = 28 clusters determined in STRUCTURE 2.3.3.

<p>Each vertical bar represents one individual.</p

Locations of <i>Mikania micrantha</i> and <i>Mikania cordata</i> populations surveyed in this study.

<p>Locations of <i>Mikania micrantha</i> and <i>Mikania cordata</i> populations surveyed in this study.</p

Genetic bottleneck of <i>Mikania micrantha</i> populations from six introduced regions in southern China.

<p><i>P</i> values are determined by a sign test under the stepwise mutation model (SMM) and the infinite allele model (IAM). <i>H_e</i>/<i>H_d</i>, the heterozygosity excess/deficiency ratio.</p

Map of sampled populations.

<p>(A) <i>Mikania micrantha</i>. (B) <i>Mikania cordata</i>.</p

Estimates of genetic diversity, and test for linkage disequilibrium and character compatibility in populations of <i>Mikania micrantha</i>.

<p><i>I_A</i>, index of association; , modified index of association; <i>IER</i>, incompatibility excess ratio.</p>*<p>, <i>P</i><0.05;</p>**<p>, <i>P</i><0.01.</p