Find research datasets worth reusing

Data set for: Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and moisture deficit stress conditions in wheat

The study material in the GWAS panel with 193 bread wheat genotypes from Indian and exotic collections was selected to map the genomic regions responsible for grain iron and Zinc content under drought and heat stress treatments. Phenotypic data: The GWAS panel was evaluated at IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m) under Irrigated (IR), Restricted Irrigated (RI) and Late sown (LS) treatment conditions over 2 years i.e. 2020 and 2021 with augmented RCBD design. Data was collected on Grain Iron and Grain zinc content along with thousand-grain weight. Around 20 g of grain sample from each of 282 genotypes from the GWAS panel under all three conditions were used for phenotyping GFeC and GZnC through high-throughput Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000; Oxford Instruments plc, Abingdon, United Kingdom) calibrated with glass beads-based values. To record TGW, manual counting of grains was followed and the weight of the grains was recorded in grams with an electronic balance. Genotypic data: Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >10%, and heterozygote frequency >50% were removed from the analysis. The remaining set of 13,947 high-quality SNPs was used in GWAS analysis.

Data from: Disentangling genetic from environmental effects on phenotypic variability of Southern rock lobster (Jasus edwardsii) postlarvae

Environmental conditions experienced during larval dispersal of marine organisms can determine size-at-settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here we investigated morphological differences in recently settled southern rock lobster (Jasus edwardsii) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction-site associated DNA sequencing (ddRADseq) to assess differences in genetic structure of recently settled recruits on the east coast of Tasmania over three months of peak settlement during 2012 (August, September and October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller individuals found at the northernmost site. Also, there was a lack of overall genetic divergence; however, significant differences in pairwise FST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, individuals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic divergence in the presence of phenotypic variation indicates that larval environmental history during dispersal of J. edwardsii could be a possible driver of the resulting phenotype of settlers.

Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population

Numerous terrestrial mammal species have experienced extensive population declines during past centuries, due largely to anthropogenic pressures. For some species, including the Eurasian otter (Lutra lutra), environmental and legal protection has more recently led to population growth and recolonisation of parts of their historic ranges. While heralded as conservation successes, only a few such recoveries have been examined from a genetic perspective, i.e. whether genetic variability and connectivity have been restored. We here use large-scale and long-term genetic monitoring data from UK otters, whose population underwent a well-documented population decline between the 1950s to 1970s, to explore the dynamics of a population re-expansion over a 21-year period. We genotyped otters from across Wales and England at five time points between 1994 and 2014 using 15 microsatellite loci. We used this combination of long-term temporal and large-scale spatial sampling to evaluate 3 hypotheses relating to genetic recovery; that (i) gene flow between sub-populations would increase over time, (ii) genetic diversity of previously isolated populations would increase, and that (iii) genetic structuring would weaken over time. Although we found an increase in inter-regional gene flow and admixture levels among subpopulations, there was no significant temporal change in either heterozygosity or allelic richness. Genetic structuring among the main sub-populations hence remained strong and showed a clear historical continuity. These findings highlight an underappreciated aspect of population recovery of endangered species, that genetic recovery may often lag behind the processes of spatial and demographic recovery. In other words, the restoration of physical connectivity of populations does not necessarily lead to genetic connectivity. Our findings emphasise the need for genetic data as an integral part of conservation monitoring, to enable the potential vulnerability of populations to be evaluated.

Chromosome-level genome assembly of Pterygoplichthys pardalis reveals its genetic basis of extensive invasion

The catfish, Pterygoplichthys pardalis, which belongs to the Loricariidae family, an invasive species which has caused huge damage to the ecological environment. However, the high-quality reference genome for the catfish has not yet been reported. In this study, we successfully assembled the first chromosome-level high-quality genome of P. pardalis using the data we produced from multiple sequencing platforms, which contains 26 chromosomes and with a scaffold N50 of 49.47 Mb. Different evaluation methods all indicate the high connectivity and accuracy of the P. pardalis genome we got. We predicated 23,859 protein-coding genes in the P. pardalis genome, and 22,169 (~92.92%) coding genes could be functionally annotated in public databases. Phylogenetic relationship analysis found P. pardalis was clustered with all the catfishes we used and diverged with them 132.5 million years ago. Besides, whole-genome collinearity analysis found that chromosome 6 of P. pardalis was aligned to two distinct chromosomes both for Ameiurus melas, Pangasianodon hypophthalmus and Ictalurus punctatus, indicating that there may have been a chromosomal fusion/fission event occurred. Furthermore, many immune-system-related genes were large-scale expanded in P. pardalis genome, which may make great contributions to their adaptive traits, even for the highly polluted environmental conditions, and successful invasion. Taken together, this study not only provides insights into the genetic basis of the successful invasion of P. pardalis, but also provides important data resources for comparative genomic analysis of P. pardalis in Siluriformes in the future.

Genet dynamics and its variation among genets of a clonal plant Convallaria keiskei

In clonal plant populations, a number of genetically identical ramets form a genet. While coexisting ramets potentially perform independently, their behaviours not only depend on ages and sizes but are also constrained by genetic background. In this study, genet dynamics and its variability among neighbouring genets were investigated based on the ramet demography of each genet in Convallaria keiskei. Genet dynamics were first formulated as a matrix model with the two components of clonal growth (clonal reproduction) and survival-transitions between ramet size classes. Then, a statistical estimation of the matrix elements was established using three datasets: aboveground demographic censuses, belowground directional rhizomatous connections and genetic identification of ramets. Finally, genet growth rates reflecting both the changes of clonal growth and ramet size growth were estimated and compared for fundamental demographic elements among genets. Over three years of aboveground annual censuses of a 28 × 2 m plot, 2,021 ramets were identified as belonging to 28 genotypes. Belowground excavation detected 515 clonal fragments. Genet growth rate of three dominant genets varied with medians of 1.13, 1.02 and 1.05; 95% credible intervals of the posterior distributions did not overlap between the genet with the largest median and the others. The variation was caused primarily by differences in clonal growth rather than survival-transitions between size classes. Clonal growth by branching was rarer than at the tips but contributed to the maintenance of the genet. Therefore, both clonal growth frequencies and connecting patterns of ramets caused the variation of genet dynamics and established genets persist for a long time through the positive growth rates, which would contribute to maintaining a population. We also conclude that fundamental demographic elements relating to clonal growth traits (the features of individual genets) strongly impact genet dynamics.

Multilocus phylogeography, population genetics and niche evolution of Australian Brown and Black-tailed Treecreepers (Aves: Climacteris)

The Carpentarian barrier across northeastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modeling of Brown and Black-tailed Treecreepers (Climacteris picumnus and C. melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and reveals a signature of a recent selective sweep in C. picumnus. No loci among 14 anonymous autosomal markers exhibited reciprocal monophyly between species, and a variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7 – 2.8 MYA, depending on the model and assumptions about generation time. Paleo-ecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the last ~600 kyr and that the area of range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.

Eastern-flowering Dogwood population genetics and ecological/environmental data

Forest fragmentation and introduced pathogens are negatively impacting trees and forests globally, including the Carolinian forest of southern Ontario, Canada. Multiple species-at-risk live in this threatened but biodiverse forest, including the endangered Cornus florida (Eastern flowering dogwood), which is now limited to fragmented woodlots, and has been decimated by the introduced fungal pathogen Discula destructiva (dogwood anthracnose). Ongoing management of C. florida in Canada is challenged by multiple knowledge gaps, two of which we aimed to address in this study. We first evaluated the association between anthracnose disease prevalence and a suite of ecological and environmental variables across 21 sites. Across our sites, larger trees tended to have the highest disease incidence, and trees on shallow slopes had the most crown dieback. We then quantified genetic diversity and gene flow and found that genetic structure has not been substantially impacted by habitat fragmentation, although dispersal typically covers short distances. However, genetic diversity is relatively low in smaller populations, and in younger trees. Localized dispersal and eroding genetic diversity may limit future adaptation and hence exacerbate population declines. We recommend that managers prioritize plantings in small populations, avoid shallow slopes, and track younger trees to evaluate age-related mortality.

Genetic variation of morphological scaling in Drosophila

Morphological scaling relationships between the sizes of individual traits and the body captures the characteristic shape of a species, and the evolution of scaling is the primary mechanism of morphological diversification. However, we have almost no knowledge of the genetic variation of scaling, which is critical if we are to understand how scaling evolves. Here we explore the genetics of population morphological scaling relationships – the scaling relationship fit to multiple genetically-distinct individuals in a population – by describing the distribution of individual scaling relationships – the genotype-specific scaling relationships that are unseen or cryptic. These individual scaling relationships harbor the genetic variation that determines relative trait growth within individuals, and theoretical studies suggest that their distribution dictates how the population scaling relationship will respond to selection. Using variation in nutrition to generate size variation within 194 isogenic lineages of Drosophila melanogaster, we reveal extensive variation in the slopes of the wing-body and leg-body scaling relationships among genotypes. This genetic variation reflects variation in the nutritionally-induced size plasticity of the wing, leg, and body. Surprisingly, we find that variation in the slope of individual scaling relationships primarily results from variation in nutritionally-induced plasticity of body size, not leg or wing size. These data allow us to predict how different selection regimes affect scaling in Drosophila and are the first step in identifying the genetic targets of such selection. More generally, our approach provides a framework for understanding the genetic variation of scaling, an important prerequisite to explaining how selection changes scaling and morphology.

Data for: Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback

Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here 'parallel evolution') often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.

Male diversity matters: Genetic structuring of insular male date palm (Phoenix dactylifera L.) revealed valuable breeding and conservation resources

Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favorable fruit production is related to quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterization of the male pollen as a superior one for each female cultivar should be the first step to establish an intensive program to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. A total number of 125 alleles was detected with an average of 8.33 alleles per locus. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of Phoenix dactylifera L. breeding programs as well as for the protection and conservation of valuable resources.

Data from: Genetic divergence along a climate gradient shapes chemical plasticity of a foundation tree species to both changing climate and herbivore damage

Climate change is threatening the persistence of many tree species via independent and interactive effects on abiotic and biotic conditions. In addition, changes in temperature, precipitation, and insect attacks can alter the traits of these trees, disrupting communities and ecosystems. For foundation species such as Populus, phytochemical traits are key mechanisms linking trees with their environment and are likely jointly determined by interactive effects of genetic divergence and variable environments throughout their geographic range. Using reciprocal Fremont cottonwood (Populus fremontii) common gardens along a steep climatic gradient, we explored how environment (garden climate and simulated herbivore damage) and genetics (tree provenance and genotype) affect both foliar chemical traits and the plasticity of these traits. We found that: 1) Constitutive and plastic chemical responses to changes in garden climate and damage varied among defense compounds, structural compounds and nitrogen. 2) For both defense and structural compounds, plastic responses to garden climate depended on the climate in which a population or genotype evolved. Specifically, trees originating from cool provenances showed higher defense plasticity in response to climate changes than trees from hotter provenances. 3) Trees from cool provenances growing in cool conditions expressed the lowest constitutive defense levels but the strongest induced (plastic) defenses. 4) The combination of hot growing conditions and simulated herbivory switched the strategy used by these genotypes, increasing constitutive defenses but erasing the capacity for induction. Because Fremont cottonwood chemistry plays a major role in shaping riparian communities and ecosystems in the southwestern US, the effects of changes in phytochemical traits can be wide-reaching. As the southwestern US is confronted with warming temperatures and insect outbreaks, these results improve our capacity to predict ecosystem consequences of climate change and inform selection of tree genotypes for conservation and restoration purposes.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on strains of Mycobacterium bovis, circulating in France, by the whole genome sequencing approach." Ciriac CHARLES

Appendix 1 Table showing the Mycobacterium bovis genome information used in this study in panel 1 The 87 genomes are from previous work (Hauer et al., 2019). The names of the genomes are highlighted with color to distinguish them within a previously defined M. bovis cluster. In Yellow Cluster I/Clonal Complex Eu3. In orange Cluster G/Family F9. In brown Cluster C/Family SB0134. In purple Cluster D/Clonal Complex Eu1. In pink the Cluster A/Family F4. In blue the Cluster F/Clonal Complex Eu2. In grey, the others. Appendix 2 Table showing the Mycobacterium bovis genome information used in this study in panel 3. The 187 genomes are of genotypes F7 and F15 (SB0821 and SB0832 respectively) which are two closely related genotypes. These genomes had already been sequenced before the start of the thesis work. Some were published with the work of Duault and collaborators and others have not yet been published (noted NA) (Duault et al., 2022). Appendix 3 Table showing the Mycobacterium bovis genome information used in this study in panel 4. The 227 genomes are of genotype SB0120-DHV. These genomes had already been sequenced before the start of the thesis work but are currently unpublished (noted NA in the columns "Date of deposit" and "Genbank biosample"). Appendix 4 Position of IS6110 insertion sites in the panel of Mycobacterium bovis strains from Pyrénées-Atlantiques (SB0821 and SB0832). The position of the start and end of IS6110 are determined with the ISMapper tool and the reference genome AF2122/97. Appendix 5 Position of IS6110 insertion sites in the Mycobacterium bovis strain panel of SB0120-DHV. Position of the start and end of IS6110 are determined with the ISMapper tool and the Mb3601 reference genome. Appendix 6 This figure from the Modenesi internship report represents a circular consensus phylogenetic tree of 300 strains of SB0120-DHV (Modenesi 2019). The strains in panel 3 are part of these 300 strains and were selected according to their sequencing quality, which explains the smaller number of strains retained (227). This tree is divided into 11 different colored clades. The posterior probability values (which correspond to the probability that these clades are true) determined with Beast (Drummond and Rambaut, 2007) are represented inside the tree.

opencc-by-4.0Dec 2022View details →

Appendix of the thesis "Acquisition of new genetic knowledge on Mycobacterium bovis strains, circulating in France, by the whole genome sequencing approach", part "4. Sequencing of new complete genomes", Ciriac CHARLES

Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric. Annex S2: Pan-genomic study performed on 12 M. bovis complete genomes. The table indicates the genes accessory. “1” shows the presence of CDS and “0” his absence. Annex S3: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS6110 is marked in green. "Indel distribution" sheet shows the indel distribution on the M. bovis genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found. Annex S4: WgSNP analysis performed on 98 M. bovis. SNPs were annotated and selected according to their specificity to an M. bovis group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position. Annex S5: Alignments of the 12 M. bovis complete genomes.

opencc-by-4.0Dec 2022View details →

Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family.Supplementary_data

This is Supplementary files for the paper "Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family". The description for each dataset is located inside files.

Genetic sex determination, sex chromosome size and sex-specific lifespan across tetrapods

Sex differences in lifespan are ubiquitous across the tree of life and exhibit broad taxonomic patterns that remain a puzzle, such as males living longer than females in birds and vice versa in mammals. The prevailing "unguarded-X" hypothesis explains sex differences in lifespan by differential expression of recessive mutations on the X or Z chromosome of the heterogametic sex but has only received indirect support to date. An alternative hypothesis is that the accumulation of deleterious mutations and repetitive elements on the Y or W chromosome might lower the survival of the heterogametic sex ("toxic Y" hypothesis). Here, we use a new database to report lower survival of the heterogametic relative to the homogametic sex across 136 species of birds, mammals, reptiles and amphibians, as expected if sex chromosomes shape sex-specific lifespans, and consistent with previous findings. We also found that the relative sizes of both the X and the Y chromosomes in mammals (but not the Z or the W chromosomes in birds) are associated with sex differences in lifespan, as predicted by the "unguarded-X" and the "toxic Y". Furthermore, we report that the relative size of the Y is negatively associated with male lifespan in mammals, so that small Y size correlates with increased male lifespan. In theory, toxic Y effects are expected to be particularly strong in mammals, and we did not find similar effects in birds. Our results confirm the role of sex chromosomes in explaining sex differences in lifespan across tetrapods and further suggest that, at least in mammals, "toxic Y" effects may play an important part in this role.

Not all roads lead to the immune system: The genetic basis of multiple sclerosis severity

Multiple sclerosis is a leading cause of neurological disability in adults. Heterogeneity in multiple sclerosis clinical presentation has posed a major challenge for identifying genetic variants associated with disease outcomes. To overcome this challenge, we used prospectively ascertained clinical outcomes data from the largest international multiple sclerosis Registry, MSBase. We assembled a cohort of deeply phenotyped individuals of European ancestry with relapse-onset multiple sclerosis. We used unbiased genome-wide association study and machine learning approaches to assess the genetic contribution to longitudinally defined multiple sclerosis severity phenotypes in 1,813 individuals. Our primary analyses did not identify any genetic variants of moderate to large effect sizes that met genome-wide significance thresholds. The strongest signal was associated with rs7289446 (β=-0.4882, P = 2.73 × 10−7), intronic to SEZ6L on chromosome 22. However, we demonstrate that clinical outcomes in relapse-onset multiple sclerosis are associated with multiple genetic loci of small effect sizes. Using a machine learning approach incorporating over 62,000 variants together with clinical and demographic variables available at multiple sclerosis disease onset, we could predict severity with an area under the receiver operator curve of 0.84 (95% CI 0.79–0.88). Our machine learning algorithm achieved positive predictive value for outcome assignation of 80% and negative predictive value of 88%. This outperformed our machine learning algorithm that contained clinical and demographic variables alone (area under the receiver operator curve 0.54, 95% CI 0.48–0.60). Secondary, sex-stratified analyses identified two genetic loci that met genome-wide significance thresholds. One in females (rs10967273; βfemale =0.8289, P = 3.52 × 10-8), the other in males (rs698805; βmale = -1.5395, P = 4.35 × 10-8), providing some evidence for sex dimorphism in multiple sclerosis severity. Tissue enrichment and pathway analyses identified an overrepresentation of genes expressed in central nervous system compartments generally, and specifically in the cerebellum (P = 0.023). These involved mitochondrial function, synaptic plasticity, oligodendroglial biology, cellular senescence, calcium and g-protein receptor signalling pathways. We further identified six variants with strong evidence for regulating clinical outcomes, the strongest signal again intronic to SEZ6L (adjusted hazard ratio 0.72, P = 4.85 × 10-4). Here we report a milestone in our progress towards understanding the clinical heterogeneity of multiple sclerosis outcomes, implicating functionally distinct mechanisms to multiple sclerosis risk. Importantly, we demonstrate that machine learning using common single nucleotide variant clusters, together with clinical variables readily available at diagnosis can improve prognostic capabilities at diagnosis, and with further validation has the potential to translate to meaningful clinical practice change.

Complex patterns shape immune genes diversity during invasion of common raccoon in Europe – selection in action despite genetic drift

Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon Procyon lotor invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific SNP markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, i.e. – less genetically diverse invasive population from Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to a new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.

Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific

The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young‐of‐the‐year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure, suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n = 1,818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size‐based investigation of population structure and phylogeography of this species in the ETP to date.

Multisite imaging of neural activity using a genetically encoded calcium sensor in the honey bee

Understanding of the neural bases for complex behaviors in Hymenoptera insect species has been limited by a lack of tools that allow measuring neuronal activity simultaneously in different brain regions. Here, we developed the first pan-neuronal genetic driver in a Hymenopteran model organism, the honey bee, and expressed the calcium indicator GCaMP6f under the control of the honey bee synapsin promoter. We show that GCaMP6f is widely expressed in the honey bee brain, allowing it to record neural activity from multiple brain regions. To assess the power of this tool, we focused on the olfactory system, recording simultaneous responses from the antennal lobe, and from the more poorly investigated lateral horn and mushroom body calyces. Neural responses to 16 distinct odorants demonstrate that odorant quality (chemical structure) and quantity are faithfully encoded in the honey bee antennal lobe. In contrast, odor coding in the lateral horn departs from this simple physico-chemical coding, supporting the role of this structure in coding the biological value of odorants. We further demonstrate robust neural responses to several bee pheromone odorants, key drivers of social behavior, in the lateral horn. Combined, these brain recordings represent the first use of a neurogenetic tool for recording large-scale neural activity in a eusocial insect, and will be of utility in assessing the neural underpinnings of olfactory and other sensory modalities and of social behaviors and cognitive abilities.

Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity

Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.