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637 results for “Population analysis”
Data from: Quantitative analysis of connectivity in populations of a semi-aquatic mammal using kinship categories and network assortativity
Analyzing the impact of anthropogenic and natural river barriers on the dispersal of aquatic and semi-aquatic species may be critical for their conservation, but no adequate genetic methods have been developed for quantifying the effect of specific barriers on current connectivity. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring how the last few generations of offspring have dispersed. In this study, we used kinship data to analyze connectivity patterns in a small semi-aquatic mammal, the Pyrenean desman, in an area comprising two river systems with close headwaters and dams of various sizes. Using a large SNP dataset from 70 specimens, we obtained kinship categories and reconstructed pedigrees. To quantify the barrier effect of specific obstacles, we constructed kinship networks and devised a method based on the assortativity coefficient, which measures the proportion between observed and expected kinship relationships across a barrier. The estimation of this parameter enabled us to infer that the most important barrier in the area was the watershed divide between the rivers, followed by a dam on one of the rivers. Other barriers did not significantly reduce the expected number of kinship relationships across them. This strategy and the information obtained with it may be crucial in determining the most important connectivity problems in an area and help develop conservation plans aimed at improving genetic exchange between populations of threatened species.
Figure 2 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 2. Neighbor-joining (Saitou and Nei 1987) cladogram, based on the net nucleotide divergence.
The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets
<p class="CxSpFirst">The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the Δ<i>K</i> method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of <i>K</i> and is sensitive to uneven sampling. If this finding holds for empirical datasets, conclusions about the scale of gene flow may have to be revised for a large number of studies. To determine the impact of method choice, we applied recently described estimators of <i>K</i> to re-estimate genetic structure in 41 empirical microsatellite datasets; 15 from a broad range of taxa and 26 focused on a diverse phylogenetic group, coral. We compared alternative estimates of <i>K</i> (Puechmaille statistics) with traditional (Δ<i>K</i> and posterior probability) estimates and found widespread disagreement of estimators across datasets. Thus, one estimator alone is insufficient for determining the optimal number of clusters regardless of study organism or evenness of sampling scheme. Subsequent analysis of molecular variance (AMOVA) between clustering solutions did not necessarily clarify which solution was best. To better infer population structure, we suggest a combination of visual inspection of STRUCTURE plots and calculation of the alternative estimators at various thresholds in addition to Δ<i>K</i>. Differences between estimators could reveal patterns with important biological implications, such as the potential for more population structure than previously estimated, as was the case for many studies reanalyzed here.</p>
Figure 2 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 2 - AFLP Autoradiogram of pigeon pea cyst nematode Heterodera cajani with EcoRI (+AAG) + MseI, (+CAG) and EcoRI (+AAA) + MseI (CTA). Lane 1 to 11: Heterodera cajani populations from Andhra Pradesh, Allahabad, Bahadurgarh, Coimbatore, Kanpur-1, Ghaziabad, Gilberga, Hisar, Delhi, Kanpur-2, andMeja.
Figure 3 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 3 - Dendograms from cluster analysis of Heterodera cajani a) for 1278 amplified restriction fragment digests using 24 primer pairs and b) the four primer pairs that suggest a similar dendogram to the full set. The using the upper tail rule the best cut procedure indicated the highest number of significant cluster partitions was 3 as in both cases with realised deviates and t statistics respectively of a) 1.47 and 4.66 and b) 1.59 and 5.04.
Figure 1 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 1 - Dendograms from cluster analysis a) for the nine biometric measurements made on second stage juveniles of eleven populations of Heterodera cajani (see Table 2 for data) b) vulval cones of cysts of the same populations. (See Table 3 for data). The using the upper tail rule the best cut procedure indicated the highest number of significant cluster partitions was for a) 2 and for b) 3 with realized deviates and t- statistics respectively of a) 2.71 and 8.56 and b) 1.04 and 3.27.
Figure 4 from: Rao U, Rao S, Rathi A, Gothalwal R, Atkinson H (2011) A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis. ZooKeys 135: 1-19. https://doi.org/10.3897/zookeys.135.1344
Figure 4 - India Map showing distances of collected 11 Heterodera cajani populations with distances in (Kilometres)
Figure 2 from: Tanga CM, Manrakhan A, Daneel JH, Mohamed SA, Khamis FM, Ekesi S (2015) Comparative analysis of development and survival of two Natal fruit fly Ceratitis rosa Karsch (Diptera, Tephritidae) populations from Kenya and South Africa. 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: 467-487. https://doi.org/10.3897/zookeys.540.9906
Figure 2 - Linear and non-linear regressions of temperature related developmental rates of immature stages of two groups of Ceratitis rosa from South Africa
Figure 1 from: Tanga CM, Manrakhan A, Daneel JH, Mohamed SA, Khamis FM, Ekesi S (2015) Comparative analysis of development and survival of two Natal fruit fly Ceratitis rosa Karsch (Diptera, Tephritidae) populations from Kenya and South Africa. 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: 467-487. https://doi.org/10.3897/zookeys.540.9906
Figure 1 - Linear and non-linear regressions of temperature related developmental rates of immature stages of two groups of Ceratitis rosa from Kenya.
Figure 3 from: Bu Y, Ma Y, Luan Y-X (2016) Paracerella Imadaté in China: the description of a new species and the analysis of genetic differences between populations (Protura, Acerentomata, Nipponentomidae). ZooKeys 604: 1-11. https://doi.org/10.3897/zookeys.604.8737
Figure 3 - Paracerella sinensis sp. n. holotype. A Tergite VII (psm= posterosubmedial) B tergite VIII C sternite I D sternite II E sternite IV F sternite VI (spm= sternal posteromedial) G sternite VII H striate band of abdominal VIII I Tergite VIII–XII J sternites VIII–XII. Arrows indicate pores. Scale bars: 20 μm.
Figure 2 from: Bu Y, Ma Y, Luan Y-X (2016) Paracerella Imadaté in China: the description of a new species and the analysis of genetic differences between populations (Protura, Acerentomata, Nipponentomidae). ZooKeys 604: 1-11. https://doi.org/10.3897/zookeys.604.8737
Figure 2 - Paracerella sinensis sp. n. holotype. A Habitus B ventral side of head (s=sensillum) C pronotum D mesonotum E metanotum F prosternum G mesosternum H metasternum I tergite I, right side J tergite III, right side. Arrows indicate pores. Scale bars: (A)100 μm, others, 20 μm.
Figure 1 from: Bu Y, Ma Y, Luan Y-X (2016) Paracerella Imadaté in China: the description of a new species and the analysis of genetic differences between populations (Protura, Acerentomata, Nipponentomidae). ZooKeys 604: 1-11. https://doi.org/10.3897/zookeys.604.8737
Figure 1 - Paracerella sinensis sp. n. holotype. A Head, dorsal view (cp = clypeal pore, fp = frontal pore) B pseudoculus C canal of maxillary gland D labial palpus E maxillary palpus (d = dorsal sensillum, v = ventral sensillum) F foretarsus, exterior view G foretarsus, interior view H foretarsus, interolateral view (paratype No. LM6-14D) I comb J female quama genitalis. Scale bars: (A, F–H) 50 μm; others, 20 μm.
Investigating population dynamics from parentage analysis in the highly endangered fan mussel Pinna nobilis
<p>Understanding dispersal patterns is a major focus for conservation biology as it influences local survival and resilience in case of local disturbance, particularly for sessile species. Dispersal can be assessed through parentage analyses by estimating family structure and self-recruitment. This study documents the family structure of a pelagic spawner, <i>Pinna nobilis</i>, which is facing a major crisis that threatens its survival as most of its populations have been decimated by a parasite, <i>Haplosporidium pinnae</i>. In this context, we focused on a single population (Peyrefite, Banyuls-sur-mer, France) where 640 individuals were sampled in 2011, 2015 and 2018 and genotyped for 22 microsatellite markers. Genetic diversity was high and homogeneous among years, with mean allele numbers ranging between 13.6 and 14.8 and observed heterozygosities (<i>Ho</i>) between 0.7121 and 0.7331. Low, but significant, genetic differentiations were found between 2011 - 2015 and 2015 - 2018. A parentage analysis described 11 clusters, including one prevailing, and revealed that 46.9 % of individuals were involved in half-sib relationships, even between years, suggesting that source populations were recurrent year after year. There were few individuals resampled between years (30 in 2015 and 14 in 2018), indicating a rapid turnover. Considering the large number of half-sib relationships but the low number of relations per individual, we conclude that <i>P. nobilis</i> exhibit homogeneous reproductive success. Self-recruitment was not detected, making this population highly vulnerable as replenishment only relies on connectivity from neighboring populations. In the context of the pandemic caused by <i>H. pinnae</i>, these results will have to be considered when choosing a location to reintroduce individuals in potential future rescue plans.</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>
Fig. 3 in Comparative analysis of the population structure of Crematogaster subdentata and Lasius neglectus in the primary and secondary ranges (Hymenoptera: Formicidae)
Fig. 3 – Scheme of the foraging areas of Crematogaster subdentata in Rostov-on-Don large accessible nests of C. subdentata in buildings and outside; inaccessible nests of C. subdentata in buildings; trees: Ac – Acer sp., Ae – Aesculus hippocastanum, Aj – Albizia julibrissin, Al – Ailanthus altissima, An – Acer negundo, C – Campsis radicans, Fr – Fraxinus sp., Gl – Gleditsia triacanta, J – Juglans regia, Mn – Morus nigra, Pa – Prunus americana, Pc – Prunus cerasus, Pp – Populus niger, Ps – Prunus spinosa, Ra – Robinia pseudoacacia, Tl – Tilia sp., Ul – Ulmus sp., V – Viburnum sp.
Figure 1 in Otolith shape analysis of three gobiid species of the Northwestern Black Sea and characterization of local populations of Neogobius melanostomus
Figure 1. – Landings of gobies on the Romanian Black Sea coast between 1970 and 2010. Data sources: FAO 2005; Creţeanu, NAFA (National Agency for Fisheries and Aquaculture Romania, pers. comm.). Uncertainty in data sources between 1989 and 2000 are indicated by dotted line. Fishing effort in terms of number of fishermen, cumulated number of months of activity for all fishermen, number of boats, tonnage and power of engines are indicated for the last period (2006 and 2010).
Population Pharmacokinetic Analysis of Daptomycin in Patients With Osteoarticular Infections
ClinicalTrials.gov study NCT03134521. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Data from: Analysis of iris surface features in populations of diverse ancestry
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Data from: "Development of the draft genome sequence of the marbled flounder Pseudopleuronectes yokohamae as a reference of population genomic analysis" in Genomic Resources Notes accepted 1 February 2015 – 31 March 2015
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Data from: Relative accuracy of three common methods of parentage analysis in natural populations
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