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19,493 results for “Populism”
Functional consequences of phenotypic variation between locally adapted populations: swimming performance and ventilation in extremophile fish
<p>Natural selection drives the evolution of traits to optimize organismal performance, but optimization of one aspect of performance can often influence other aspects of performance. Here, we asked how phenotypic variation between locally adapted fish populations affects locomotion and ventilation, testing for functional trade-offs and trait-performance correlations. Specifically, we investigated two populations of livebearing fish (<em>Poecilia mexicana</em>) that inhabit distinct habitat types (hydrogen-sulfide-rich springs and adjacent nonsulfidic streams). For each individual, we quantified different metrics of burst swimming during simulated predator attacks, steady swimming, as well as gill ventilation. Coinciding with predictions, we documented significant population differences in all aspects of performance, with fish from sulfidic habitats exhibiting higher steady swimming performance and higher ventilation capacity, but slower burst swimming. There was a significant functional trade-off between steady and burst swimming, but not between different aspects of locomotion and ventilation. While our findings about population differences in locomotion performance largely parallel the results from previous studies, we provide novel insights about how morphological variation might impact ventilation and ultimately oxygen acquisition. Overall, our analyses provided insights into the functional consequences of previously documented phenotypic variation, which will help to disentangle the effects of different sources of selection that may coincide along complex environmental gradients.</p>
Data from: Selection for life-history traits to maximize population growth in an invasive marine species
Species establishing outside their natural range, negatively impacting local ecosystems, are of increasing global concern. They often display life-history features characteristic for r-selected populations with fast growth and high reproduction rates to achieve positive population growth rates (r) in invaded habitats. Here, we demonstrate substantially earlier maturation at a 2 orders of magnitude lower body mass at first reproduction in invasive compared to native populations of the comb jelly Mnemiopsis leidyi. Empirical results are corroborated by a theoretical model for competing life-history traits that predicts maturation at the smallest possible size to optimize r, while individual lifetime reproductive success (R0), optimized in native populations, is near constant over a large range of intermediate maturation sizes. We suggest that high variability in reproductive tactics in native populations is an underappreciated determinant of invasiveness, acting as substrate upon which selection can act during the invasion process.
Data from: Old-growth forests buffer climate-sensitive bird populations from warming
Aim: Habitat loss and climate change constitute two of the greatest threats to biodiversity worldwide, and theory predicts that these factors may act synergistically to affect population trajectories. Recent evidence indicates that structurally complex old-growth forest can be cooler than other forest types during spring and summer months, thereby offering potential to buffer populations from negative effects of warming. Old growth may also have higher food and nest-site availability for certain species, which could have disproportionate fitness benefits as species approach their thermal limits. Location: Pacific Northwestern United States. Methods: We predicted that negative effects of climate change on 30-year population trends of old-growth-associated birds should be dampened in landscapes with high proportions of old-growth forest. We modelled population trends from Breeding Bird Survey data for 13 species as a function of temperature change and proportion old-growth forest. Results: We found a significant negative effect of summer warming on only two species. However, in both of these species, this relationship between warming and population decline was not only reduced but reversed, in old-growth-dominated landscapes. Across all 13 species, evidence for a buffering effect of old-growth forest increased with the degree to which species were negatively influenced by summer warming. Main conclusions: These findings suggest that old-growth forests may buffer the negative effects of climate change for those species that are most sensitive to temperature increases. Our study highlights a mechanism whereby management strategies to curb degradation and loss of old-growth forests—in addition to protecting habitat—could enhance biodiversity persistence in the face of climate warming.
Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for non-model organisms, potentially revolutionising the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (1) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci, and; (2) quantify error rates for loci, alleles and SNPs. As an empirical example we use a double digest RAD dataset of a non-model plant species, Berberis alpina, collected from high altitude mountains in Mexico.
Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains
<p>We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of 'personalized medicine'. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species.</p> <p>Here we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically characterize wild populations of zebrafish from India, Nepal and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic and evolutionary studies in Danio rerio.</p>
Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness
<p>Multiple, simultaneous environmental changes, in climatic/abiotic factors, in interacting species, and in direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate (lambda) from high and low levels of an identified driver from demographic studies of terrestrial plants. Among abiotic drivers, natural disturbance (not climate), and among biotic drivers, interactions with neighboring plants had the strongest effects on lambda. However, when drivers were combined into the three main types, their average effects on lambda did not differ. For the subset of studies that measured both the average and variability of the driver, lambda was more sensitive to one standard deviation of change in abiotic drivers relative to biotic drivers, but sensitivity to biotic drivers was still substantial. Similar impact magnitudes for abiotic/biotic/anthropogenic drivers holds for plants of different growth forms, for different latitudinal zones, and for biomes characterized by harsher or milder abiotic conditions, suggesting that all three drivers have equivalent impacts across a variety of contexts. Thus the best available information about the integrated effects of drivers on all demographic rates provides no justification for ignoring drivers of any of these three types when projecting ecological and evolutionary responses of populations and of biodiversity to environmental changes.</p>
Data from: The socially parasitic ant Polyergus mexicanus has host-associated genetic population structure and related neighboring nests
<p>The genetic structure of populations can be both a cause and a consequence of ecological interactions. For parasites, genetic structure may be a consequence of preferences for host species or of mating behavior. Conversely, genetic structure can determine where conspecific interactions among parasites lay on a spectrum from cooperation to conflict. We used microsatellite loci to characterize the genetic structure of a population of the socially parasitic dulotic (aka "slave-making") ant (<i>Polyergus mexicanus</i>), which is known for its host-specificity and conspecific aggression. First, we assessed whether the pattern of host species use by the parasite has influenced parasite population structure. We found that host species use was correlated with subpopulation structure, but this correlation was imperfect: some subpopulations used one host species exclusively, while others used several. Second, we examined the viscosity of the parasite population by measuring the relatedness of pairs of neighboring parasitic ant nests at varying distances from each other. Although natural history observations of local dispersal by queens suggested the potential for viscosity, there was no strong correlation between relatedness and distance between nests. However, 35% of nests had a closely related neighboring nest, indicating that kinship could potentially affect the nature of some interactions between nests of this social parasite. Our findings confirm that ecological forces like host species selection can shape the genetic structure of parasite populations, and that such genetic structure has the potential to influence parasite-parasite interactions in social parasites via inclusive fitness.</p>
Data and code from: Phenotypic memory drives population growth and extinction risk in a noisy environment
<p>Random environmental fluctuations pose major threats to wild populations. As patterns of environmental noise are themselves altered by global change, there is growing need to identify general mechanisms underlying their effects on population dynamics. This notably requires understanding and predicting population responses to the color of environmental noise, i.e. its temporal autocorrelation pattern. Here, we show experimentally that environmental autocorrelation has a large influence on population dynamics and extinction rates, which can be predicted accurately provided that a memory of past environment is accounted for. We exposed near to 1000 lines of the microalgae <em>Dunaliella salina</em> to randomly fluctuating salinity, with autocorrelation ranging from negative to highly positive. We found lower population growth, and twice as many extinctions, under lower autocorrelation. These responses closely matched predictions based on a tolerance curve with environmental memory, showing that non-genetic inheritance can be a major driver of population dynamics in randomly fluctuating environments. </p>
Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion
Rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction and magnitude of phenotypic evolution during invasion has been underestimated. We explored the utility of niche-shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded from the northeastern coastline of Japan to North America, Europe and northwestern Africa within the last 100 years. A genetically-informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations and as predicted, non-native populations had greater tolerance for ecologically-relevant extreme heat (40ºC) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically-informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions, and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
Data from: Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana
The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter‐population crosses may therefore exhibit heterosis (increased fitness relative to intra‐population crosses). Low genetic diversity and greater genetic distance between populations should increase the magnitude of heterosis. Moreover, drift and selection should remove strongly deleterious recessive alleles from individual populations, resulting in reduced inbreeding depression. To estimate heterosis, we crossed 90 independent line pairs of Arabidopsis thaliana from 15 pairs of natural populations sampled across Fennoscandia, and crossed an additional 41 line pairs from a subset of 4 of these populations to estimate inbreeding depression. We measured lifetime fitness of crosses relative to parents in a large outdoor common garden (8448 plants in total) in central Sweden. To examine the effects of genetic diversity and genetic distance on heterosis, we genotyped parental lines for 869 SNPs. Overall, genetic variation within populations was low (median expected heterozygosity = 0.02), and genetic differentiation was high (median FST = 0.82). Crosses between 10 of 15 population pairs exhibited significant heterosis, with magnitudes of heterosis as high as 117%. We found no significant inbreeding depression, suggesting that the observed heterosis is due to fixation of mildly deleterious alleles within populations. Widespread and substantial heterosis indicates an important role for drift in shaping genetic variation, but there was no significant relationship between fitness of crosses relative to parents and genetic diversity or genetic distance between populations.
Skull shape of a widely-distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations
<p>The biogeographical distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences – geometric morphometrics – to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behaviour, and phenotypic differentiation, allowing us to ask if populations can be distinguished and if patterns of variation indicate adaptability to changing environmental conditions. We analysed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using Principal Components Analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbour similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation - 76% - remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g. specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetics-based conservation studies.</p>
The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
<p class="western"><span>Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. </span></p> <p class="western"><span>The recent analysis of replicate populations from two different </span><span><i>Drosophila simulans</i></span><span> founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. </span></p> <p class="western"><span>Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations.</span></p> <p class="western"> </p>
A transcriptome for the early-branching fern Botrychium lunaria enables fine-grained resolution of population structure
<p>File S1: Alignment of Botrychium CRY2cA sequences used to infer the genus-level phylogeny.</p> <p>File S2: Peptide sequences used to infer the orthogroups named according species names or identifiers (see Table S1).</p> <p>File S3: Alignments of the orthogroup sequences subset used to infer the phylogenomy.</p> <p>File S4: Output files from modeltest-ng named by orthogroup names.</p> <p>File S5: Output files from raxml-ng named by orthogroup names.</p>
The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)
<p>Species often experience spatial <span class="NormalTextRun SCXW235808685 BCX2">environmental </span><span class="NormalTextRun SCXW235808685 BCX2">heterogeneity </span><span class="NormalTextRun SCXW235808685 BCX2">across their range</span><span class="NormalTextRun SCXW235808685 BCX2">, </span><span class="NormalTextRun SCXW235808685 BCX2">and </span><span class="NormalTextRun SCXW235808685 BCX2">populations </span><span class="NormalTextRun SCXW235808685 BCX2">may exhibit </span><span class="NormalTextRun SCXW235808685 BCX2">signatures </span><span class="NormalTextRun SCXW235808685 BCX2">of adaptation to local environmental </span><span class="NormalTextRun SCXW235808685 BCX2">characteristics.</span><span class="NormalTextRun SCXW235808685 BCX2"> Other population</span><span class="NormalTextRun SCXW235808685 BCX2"> genetic</span><span class="NormalTextRun SCXW235808685 BCX2"> processes, </span><span class="NormalTextRun SCXW235808685 BCX2">such as </span><span class="NormalTextRun SCXW235808685 BCX2">migration and genetic drift, </span><span class="NormalTextRun SCXW235808685 BCX2">can </span><span class="NormalTextRun SCXW235808685 BCX2">impede the effect</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2"> of </span><span class="NormalTextRun SCXW235808685 BCX2">local adaptation</span><span class="NormalTextRun SCXW235808685 BCX2">. Genetic drift </span><span class="NormalTextRun SCXW235808685 BCX2">in particular </span><span class="NormalTextRun SCXW235808685 BCX2">can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects lead</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2"> to decreases in genetic variation in the direction of the expansion. </span><span class="NormalTextRun SCXW235808685 BCX2">Here </span><span class="NormalTextRun SCXW235808685 BCX2">we explore the </span><span class="NormalTextRun SCXW235808685 BCX2">genetic diversity</span><span class="NormalTextRun SCXW235808685 BCX2"> of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. </span><span class="NormalTextRun SCXW235808685 BCX2">Based on our analyses of a large SNP dataset, we find evidence </span><span class="NormalTextRun SCXW235808685 BCX2">that both </span><span class="NormalTextRun SCXW235808685 BCX2">climate and demographic history</span><span class="NormalTextRun SCXW235808685 BCX2"> </span><span class="NormalTextRun SCXW235808685 BCX2">have </span><span class="NormalTextRun SCXW235808685 BCX2">shape</span><span class="NormalTextRun SCXW235808685 BCX2">d</span><span class="NormalTextRun SCXW235808685 BCX2"> the </span><span class="NormalTextRun SCXW235808685 BCX2">genetic</span><span class="NormalTextRun SCXW235808685 BCX2"> structure of</span><span class="NormalTextRun SCXW235808685 BCX2"> populations. </span><span class="NormalTextRun SCXW235808685 BCX2">P</span><span class="NormalTextRun SCXW235808685 BCX2">ronounced genetic differentiation</span><span class="NormalTextRun SCXW235808685 BCX2"> was evident </span><span class="NormalTextRun SCXW235808685 BCX2">between populations occupying cold versus hot desert</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2">,</span><span class="NormalTextRun SCXW235808685 BCX2"> and </span><span class="NormalTextRun SCXW235808685 BCX2">we </span><span class="NormalTextRun SCXW235808685 BCX2">detected numerous loci </span><span class="NormalTextRun SCXW235808685 BCX2">with </span><span class="NormalTextRun SCXW235808685 BCX2">significant association</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2"> with climate. The genetic signal of founder effect</span><span class="NormalTextRun SCXW235808685 BCX2">s</span><span class="NormalTextRun SCXW235808685 BCX2">, however, is still present in the genomes of the recently expanded populations</span><span class="NormalTextRun SCXW235808685 BCX2">, </span><span class="NormalTextRun SCXW235808685 BCX2">which</span><span class="NormalTextRun SCXW235808685 BCX2"> comprise subsets of genetic variation found in the southern populations, and </span><span class="NormalTextRun SCXW235808685 BCX2">we found substantial evidence that </span><span class="NormalTextRun SCXW235808685 BCX2">genetic diversity of lizards differs along the two colonization routes.</span></p>
Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations
<p><b>PREMISE </b></p> <p>Across taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments.</p> <p><b>METHODS </b></p> <p>We used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (<i>Mimulus cardinalis</i>).</p> <p><b>RESULTS </b></p> <p>We mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats.</p> <p><b>CONCLUSIONS </b></p> <p>Our results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates. </p>
Exploring phenotypic diversity of pigmented traits and iris features in Pakistani population
<p><span>Phenotypic variations of eye color, skin color, and iris surface features have been well-explored in certain populations. However, there has been comparatively little research on variations in these features in Pakistani population. The aim of this study is to</span> discover phenotypic diversity and correlations of pigmented traits and iris surface features in Punjab and Khyber-Pakhtunkhwa (KPK)<b> </b>province of Pakistan<b>.</b> Digital images of eyes and skin were examined by investigators to determine color using Fitzpatrick Phototype Scale. Similarly, iris patterns were characterized by Edward iris feature software and association studies were conducted through SPSS program. Intermediate eye color was frequent in KPK (44%) while brown was higher in Punjab (47%). <span>Contrarily</span>, light to medium brown skin color was recurring (55%) in Punjab whereas lighter skin color prevailed in KPK (69%). Furthermore, Fuchs' crypts were significantly correlated with contraction furrows in both populations. Likewise, crypts were significantly associated with Wolfflin nodules and furrows were significantly related to conjunctival melanosis and pigment spots in KPK sample set. Based on unique iris patterns, these phenotypic traits would be helpful for individuals' discrimination in the population<b>. </b>In future, there is need to explore genetic associations and functional differences of these traits.</p>
Population genetic assessment of newly discovered, extremely small populations of Xanthocyparis Vietnamensis from southwestern China
<p><i>Xanthocyparis vietnamensis</i> is an endangered species that is currently restricted to karst montane areas in southwestern China and Vietnam. This rare conifer was first recorded in 2002 from northern Vietnam and then in 2013 from Guangxi, China, yet little is known about its genetic diversity and population structure. We developed expressed sequence tag microsatellite markers (EST-SSR) for <i>X. vietnamensis</i>. Illumina HiSeq data were used to reconstruct the transcriptome of this species by de novo assembly. Based on this transcriptome, 20 SSR markers were designed and successfully amplified, and no loci with excessive null allele was detected. These polymorphic loci were then employed to access the genetic diversity and population structure of <i>X. vietnamensis</i>. As well, they could be useful in promoting sustainable forest management strategies for this species in the vulnerable karst ecosystem.</p>
Parental population range expansion before secondary contact promotes heterosis
<p>Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing where neutral or slightly deleterious mutations drift to high frequency at the expansion front. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative effects of Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening reproductive isolation. When BDMIs are linked to such recessive deleterious alleles the fitness benefit of introgression at these loci can facilitate introgression at the BDMIs. The extent to which this occurs depends on the strength of selection against the linked deleterious alleles and the distribution of recombination across the chromosome. Finally, surfing of neutral loci can alter the expected pattern of population ancestry, thus accounting for historical population expansion is necessary to develop accurate null genomic models of secondary-contact hybrid zones.</p>
Population structure of giant clams (sub-family: Tridacninae) across Palau: implications for conservation
<p>Giant clams (Sub-family: Tridacninae) are an important food and economic resource for the Republic of Palau. Previous surveys of giant clams conducted over 20 years ago found diverse, localized populations across Helen Reef and the Rock Islands Southern Lagoon. This study updates population structure data for Palauan giant clams and investigates the impacts of conservation on these important bivalves. We surveyed eleven sites within fringing, barrier, atoll, and oceanic reefs across the Palauan archipelago (total area = 1650m<sup>2</sup>). A total of 831 clams were measured across seven species (<i>Tridacna crocea, T. maxima, T. noae, T. squamosa, T. derasa, T. gigas, </i>and <i>Hippopus hippopus</i>). In addition, this is the first documented case of <i>T. noae</i> in Palau. Our measurements show that giant clams in Palau are among the most abundant and densely distributed compared to other Indo-Pacific reefs. <i>T. crocea </i>exhibited the highest abundance (521 individuals) and density (20.0 ± 2.9 per 50m<sup>2</sup>) of all species in this survey. However, high demand from local and international markets may have resulted in low average shell lengths and reduced abundances of adult clams within the most abundant species: <i>T. crocea, T. maxima, </i>and <i>T. squamosa</i>. Despite these harvesting pressures, Palau's incorporation of bottom-up traditional and modern conservation initiatives has positively impacted <i>T. crocea</i>, the most targeted species by local fishers. Within the Ngermedellim Marine Sanctuary, <i>T. crocea </i>exhibit high abundances of recruits and adults, suggesting that protection from fishing has increased replenishment rates and reduced mortality within this conservation area. As these bivalves continue to be exploited, we suggest that continued protection of and the implementation of size-limits will enable giant clams to remain abundant and diverse in Palau.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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