Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect ...data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both "recent" and "deep" timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus.
Climate‐induced expansion of invasive hybridization (breeding between invasive and native species) poses a significant threat to the persistence of many native species worldwide. In the northern U.S. ...Rocky Mountains, hybridization between native cutthroat trout and non‐native rainbow trout has increased in recent decades due, in part, to climate‐driven increases in water temperature. It has been postulated that invasive hybridization may enhance physiological tolerance to climate‐induced thermal stress because laboratory studies indicate that rainbow trout have a higher thermal tolerance than cutthroat trout. Here, we assessed whether invasive hybridization improves cardiac performance response to acute water temperature stress of native wild trout populations. We collected trout from four streams with a wide range of non‐native admixture among individuals and with different temperature and streamflow regimes in the upper Flathead River drainage, USA. We measured individual cardiac performance (maximum heart rate, “MaxHR”, and temperature at arrhythmia, “ArrTemp”) during laboratory trials with increasing water temperatures (10–28°C). Across the study populations, we observed substantial variation in cardiac performance of individual trout when exposed to thermal stress. Notably, we found significant differences in the cardiac response to thermal regimes among native cutthroat trout populations, suggesting the importance of genotype‐by‐environment interactions in shaping the physiological performance of native cutthroat trout. However, rainbow trout admixture had no significant effect on cardiac performance (MaxHR and ArrTemp) within any of the three populations. Our results indicate that invasive hybridization with a warmer‐adapted species does not enhance the cardiac performance of native trout under warming conditions. Maintaining numerous populations across thermally and hydrologically diverse stream environments will be crucial for native trout to adapt and persist in a warming climate.
Abstract
Variation in life history traits can arise from both genetic and environmental factors. We investigated reproductive activity and variation in some life history traits among four lizard ...species Sceloporus bicanthalis, S. subniger (viviparous), S. aeneus and S. scalaris (oviparous) from different populations of the S. scalaris group. We consider that the phylogenetic history of the group might explain the similarities in the reproductive and life history traits. In oviparous species, reproductive activity was seasonal, as well as the viviparous S. subniger, but S. bicanthalis showed continuous breeding. Sceloporus aeneus showed the smallest snout–vent length (SVL) at sexual maturity. There were also differences in SVL and clutch/litter size among species. Clutch/litter size was positively correlated with female SVL in most species. However, egg mass/volume did not vary among species or populations. Among populations within a species, there were differences in SVL (S. aeneus), clutch size and egg volume (S. scalaris) for oviparous species. In addition, similarities in SVL (S. scalaris, S. bicanthalis), egg mass (S. scalaris) and litter size (S. bicanthalis) were found in both oviparous and viviparous species. These results showed that variation in these life history traits are due to environmental factors and the evolutionary history of the group.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used ...genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)-insectivores and piscivores-that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. "Gerrards" are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence.
Genomic divergence was high between sympatric insectivores and piscivores (Formula: see text = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (Formula: see text = 0.159) that are > 500 km apart. A window-based Formula: see text analysis did not reveal "islands" of genomic differentiation; however, the window with highest Formula: see text estimate did include a gene associated with insulin secretion. Although we explored the use of the "Local score" approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs.
Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences.
A considerable amount of evidence has favored ecological host-fitting, rather than coevolution, as the main mechanism responsible for trypanosome divergence. Nevertheless, beyond the study of human ...pathogenic trypanosomes, the genetic basis of host specificity among trypanosomes isolated from forest-inhabiting hosts remains largely unknown.
To test possible scenarios on ecological host-fitting and coevolution, we combined a host capture recapture strategy with parasite genetic data and studied the genetic variation, population dynamics and phylogenetic relationships of Trypanosoma terrestris, a recently described trypanosome species isolated from lowland tapirs in the Brazilian Pantanal and Atlantic Forest biomes.
We made inferences of T. terrestris population structure at three possible sources of genetic variation: geography, tapir hosts and 'putative' vectors. We found evidence of a bottleneck affecting the contemporary patterns of parasite genetic structure, resulting in little genetic diversity and no evidence of genetic structure among hosts or biomes. Despite this, a strongly divergent haplotype was recorded at a microgeographical scale in the landscape of Nhecolândia in the Pantanal. However, although tapirs are promoting the dispersion of the parasites through the landscape, neither geographical barriers nor tapir hosts were involved in the isolation of this haplotype. Taken together, these findings suggest that either host-switching promoted by putative vectors or declining tapir population densities are influencing the current parasite population dynamics and genetic structure. Similarly, phylogenetic analyses revealed that T. terrestris is strongly linked to the evolutionary history of its perissodactyl hosts, suggesting a coevolving scenario between Perissodactyla and their trypanosomes. Additionally, T. terrestris and T. grayi are closely related, further indicating that host-switching is a common feature promoting trypanosome evolution.
This study provides two lines of evidence, both micro- and macroevolutionary, suggesting that both host-switching by ecological fitting and coevolution are two important and non-mutually-exclusive processes driving the evolution of trypanosomes. In line with other parasite systems, our results support that even in the face of host specialization and coevolution, host-switching may be common and is an important determinant of parasite diversification.
Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing ...non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal-likelihood scores competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation (HME), smoothed harmonic mean estimation (sHME), path-sampling/thermodynamic integration (PS), and stepping-stone (SS) analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that HME and sHME perform poorly compared with PS and SS marginal-likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor delimitation (BFD) of species showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, BFD through PS and SS analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical data sets, harmonic and smoothed harmonic mean marginal-likelihood estimators provided much higher marginal-likelihood estimates than PS and SS estimators. The AICM displayed poor repeatability in both simulated and empirical data sets, and produced inconsistent model rankings across replicate runs with the empirical data. Our results suggest that species delimitation through the use of Bayes factors with marginal-likelihood estimates via PS or SS analyses provide a useful and complementary alternative to existing species delimitation methods.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NMLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Silicon detection is a mature technology for registering the passage of charged particles. At the same time it continues to evolve toward increasing radiation tolerance as well as precision and ...adaptability. For these reasons it is likely to remain a critical element of detection of systems associated with extraterrestrial exploration. Silicon sensor leakage current and depletion voltage depend on the integrated fluence received by the sensor and on its thermal history during and after the irradiation process. For minimal assumptions on shielding and hence on the particle energy spectrum, and using published data on Martian ground temperature, we predict the leakage current density and the depletion voltage, as a function of time, of silicon sensors in transit to and deployed continuously on the Mars surface for a duration of up to 28 Earth-years, for several sensor geometries and a worst-case temperature scenario.
We tested the hypothesis that underrepresented students in active-learning classrooms experience narrower achievement gaps than underrepresented students in traditional lecturing classrooms, averaged ...across all science, technology, engineering, and mathematics (STEM) fields and courses. We conducted a comprehensive search for both published and unpublished studies that compared the performance of underrepresented students to their overrepresented classmates in active-learning and traditional-lecturing treatments. This search resulted in data on student examination scores from 15 studies (9,238 total students) and data on student failure rates from 26 studies (44,606 total students). Bayesian regression analyses showed that on average, active learning reduced achievement gaps in examination scores by 33% and narrowed gaps in passing rates by 45%. The reported proportion of time that students spend on in-class activities was important, as only classes that implemented high-intensity active learning narrowed achievement gaps. Sensitivity analyses showed that the conclusions are robust to sampling bias and other issues. To explain the extensive variation in efficacy observed among studies, we propose the heads-and-hearts hypothesis, which holds that meaningful reductions in achievement gaps only occur when course designs combine deliberate practice with inclusive teaching. Our results support calls to replace traditional lecturing with evidence-based, active-learning course designs across the STEM disciplines and suggest that innovations in instructional strategies can increase equity in higher education.
Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated ...by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes.
Proliferation of genome-scale studies on aquatic species have resulted from the decreasing costs of high-throughput sequencing combined with novel computational approaches.
Our increasing understanding of the genomes of aquatic species has enabled the annotation of loci that are adaptive, sex linked, and associated with phenotype, allowing the inference of evolutionary and demo-genetic processes from spatio-temporal genetic patterns.
Recent improvements in climate and habitat data for aquatic systems provide a more precise characterization of aquatic niches, facilitating landscape genomics.
Many landscape genetic analytical methods have recently been developed specifically for aquatic systems.
We provide a list of spatial and genomic resources as part of a ‘roadmap’ to guide future aquatic landscape genomic studies.
The operational experience and requirements to ensure optimum data quality and data taking efficiency with the 4-layer ATLAS Pixel Detector are discussed. The detector has undergone significant ...hardware and software upgrades to meet the challenges imposed by the Large Hadron Collider (LHC). The LHC is exceeding expectations for instantaneous luminosity by more than a factor of two (to more than 2×1034 cm−2 s−1). Emphasizing radiation damage effects, the key status and performance metrics are described.
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