Find research datasets worth reusing

Figure 11. Morphotype B in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 11. Morphotype B, CE1130, Nais communis/variabilis. A, anterior ventral, segment II; B, posterial ventral, segment unknown; C, dorsal. Scale bars: 3 Mm.

Figure 4. Morphotype A2 in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 4. Morphotype A2, CE1143, Nais communis/variabilis. A, anterior ventral, segment III; B, posterior ventral, segment IX; C, dorsal. Scale bars: 3 Mm.

Figure 15. Morphotype D in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 15. Morphotype D, CE3300 (A), CE4096 (B), and CE1919 (C), Nais elinguis. A, anterior ventral, segment II; B, posterior ventral, segment XI; C, dorsal. Scale bars: 3 Mm.

Figure 20. Morphotype G in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 20. Morphotype G, CE1263, Nais christinae. A, anterior ventral, segment II; B, posterior ventral, segment VII; C, dorsal. Scale bars: 3 Mm.

Figure 19. Morphotype F in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 19. Morphotype F, CE2901, Nais barbata. A, anterior ventral, segment II; B, posterior ventral, segment VI; C, dorsal. Scale bars: 3 Mm.

Figure 7. Morphotype A3 in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 7. Morphotype A3: CE1144 (A), CE3656 (B), CE3500 (C), Nais communis/variabilis. A, anterior ventral, segment IV; B, posterior ventral, segment XI; C, dorsal. Scale bars: 3 Mm.

Figure 2. Morphotype A1 in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 2. Morphotype A1, CE3494, Nais communis/variabilis. A, anterior ventral, segment II; B, posterior ventral, segment VIII; C, dorsal. Scale bars: 3 Mm.

Figure 3. Morphotype A1 in Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae)

Figure 3. Morphotype A1, CE4104, Nais communis/variabilis. A, anterior ventral, segment II; B, posterior ventral, segment XII; C, dorsal. Scale bars: 3 Mm.

Life‐stage‐dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas

Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using ddRAD-derived SNPs. A reduced proportion of homozygotes with a chromosomal inversion located in LG1 was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No neutral genetic differences were found between samples from the Northern cod stock; however, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: 1) the Newfoundland Atlantic Coast, 2) eastern and southern Gulf of St. Lawrence and Burgeo Bank, and 3) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote rebuilding.

Stan code from: Branching networks can have opposing influences on genetic variation in riverine metapopulations

Aim: Fractal networks, represented by branching complexity in rivers, are ubiquitous in nature. In rivers, the number of either distal (e.g., in headwater streams) or confluent (e.g., in mainstems) locations can be increased along with their branching complexity. Distal- or confluent-spatial locations can result in fewer or greater corridor linkages that can alter genetic divergence at the metapopulation scale. These mechanisms underlying the resulting genetic structuring remain poorly understood at the metapopulation scale, particularly in terms of the roles of species-specific dispersal traits. The objective of this study is to mechanistically understand how branching complexity can simultaneously influence genetic divergence in opposite directions. Location: Northeastern Japan Methods: To evaluate the integrated influences of network complexity and species dispersal on genetic divergence among populations at the catchment scale, we modelled metapopulation genetic dynamics under a Bayesian inference framework by adapting empirical genetic data from four macroinvertebrate species. Simulations were then performed using empirical and virtual species-characteristics on virtual river networks. Results: Our simulation experiments showed that both greater landscape connectivity (resulting from shorter watercourse distance) and greater isolation of distal locations occurred in the more-branched river networks. These two spatial features have negative and positive influences on genetic divergence, with their relative importance varying among different species and dispersal characteristics. Specifically, genetic divergence at the metapopulation scale increased for species having higher downstream-biased dispersal but decreased for species having higher upstream-biased dispersal. Distal populations (e.g., in headwaters) have higher genetic independence when downstream-biased asymmetry is higher. Main conclusions: We found a strong association between species dispersal and evolutionary processes such as gene flow and genetic drift. This association mediates the pervasive influences of branching complexity on genetic-divergence in the metapopulation. It also highlights the importance of considering species dispersal-patterns when developing management strategies in the face of rapid environmental-change scenarios.

Genetic control of arbuscular mycorrhizal colonization by Rhizophagus intraradices in Helianthus annuus (L.)

Plant symbiosis with arbuscular mycorrhizal (AM) fungi provides many benefits, including increased nutrient uptake, drought tolerance, and belowground pathogen resistance. To develop a better understanding of the genetic architecture of mycorrhizal symbiosis, we conducted a genome-wide association study (GWAS) of this plant-fungal interaction in cultivated sunflower. A diversity panel of cultivated sunflower (Helianthus annuus L.) was phenotyped for root colonization under inoculation with the AM fungus Rhizophagus intraradices. Using a mixed linear model approach with a high-density genetic map, we identified genomic regions that are likely associated with R. intraradices colonization in sunflower. Additionally, we used a set of twelve diverse lines to assess the effect that inoculation with R. intraradices has on dried shoot biomass and macronutrient uptake. Colonization amongst lines in the mapping panel ranged from 0-70% and was not correlated with mycorrhizal growth response, shoot phosphorus response, or shoot potassium response among the Core 12 lines. Association mapping yielded three single nucleotide polymorphisms (SNPs) that were significantly associated with R. intraradices colonization. This is the first study to use GWAS to identify genomic regions associated with AM colonization in an Asterid eudicot species. Three genes of interest identified from the regions containing these SNPs are likely related to plant defense.

Population genetics informs the management of a controversial Australian waterbird

Widespread degradation across Australia's inland wetland network has contributed to severe declines for many waterbird species. In contrast, breeding colonies of the Australian white ibis (Threskiornis molucca) have increased in urbanised areas along the coast, but the level of dispersal and gene flow between inland and coastal areas remain unknown. This study uses single nucleotide polymorphisms (SNPs) to ascertain the variables influencing genetic connectivity among several inland and urban colonies of white ibis across south-eastern Australia between 2015 and 2018. The contemporary effective population size was estimated, and this value was used in simulations to evaluate the impact of various management scenarios on future genetic diversity. We found no significant differences in allele frequencies between localities, or robust evidence of site fidelity, therefore suggesting widespread dispersal and gene flow between inland and urban colonies. Furthermore, effective sizes were large enough to maintain genetic diversity into the future under various realistic management scenarios. However, the lack of genetic partitioning found suggests that urban management of the ibis should not be undertaken in isolation of the conservation requirements of inland colonies.

opencc-by-4.0Sep 2021View details →

Raw data for Characterization of the genetic switch from phage ɸ13 important for human colonization by Staphylococcus aureus

Raw data for the manuscript with the title "Characterization of the genetic switch from phage ɸ13 important for human colonization by Staphylococcus aureus". All data produced in the study can be found in this Excel file.

A genetically based ecological trade-off contributes to setting a geographic range limit

Understanding the ecological factors that shape geographic range limits and the evolutionary constraints that prevent populations from adaptively evolving beyond these limits is an unresolved question. Here, we investigated why the euryhaline fish, Poecila reticulata, is confined to freshwater within its native range, despite being tolerant of brackish water. We hypothesized that competitive interactions with a close relative, Poecilia picta, in brackish water prevents P. reticulata from colonizing brackish water. Using a combination of field transplant, common garden breeding, and laboratory behavior experiments we find support for this hypothesis, as P. reticulata are behaviorally subordinate and have lower survival in brackish water with P. picta. We also found a negative genetic correlation between P. reticulata growth in brackish water versus freshwater in the presence of P. picta, suggesting a genetically based trade-off between salinity tolerance and competitive ability could constrain adaptive evolution at the range limit.

Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape

The dataset consists of 9 microsatellite markers used to analyze reticulated flatwoods salamanders' (Ambystoma bishopi) population structure on Eglin AFB. Samples came from various breeding ponds and allele sizes were scored using GeneMapper (GeneMapper v4.0; Applied Biosystems). Data was collected via allele scoring in GeneMapper by two independent researchers. Allele sizes for each individual have been re-formatted for various programs using the microsatellite Add-in in Excel as well as by using the GenAlEx extension in Excel.

Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura,restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

Do genetic differences in growth thermal reaction norms maintain genetic variation in timing of diapause induction?

<ol> <li>An optimal timing for diapause induction through the sexual production of dormant propagules is expected in organisms with temporary populations. Yet, empirical studies often find high within-population genetic variation in the sexual production of such propagules, suggesting that this is a common feature of such organisms.</li> <li>Here, we hypothesize that genetic variation in the propensity to produce dormant propagules, Pd, is maintained by a genotype-by-environment interaction in clonal reproductive rates, where fast-growing genotypes within an environment should delay diapause relative to slow-growing genotypes. From this, we derive two predictions. First, if reaction norms of clonal reproduction cross between two environments, the genetic correlation of Pd between these environments should be negative. Second, the correlation between plasticity values of clonal reproduction and Pd should be negative.</li> <li>We tested these predictions by quantifying ephippia production in genotypes of a population of the facultative sexual cladoceran Daphnia magna at two temperatures. The population biomass at the onset of ephippia production was used as a measure of Pd, whereas juvenile somatic growth rate was used as a proxy for clonal reproductive rate. Plasticity for both measurements was derived from thermal reaction norms.</li> <li>Our results did not support either prediction, as neither the genetic correlation of Pd between environments, nor the correlation between plasticity values of growth and Pd were found to be significant.</li> <li>Our results suggest that genetic variation in the timing of diapause is not maintained by genetic differences in thermal clonal reproduction reaction norms. We propose as an alternative hypothesis that if there is across year variation in how stochastically the environment deteriorates, fluctuating selection may favor genotypes with different Pd between years.</li> </ol>

Pronounced genetic separation among varieties of the Primula cusickiana species complex, a Great Basin endemic

Distinguishing between populations with strong genetic structure and unique species is a common challenge in systematics, especially for taxa occurring in fragmented habitats where allopatric speciation may be widespread and distinct groups may be morphologically similar. Such is often the case with species complexes across sky island environments. In these scenarios, biogeography may help to explain the taxonomic relations between species complex members, and restriction site-associated DNA (RAD) sequencing methods are commonly used to compare closely related species across thousands of loci. Here we use RADseq to clarify the boundaries separating the geographically distinct but morphologically similar varieties of the Primula cusickiana species complex, and to contextualize past findings of strong genetic structure among populations within varieties. Our genetic analyses demonstrate pronounced separation between isolated populations of this Great Basin endemic, indicating that the current varietal classification of complex members is inaccurate, and emphasizing their conservation importance. We discuss how these results correspond to recent biogeographical models used to describe the distribution of other sky island taxa in western North America. Our findings also fit into a wider trend observed for alpine Primula species complexes, and we consider how edaphic specialization and heterostylous breeding systems may be contributing to frequent diversification via allopatric speciation in this genus.

IUCN Red List protects avian genetic diversity

Despite well-established links between low genetic diversity and extinction processes, intra-specific genetic diversity is rarely considered in global conservation assessments, potentially leading to biased estimates of species' extinction risk. We show that birds ranked as "threatened" by the IUCN Red List have lower intra-specific genetic diversity than "non-threatened" species, confirming that threat criteria, used by the IUCN, effectively protect genetically depleted species. However, some "non-threatened" species harbour low levels of genetic diversity, indicating an undetected vulnerability to global change. Global conservation assessments will benefit from explicitly integrating relevant genetic and genomic diversity-based measures in estimates of species' extinction risk.