Signal level comparison between TerraSAR-X and COSMO-SkyMed SAR Sensors

International audienceSoil and vegetation biophysical parameter retrieval using synthetic-aperture-radar images requires radiometrically well-calibrated sensors. In this letter, a comparison of signal levels between TerraSAR-X (TSX) and the COSMO-SkyMed (CSK) constellation (CSK1, CSK2, CSK3, and CSK4) was carried out in order to analyze the ability to use jointly all current X-band sensors. The analysis of the X-band signal over forest stands showed a stable signal (variation lower than 1 dB) over time for each of the studied sensors, but a significant difference was observed between the different X-band sensors. Differences between radar signals were higher in HH than in HV polarization. TSX and CSK4 showed similar backscatter signals, with signal level differences of 0.6 dB in HH and 1.4 dB in HV. The CSK3 signal was observed to be lower than those from TSX and CSK4 by about 2.1 dB and 1.5 dB in HH against 3.2 dB and 1.8 dB in HV, respectively. Moreover, CSK2 and CSK1 which showed slightly different backscatter signals (within 1.1 dB in HH and 1.9 dB in HV) had signal levels lower than those obtained from TSX (2.2-3.3 dB in HH and 3.2-5.1 dB in HV for about 29° incidence angle). These results show that it is currently difficult to use jointly the available X-band satellites (CSK and TSX) for estimating the biophysical parameters of soil or vegetation. This is due to the significant difference in the radar signal level between some of the analyzed satellites, which will cause a high overor underestimation of biophysical parameters

Irrigated grassland monitoring using a time series of terraSAR-X and COSMO-skyMed X-Band SAR Data

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SYNERGIE [Axe_IRSTEA]TETIS-ATTOSInternational audienceThe objective of this study was to analyze the sensitivity of radar signals in the X-band in irrigated grassland conditions. The backscattered radar signals were analyzed according to soil moisture and vegetation parameters using linear regression models. A time series of radar (TerraSAR-X and COSMO-SkyMed) and optical (SPOT and LANDSAT) images was acquired at a high temporal frequency in 2013 over a small agricultural region in southeastern France. Ground measurements were conducted simultaneously with the satellite data acquisitions during several grassland growing cycles to monitor the evolution of the soil and vegetation characteristics. The comparison between the Normalized Difference Vegetation Index (NDVI) computed from optical images and the in situ Leaf Area Index (LAI) showed a logarithmic relationship with a greater scattering for the dates corresponding to vegetation well developed before the harvest. The correlation between the NDVI and the vegetation parameters (LAI, vegetation height, biomass, and vegetation water content) was high at the beginning of the growth cycle. This correlation became insensitive at a certain threshold corresponding to high vegetation (LAI ~2.5 m2/m2). Results showed that the radar signal depends on variations in soil moisture, with a higher sensitivity to soil moisture for biomass lower than 1 kg/m². HH and HV polarizations had approximately similar sensitivities to soil moisture. The penetration depth of the radar wave in the X-band was high, even for dense and high vegetation; flooded areas were visible in the images with higher detection potential in HH polarization than in HV polarization, even for vegetation heights reaching 1 m. Lower sensitivity was observed at the X-band between the radar signal and the vegetation parameters with very limited potential of the X-band to monitor grassland growth. These results showed that it is possible to track gravity irrigation and soil moisture variations from SAR X-band images acquired at high spatial resolution (an incidence angle near 30°)

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens

A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly mutable site in the βA-globin gene has contributed to an evolutionary change in hemoglobin (Hb) function in high-altitude Andean house wrens (Troglodytes aedon). Results of experiments on native Hb variants and engineered, recombinant Hb mutants demonstrate that a nonsynonymous mutation at a CpG dinucleotide in the βA-globin gene is responsible for an evolved difference in Hb–O2 affinity between high- and low-altitude house wren populations. Moreover, patterns of genomic differentiation between high- and low-altitude populations suggest that altitudinal differentiation in allele frequencies at the causal amino acid polymorphism reflects a history of spatially varying selection. The experimental results highlight the influence of mutation rate on the genetic basis of phenotypic evolution by demonstrating that a large-effect allele at a highly mutable CpG site has promoted physiological differentiation in blood O2 transport capacity between house wren populations that are native to different elevations

The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP

The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis

Background Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis. Results Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species\u27 range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America. Conclusion We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously

A geographic cline induced by negative frequency-dependent selection

<p>Abstract</p> <p>Background</p> <p>Establishment of geographic morph frequency clines is difficult to explain in organisms with limited gene flow. Balancing selection, such as negative frequency-dependent selection (NFDS), is instead suggested to establish a morph frequency cline on a geographic scale at least theoretically. Here we tested whether a large-scale smooth cline in morph frequency is established by NFDS in the female-dimorphic damselfly, <it>Ischnura senegalensis</it>, where andromorphs and gynomorphs are maintained by NFDS.</p> <p>Results</p> <p>We found a large-scale latitudinal cline in the morph frequency: andromorph frequency ranged from 0.05 (South) to 0.79 (North). Based on the empirical data on the numbers of eggs, the number of ovariole, abdomen length and latitude, the potential fitness of andromorphs was estimated to be lower than that of gynomorphs in the south, and higher in the north, suggesting the gene-by-environment interaction. From the morph-specific latitudinal cline in potential fitness, the frequency of andromorphs was expected to shift from 0 to 1 without NFDS, because a morph with higher potential fitness wins completely and the two morphs will switch at some point. In contrast, NFDS led to the coexistence of two morphs with different potential fitness in a certain geographic range along latitude due to rare morph advantage, and resulted in a smooth geographic cline of morph frequency.</p> <p>Conclusion</p> <p>Our results provide suggestive evidence that the combination of NFDS and gene-by-environment interaction, i.e., multi-selection pressure on color morphs, can explain the geographic cline in morph frequency in the current system.</p

The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis

<p>Abstract</p> <p>Background</p> <p>Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, <it>Cardinalis cardinalis</it>.</p> <p>Results</p> <p>Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America.</p> <p>Conclusion</p> <p>We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in <it>C. cardinalis</it>. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously.</p

Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene—or both—have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area