Find research datasets worth reusing

Fig. 4 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems

Fig. 4. Amobia burnsi (Malloch, 1930), ♂, NSW, North Head, Sydney Harbour, 14 Feb. 1978, G. Daniels leg. (AM) A. Habitus, lateral view. B. Head, lateral view. C. Habitus, dorsal view. D. Head, dorsal view. E. Abdomen, dorsal view. F. Left wing, dorsal view. G. Head, anterior view. Scale bars: 1 mm.

Fig. 1 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems

Fig. 1. Maximum likelihood phylogenetic tree indicating the placement of Amobia among the global Miltogramminae, inferred from COI, CYTB, ND4 and EF1α sequence data. With the exception of the three newly sequenced Australian Amobia and Macronychia rubesca, data was acquired from Piwczyński et al. (2017). Node support values are shown for both maximum likelihood analysis (bootstrap support, 1000 iterations; in bold font) and Bayesian analysis (posterior probability, 40 million generations), 'NA' indicates nodes resolved that were not resolved by the Bayesian analysis. Branch length scale = 0.3 nucleotide substitutions per site (calculated by the GTR+G nucleotide substitution model).

Fig. 6 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems

Fig. 6. Amobia serpenta sp. nov., holotype, ♂, NT, Serpentine Gorge, West MacDonnell National Park, 13 Nov. 2017, Johnston, Wallman and Szpila leg. (ANIC). A. Habitus, lateral view. B. Head, lateral view. C. Habitus, dorsal view. D. Head, dorsal view. E. Abdomen, dorsal view. F. Left wing, dorsal view. G. Head, anterior view. Scale bars: 1 mm.

Fig. 3 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems

Fig. 3. Amobia auriceps (Baranov, 1935), male terminalia, QLD, Cairns, 1919, J.F. Illingworth leg. (BM). A. Epandrium, cerci, surstyli and phallus, posterior view. B. Epandrium, cerci, surstyli, phallus and pre-gonite, lateral view. Abbreviations: c = cercus; d = distal lobe of phallus; s = surstylus; p = pregonite. Scale bars: 100 µm.

Fig. 5 in Taxonomic revision of Australian Amobia Robineau-Desvoidy, 1830 (Sarcophagidae: Miltogramminae): integrating morphology and genetics finds a new species and tackles old problems

Fig. 5. Amobia burnsi (Malloch, 1930), male terminalia, NT, 15 km N Katherine, 16 May 2005, R.W. Matthews leg (ANIC). A. Epandrium, cerci, surstyli and phallus, posterior view. B. Epandrium, cerci, surstyli, phallus and pre-gonite, lateral view. C. SEM image of epandrium, gonites, cerci and surstyli, posterior view. D. SEM image of epandrium, gonites, phallus, cerci and surstyli, lateral view. Abbreviations: c = cercus; d = distal lobe of phallus; s = surstylus; p = pre-gonite. Scale bars: 100 µm.

opencc-zeroDec 2023View details →

dryad40/100

Data from: harnessing the power of regional baselines for broad-scale genetic stock identification: a multistage, integrated, and cost-effective approach

In mixed-stock fishery analyses, genetic stock identification (GSI) estimates the contribution of each population to a mixture and is typically conducted at a regional scale using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines due to non-overlapping populations and genetic markers. In cases where the mixture contains stocks spanning across a wide area, a broad-scale baseline is created, but often at the cost of resolution. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analysis of mixtures containing individuals from a broad geographic range. This method employs a multistage framework that allows disparate baselines to be used in a single integrated process that produces estimates along with the propagated errors from each stage. All individuals in the mixture sample are required to be genotyped for all genetic markers in the baselines used by this model, but the baselines do not require overlap in genetic markers or populations representing the broad-scale or regional baselines. We demonstrate our integrated multistage GSI model using a synthesized data set made up of Chinook salmon, Oncorhynchus tshawytscha, from the North Bering Sea of Alaska. The data set is designed to be run using R package, Ms.GSI, and it does not represent the composition of the real fishery. The results show an improved accuracy for estimates using an integrated multistage framework, compared to the conventional framework of using separate hierarchical steps. The integrated multistage framework allows GSI of a wide geographic area without first developing a large scale, high-resolution genetic baseline or dividing a mixture sample into smaller regions beforehand. This approach is more cost-effective than updating range-wide baselines with all regionally important markers.

dryad40/100

High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 SNP makers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and P. glauca based on 27,052 makers and 11,609 gene sequences. Altogether, these two linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed herein opens new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.

opencc-zeroJan 2024View details →

Figure 6 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 6. Variation of the live adult male paratype GZNU20220705001 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view.

Figure 1 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 1. Sampling localities of Rana zhijinensis Luo, Xiao & Zhou, sp. nov., R. culaiensis, R. hanluica, and R. omeimontis in Guizhou Province, China. A. Guiguo Town, Zhijin County; B. Supu Town, Qianxi County; C. Zhujianshan Nature Reserve, Huangping County; D. Leigongshan National Nature Reserve, Leishan County.

Figure 2 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 2. Phylogenetic tree based on three mitochondrial genes and six nuclear genes. A. Maternal tree; B. Nuclear gene tree. In both phylogenetic tree, ultrafast bootstrap support (UFB) values from ML analyses/Bayesian posterior probabilities (BPP) from BI analyses are given beside nodes. Scale bars denote nucleotide substitutions per sites for mitochondrial and nuclear genes.

Figure 5 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 5. Morphological features of the live adult male holotype GZNU2018081606 of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. A. Dorsolateral view; B. Dorsal view; C. Ventral view; D. Egg cluster; E. Ventral view of hand and dark gray-blackish nuptial pad; F. Ventral view of foot.

Figure 4 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 4. Haplotype networks of Rana zhijinensis Luo, Xiao & Zhou, sp. nov. and its related species constructed based on the nuclear gene sequences. Different species of the R. japonica group are shown as different colors.

Figure 3 in Description of a new species of the genus Rana (Anura: Ranidae) from western Guizhou, China, integrating morphological and molecular genetic data

Figure 3. Phylogenetic tree based on four mitochondrial genes and six nuclear genes. In this phylogenetic tree, UFB from ML analyses/ BPP from BI analyses are given beside nodes. The scale bar represents 0.03 nucleotide substitutions per site. Red lines represent species delimitation results of bPTP and BPP.

Fig. 5 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

Fig. 5. Decision tree used for specimens euthanized to obtain tissue. Blue indicates steps in the decision tree. Green indicates procedures that will lead to preservation of tissues for genetic study. Purple indicates procedures that lead to achieving multiple goals, including cell culture and obtaining gametes for current or future ARTs. NOTE: Breeding and IVF can result in offspring that can be used for genetic purposes, thereby achieving multiple goals.

Fig. 6 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

Fig. 6. Decision tree used to obtain tissue from live animals. Blue indicates steps in the decision tree. Green indicates procedures that will lead to preservation of tissues for genetic study. Purple indicates procedures that lead to achieving multiple goals, including obtaining gametes for current or future ARTs. NOTE: Breeding and IVF can result in offspring that can be used for genetic purposes, thereby achieving multiple goals.

Fig. 4 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

Fig. 4. Length of time from cell culture initiation to freezing for amphibian cell lines in San Diego Zoo's Frozen Zoo®. Low = 19 days; high = 596 days; average = 154 days.

Fig. 3 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

Fig. 3. The "tissue piecing" protocol used to preserve viable cells for establishment of cell lines in the future. A) Tissue is cut into long, thin strips. B) Tissue is diced into 1 mm3 fragments before adding medium containing 10% DMSO as a cryoprotectant. C) Prepared tissue is stored in LN2 until future cell culture is possible; those without cell culture capability can transport samples using a dry shipper to maintain cold-chain.

Fig. 2 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

Fig. 2. Procedures used to obtain amphibian eggs or sperm for use in ARTs. A) Gravid female Leopard Frog (Lithobates sp.) after gonadotropic hormone injection. B) Expressing eggs into container by pressing on abdomen and pushing thumb toward cloaca; eggs can be fertilized (i.e., IVF) by fresh or cryopreserved sperm. Sperm can similarly be released from males by pushing towards the cloaca and releasing sperm naturally (in season) or after injection of gonadotropic hormones (e.g., HIS).

Fig. 1 in P e r s p e c t i v e Integrating current methods for the preservation of amphibian genetic resources and viable tissues to achieve best practices for species conservation

Fig. 1. Role of genetic resource collections in the research and conservation of amphibians. Green indicates the storage of tissues in biobanks. Purple indicates procedures associated with ARTs that lead to achieving multiple goals in amphibian research and conservation. Asterisk (*) denotes tissue or methodologies that are not currently used in ARTs but may be possible in the future. NOTE: For a more complete list of ARTs reference Clulow et al. (2014).