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opencc-zeroDec 2013View details →

Data from: Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.

opencc-zeroDec 2010View details →

Data from: Detection of outlier loci and their utility for fisheries management

Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific ("outlier") effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide ("neutral") effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments, however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening >11,000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among-sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.

opencc-zeroDec 2017View details →

Data from: Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species

Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species and thus their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less-successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.

opencc-by-4.0Jul 2021View details →

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

Assembled sequence alignments and phylogenetic trees for plastomes and nuclear loci for 24 samples of Crataegus.

opencc-zeroDec 2015View details →

Data from: Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations - "outlier loci" (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated FST when sequenced in new samples from the original locations, and also not to follow predictable geographical patterns of elevated FST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of FST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased FST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared to more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated FST in geographically distant locations. We discuss possible explanations for this unexpected result.

opencc-zeroJul 2021View details →

Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.

opennotspecifiedMay 2011View details →

Fig. 1 in Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci

Fig. 1. Simultaneous-analysis parsimony JK tree of all morphological and molecular characters with parsimony JK values above each branch, and likelihood BS values (for the matrix of all nucleotide characters) below each branch. Clades in the parsimony JK tree that were contradicted by clades in the likelihood BS tree are indicated by XX, with BS support for the highest contradictory likelihood clade listed.

opencc-zeroAug 2021View details →

UK dogs data from: Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci

Background: Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems across countries. In this study, we incorporated routinely assessed CHD records and genotype data of German Shepherd dogs from two countries (UK and Sweden) to perform genome-wide association studies (GWAS) within populations using different variations of CHD phenotypes. As phenotypes, dogs were either classified into cases and controls based on the Fédération Cynologique Internationale (FCI) five-level grading of the worst hip or the FCI grade was treated as an ordinal trait. In a subsequent meta-analysis, we added publicly available data from a Finnish population and performed the GWAS across all populations. Genetic associations for the CHD phenotypes were evaluated in a linear mixed model using 62,089 SNPs. Results: Multiple SNPs with genome-wide significant and suggestive associations were detected in single-population GWAS and the meta-analysis. Few of these SNPs overlapped between populations or between single-population GWAS and the meta-analysis, suggesting that many CHD-related QTL are population-specific. More significant or suggestive SNPs were identified when FCI grades were used as phenotypes in comparison to the case-control approach. MED13 (Chr 9) and PLEKHA7 (Chr 21) emerged as novel positional candidate genes associated with hip dysplasia. Conclusions: Our findings confirm the complex genetic nature of hip dysplasia in dogs, with multiple loci associated with the trait, most of which are population-specific. Routinely assessed CHD information collected across countries provide an opportunity to increase sample sizes and statistical power for association studies. While the lack of standardisation of CHD assessment schemes across countries poses a challenge, we showed that conversion of traits can be utilised to overcome this obstacle.

opennotspecifiedJan 2012View details →

FIGURES 1–2 in High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.

FIGURES 1–2. Helichus cordubensis: 1, male genitalia, ventral view; 2, lateral view of same. Locality of specimen used for the illustration: "Alta Gracia, La Granja. Sierra de Córdoba, Cordoba province, Argentina".

FIGURE 10 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 10. Fruit surface (SEM) of Atraphaxis davurica (A–C), A. davurica var. chikoensis (D), A. selengensis (E–F) from RUSSIA, Buryatia, A. pungens (G–H), A. frutescens (I): A, B—Selenginsky d., Dede-Sutoy, Kazanovsky ID 965 (NSK). C—Borgoysky Ridge, Peshkova & Tarasova 953 (NSK). D—the Kudara river, Kursky (LE). E—Selenginsky d., Deben, Badmaeva (MW). F—Dzhidinsky d., Ust-Kyakhta, Peshkova & Tarasova 2698 (NSK). G—RUSSIA, Altai Rep., Kosh-Agach d., the Kokorya river, Gordeeva & Ustiantseva (LE). H—MONGOLIA, Khovd aimag, Sherin & Shalimov (ALTB). I—MONGOLIA, SW Mongolia, Baytag-Bogdo, Gubanov 2551 (MW). Scale Bar = 30 µm.

FIGURE 8 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 8. Stigmas (SEM) of Atraphaxis davurica (A–B, E), A. davurica var. chikoensis (C–D), A. selengensis (F) from RUSSIA, Buryatia, and A. pungens (G–I): A—Selenginsky d., Novoselenginsk, Kazanovsky 42812 (MW). B—Selenginsky d., Dede-Sutoy, Kazanovsky ID 965 (NSK). C—Khentei- Chikoy Highlands, Anagustay, Maximova (LE). D—the Kudara river, Khankharnegu, Kursky (LE). E—Dzidinsky d., Borgoysky Ridge, Peshkova & Tarasova 953 (NSK). F—Selenginsky d., Deben, Badmaeva (MW). G—RUSSIA, Khakassia, Askiz d., Kazanovka, Skvortsov (MW). H—RUSSIA, Altai Rep., Kosh-Agach d., the Kokorya river, Gordeeva & Ustiantseva (LE). I—MONGOLIA, Central aimag, Budantsev et al. 27 (MW). Scale Bar = 100 µm (B, D–F, H–I); =200 µm (A); =300 µm (C, G).

FIGURE 6 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 6. Perianths of Atraphaxis davurica (A–D), A. davurica var. chikoensis (E–F) from RUSSIA, Buryatia, A. pungens (G–I), A. selengensis (J–L) from RUSSIA, Buryatia, and A. frutescens (M–O) from RUSSIA, Tuva. A—Mukhorshibirsky d., Podlopatki, Abramova et al. (MW). В—Selenginsky d., Lake Sulfatnoye, Badmaeva (MW). C—Selenginsky d., Zurgan-Debe, Chepinoga & Rosbah 16359 (UUH, IRKU). D—Dzhidinsky d., Erkhirik, Badmaeva (MW). E—the Kudara river, Khankharnegu, Kursky (LE). F—Khentei-Chikoy Highlands, Anagustay, Maximova (LE). G—MONGOLIA, Bulgan aimak, Khangai, 90 km NEE of Kharkharin, Gubanov 3563 (MW). H—RUSSIA, Khakassia, Shira d., Fyrkal, Kostikov (NS). I—RUSSIA, Altai Rep., Kosh- Agach d., Chuya, Kamelin et al. (LE). J—Selenginsky d., Enkhor, Korolyuk 236 (UUH). K—Dzhidinsky d., Ust-Kyakhta, Ubur-Dzokoy, Peshkova & Skudenkova 2700 (NSK). L—Selenginsk, Schukin (MW). M—Ulug-Khem d., the Senek River, Lomonosova, Medvedeva 547 (MW). N—Pyi-Khemsky d., Uyuk ridge, the Yenisei River, Kostikov (NS). O—Ulug-Khem d.,Torgalyk, Schreter (MW). Scale Bar =1 mm (A–K, M–O); =0.5 mm (L).

FIGURE 7 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 7. Stigmas of Atraphaxis davurica (A–G), A. davurica var. chikoensis (H–I), A. selengensis (J) from RUSSIA, Buryatia, A. pungens (K–M), and A. frutescens (N–O). A—Selenginsky d., lake Gusinoye, Sandanov sd 15-166 (UUH). B—Selenginsky d., Dede-Sutoy, Shamanova ID 18122 (IRK). C–D— Mukhorshibsky d., Podlopatki, Abramova et al. (MW). E—Selenginsky d., Zurgan-Debe. Chepinoga & Rosbah 16359 (UUH, IRKU). F, G—Dzhidinsky d., Borgoysky Ridge, Dyrestuy, Pozdnyakova (UUH). H—The Kudara river, Khankharnegu, Kursky. (LE). I—Khentei- Chikoy Highlands, Anagustay, Maximova (LE, Holotype). J—Dzhidinsky d., Ust-Kyakhta, Ubur-Dzokoy, Peshkova & Skudenkova 2700 (NSK). K—RUSSIA, Khakassia, Askiz d., Kazanovka, Skvortsov (MW). L—MONGOLIA Central aimag, Mt. Dzamryn-Ula, Budantsev et al. 27 (MW). M—MONGOLIA, Bulgan aimag, Khangai, Kharkharin, Gubanov 3563 (MW). N, O—RUSSIA, Hortus Upsaliensis, Ehrhart 2744 (MW). Scale Bar = 0.5 mm (A, C, E, F, H); = 1 mm (I); = 0.2 mm (B, D, G, J–M); =0.1 mm (N, O).

FIGURE 3 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 3. Thyrses of Atraphaxis davurica (A), A. davurica var. chikoensis (B), A. pungens (C), A. selengensis (D–E) and A. frutescens from RUSSIA (F). A—Buryatia, Mukhorshibirsky d., Podlopatki, Abramova et al. (MW). B—Buryatia, Khentei-Chikoy Highlands, Anagustay, Maximova (LE). C—Khakassia, Askiz d., Kazanovka, Skvortsov (MW). D—Buryatia, Selenginsk, Poplavskaya & Sukachev 3286 (LE). E—Buryatia, Selenginsk, Daeva (MHA, Holotype). F—Novosibirsk region, Ordynsky d., Antonovo, Kostikov (NS)

FIGURE 4 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 4. Ochreas and ochreolas of Atraphaxis davurica (A–F), A. davurica var. chikoensis (G–I), A. selengensis (J–M) from RUSSIA, Buryatia, and A. pungens (N–O) from RUSSIA, Khakassia. A, C—Selenginsky d., lake Krugloye, Badmaeva (MW). B—Dzhidinsky d., Dyrestuy, Badmaeva (MW). D—Selenginsky d., lake Gusinoye, Sandanov Sd 15-166 (UUH). E—Selenginsky d., Dede-Sutoy, Shamanova ID 18122 (IRK). F—Selenginsky d., Gusinoosersk, Makeeva (MW). G–I—Khentei-Chikoy Highlands, Anagustay, Maximova (LE). J—Dzhidinsky d., Ust-Kyakhta, Ubur-Dzokoy, Peshkova & Skudenkova 2700 (NSK). K, L—Selenginsky d., Enkhor, Korolyuk 236 (UUH). M—Selenginsk d., Novoselenginsk, Peshkova & Skudenkova 1499 (NSK). N, O—Askiz d., Kazanovka, Skvortsov (MW). Scale Bar =1 mm.

FIGURE 2 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 2. Atraphaxis davurica (A), A. davurica var. chikoensis (B), A. pungens (C), A. selengensis (D–E) from RUSSIA, and A. frutescens from MONGOLIA (F). A—Buryatia, Mukhorshibirsky d., Podlopatki, Abramova et al. (MW). B—Buryatia, Khentei-Chikoy Highlands, Anagustay, Maximova (LE). C—Khakassia, Askiz d., Kazanovka, Skvortsov (MW). D—Buryatia, Selenginsk, Schukin (LE). E—Buryatia, Selenginsk, Daeva (MHA, Holotype). F—Khovd aimag, Bulgan, Gubanov 7503 (MW).

FIGURE 5 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 5. Leaf blades of A. davurica (A–D), A. davurica var. chikoensis (E), A. selengensis (F–G) from RUSSIA, Buryatia, A. frutescens (H–I) from MONGOLIA, A. pungens (J–L) from RUSSIA. A—Selenginsky d., lake Gusinoye, the Silve River, Verkhozina et al. 2396, ID1273 (IRK). B—Selenginsky d., lake Gusinoye, Badmaeva (MW). C—Selenginsky d., Gusinoosersk, lake Gusinoye, Urbanavichene Br-u-117 (MW). D—Selenginsk d., lake Sulfatnoye, Badmaeva s.n. (MW). E—Khentei-Chikoy Highlands, Anagustay, Maximova (LE, Holotype). F, G—Selenginsky d., Enkhor, Korolyuk 236 (UUH). H, I—Mongol Altay, Bayan-Olygiy aimag, the Bulgan river, Kamelin et al. 2298. (MW). J—Khakassia, Askiz d., Kazanovka, Skvortsov (MW). K—Tuva, Kyzyl d., Sukpak, Kostikov (NS). L—Khakassia, Ordzhonikidze d., Iyus, Mt. Sunduk, Kostikov (NS). Scale Bar =1 mm.

FIGURE 1 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 1. The results of ML and BI analyses applied to the combined chloroplast data set (trnL(UAA) intron + trnL-trnF IGS and rpl32- trnL (UAG) IGS) of Atraphaxis with Bactria ovczinnikovii taken as an outgroup. Numbers above or below branches indicate the aLRT support values equal or more than 0.7 / the posterior probabilities from Bayesian analysis equal or more than 0.9.

FIGURE 9 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 9. Fruits of Atraphaxis davurica (A–D), A. selengensis (E–F) from RUSSIA, Buryatia, A. pungens (G–H), and A. frutescens (I). A—Dzhidinsky d., Borgoysky Ridge, Dyrestuy, Pozdnyakova (UUH). B—Dzhidinsky d., Borgoysky Ridge, between Temnik and Dzhida, Smirnov 2654 (LE). C—Selenginsky d., Lake Gusinoye, Badmaeva (MW). D—Kyakhtinsky d., vill. Altai, Friesen 479 (NSK). E— Selenginsky d., Enkhor, Korolyuk 236 (UUH). F—Selenginsky d., Novoselenginsk, Peshkova & Skudenkova 1444 (NSK). G—RUSSIA, Altai Rep., Kosh-Agach d., Chuya, Kamelin et al. (LE). H—MONGOLIA, Central aimag, Mt. Dzamryn-Ula, Budantsev et al. 27 (MW). I—RUSSIA, Hortus Upsaliensis, Ehrhart 2744 (MW). Scale Bar =1 mm

FIGURE 11 in A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: II. Atraphaxis selengensis spec. nov., and A. davurica Jaub. & Spach from Russian Transbaikalia

FIGURE 11. Pollen (SEM) of Atraphaxis selengensis (A, B), A. davurica (C–G), A. davurica var. chikoensis (H–J) from RUSSIA, Buryatia, and A. pungens (K–L) from RUSSIA, Khakassia. A, B—Dzhidinsky d., Ust-Kyakhta, Peshkova, Tarasova 2698 (NSK). C, D—Kyakhta d., Ust-Kiran, Peshkova, Skudenkova 170 (MW). E–G—Dzhidinsky d., Petropavlovka, Peshkova, Tarasova 504 (NSK). H–J—Khentei-Chikoy Highlands, Anagustay, Maximova (LE). K, L—Askiz d., Kazanovka, Skvortsov s.n. (MW). Scale Bar = 10 µm (A, C–F, H, K–L); = 3 µm (B, I–J); = 1 µm (G).