Population Structuring Research Articles

A spatial statistical approach for identifying population structuring of marine fish species: European sprat as a case study

AbstractMany marine fish species are widely distributed over large areas. Failing to acknowledge that such species may be composed of distinct populations may result in overestimation of the stock's true harvest potential. To avoid overexploitation, ways to identify population structuring are therefore needed. In this study, we developed and applied a statistical approach to identify biologically relevant population boundaries for a widely distributed marine fish species, European sprat (Sprattus sprattus). Specifically, we compiled and standardized multiple trawl-survey data sets and used a range of statistical tools to assess whether the current management boundaries adequately account for potential population structuring. Our results demonstrate regional differences in spatial abundance patterns, temporal dynamics and population demographics. These findings are in line with recent genetic studies of sprat, indicating reproductive isolation between the Baltic Sea/Kattegat and a larger cluster containing the North-, Irish-, Celtic Sea, and Bay of Biscay. Since relying on routinely collected survey data, our statistical approach can be a cost-effective complement to population genetic methods for detecting population structuring. These can be used to guide spatial management efforts and ensure sustainable exploitation, especially under climate change and the expected changes in species distributions across current management borders.

Abiotic drivers shape seed inputs and outputs in a tropical wetland on Croton trinitatis population

BackgroundPredicting how natural and anthropogenic drivers shape different ecological indicators, such as plant populations along environmental gradients, can be a relevant tool for establishing management and conservation criteria of tropical wetlands. We aimed to assess the effects of seasonal flood disturbance, type of grasslands and topographical conditions on Croton trinitatis population distribution in a tropical wetland.MethodsThe study was carried out in a seasonally flooded grassland (Central-West Brazil). We conducted samplings of soil on the dry and flood hydrophases of the Pantanal. We took the samples in eight seasonal ponds, with 1 km interval between them. Transects were marked during the flood period, observing the water level, one in the lowest zone, in the middle of the pond = low (ca. 60 cm deep), one at the pond edge = mid (ca. 30 cm deep) and one in the higher zone, on the external part = high (ca. 1 cm deep).ResultsThe results showed that the topography, seasonality, and types of grassland determine differences in the abundance patterns of adult plants and seedlings, and seed bank and seed predation. The abiotic factors can shape plant population-related ecological processes and patterns, with outputs (germination and predation) and inputs (local dispersion and from neighbouring areas) of proportional seeds for the population maintenance in this environment.ConclusionWe emphasize the importance of these findings, to show that abiotic factors are not the only ones to be considered in ecological studies of distribution and structuring of populations in habitats with extreme seasonal events.

Distance to coastline modulates morphology and population structure in a coastal amphibian

Abstract Salinization due to sea-level rise and marine submersions is expected to strongly impact coastal ecosystems. Exposure to salinity can negatively impact biodiversity especially in coastal wetlands. To understand comprehensively the consequences of environmental salinization on coastal biodiversity, it is essential to document how coastal species currently respond to exposure to salinity. In this study, we investigated how variations of environmental salinity relative to the distance to the ocean influence population structure (age ratio and sex ratio), and individual hydro-mineral balance (osmolality) and morphology (size, mass, condition) in the western spadefoot toad (Pelobates cultripes) in two populations from the French Atlantic coast. We show that distance to coastline strongly influences exposure to salt on a small spatial scale. Some variables (e.g., abundances, osmolality, morphology) responded similarly in both sites and may be related to salt deposition due to landward sea-spray. Interestingly, other variables (sex ratio and age ratio) displayed site-specific responses and appeared to be linked to the salinity of breeding sites. Distance to the shoreline appears to be a critical population structuring factor in this coastal salt-tolerant species. Future studies should investigate how distance to shoreline—and thus environmental salinity—can ultimately affect individual performances and fitness.

DNA marker-based auditing of genetic diversity and population structuring of Indian mango (Mangifera indica L.) elites

DNA marker-based auditing of genetic diversity and population structuring of Indian mango (Mangifera indica L.) elites

How do genetic relatedness and spatial proximity shape African swine fever infections in wild boar?

The importance of social and spatial structuring of wildlife populations for disease spread, though widely recognized, is still poorly understood in many host-pathogen systems. In particular, system-specific kin relationships among hosts can create contact heterogeneities and differential disease transmission rates. Here, we investigate how distance-dependent infection risk is influenced by genetic relatedness in a novel host-pathogen system: wild boar (Sus scrofa) and African swine fever (ASF). We hypothesized that infection risk would correlate positively with proximity and relatedness to ASF-infected individuals but expected those relationships to weaken with the distance between individuals due to decay in contact rates and genetic similarity. We genotyped 323 wild boar samples (243 ASF-negative and 80 ASF-positive) collected in north-eastern Poland in 2014-2016 and modelled the effects of geographic distance, genetic relatedness and ASF virus transmission mode (direct or carcass-based) on the probability of ASF infection. Infection risk was positively associated with spatial proximity and genetic relatedness to infected individuals with generally stronger effect of distance. In the high-contact zone (0-2km), infection risk was shaped by the presence of infected individuals rather than by relatedness to them. In the medium-contact zone (2-5km), infection risk decreased but was still associated with relatedness and paired infections were more frequent among relatives. At farther distances, infection risk further declined with relatedness and proximity to positive individuals, and was 60% lower among un-related individuals in the no-contact zone (33% in10-20km) compared among relatives in the high-contact zone (93% in 0-2km). Transmission mode influenced the relationship between proximity or relatedness and infection risk. Our results indicate that the presence of nearby infected individuals is most important for shaping ASF infection rates through carcass-based transmission, while relatedness plays an important role in shaping transmission rates between live animals.

Population Genetics of Brook Trout in the Southern Appalachian Mountains

AbstractBroad‐scale patterns of genetic diversity for Brook Trout Salvelinus fontinalis remain poorly understood across their endemic range in the eastern United States. We characterized variation at 12 microsatellite loci in 22,020 Brook Trout among 836 populations from Georgia, USA, to Quebec, Canada, to the western Great Lakes region. Within‐population diversity was typically lower in the southern Appalachian Mountains relative to the mid‐Atlantic and northeastern regions. Effective population sizes in the southern Appalachians were often very small, with many estimates less than 30 individuals. The population genetics of Brook Trout in the southern Appalachians are far more complex than a conventionally held simple “northern” versus “southern” dichotomy would suggest. Contemporary population genetic variation was consistent with geographic expansion of Brook Trout from Mississippian, mid‐Atlantic, and Acadian glacial refugia as well as differentiation among drainages within these broader clades. Genetic variation was pronounced among drainages (57.4% of overall variation occurred among 10‐digit hydrologic unit code [HUC10] units or larger units) but was considerable even at fine spatial scales (13% of variation occurred among collections within HUC12 drainage units). Remarkably, 87.2% of individuals were correctly assigned to their collection of origin. While comparisons with fish from existing major hatcheries showed impacts of stocking in some populations, genetic introgression did not overwhelm the signal of broad‐scale patterns of population genetic structure. Although our results reveal deep genetic structure in Brook Trout over broad spatial extents, fine‐scale population structuring is prevalent across the southern Appalachians. Our findings highlight the distinctiveness and vulnerability of many Brook Trout populations in the southern Appalachians and have important implications for wild Brook Trout management. To facilitate application of our findings by conservation practitioners, we provide an interactive online visualization tool to allow our results to be explored at management‐relevant scales.

Woody species diversity, structural composition, and human use of church forests in central Ethiopia

Church forests on the premises of Ethiopian Orthodox Churches have been recognized as refugia of tropical plant biodiversity within the predominantly agricultural landscape matrix. Understanding the species composition, population structure, and human use of trees in forested areas is crucial for sustainable conservation efforts. We investigated these features in mixed natural-planted church forests in central Ethiopia. Three forests associated with churches for 37–50 years were surveyed to assess: (i) the diversity and population characteristics of woody species depending on the age of the church forest, (ii) the use of trees by humans, and (iii) church forests’ contribution to the conservation of threatened species. Vegetation and ethnobotanical data were collected via forest inventory of 24 plots sized 0.04 ha and through a rapid rural appraisal conducted in 120 households. Thirty woody species, twenty-eight indigenous species, and two exotic species were identified. The three church forests were floristically different, with only four tree species in common. Most indices of diversity and population structural parameters of woody species were higher in older than in younger church forests, presumably due to a longer tradition of forest conservation. All church forests presented inverse J-shaped size-class distributions, indicative of populations with good recruitment potential. Woody species were mainly used for medicine, construction wood, and firewood. Eighteen threatened species were recorded; however, few conservation activities besides social taboos were revealed in the examined forests. Our findings highlight the role of church forests in the conservation of woody species diversity, and the need to strengthen current strategies to support long-term biodiversity conservation.

Year-Round Dive Characteristics of Male Beluga Whales From the Eastern Beaufort Sea Population Indicate Seasonal Shifts in Foraging Strategies

Dive behavior represents multiple ecological functions for marine mammals, but our understanding of dive characteristics is typically limited by the resolution or longevity of tagging studies. Knowledge on the time-depth structures of dives can provide insight into the behaviors represented by vertical movements; furthering our understanding of the ecological importance of habitats occupied, seasonal shifts in activity, and the energetic consequences of targeting prey at a given depth. Given our incomplete understanding of Eastern Beaufort Sea (EBS) beluga whale behavior over an annual cycle, we aimed to characterize dives made by belugas, with a focus on analyzing shifts in foraging strategies. Objectives were to (i) characterize and classify the range of beluga-specific dive types over an annual cycle, (ii) propose dive functions based on optimal foraging theory, physiology, and association with environmental variables, and (iii) identify whether belugas undergo seasonal shifts in the frequency of dives associated with variable foraging strategies. Satellite-linked time-depth-recorders (TDRs) were attached to 13 male belugas from the EBS population in 2018 and 2019, and depth data were collected in time series at a 75 s sampling interval. Tags collected data for between 13 and 357 days, including three tags which collected data across all months. A total of 90,211 dives were identified and characterized by twelve time and depth metrics and classified into eight dive types using a Gaussian mixed modeling and hierarchical clustering analysis approach. Dive structures identify various seasonal behaviors and indicate year-round foraging. Shallower and more frequent diving during winter in the Bering Sea indicate foraging may be energetically cheaper, but less rewarding than deeper diving during summer in the Beaufort Sea and Arctic Archipelago, which frequently exceeded the aerobic dive limit previously calculated for this population. Structure, frequency and association with environmental variables supports the use of other dives in recovery, transiting, and navigating through sea ice. The current study provides the first comprehensive description of the year-round dive structures of any beluga population, providing baseline information to allow improved characterization and to monitor how this population may respond to environmental change and increasing anthropogenic stressors.

Genetic structuring of parental populations of coffee (Coffea canephora Pierre ex A. Froehner) breeding in Côte d’Ivoire using SNP markers

Description. Coffee cultivation plays an important economic and social role in Côte d'Ivoire. Among the dozens of Coffea species, only Coffea canephora, also known as robusta, is grown in the country. The genetic improvement of this species has been the subject of a selection program set up by the National Center for Agronomic Research (CNRA). This program involves two basic genetic groups, Guinean and Congolese. These groups have been determined using enzymatic markers which are known to be less informative. So little is known about the reliability of the genetic structuring of the parental populations. Objectives. The objective of this work is to refine the genetic structuring of the parental populations used to set up the C. canephora breeding program in Côte d'Ivoire using SNP markers and to relate this structure to test values in the genotypes concerned. Method. Sixty-six individuals representing parental genotypes of the two populations were analyzed using 200 SNPs markers. The parameters of genetic diversity were calculated and then the genetic structure was determined. The yield over four years of production, susceptibility to rust, and bean size have been evaluated. Results of these agronomic traits have been included in this analysis. The Guinean genotypes were crossed with a Congolese tester named 464 and the Congolese individuals were crossed with a Guinean tester 410, for assessing their combining ability. Results. The analysis of molecular variance (AMOVA) revealed that 75% of the total variation was due to variation between populations. Bayesian classification and Principal Coordinates Analysis (PCoA) structure the 66 genotypes into two main groups of Guineans and Congoleses. While the Guinean group appears to be homogeneous, the Congolese group is split into four subgroups of SG1, SG2, B and C. Maximum test values are found for the SG1 and SG2 subgroups. The Guinean group showed lower performance. It is important in this group to select the best progenitors. Conclusions. SNP markers were effective in genetic structuring of the population. This study also allows the identification of a genotype that was not determined. The use of this set of markers will be useful for the control of future progenitors. The same genetic progress can be achieved by crossing SG1 or SG2 with a good Guinean male. It seems important to make a selection among the Guineans before crossing them with a Congolese tester.

Population structuration and chromosomal features homogeneity in Parodon nasus (Characiformes: Parodontidae): A comparison between Lower and Upper Paraná River representatives

ABSTRACT The ichthyofauna of the La Plata hydrographic basin is divided into Upper and Lower Paraná River systems due to the geographic isolation of the Sete Quedas waterfalls, currently flooded by the lake of the Itaipu dam. In Parodontidae, pairs of species, or groups of cryptic species were described between these systems. Although genetic isolation and speciation have already been proposed in other species in the group, Parodon nasus has been maintained as a valid species and distributed throughout the La Plata river basin. In this perspective, specimens of P. nasus from four different sampling sites in the Upper and Lower Paraná River systems were compared regarding the karyotypes, molecular analyzes of population biology and species delimitation to investigate their genetic and population isolation in the La Plata river basin. Despite a geographic barrier and the immense geographic distance separating the specimens sampled from the Lower Paraná River system compared to those from the Upper Paraná River, the data obtained showed P. nasus as a unique taxon. Thus, unlike other species of Parodontidae that showed diversification when comparing the groups residing in the Lower versus Upper Paraná River, P. nasus showed a population structure and a karyotypic homogeneity.

Fucoid seaweeds on the Russian Arctic coast: using traditions and ecological monitoring

In recent years, harvest and cultivation of marine biological resources, including commercial seaweeds, has increased significantly. The task of this research was the ecological monitoring of commercial fucoid seaweeds beds in coastal waters of the Barents and White Seas. Data of seasonal supervision at stationary biological station and materials of expedition works on Murmansk coast were analyzed. The species, age, generative and spatial structures of fucoid populations in different biotopes of the littoral were studied. It was found that species composition of phytocenoses and quantitative parameters of commercial fucoids varied significantly in open and closed bays, as well as in algae living in the lower and upper littoral. The average biomass of fucoids in semi-closed inlets varied from 2.8±0.6 to 17.7±2.9 kg/m2, depending on dominant species in community, the structure of substrate and impact of waves. The results indicate that phytocenoses of fucoid algae under the influence of changing environmental factors largely ensure the integrity of littoral ecosystem. For rational harvest and cultivation of commercial fucoids, as well as the restoration of disturbed phytocenoses after the removal of some algae, it is recommended to use the technology of synchronization of harvesting with life cycles of seaweeds.

COI gene sequencing reveals genetic population structuring and a separate lineage of the green tiger prawn Penaeus semisulcatus in the Gulf of Suez and the Bitter Lakes, Egypt

The green tiger prawn Penaeus semisulcatus is one of the major commercial trawl crustaceans in the Red Sea, the Arabian Gulf, and the Indian Ocean. Herein, we aimed to assess its genetic diversity and phylogeographic criteria in the North West (NW) of the Red Sea. Prawn samples were collected from the Bitter Lakes; the North; and the South of the Gulf of Suez in Egypt. The hypervariable, 5´ barcode area of the Cytochrome oxidase subunit 1 (COI) gene was PCR-amplified and sequenced in all samples. The resulting sequences were subjected to several genetic, phylogenetic, and population genetics' analyses. Consequently, clear signs of genetic populations’ diversity, expansion; and possible structuring were identified in different areas in the NW Red Sea. Furthermore, extremely discordant genetic connectivity was found between the populations around the Arabian Plate (i.e. of the Red Sea and Strait of Hormuz) and the IndoWest Pacific, resulting in characterizing the Arabian plate populations as a separate lineage of P. semisulcatus. Based on these findings, it is important to investigate whether there are other discriminative genomic, morphological and/or morphometric differences among the genetically identified lineages and populations. Consequently, differential conservational strategies of different populations of this species should be applied in the studied areas.

Genetic Diversity of Schistosoma haematobium in Sub-Saharan Africa: A Systematic Review

Urogenital schistosomiasis caused by the parasite Schistosoma haematobium is the most common form of schistosomiasis. This parasite has a high potential for genetic exchange within parasite populations giving rise to the genetic diversity that is important for its survival. Genetic differences may lead to some parasite strains being more immunogenic which may have a negative impact on management and control of schistosomiasis. Therefore, understanding these genetic differences in the parasite may lead to better management of the disease. The aim of this review was to systematically review scientific literature on the genetic diversity and population structuring of S. haematobium and the methods used across sub-Saharan African countries. A literature search was done on PubMed, African Journals online and Google scholar using predefined search terms such as urinary schistosomiasis, S. haematobium, genetic diversity in sub-Saharan Africa in combination with Boolean operators (AND, OR). The search included studies published from 2000-2020 that emphasised on genetic diversity of S. haematobium in sub-Saharan Africa. A country in sub-Saharan Africa was included if had a study that determined the genetic diversity of S. haematobium Sixteen study articles from 18 sub-Saharan African countries met the inclusion criteria The genetic diversity of S. haematobium varied from low to high using different methods. Most studies conducted in these countries showed a high genetic diversity of S. haematobium 18/36 (50%) studies. Four methods namely, restriction fragment length polymorphism, randomly amplified polymorphic DNA, DNA barcoding and Microsatellite markers were used to determine diversity In these studies, measures of genetic diversity such as number of alleles per minute or allelic richness, heterozygosity, number of genotypes and unique haplotypes were used. Microsatellites were the most commonly used method and the studies reported number of alleles per locus ranging from 2-19 alleles per locus and heterozygosity of 6 to 71% in some studies. . The highest number of studies were conducted in West Africa Nigeria and Zimbabwe , 4/36(11%) each. Results show the need for continued monitoring of genetic variations in S. haematobium in sub- Saharan Africa. This will aid in understanding the epidemiology of disease, advancing novel treatment and vaccine strategies.

Flower structures of black mulberry (Morus nigra) trees

This study investigated the flower structures of a black mulberry population in Tokat province and its surroundings. Of the investigated black mulberry trees of the population, 49% were identified as monoecious-male, 43% as dioecious-female, 5.7% as dioecious-male and 2.3% as monoecious-mixed. Generally, four stamens were identified in male flowers and especially in mixed catkins, 3 or 2 stamens were also identified in male flowers. Female flowers were composed of a long two-lobed stigma and an ovary. Catkin lengths of male flowers varied between 42.7-22.8 mm and catkin lengths of female flowers varied between 24.1-4.3 mm. The number of male flowers per catkin varied between 26.36-10.62 in dioecious trees and 26.3-14.1 in monoecious trees. The number of female flowers per catkin varied between 36.16-13.5 in monoecious trees and between 52.0-15.6 in dioecious trees. There were significant differences in the phenological stages of the flowers. Flowering lasted about 60 days in all genotypes.

Craniological sources on the problem of ethnogenesis of the Narym Selkups

The Narym Selkups are an indigenous population of the Middle Ob River region speaking various dialects of the Selkup language related to the South-Samodian branch of the Ural language family. In the course of the study of Medieval and relatively recent burial grounds in the territory of the Narym Ob area of Tomsk Oblast, considerable amount of craniological material has been collected, which constitutes an important historical source for solving general problems of their origins. According to the archaeological and ethnographic materials, the Medieval burials were left by direct ascendants of modern Narym Selkups, whereas the materials from the later burial grounds are directly associated with their specific local-dialect groups. This paper is aimed to introduce into scien-tific discourse virtually all craniological materials known today from the burial grounds left by the Narym Selkups, and, on the basis of the results of group cross-correlation, to identify trends of the territorial variability of the whole community. Significant increase of new finds from the vast territory of the Middle Ob region, population-driven approach to the data analysis and development of the craniometric technique warranted re-grouping of the finds by the territorial principle and their repeated measurement and analysis. In view of the current problem, all cranio-logical materials were grouped into ten sampling series, five of which are published for the first time (the burial ground of Ostyatskaya Gora and four combined craniological series from the burial grounds of Lower Chulym, Narym Ob, Upper Ket, and the Tym and Vasyugan rivers). Analysis of the variability of the series from the Narym Ob region in chronological and geographical bands showed their weak variability in space and time. Therefore, prior to the Russian colonization of Siberia, this region of the Middle Ob area was not invaded by considerably large groups of people of different anthropological appearance. All studied craniological series were samples from the single unity. Although the territorial variability of the anthropological features within the groups of the Narym Selkups is not large, in some cases an influence of territorially closest neighbours on the anthropological structures of particular Selkup populations can be discerned. It appeared that the southern groups exhibit resemblance with their territorially closest Turkic populations of the Chulym and Lower Tom regions, while in the composition of other Narym groups, there have been identified an admixture of the component genetically related to the Turkic populations of the Western-Siberian forest-steppe — Barabino and Tobol-Irtysh Tatars, and, although being very weak, an influence of the Ob Ugric populations can be discerned.

Seascape Genomics Reveals Metapopulation Connectivity Network of Paramuricea biscaya in the Northern Gulf of Mexico

The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore, central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized disturbance. Understanding these source-sink dynamics is essential to guide restoration efforts and for the study of ecology and evolution in the ocean. The patterns and mechanisms of connectivity in the deep-sea (>200 m deep) are largely understudied. In this study, we investigated the spatial diversity patterns and metapopulation connectivity of the octocoral Paramuricea biscaya throughout the northern Gulf of Mexico (GoM). Paramuricea biscaya is one of the most abundant corals on the lower continental slope (between 1,200 and 2,500 m) in the GoM. The 2010 Deepwater Horizon oil spill (DWH) directly impacted populations of this species and thus are considered primary targets for restoration. We used a combination of seascape genomic analyses, high-resolution ocean circulation modeling, and larval dispersal simulations to quantify the degree of population structuring and connectivity among P. biscaya populations. Evidence supports the hypotheses that the genetic diversity of P. biscaya is structured by depth, and that larval dispersal among connected populations is asymmetric due to dominant ocean circulation patterns. Our results suggest that there are intermediate unsampled populations in the central GoM that serve as stepping stones for dispersal. The data suggest that the DeSoto Canyon area, and possibly the West Florida Escarpment, critically act as sources of larvae for areas impacted by the DWH oil spill in the Mississippi Canyon. This work illustrates that the management of deep-sea marine protected areas should incorporate knowledge of connectivity networks and depth-dependent processes throughout the water column.

POLYMORPHISM OF THE Β-LACTOGLOBULIN GENE AND DAIRY PRODUCTIVITY OF DIFFERENT SHEEP’S GENOTYPES

POLYMORPHISM OF THE Β-LACTOGLOBULIN GENE AND DAIRY PRODUCTIVITY OF DIFFERENT SHEEP’S GENOTYPES

Relaxation time of brain tissue in the elderly assessed by synthetic MRI.

BackgroundSynthetic MRI (SyMRI) is a quantitative technique that allows measurements of T1 and T2 relaxation times (RTs). Brain RT evolution across lifespan is well described for the younger population. The aim was to study RTs of brain parenchyma in a healthy geriatric population in order to define the normal value of structures in this group population. Normal values for geriatric population could help find biomarker for age‐related brain disease.Materials and methodsFifty‐four normal‐functioning individuals (22 females, 32 males) with mean age of 83 years (range 56–98) underwent SyMRI. RT values in manually defined ROIs (centrum semiovale, middle cerebellar peduncles, thalamus, and insular cortex) and in segmented whole‐brain components (brain parenchyma, gray matter, white matter, myelin, CSF, and stromal structures) were extracted from the SyMRI segmentation software. Patients' results were combined into the group age. Main ROI‐based and whole‐brain results were compared for the all dataset and for age group results as well.ResultsFor white matter, RTs between ROI‐based analyses and whole‐brain results for T2 and for T1 were statistically different and a trend of increasing T1 in centrum semiovale and cerebellar peduncle was observed. For gray matter, thalamic T1 was statistically different from insular T1. A difference was also found between left and right insula (p < .0001). T1 RTs of ROI‐based and whole‐brain‐based analyses were statistically different (p < .0001). No significant difference in T1 and T2 was found between age groups on ROI‐based analysis, but T1 in centrum semiovale and thalamus increased with age. No statistical difference between age groups was found for the various segmented volumes except for myelin between 65–74 years of age and the 95–105 years of age groups (p = .038).ConclusionsSyMRI is a new tool that allows faster imaging and permits to obtain quantitative T1 and T2. By defining RT values of different brain components of normal‐functioning elderly individuals, this technique may be used as a biomarker for clinical disorders like dementia.

Broadscale Population Structure and Hatchery Introgression of Midwestern Brook Trout

AbstractBrook Trout Salvelinus fontinalis have faced significant declines throughout their native range and have been stocked in Midwestern waters since the late 1800s to offset such losses. Several studies have investigated the genetic effects of these stockings, but these efforts have been confined to relatively small spatial scales. In this study, we compiled 8,454 Brook Trout microsatellite genotypes from 188 wild Midwestern populations and 26 hatchery strains to provide novel insights of broadscale population structure, regional patterns of genetic diversity, and estimates of hatchery introgression for inland Wisconsin populations. Our results indicate high levels of differentiation among our study populations, a lack of hydrological population structuring, lower estimates of genetic diversity in the Driftless Area, and that hatchery introgression has been largely confined to regions of inland Wisconsin that have been heavily affected by anthropogenic disturbances (i.e., the Driftless Area). We also provide evidence that populations may be able to purge hatchery‐derived alleles, discuss possible mechanisms behind this phenomenon, and consider their relevance to accurate estimation of hatchery introgression. Collectively, these results summarize the genetic effects of over a century of anthropogenic disturbance on native Brook Trout populations and emphasize the importance of integrating historical data into contemporary genetic research of intensively managed species.

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.

Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales─picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure-function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.