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FIGURE 3. A in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity

FIGURE 3. A) Distribution of the Glandulocaudinae and the topographic and tectonic features of SE South America. Double lines corresponds to the main axes of Quaternary tectonics in the area (according to Saadi, 1993; Saadi et al., 2002 and Riccomini et al. 2001) B) The same area showed within the contest of major tectonic provinces of South American Platform. I – South American Platform; II – Patagonian massif; III – Andean orogenic belt; IV – foreland basins; AM = Amazon craton; SL = São Luis craton; SF = São Francisco craton; LA = Luiz Alves craton; RP = Rio de la Plata craton; B = Borborema province; T = Tocantins province; M = Mantiqueira province; DF = Dom Feliciano belt. (Modified from Cordani et al., 2000).

FIGURE 2. Phylogenetic relationships between T. cinnabarinus and T. urticae inferred from ITS2 in Genetic Relationship between the Carmine Spider Mite Tetranychus cinnabarinus (Boisduval) and the Two-spotted Mite T. urticae Koch in China Based on the mtDNA COI and rDNA ITS2 Sequences

FIGURE 2. Phylogenetic relationships between T. cinnabarinus and T. urticae inferred from ITS2 data of Neighbor- Joining methods. Phylogenetic tree was established by MEGA based on Kimura-2-parameter distance. Numbers on branches indicate the percentage of 100 bootstraps supporting the branching pattern shown. Two sequences of T. evansi and T. pacificus were used as outgroups.

FIGURE 1 in Genetic Relationship between the Carmine Spider Mite Tetranychus cinnabarinus (Boisduval) and the Two-spotted Mite T. urticae Koch in China Based on the mtDNA COI and rDNA ITS2 Sequences

FIGURE 1. Phylogenetic tree inferred from COI sequences of various samples of T. urticae and T. cinnabarinus. The Neighbor-Joining (NJ) method was used based on distances calculated using Kimura-2-parameter correction method. Numbers on branches indicate the percentage of 100 bootstraps supporting the branching pattern shown. The species Petrobia harti and Bryobia kissophila were used as outgroups. Mite colouration for each sample is indicated in brackets: (R) means red form of T. urticae; (G) means green form of T. urticae.

FIGURE 1 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity

FIGURE 1. Representatives of the Glandulocaudinae and their caudal organs. A) Lophiobrycon weitzmani; paratype, LIRP 4338, photo by R.M.C. Castro; B) Glandulocauda melanogenys, uncatalogued specimens, collected at Estação Biológica de Boracéia, Rio Guaratuba basin, photo by J.C. Nolasco C) Mimagoniates microlepis, photo by R.L. Corte. Arrows indicate the caudal-fin rays 11 and 12. (modified from Menezes & Weitzman, 1990 and Castro et al. 2003).

FIGURE 1 in An interactive identification key for genets and oyans (Carnivora, Viverridae, Genettinae, Genetta spp. and Poiana spp.) using Xper²

FIGURE 1. Xper² interface showing the three columns with adjustable labels: (left) identification procedure, with character partitions ("Groups"), characters ("Descriptors"), character states ("States") and characters used ("Description in progress"); (central) contextual information on taxa and characters, with "Definition" and "Images"; (right) list of "Remaining taxa" and "Dismissed taxa".

opencc-zeroOct 2019View details →

Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and inter-population spatial scales

Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.

opencc-zeroOct 2019View details →

Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.

Data from: Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore

Harvest can disrupt wildlife populations by removing adults with naturally high survival. This can reshape sociospatial structure, genetic composition, fitness, and potentially affect evolution. Genetic tools can detect changes in local, fine-scale genetic structure (FGS) and assess the interplay between harvest-caused social and FGS in populations. We used data on 1,614 brown bears, Ursus arctos, genotyped with 16 microsatellites, to investigate whether harvest intensity (mean low: 0.13 from 1990-2005, mean high: 0.28 from 2006-2011) caused changes in FGS among matrilines (8 matrilines; 109 females ≥ 4 years of age), sex-specific survival and putative dispersal distances, female spatial genetic autocorrelation, matriline persistence, and male mating patterns. Increased harvest decreased FGS of matrilines. Female dispersal distances decreased and male reproductive success was redistributed more evenly. Adult males had lower survival during high harvest, suggesting that higher male turnover caused this redistribution and helped explain decreased structure among matrilines, despite shorter female dispersal distances. Adult female survival and survival probability of both mother and daughter were lower during high harvest, indicating that matriline persistence was also lower. Our findings indicate a crucial role of regulated harvest in shaping populations, decreasing differences among 'groups', even for solitary-living species, and potentially altering the evolutionary trajectory of wild populations.

Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides butterfly populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

Data from: The genetic landscape of axonal neuropathies in the middle aged and elderly: focus on MME (supplementary information)

OBJECTIVE: To test the hypothesis that monogenic neuropathies such as Charcot-Marie-Tooth disease (CMT) contribute to frequent but often unexplained neuropathies in the elderly, we performed genetic analysis of 230 patients with unexplained axonal neuropathies and disease onset >35 years. METHODS: We recruited patients, collected clinical data and conducted whole-exome sequencing (WES, n=126) and MME single-gene sequencing (n=104). We further queried WES repositories for MME variants and measured blood levels of the MME-encoded protein neprilysin. RESULTS: In the WES cohort, the overall detection rate for assumed disease-causing variants in genes for CMT or other conditions associated with neuropathies was 18.3% (familial cases 26.4%, apparently sporadic cases 12.3%). MME was most frequently involved and accounted for 34.8% of genetically solved cases. The relevance of MME for late-onset neuropathies was further supported by detection of a comparable proportion of cases in an independent patient sample, preponderance of MME variants among patients compared to population frequencies, retrieval of additional late-onset neuropathy patients with MME variants from WES repositories, and low neprilysin levels in patients' blood samples. Transmission of MME variants was often consistent with an incompletely penetrant autosomal dominant trait and less frequently with autosomal recessive inheritance. CONCLUSIONS: A detectable fraction of unexplained late-onset axonal neuropathies is genetically determined, either by variants in CMT genes or genes involved in other conditions that affect the peripheral nerves and can mimic a CMT phenotype. MME variants can act as completely penetrant recessive alleles but also confer dominantly inherited susceptibility to axonal neuropathies in an aging population.

Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean

Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.

Data from: Genetic structuring among colonies of a pantropical seabird: Implication for subspecies validation and conservation

Appendix S1 <table> <tbody> <tr> <td>Table S1</td> <td>Details of field researchers and licences under which they took blood samples from white-tailed tropicbirds from populations in the years of study</td> </tr> <tr> <td>Table S2</td> <td>Morphometrics of 616 individual white-tailed tropicbirds from 11 populations. Population codes are as described in Table 1.</td> </tr> <tr> <td>Table S3</td> <td>Raw microsatellite genotypes for 382 individual White-tailed tropicbird from 13 populations. Population codes are as described in Table 1</td> </tr> <tr> <td>Table S4</td> <td>Details of mtDNA sequences </td> </tr> <tr> <td>Table S5</td> <td>Tests of bottleneck (P-values for one-tailed Wilcoxon's signed rank test for heterozygosity excess) based on 10 microsatellites in 13 populations of Phaethon lepturus</td> </tr> <tr> <td>Table S6</td> <td>Pairwise FST estimates based on nuclear microsatellite variation (above diagonal), and ΦST estimates based on mtDNA sequence (below diagonal) for 11 populations with sample sizes >5 ('Pop's) of Phaethon lepturus (see Table 1 for population codes)</td> </tr> </tbody> </table>

Data from: Genetic Variation in Plethodon cinereus and Plethodon hubrichti from in and Around a Contact Zone

Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk—particularly in range-restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~ 18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red-backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.

Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across a SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.

Transcriptome dataset to: Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development

This collection contains RNA-seq data obtained from young flower buds of Silene latifolia for each sample in the main manuscript in triplicate (male, female, two generations of hermaphrodites). The RNA was isolated from adult plants of U15 population and two subsequent generations, made by full-sib mating (U15=15 generations, U16=16 generations, U17=17 generations). The petals and sepals were removed before RNA-isolation. To avoid the bias made by sampling of old flower buds, only the first flowers were always sampled. The deposited RNA-seq data were not processed.

Data from: Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts

Several studies have demonstrated the ecological consequences of genetic variation within a single plant species. For example, these studies show that individual plant genotypes support unique composition of the plants' associated arthropod community. By contrast, fewer studies have explored how plant genetic variation may influence evolutionary dynamics in the plant's associated species. Here, we examine how aphids respond evolutionarily to genetic variation in their host plant. We conducted two experiments to examine local adaptation and rapid evolution of the free-feeding aphid Chaitophorus populicola across genetic variants of its host plant, Populus angustifolia. To test for local adaptation, we collected tree cuttings and aphid colonies from three sites along an elevation / climate gradient and conducted a reciprocal transplant experiment. In general, home aphids (aphid transplanted onto trees from the same site) produced 1.7-3.4 times as many offspring as foreign aphids (aphids transplanted onto trees from different sites). To test for rapid evolution, we used 4 clonally replicated aphid genotypes and transplanted each onto 5 clonally replicated P. angustifolia genotypes. Each tree genotype started with the same aphid genotype composition. After 21 days (~two aphid generations), aphid genotype composition changed (i.e. aphids evolved) and some tree genotypes supported unique evolutionary trajectories of aphids. These results suggest that plant evolution in response to human perturbation, such as climate change and invasive species will also result in evolutionary responses in strongly interacting species that could cascade to affect whole communities.

Wild strawberry shows genetic variation in tolerance but not resistance to a generalist herbivore

Plants' defenses against herbivores usually include both resistance and tolerance mechanisms. Their deployment has predominantly been studied in either single plant genotypes, or multiple genotypes exposed to single herbivores. In natural situations, however, most plants are attacked by multiple herbivores. Therefore, aims of this study were to assess and compare effects of single and multiple herbivores on plant resistance and tolerance traits, and the consequences for overall plant performance. For this, we exposed multiple genotypes of wild woodland strawberry (Fragaria vesca) to jasmonic acid (JA), to mimic chewing herbivory and induce the plants' defense responses, then introduced the generalist herbivore Spodoptera littoralis to feed on them. We found that woodland strawberry consistently showed resistance to S. littoralis herbivory, with no significant genetic variation between the genotypes. By contrast, the studied genotypes showed high variation in tolerance, suggesting evolutionary potential in this trait. Prior JA application did not alter these patterns, although it induced an even higher level of resistance in all tested genotypes. The study provides novel information that may be useful for breeders seeking to exploit tolerance and resistance mechanisms to improve strawberry crops' viability and yields, particularly when multiple herbivores pose significant threats.

Growth-defense tradeoffs shape the genetic composition of aspen forests

All organisms experience fundamental conflicts between divergent metabolic processes. In plants, a pivotal conflict occurs between allocation to growth, which accelerates resource acquisition, and to defense, which protects existing tissue against herbivory. Tradeoffs between growth and defense traits are not universally observed, and a fundamental prediction of plant evolutionary ecology is that context-dependence of these tradeoffs contributes to the maintenance of intraspecific variation in defense. This prediction has rarely been tested, however, and the evolutionary consequences of growth-defense tradeoffs in different environments are poorly understood. Here we show that intraspecific trait tradeoffs interact with competitive environment to drive natural selection of tree genotypes corresponding to their growth-defense phenotypes. Our results show for the first time that a functional trait tradeoff, when coupled with environmental variation, causes real-time divergence in the genetic architecture of forest stands. Specifically, competitive selection for faster growth resulted in dominance by fast-growing tree genotypes that were poorly defended against natural enemies. This outcome is a signature example of eco-evolutionary dynamics: competitive interactions affected microevolutionary trajectories on a timescale relevant to subsequent ecological interactions. Eco-evolutionary drivers of tree growth and defense are thus critical to stand-level trait variation, which structures communities and ecosystems over expansive spatiotemporal scales.

opennotspecifiedMar 2018View details →

Figure 3 in Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis, the spot-tailed earless lizards of Texas

Figure 3. Hind limb blotches of (a) Holbrookia lacerata lacerata (UTA R 63333) and (b) H. l. subcaudalis (UTA R 63303). In H. l. lacerata, most blotches are oblong and fused into bands. In H. l. subcaudalis, blotches are ellipsoid.