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opencc-zeroJun 2020View details →

Data from: Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens

High-throughput sequencing (HTS) technologies offer new promise to support surveillance programs targeting marine non-indigenous species (NIS). Metabarcoding might surpass traditional monitoring methods, for example through its ability to detect rare species, a key feature in early detection of NIS. Another interest of this approach is the identification of organisms difficult to identify based on morphology only (e.g., early developmental stages), making it relevant in the context of management programs. Because many marine benthic NIS have a bi-phasic bentho-pelagic life cycle, targeting their pelagic larval stages in zooplankton may allow early detection and assessment of their establishment and potential spread. We illustrate this approach with an analysis of bulk-DNA retrieved from a time-series of zooplankton samples collected over 22 months in one bay in Brittany (France). Using HTS of amplicons obtained with two markers (COI and 18S) and a metabarcoding approach, 12 NIS were identified and their temporal larval dynamics were monitored. Importantly, we chose to focus on a closed list of species, from four metazoan classes encompassing 52 NIS reported within the study area or nearby seas, with molecular references available or obtained locally for 42 of them. The use of a custom-designed database allowed the detection of three NIS otherwise not detected when using public databases. Interestingly, NIS known to have a short-lived larval stage were detected (e.g., the bryozoan Bugula neritina or the tunicate Corella eumyota). For two molluscs Ruditapes philippinarum and Crepidula fornicata, metabarcoding results were compared to those obtained using traditional methods (i.e., barcoding of individual larvae and morphology, respectively) to show the reliability of the approach in detecting and assessing the extent of their reproductive periods. Our results also revealed that the Pacific oyster Crassostrea gigas, a notorious invasive species, failed to reproduce in the study bay, showing that metabarcoding on larval stages also provides information regarding the establishment success (or failure) of NIS. While metabarcoding has its limitations and biases, this study demonstrates its effectiveness for surveillance of targeted NIS, notably to support management strategies like the European Marine Strategy Framework Directive (MSFD).

opencc-zeroOct 2020View details →

Bamboo phenology and life cycle drive seasonal and long-term functioning of Amazonian bamboo-dominated forests

1. Bamboo-dominated forests (BDF) extend over large areas in the drought-prone Southwestern Amazon, yet little is known about the dynamics of these ecosystems. Here, we investigate the hypothesis that bamboo modulates large-scale ecosystem dynamics through competition with coexisting trees for water. 2. We examined spatio-temporal patterns of remotely sensed metrics (Enhanced Vegetation Index [EVI], Normalized Difference Moisture Index [NDMI]) in >300 Landsat images as proxies for canopy leaf phenology and water content at two time scales: (1) a complete bamboo life cycle (~28 years), and (2) the seasonal cycle; and at two spatial scales: (a) comparing adjacent areas of BDF vs. Terra-firme forests (TFF) to investigate regional dynamics, and (b) comparing the vegetation classes of bamboo, trees in BDF, and trees in TFF to investigate the effects of bamboo on coexisting trees. 3. At the regional scale, BDF showed higher EVI (leaf area density) and lower NDMI (water content) than nearby TFF but these differences disappeared as bamboo died, suggesting a strong influence of bamboo life-stage in the functioning of these forests. BDF seasonal cycle showed a bimodal EVI pattern as trees and bamboos had asynchronized leaf production peaks. 4. At the scale of vegetation classes, trees in BDF showed lower NDMI (i.e., water content) than trees in TFF except after bamboo mortality, indicating a release from competition with bamboo for water. Canopy water content of trees in BDF was also reduced during bamboo dry-season greening (increased EVI ~ leaf production) due to increased water demands. Nevertheless, long-term and seasonal phenology of trees in BDF did not differ from that of trees in TFF suggesting a potential selection for drought-tolerant trees in BDF. 5. Synthesis. Bamboo-dominated forests have received less attention than other Amazonian forests and their functional dynamics are commonly ignored or misinterpreted. Using remote sensing to characterize forest phenology and water content, we show the distinctive seasonal and long-term dynamics of BDF and coexisting trees and the importance of bamboo competition for water in shaping this ecosystem. Our results suggest a potential selection for drought-tolerant trees in BDF since they maintain the same EVI as trees in bamboo-free forests but with lower water content. A better characterization of BDF and their cyclical dynamics is crucial for accurately interpreting Amazonian forests' responses to extreme climatic events such as high temperatures and droughts.

opencc-by-4.0Sep 2020View details →

Life Cycle Environmental Impact of Houston METRO System – Evaluation of Electric Alternatives

In the Greater Houston Area, mobile sources (on- and off-road vehicles) contribute the highest share of nitrogen oxide (NOx) emissions and second-highest share of volatile organic (VOC) emissions. The Houston METRO system is a key element in Houston's infrastructure that can be expanded to lower emissions of criteria air pollutants (CAPs) and greenhouse gases (GHGs) and improve regional air quality. Currently, there is no comparative study for relative emissions and environmental impacts between passenger automobiles and METRO routes in Houston. Our research addressed this critical gap and developed environmental life cycle assessment for conventional diesel buses, diesel hybrid buses, and alternative electric buses in Houston using the GREET model. The life cycle GHG emissions of electric buses are slightly lower than the other two types of buses. However, all the other major emissions such as CO, NOx, PM10, PM2.5, VOCs, SOx, N2O, CH4, black carbon and primary organic carbon associated with electric buses are higher than diesel buses, thus causing higher environmental cost of electric buses than diesel buses. The life cycle costs of buses are very sensitive to future diesel and electricity prices. The results from this project would serve as a guiding framework to evaluate the effects of the decision to expand the METRO system and estimate the contribution of the METRO system in realizing the Greater Houston Area's environmental objectives.

FIGURE 5. Alecton discoidalis last instar larva. A, B in Description of life cycle and preimaginal stages of Alecton discoidalis Laporte 1833 (Coleoptera: Lampyridae) under laboratory conditions

FIGURE 5. Alecton discoidalis last instar larva. A, B: dorsal and ventral habitus. C, D: dorsal and ventral view of the larva head. E: right antenna (dorsal view). F: left maxilla (ventral view). G: left mandible (dorsal view). Scale bar for F and G (3 mm).

FIGURE 3 in Description of life cycle and preimaginal stages of Alecton discoidalis Laporte 1833 (Coleoptera: Lampyridae) under laboratory conditions

FIGURE 3. Duration of immature stages of Alecton discoidalis. Beyond the original larvae reared from eggs, additional larvae were collected from the field and reared in the laboratory. These additional larvae were not included in the E-L7 life stage duration calculations but were included in the dataset for PP and P durations (above). Duration of eighth larval instar was not included because this larva died as an 8th instar larva (see Table 1).

FIGURE 2. A in Description of life cycle and preimaginal stages of Alecton discoidalis Laporte 1833 (Coleoptera: Lampyridae) under laboratory conditions

FIGURE 2. A: Alecton discoidalis, newly emerged brachypterous female and alate male. B: A. discoidalis, eggs and newly hatched first instar larva.

FIGURE 1. A in Description of life cycle and preimaginal stages of Alecton discoidalis Laporte 1833 (Coleoptera: Lampyridae) under laboratory conditions

FIGURE 1. A: Habitat of collection site, near of the Water Reservoir Caunavaco, Pan de Matanzas, Cuba. B: Specific area where Alecton discoidalis larvae were found, along trail to the Water Reservoir Caunavaco. C: Microhabitat where larvae were collected.

FIGURE 4 in Description of life cycle and preimaginal stages of Alecton discoidalis Laporte 1833 (Coleoptera: Lampyridae) under laboratory conditions

FIGURE 4. Measurements taken across larval instars of Alecton discoidalis, both sexes. The eighth larval instar was not measured due to the sole specimen (a female) reaching this instar died before pupating (i.e. before reaching the end of the eighth instar).

opencc-zeroDec 2014View details →

Data from: Signatures of natural selection between life cycle stages separated by metamorphosis in European eel

Background: Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages when comparing the genetic associations between glass eels and silver eels. Results: We used two sets of markers to test for selection: first, we genotyped individuals using a panel of 80 coding-gene single nucleotide polymorphisms (SNPs) developed in American eel; second, we investigated selection at the genome level using a total of 153,423 RAD-sequencing generated SNPs widely distributed across the genome. Using the RAD approach, outlier tests identified a total of 2413 (1.57 %) potentially selected SNPs. Functional annotation analysis identified signal transduction pathways as the most over-represented group of genes, including MAPK/Erk signalling, calcium signalling and GnRH (gonadotropin-releasing hormone) signalling. Many of the over-represented pathways were related to growth, while others could result from the different conditions that eels inhabit during their life cycle. Conclusions: The observation of different genes and gene pathways under selection when comparing glass eels vs. silver eels supports the adaptive decoupling hypothesis for the benefits of metamorphosis. Partitioning the life cycle into discrete morphological phases may be overall beneficial since it allows the different life stages to respond independently to their unique selection pressures. This might translate into a more effective use of food and niche resources and/or performance of phase-specific tasks (e.g. feeding in the case of glass eels, migrating and reproducing in the case of silver eels).

opencc-zeroMar 2020View details →

Data from: Description of a new species of Hedruris Nitzsch, 1821 (Nematoda, Hedruridae) from freshwater turtles in Argentina, with information on its life cycle and a review of the genus's host and geographic distribution

Hedruris dratini n. sp. (Nematoda, Hedruridae) is described from freshwater turtles in Argentina and information about its life cycle provided. The new species differs from the remaining species of the genus by possessing an excretory pore, and the nerve ring and deirids being positioned at equal distance from the anterior end. Additionally, H. dratini n. sp. has mammilated eggs and males possess nine pairs of caudal papillae. The first life cycle within the genus including an amphipod as intermediate host and a reptile as a definitive host is presented. Furthermore, the host and geographic distribution of species of the genus Hedruris Nitzsch, 1821 are analyzed. Although the genus has a cosmopolitan distribution and parasitizes a great diversity of hosts, the majority of its species follow a Gondwanian distribution and its preferred hosts are amphibians.

opencc-zeroDec 2012View details →

Data from: A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages

Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

opencc-zeroDec 2010View details →

Data from: Climate effects on life cycle variation and population genetic architecture of the black bean aphid, Aphis fabae

Aphid species commonly have different reproductive modes ranging from cyclical to obligate parthenogenesis. The distribution of life cycle variation in aphids is generally determined by ecological forces, mainly climate, because only sexually produced diapausing eggs can survive harsh winters. Aphids are thus interesting models to investigate intrinsic and environmental factors shaping the competition among sexual and asexual lineages. We conducted a Europe-wide sampling of black bean aphids, Aphis fabae, and combined population genetic analyses based on microsatellite data with an experimental determination of life cycle strategies. Aphids were collected from broad beans (Vicia faba) as well as some Chenopodiaceae, but we detected no genetic differentiation between aphids from different host plants. Consistent with model predictions, life cycle variation was related to climate, with aphids from areas with cold winters investing more in sexual reproduction than aphids from areas with mild winters. Accordingly, only populations from mild areas exhibited a clear genetic signature of clonal reproduction. These differences arise despite substantial gene flow over large distances, which was evident from a very low geographic population structure and a lack of isolation-by-distance among 18 sites across distances of more than 1000 kilometres. There was virtually no genetic differentiation between aphids with different reproductive modes, suggesting that new asexual lineages are formed continuously. Indeed, a surprising number of A. fabae genotypes even from colder climates produced some parthenogenetic offspring under simulated winter conditions. From this we predict that a shift to predominantly asexual reproduction could take place rapidly in under climate warming.

opencc-zeroDec 2015View details →

Data from: Genotypic diversity mitigates negative effects of density on plant performance: a field experiment and life-cycle analysis of common evening primrose Oenothera biennis

1.Genotypic diversity in plant populations is known to enhance plant performance and ecosystem function. Nonetheless, the effect of genotypic diversity has rarely been examined across a population's lifecycle despite the expectation that changing conditions, such as population density, will alter the benefits of diversity. 2.We simultaneously manipulated a component of genotypic diversity (richness, the number of genotypes) and density of common evening primrose Oenothera biennis to address the consequences for herbivory and lifetime fitness in a two-year field experiment that spanned seed germination to life-time fruit production. We genotyped >1100 seedlings with microsatellite DNA markers to determine realized diversity and density in plots sown with O.biennis seeds. Our design achieved quantitative variation in plant density and diversity, with one to 44 individuals established in field plots and two to eight genotypes per polyculture plot (based on microsatellite analysis of reproductive plants). 3.We found a strong interaction between seed density and genetic diversity, with germination and establishment being 24% higher in genetic polycultures than monocultures, but only at low seed density. At high seed density, the opposite pattern emerged, with polycultures having 12% fewer individuals established than monocultures. Initial effects of emergence on plot density persisted through to the fruiting stage. 4.Higher plant densities result in increased mortality, decreased probability of reproduction, decreased plant height, and lower levels of life-time fruit production per plant. Increasing genotypic diversity increased the probability of reproduction overall, and showed a significant interaction with plant density mitigating the negative effects of high density on individual height and lifetime fruit production. 5.Synthesis. Plant density and genotypic diversity interacted from the very earliest stages of seed germination and establishment of O. biennis. This effect persisted over the two-year life-cycle of plants, and genotypic diversity buffered against the negative fitness consequences of high plant density. These results imply a dynamic interplay between the long-held paradigm of density effects in plant ecology and the genetic structure of populations.

opencc-zeroDec 2015View details →

Data from: Functional traits as predictors of vital rates across the life cycle of tropical trees

The 'functional traits' of species have been heralded as promising predictors for species' demographic rates and life history. Multiple studies have linked plant species' demographic rates to commonly measured traits. However, predictive power is usually low – raising questions about the practical usefulness of traits – and analyses have been limited to size-independent univariate approaches restricted to a particular life stage. Here we directly evaluated the predictive power of multiple traits simultaneously across the entire life cycle of 136 tropical tree species from central Panama. Using a model-averaging approach, we related wood density, seed mass, leaf mass per area and adult stature (maximum diameter) to onset of reproduction, seed production, seedling establishment, and growth and survival at seedling, sapling and adult stages. Three of the four traits analysed here (wood density, seed mass and adult stature) typically explained 20–60% of interspecific variation at a given vital rate and life stage. There were strong shifts in the importance of different traits throughout the life cycle of trees, with seed mass and adult stature being most important early in life, and wood density becoming most important after establishment. Every trait had opposing effects on different vital rates or at different life stages; for example, seed mass was associated with higher seedling establishment and lower initial survival, wood density with higher survival and lower growth, and adult stature with decreased juvenile but increased adult growth and survival. Forest dynamics are driven by the combined effects of all demographic processes across the full life cycle. Application of a multitrait and full-life cycle approach revealed the full role of key traits, and illuminated how trait effects on demography change through the life cycle. The effects of traits on one life stage or vital rate were sometimes offset by opposing effects at another stage, revealing the danger of drawing broad conclusions about functional trait–demography relationships from analysis of a single life stage or vital rate. Robust ecological and evolutionary conclusions about the roles of functional traits rely on an understanding of the relationships of traits to vital rates across all life stages.

opencc-zeroDec 2014View details →

Data from: Affinity, life cycle, and intracellular complexity of organic-walled 2 microfossils from the Mesoproterozoic of Shanxi, China

Light microscope and scanning electron microscope observations on new material of unicellular microfossils Dictyosphaera macroreticulata and Shuiyousphaeridium macroreticulatum, from the Mesoproterozoic Ruyang Group in China, provide insights into the microorganisms' biological affinity, life cycle and cellular complexity. Gigantosphaeridium fibratum n. gen. et sp., is described and is one of the largest Mesoproterozoic microfossils recorded. Phenotypic characters of vesicle ornamentation and excystment structures, properties of resistance and cell wall structure in Dictyosphaera and Shuiyousphaeridium are all diagnostic of microalgal cysts. The wide size ranges of the various morphotypes indicate growth phases compatible with the development of reproductive cysts. Conspecific biologically, each morphotype represents an asexual (resting cyst) or sexual (zygotic cyst) stage in the life cycle, respectively. We reconstruct this hypothetical life cycle and infer that the organism demonstrates a reproductive strategy of alternation of heteromorphic generations. Similarly in Gigantosphaeridium, a metabolically expensive vesicle with processes suggests its protective role as a zygotic cyst. In combination with all these characters and from the resemblance to extant green algae, we propose the placement of these ancient microorganisms in the stem group of Chloroplastida (Viridiplantae). A cell wall composed of primary and secondary layers in Dictyosphaera and Shuiyouisphaeridium required a high cellular complexity for their synthesis and the presence of an endomembrane system and the Golgi apparatus. The plastid was also present, accepting the organism was photosynthetic. The biota reveals a high degree of morphological and cell structural complexity, and provides an insight into ongoing eukaryotic evolution and the development of complex life cycles with sexual reproduction by 1200 Ma.

opencc-zeroDec 2013View details →

Data from: Fine-scale spatial genetic dynamics over the life-cycle of the tropical tree Prunus africana

Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.

opencc-zeroDec 2013View details →

Data from: The trophic vacuum and the evolution of complex life cycles in trophically-transmitted helminths

Parasitic worms (helminths) frequently have complex life cycles in which they are transmitted trophically between two or more successive hosts. Sexual reproduction often takes place in high trophic-level (TL) vertebrates, where parasites can grow to large sizes with high fecundity. Direct infection of high TL hosts, while advantageous, may be unachievable for parasites constrained to transmit trophically, because helminth propagules are unlikely to be ingested by large predators. Lack of niche overlap between propagule and definitive host (the trophic transmission vacuum) may explain the origin and/or maintenance of intermediate hosts, which overcome this transmission barrier. We show that nematodes infecting high TL definitive hosts tend to have more successive hosts in their life cycles. This relationship was modest, though, driven mainly by the minimum TL of hosts, suggesting that the shortest trophic chains leading to a host define the boundaries of the transmission vacuum. We also show that alternative modes of transmission, like host penetration, allow nematodes to reach high TLs without intermediate hosts. We suggest that widespread omnivory as well as parasite adaptations to increase transmission probably reduce, but do not eliminate, the barriers to the transmission of helminths through the food web.