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Nq microsatellite data for COLONY
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Data from: Mating system of Caiman yacare (Reptilia Alligatoridae) described from microsatellite genotypes
The yacare caiman (Caiman yacare) is a reptile from South America and 1 of the 2 crocodilian species present in Argentina. The degradation of their natural habitat and strong hunting pressure led to a sharp numerical decline of wild populations. Nowadays, C. yacare is included in Appendix II of CITES, and ranching practices in some areas in Argentina are helping hatching success. In this context, it is important to better understand the population structure and mating system of the species. To do this, we amplified 10 microsatellite markers (SSRs) in 148 individuals of 13 C. yacare nests. All of the markers were polymorphic with 2–12 alleles per locus, with allelic sizes ranging between 154 and 400 bp and medium levels of polymorphism (H o = 0.152–0.551 and H e = 0.221–0.621). We were able to determine the maternal genotype in 9 out of 13 nests. In 6 of them we found more than 1 paternal genotype, with a maximum of 3 fathers for a single nest. This study is the first to provide evidence of multiple paternity behavior. These findings will be useful to improve management and conservation strategies for the species.
Microsatellite genotypes of Camellia oleifera for GenoDive analysis
<p><i>Camellia oleifera</i>, a hexaploid evergreen broadleaf shrub or small tree, is the dominant woody oilseed crop in China. Understanding the spatial pattern of genetic diversity in wild <i>C. oleifera</i> is essential for conservation and utilization of genetic resources. Six wild <i>C. oleifera</i> populations were sampled along a latitudinal gradient in subtropical evergreen broadleaf forests of Southern China. A new high-throughput sequencing-based microsatellite genotyping method was developed to resolve allele dosage uncertainty in hexaploid wild <i>C. oleifera </i>with 35 microsatellite markers. Finally, the dataset of mcrosatellite genotypes was generated with corrected allele dosages. In addition, another dataset of microsatellite genotypes with uncorrected allele dosages (showing only different alleles) was generated, for mimicking the situation of current microsatellite genotyping methods.</p>
Guppy MHC and microsatellite genotypes, gyrodactylid infection trials, and analysis code
<p>Natural host populations differ in their susceptibility to infection by parasites, and these intra-population differences are still an incompletely understood component of host-parasite dynamics. In this study, we used controlled infection experiments with wild-caught guppies (<em>Poecilia reticulata</em>) and their ectoparasite <em>Gyrodactylus turnbulli</em> to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with Major Histocompatibility Complex (MHC) 'supertypes'. Controlling for intra-population differences and potential inbreeding variance, we found a significant negative relationship between individual-level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype-specific effects. We conclude that population-level differences in host infection susceptibility likely reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.</p>
Fig. 1 in Microsatellite variation and population genetic structure of a neotropical endangered Bryconinae species Brycon insignis Steindachner, 1877: implications for its conservation and sustainable management
Fig. 1. Location of sampling sites of Brycon insignis in drainages in Southeastern Brazil. Power Company Hatchery (PCH), São João River (SJR), Paraíba do Sul River (PSR), Imbé River (IMR), Muriaé River (MUR) and Itabapoana River (ITR).
Microsatellite data of Avicennia marina from Gazi Bay, Kenya
<p>Mangrove ecosystems along the East African coast are often characterized by a disjunct zonation of seaward and landward <i>Avicennia marina</i>. This disjunct zonation may be maintained through different positions in the tidal frame, yielding different dispersal settings. The spatial configuration of the landscape and coastal processes such as tides and waves are expected to largely influence the extent of propagule transport and subsequent regeneration. We hypothesized that landward sites would keep a stronger genetic structure over short distance in comparison to enhanced gene flow among regularly flooded seaward fringes. We tested this hypothesis from densely vegetated <i>A. marina</i> transects of a well-documented mangrove system (Gazi Bay, Kenya) and estimated local gene flow and kinship-based fine scale genetic structure. Ten polymorphic microsatellite markers in 457 <i>A. marina</i> trees revealed no overall significant difference in levels of allele or gene diversities between sites that differ in hydrological proximity. Genetic structure and connectivity of <i>A. marina</i> populations however indicated an overall effect of geographic distance and revealed a pronounced distinction between channels and topographic setting. Migration models allowed to infer gene flow directionality among channels, and indicated a bidirectional steppingstone between seaward and nearest located landward stands. Admixed gene pools without any fine-scale structure were found within the wider and more exposed Kidogoweni river estuary, suggesting open systems. Elevated kinship values and structure over 5 to 20 m distance were only detected in two distant landward and seaward transects near the mouth of the Mkurumuji River, indicating local retention and establishment. Overall, our findings show that patterns of <i>A. marina</i> connectivity are explained by hydrological proximity, channel network structure, and hydrokinetic energy, rather<i> </i>than just their positioning as disjunct landward or seaward zones.</p>
Figure 5 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 5 - Simplified network of Bactrocera carambolae and Bactrocera dorsalis groups, and the sequential disconnection of the network. The network was constructed using eight SSRs. Scanning was done for decreasing thresholds A is the fully connected network B is the percolation threshold (Dp = 0.20, with all links corresponding to distances superior to Dp excluded). DP, JK, and NT are connecting between Bactrocera carambolae and Bactrocera dorsalis groups. Red dashed lines with number are corresponded to the threshold values, revealing serial disconnection of the network C is the lowest threshold (thr = 0.15).
Figure 4 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 4 - Simplified network of seven Bactrocera carambolae populations, and the sequential forms of cluster. The network was constructed using eight SSRs. Scanning was done for decreasing thresholds A is the fully connected network B is the percolation threshold (Dp = 0.52, with all links corresponding to distances superior to Dp excluded). JK plays an important role connecting between native and introduced populations C–D are the lower thresholds chosen (thr = 0.40 and 0.15, respectively) to reveal sub-structured network.
Figure 3 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 3 - The individual admixture plot for K = 3. Each bar reveals a single individual. Each color of bars represents each genetic cluster. Samples of Bactrocera carambolae belong to clusters 2 and 3 (green and blue, respectively) while samples of Bactrocera dorsalis belong to cluster 1 (red). Potential hybrids have a proportion of genetic cluster (Q) between 0.100 to 0.900 (0.100 ≤ Q ≤ 0.900) as identified with asterisk (*).
Figure 1 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 1 - Sampling collections of Bactrocera carambolae and Bactrocera dorsalis in this study. Seven populations of Bactrocera carambolae (blue dots) were collected from Southeast Asia and Suriname. Three populations of Bactrocera dorsalis (red dots) were sampled from East and Southeast Asia. Two other unidentified populations (purple dots) were included. Information for each population is described in Table 1.
Figure 6 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 6 - Simplified network of the SY5 strain and wild populations, and the sequential disconnection of the network. The network was constructed using seven SSRs. Scanning was done for decreasing thresholds A is the fully connected network B is the percolation threshold (Dp = 0.23, with all links corresponding to distances superior to Dp excluded). DP, JK, and NT are connecting between Bactrocera carambolae and Bactrocera dorsalis groups C is the lowest threshold (thr = 0.15). Red dashed lines with number are corresponded to the threshold values, revealing serial disconnection of the network.
Figure 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 2 - Three-dimensional plot of Principal Coordinate Analysis (PCoA) and STRUCTURE analysis. A the planes of the first three principal coordinates explain 43.65%, 20.13%, and 16.91% of total genetic variation, respectively, for seven Bactrocera carambolae populations using eight SSRs B the planes of the first three principal coordinates explain 33.05%, 23.17%, and 15.87%, respectively, for Bactrocera carambolae and Bactrocera dorsalis groups using eight SSRs C the planes of the first three principal coordinates explain 30.50%, 22.14%, and 18.53%, respectively, for the SY5 strain and wild populations using seven SSRs. Pie graphs, consisting of different colored sections, represent co-ancestor distribution of 185, 289, and 321 individuals in A two, B three, and C two hypothetical clusters, respectively.
Spotted turtle dispersal microsatellite DNA sex and site data
<p>Sex-biased dispersal is common in many animals, with male-biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male-male competition and a lack of male parental care. Few studies of sex-biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male-biased dispersal as expected. We tested for sex-biased dispersal in the endangered freshwater turtle, the spotted turtle (<em>Clemmys</em> <em>guttata</em>) by investigating fine-scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances < 25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy-Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex-biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of < 25 km in <em>C</em>. <em>guttata</em>, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size.</p>
Sheepnose mussel (P. cyphyus) microsatellite dataset for population genetic analysis
<p class="Body">North American freshwater mussel species have experienced substantial range fragmentation and population reductions. These impacts have the potential to reduce genetic connectivity among populations and increase the risk of losing genetic diversity. Thirteen microsatellite loci and an 883 bp fragment of the mitochondrial ND1 gene were used to assess genetic diversity, population structure, contemporary migration rates, and population size changes across the range of the Sheepnose mussel (<em>Plethobasus cyphyus</em>). Population structure analyses reveal five populations, three in the Upper Mississippi River Basin and two in the Ohio River Basin. Sampling locations exhibit a high degree of genetic diversity and contemporary migration estimates indicate that migration between populations within river basins is occurring, although at low rates. but no migration is occurring between the Ohio and Mississippi river basins. No evidence of bottlenecks was detected, and almost all locations exhibited the signature of population expansion. Our results indicate that although anthropogenic activity has altered the landscape across the range of the Sheepnose, these activities have yet to be reflected in losses of genetic diversity. Efforts to conserve Sheepnose populations should focus on maintaining existing habitats and fostering genetic connectivity between extant demes to conserve remaining genetic diversity for future viable Sheepnose populations.</p>
A Phase II Study of Futibatinib and Pembrolizumab in Metastatic Microsatellite Stable Endometrial Carcinoma
ClinicalTrials.gov study NCT05036681. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study to Assess Efficacy of RXC004 +/- Nivolumab in Ring Finger Protein 43 (RNF43) or R-spondin (RSPO) Aberrated, Metastatic, Microsatellite Stable, Colorectal Cancer After Progression on Standard o
ClinicalTrials.gov study NCT04907539. IPD Sharing: NO. Countries: 4. Publications: 0.
Anti-PD-1 Antibody Plus Regorafenib in Refractory Microsatellite Stable Metastatic Colorectal Cancer
ClinicalTrials.gov study NCT05942768. IPD Sharing: YES. Countries: 1. Publications: 0.
A Study to Evaluate the Efficacy and Safety of Standard-of-Care Chemotherapy and Bevacizumab With or Without INCA33890 in the First-Line Treatment of Metastatic Microsatellite Stable Colorectal Cancer
ClinicalTrials.gov study NCT07284849. IPD Sharing: YES. Countries: 0. Publications: 0.
Efficacy and Safety of Olaparib in Pretreated Patients With Measurable Colorectal Cancer, Stratified by Microsatellite Instability (MSI) Status
ClinicalTrials.gov study NCT00912743. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study of Nivolumab and Relatlimab in Patients With Microsatellite Stable (MSS) Advanced Colorectal Cancer
ClinicalTrials.gov study NCT03642067. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
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