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FIGURES 46–60 in Morphological, ecological and molecular characterization of Pyropia vietnamensis (Bangiales, Rhodophyta) from the Konkan region, India

FIGURES 46–60. Cross section of blade passing through Spermatangia. Scale bar = 10μm. 46. Redi. 47. Harihareshwar. 48. Palshet 49. Dona Paula. 50. Hedavi I. 51. Vagathor. 52. Kolthare. 53. Anjuna. 54. Malvan I. 55. Purnagad I. 56. Hedavi II. 57. Malvan II. 58.Shekhadi. 59. Velaneshwar. 60. Purnagad II.

FIGURES 28–30 in Morphological, ecological and molecular characterization of Pyropia vietnamensis (Bangiales, Rhodophyta) from the Konkan region, India

FIGURES 28–30. Spinulose margin of thallus. Scale bar = 10μm. 28. Kolthare. 29. Harihareshwar. 30. Shekhadi.

FIGURES 16–27 in Morphological, ecological and molecular characterization of Pyropia vietnamensis (Bangiales, Rhodophyta) from the Konkan region, India

FIGURES 16–27. Spinulose margin of thallus. Scale bar = 10μm. 16. Anjuna. 17. Vagathor. 18. Malvan II. 29. Velaneshwar. 20. Hedavi II. 21. Purnagad I. 22. Redi. 23. Hedavi I. 24. Malvan I. 25. Dona Paula. 26. Palshet 27. Purnagad II

FIGURES 1–15 in Morphological, ecological and molecular characterization of Pyropia vietnamensis (Bangiales, Rhodophyta) from the Konkan region, India

FIGURES 1–15. Habit of Pyropia vietnamensis. 1. Harihareshwar (ARC- P- 31). 2. Shekhadi (ARC- P- 80). 3. Kolthare (ARC- P- 23). 4. Palshet (ARC- P- 3). 5. Malvan (ARC- P- 48). 6. Malvan (ARC- P- 69). 7. Purnagad (ARC- P- 21). 8. Purnagad (ARC- P-22). 9. Velaneshwar (ARC- P- 8). 10. Anjuna (ARC- P- 192). 11. Hedavi (ARC- P- 12). 12. Vagathor (ARC- P- 196). 13. Hedavi (ARC- P- 20). 14. Dona Paula (ARC- P- 183). 15. Redi (ARC- P- 73).

FIGURES 31–45 in Morphological, ecological and molecular characterization of Pyropia vietnamensis (Bangiales, Rhodophyta) from the Konkan region, India

FIGURES 31–45. Cross section of blade passing through vegetative area. Scale bar = 10μm. 31. Redi. 32. Hedavi 1. 33. Kolthare. 34. Vagathor. 35. Purnagad II. 36. Harihareshwar. 37. Dona Paula. 38. Hedavi II. 39. Malvan II. 40. Velaneshwar. 41. Anjuna. 42. Malvan I. 43. Palshet. 44. Purnagad I. 45. Shekhadi.

FIGURE 4 in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data

FIGURE 4. Idiograms of the four populations showing CMA 3 bands (yellow), 35S (red) and 5S (green) signals. A. S. litoralis; B. S. virgaurea (Livorno); C. S. virgaurea (Monte Pisano); D. S. virgaurea (Tre Potenze). Scale bar: 5 μm.

FIGURE 2 in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data

FIGURE 2. Chromomycin banding showing the GC-rich DNA regions. A. S. litoralis (partial metaphase); B. S. virgaurea (Livorno; partial metaphase); C. S. virgaurea (Monte Pisano); D. S. virgaurea (Tre Potenze). Scale bar: 10 μm.

FIGURE 1. Schiff stained metaphase plates. A. S in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data

FIGURE 1. Schiff stained metaphase plates. A. S. litoralis; B. S. virgaurea (Livorno); C. S. virgaurea (Monte Pisano); D. S. virgaurea (Tre Potenze). Scale bar: 10 μm.

FIGURE 3. FISH showing the chromosomes with 35S in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data

FIGURE 3. FISH showing the chromosomes with 35S (red) and 5S (green) signals. A. Partial metaphase of S. litoralis; B. Partial metaphase of S. virgaurea (Livorno); C. S. virgaurea (Monte Pisano); D. S. virgaurea (Tre Potenze). Scale bar: 10 μm.

FIGURE 5 in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data

FIGURE 5. Grime triangle showing CSR strategies calculated for each single individual. Empty dots: S. litoralis; diamonds: S. virgaurea (Livorno); filled squares: S. virgaurea (Monte Pisano); stars: S. virgaurea (Tre Potenze).

opencc-zeroDec 2017View details →

Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, since the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery reared parrs.

opencc-zeroAug 2019View details →

Data from: Genotyping-in-Thousands by sequencing (GT-seq) panel development and application to minimally-invasive DNA samples to support studies in molecular ecology

Minimally-invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping-by-sequencing approaches, which have been traditionally developed for high-quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping-in-Thousands by sequencing (GT-seq), a multiplex amplicon sequencing approach, to effectively genotype minimally-invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT-seq from a de novo restriction-site associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT-seq for the same individuals found low rates of genotyping error (GT-seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT-seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT-seq and RADseq datasets, as were inferred patterns of population structure. Overall, GT-seq can be effectively applied to low quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally-invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era.

opencc-zeroDec 2013View details →

Data from: Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

opencc-zeroDec 2017View details →

Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.

opencc-zeroDec 2014View details →

Data from: Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards

Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal 'trunk-ground' anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates.

Figure 4 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data

Figure 4. Time-calibrated phylogram from the partitioned BEAST analyses of the combined dataset (COI and 16s). Bayesian inference (BI) and maximum likelihood (ML) reconstructions provided very similar and largely overlapping topologies. Numbers below nodes are BI posterior probabilities (only values> 0.95 are shown) and ML bootstrap values (only values> 70% are shown). Numbers above nodes are estimated dates of diversification. Terminal taxa labels refer to individual sequence numbers used in Table 2.

Figure 2 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data

Figure 2. Paramera of male at left (lateral and dorsal views) and parts of left valves of female Propomacrus at right. The dashed line separates different scales and sexes. (a–d): 'P. cypriacus'; (e–h) P. bimucronatus from the Lebanon; (i–l): P. bimucronatus from Turkey; a, g and k: basal parts of valves; d, h and l: distal parts of valves.

Figure 1 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data

Figure 1. Map of Cyprus with new and previous records of P. cypriacus. Localities where unsuccessful searches were performed are also shown.

Figure 3 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data

Figure 3. Protibiae of P. bimucronatus (left) from Turkey (upper), the Lebanon (middle), and Greece (lower), and 'P. cypriacus' (upper right: holotype; middle and lower: paratypes; Vretsia, Cyprus, leg. Makris). All photos are at the same scale.