Vavilov's ideas formed a solid scientific basis for the long-term efforts on securing PGR in ex situ genebanks, both internationally and in Russia. The collection of seeds and living plants at the N.I. Vavilov All Russian Institute of Plant Genetic Resources (VIR) is one of the oldest in the world. The size of the collection increased from 301 accessions in 1901 to over 330,000 accessions in 2017, now representing 64 botanical families, 376 genera, and 2169 species. Acquisition was mainly focused on crops that are suitable for cultivation in Russia such as potatoes, barley, wheat, sorghum, beans, vegetables, forage species, and many others. For over a century, VIR has been providing the materials for breeding programs and research, which resulted in developing new cultivars with unique characteristics such as high yield combined with deceased resistance, improved storability, cold and drought tolerance, or ability to grow on deserts and polluted lands. The main field collection near St. Petersburg and 11 main branches across the country covering a wide spectrum of climatic conditions combined with modern seed storage, in vitro and cryobank facilities, and molecular laboratories form a solid platform for breeding, regeneration, and evaluation of accessions in the collection. This article gives a brief overview of VIR as the leading genebank and breeding center in Russia, its main activities in conservation and utilization of PGR for national food security and its role in developing national policies in this area.N.I. Vavilov was among the first scientists who recognized the high potential value of plant genetic resources (PGR) for humankind. In addition to his fundamental work on the centers of crop origin, he emphasized the importance of collection and  Ex situ collections of cultivated plants and their wild relatives are the basic components of food and environmental security of each sovereign country, including Russia. Their relevance and strategic importance have been recognized in the past decades due to enormous genetic erosion and worldwide extinction of crop varieties, species, and even genera. According to the Food and Agricultural Organization of the United Nations (FAO) (1998), 75% of the world's crop genetic diversity was lost in the 20th century. Moreover, the number and assortment of cultivated plants and their wild species have been significantly reduced. Only 30 agricultural crops provide for 95% of humankind's requirements in high-calorie plant-derived food, and 4 of them, rice, wheat, maize, and potatoes, cover more than 60% of our demand in energy and proteins.Contemporary losses of the diversity and a small number of crops used in production under the global and local climate changes present a serious threat to the entire worldwide community and aggravate the problem of food security. Therefore, in Russia as in many other countries, conservation and sustainable utilization of PGR have acquired national and strategic importance.ex situ is one of the oldest in the world. It was established in October 1894 as the Bureau of Applied Botany under the Scientific Committee at the Ministry of State Property of the Russian Empire. The Bureau gradually evolved into the N.I. Vavilov Institute of Plant Genetic Resources, or VIR, which became the national center of conservation, research, and utilization of PGR.The Russian collection of plant genetic resources (PGR) 2The present status of VIR's collection is the result of the collective efforts of several generations of world-renowned scientists and explorers. The central, and probably the most internationally acknowledged figure in VIR history is Nikolai Ivanovich Vavilov. He was among the first scientists who recognized the exceptional importance and potential value of collecting and preserving the genetic diversity of crop varieties and their wild relatives for humankind. He also laid the foundation for the national and global strategies in PGR conservation and sustainable utilization. Vavilov's theory of the centers of crop origin, his law of homologous series in hereditary variation, fundamental works on geographic distribution of genes, the role of source material in breeding practice, and other publications are internationally renowned. Science historians and Vavilov's biographers usually highlight two stages in his program development. The first stage (1917–1929) was mainly devoted to the collection and research of world genetic resources of staple crops and their wild relatives. The second stage (1929–1940) was mainly focused on a wide-scale scientific synthesis of the acquired knowledge and development of a theoretical basis of crop biology and breeding.3–5The active research and collection work commenced by Vavilov and his team was continued throughout 20th century, but only hampered by World Wars I and II. By 1901, VIR collection of PGR was composed of 301 accessions. In 2015, this number increased to 325,000 unique accessions . During The activities in monitoring, collecting, conservation, documentation, comprehensive study, and effective utilization of global PGR are ongoing and creatively developed on the basis of modern science and technology achievements, with due regard to new economic and political trends.in vitro (750 accessions), and in cryopreservation (1824 accessions). Being the fourth in the world in the number of the preserved accessions, VIR maintains probably the richest botanical, genetic, geographic, and ecological diversity of plant germplasm.The dynamic change of accession numbers in VIR collection during the past years is presented in in vitro or cryogenic storage  of major crops for targeted utilization in breeding programs. New effective alleles, rare ones or those earlier ignored by breeders, which determine photoperiodic sensitivity and response to vernalization, resistance to pathogens and other traits, were identified and mapped. Marking and molecular mapping quantitative trait loci allowed researchers to find, identify, and perform a controlled transfer of chromosome loci determining expression of economically useful traits such as resistance to biotic and abiotic stressors, quality, and productivity. Genetic diversity of accessions in the collection studied by conventional technologies and innovative molecular genetic approaches, including genomics, molecular marking, mapping, and bioinformatics, serves as a powerful base of valuable source material and an instrumental mechanism of effective breeding development. We believe that the diversity of the collection materials, provided that they are safely conserved and sustainably utilized, may promote breeding technologies and priority trends in the 21st century breeding, which are oriented toward the development of high-quality food, optimization of animal feed production, global climate change, “nordification” of crop production, development of novel agro-, bio-, food, chemical, and industrial technologies, biologization and ecologization of agriculture, and resource- and energy-saving policies.13As the national genetic resources center with over 120 years of history, VIR has been responsible for mobilization, conservation, evaluation, and utilization of PGR in Russia and involved in the development of relevant governmental programs and legal instruments. In addition to VIR collection, ∼50,000 accessions of PGR are held by other organizations in Russia: research institutions, breeding centers, universities, botanical gardens, commercial plant breeding and seed production companies, and on farms. Over 1600 species of crop wild relatives occur in Russia within their natural populations—they are potential carriers of alleles valuable for breeding. Many of them are now under the threat of extinction and require measures toward their safeguarding.The problems of PGR conservation in genebanks, within natural plant communities and on farms, and their sustainable utilization are listed among the five top priorities of national security in most of the world's countries, including Russia. These problems need to be solved both at national and international levels, because countries are not self-sufficient and depend on each other in the context of PGR. To find a successful solution to such problems, relevant international documents have been developed such as the Convention on Biological Diversity, 1992; Global Plan of Action for Plant Genetic Resources for Food and Agriculture, 1996, 2011; International Treaty on Plant Genetic Resources for Food and Agriculture, 2004; and Nagoya Protocol on Access to Genetic Resources, 2011. However, with new challenges of globalization and emergence of new technologies, climate change and rapid genetic erosion, profound modifications should be made in the national and international policies in the area of crop agricultural biodiversity conservation and utilization.The importance of VIR's collections and activities in providing solutions to plant breeding and production problems in Russia as well as their role in solving the problem of food supply has been emphasized at several international forums. The former minister of agriculture, E.B. Skrynnik, informed the delegates at the FAO World Summit on Food Security  that Russia is ready to make VIR's collection available for the worldwide community, considering possible climate changes and the common interest of all countries in the reduction of the starvation and poverty level in the world. However, Russia has not yet joined the International Treaty on Plant Genetic Resources for Food and Agriculture; hence, international distribution of accessions from VIR genebank has been accomplished based on bilateral agreements rather than SMTA.In 2006, VIR developed and proposed the draft of the National Program “Conservation and Sustainable Utilization of Crop Genetic Resources,” which envisaged necessary budget funding for effective coordination of PGR activities at the national, regional, and international levels. Despite the first approval, the program was not funded or implemented. Later, genetic resources conservation was prioritized in the list of national programs, which was approved by the President and Government of the Russian Federation. Most recently, joint efforts of the Russian Ministry of Agriculture and VIR helped to develop and coordinate at the ministerial level of stakeholders the draft Federal Law “Concerning Plant Genetic Resources for Agricultural Production,” which will regulate the activities in the areas of collection, regeneration, storage, research, and sustainable utilization of PGR and their collection for agricultural production in the Russian Federation.ex situ and in situ conservation of genetic resources, development of fundamental and applied research in the area of agricultural biodiversity, avoiding duplication of activities, enhancement of valuable plant diversity mobilization possibilities, expansion of the national genetic diversity by targeted collecting missions over Russia and other countries, as well as through international germplasm exchange, and efficient and sustainable utilization of bioresources with the help of new technologies and scientific achievements.The main idea of the proposed National Program is to combine governmental and nongovernmental measures to create the most favorable environment for secure ex situ collections. It will also open the floor for further discussion and adoption of new international agreements, including the issues of access and benefit sharing as well as to implement large-scale and mutually beneficial international and regional cooperation, while observing the national interests.The National Program will support effective coordination of PGR-related activities within the country and help to establish solid partnerships between governmental and private institutions holding Thus, the proposed National Program on Genetic Resources of Cultivated Plants and Their Wild Relatives of the Russian Federation represents the basic instrument and main mechanism in achieving the goals of mobilization, conservation, and sustainable utilization of agricultural biodiversity components, as it would help to implement relevant activities at the national and international levels. The National Program will become an integral part of the National Strategy and National Plan of Action in the area of biodiversity conservation in the Russian Federation.


Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST), and ocean turbidity (KD490) on population‐level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h. rubellus from the SW Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h. homarus from the tropical region in‐between. Virtual passive Lagrangian particles advected using satellite‐derived ocean surface currents were used to simulate larval dispersal. In the SW Indian Ocean, the dispersion of particles tracked over a 4‐month period provided insight into a steep genetic gradient observed at the Delagoa Bight, which separates P. h. rubellus and P. h. homarus. South of the contact zone, particles were advected southwestwards by prevailing boundary currents or were retained in nearshore eddies close to release locations. Some particles released in southeast Madagascar dispersed across the Mozambique Channel and reached the African shelf. Dispersal was characterized by high seasonal and inter‐annual variability, and a large proportion of particles were dispersed far offshore and presumably lost. In the NW Indian Ocean, particles were retained within the Arabian Sea. Larval retention and self‐recruitment in the Arabian Sea could explain the recent genetic divergence between P. h. megasculptus and P. h. homarus. Geographic distance and minimum SST were significantly associated with genetic differentiation in multivariate analysis, suggesting that larval tolerance to SST plays a role in shaping the population structure of P. homarus.This study examines the fine‐scale population genetic structure and phylogeography of the spiny lobster  SeascapPanulirus homarus is widespread in the Indo‐West Pacific, extending northwards from southeastern Africa to the Arabian Sea, and eastwards to Japan, Indonesia, and northern Australia  from the Southwest (SW) Indian Ocean is the most divergent and possibly a separate species based on phylogenetic analyses using mitochondrial and nuclear markers  is widespread in intervening areas  from the Northwest (NW) Indian Ocean (mainly Arabian Sea) remains unclear. Neither Singh et al.  evaluate potential phylogeographic boundary zones; (b) use virtual particle tracking simulations to infer larval dispersal patterns based on surface currents; and (c) determine the extent to which genetic structure correlates with environmental variables and simulated larval movement.We used biological information, habitats, and ocean surface currents in a seascape genetics approach to explore the genetic structure observed within the 22.1Panulirus homarus specimens were collected from 15 sites in the Western Indian Ocean: five sites from eastern South Africa, three from Mozambique, one each in southern Madagascar, Kenya and Yemen, and four in Oman , 53 in the P. h. megasculptus group , and 175 in the P. h. rubellus group . DNA was extracted from pereiopod tissue using the Zymo gDNA Universal DNA extraction kit , as per the manufacturers protocol.A total of 271 A panel of 21 microsatellite loci, consisting of eight loci  described by Dao, Todd, and Jerry  and 13 lPCR products were carried out in 10 µl volume reactions, which contained 5 µl of 1× Kapa 2G Fast Multiplex Mastermix (Kapa Biosystems), 0.2 µmol/L of each primer, and 1 µl of 10–50 ng of genomic DNA. For multiplexes A, B, C, and Orn 17, cycling conditions were as follows: an initial denaturation at 95°C for 5 min, followed by 28 cycles of denaturation at 95°C for 30 s, annealing at 60°C for 90 s, extension at 72°C for 30 s, and a final extension step at 60°C for 30 min. For multiplexes E, F, and G, cycling conditions were as follows: an initial denaturation step at 95°C for 15 min, 32 cycles of denaturation at 94°C for 30 s, annealing at 60°C for 90 s, extension for 72°C for 60 s, and a final extension at 72°C for 30 min.FST values using paired t tests.Fragment analysis of amplified products was done at Central Analytical Facility at Stellenbosch University, South Africa. GeneMarker v. 2.4.0 (Soft Genetics) was used to score the genotypes. To monitor the consistency in genotype scoring, 20% of the samples were re‐amplified and scored. Individuals with <20% missing data were considered for further analyses. Microchecker v.2.2.3  and Pophelper  were used to identify the number of genetic clusters (K) that fit the data best  ranged from 1 to 12. The spatial model was employed, with and without accounting for null alleles. The correlated allele frequencies model was chosen to detect subtle genetic structure . The genetic distances (FST/(1 – FST) were regressed against the geographic distances (straight‐line distances on Google Earth) with 1,000 randomizations between populations.The null hypothesis of isolation by distance was examined by testing the relationship between genetic and geographic distance using a Mantel test. The analysis was carried out using the program IBDWS , geography, and environment was tested using the multivariate multiple regression approach of a distance‐based redundancy analysis (dbRDA) , sea surface temperature , and turbidity  were obtained from the GMIS Marine Geodatabase (mcc.jrc.ec.europa.eu), based on the NASA MODIS terra satellite at a 4‐km spatial resolution. Data were collected from 2012 to 2015, coinciding with the genetic sampling regime. A matrix of genetic differentiation between sampling sites (FST) was used as the response variable, and mean measurements of environmental variables , and larval recruits (based on estimates from ocean modeling simulations as the number of larvae that reach settlement at each site on the coast) were used as the explanatory variables. The dbRDA analysis was carried out using the “capscale” function in the Vegan package  to subtropical conditions (P. h. rubellus preference)  Berry, , 1974a .e Berry, . The Euce Berry, . The “va2.5We explored the effects of ocean circulation on larval dispersal and settlement, and hence genetic differentiation, in the virtual particle tracking tool, Parcels v.0.9  which provides daily average surface ocean current estimates for the world's oceans at 25‐km spatial resolution by merging data from multiple satellite altimeter missions with gravity models and combining these with Ekman currents (at surface and 15 m depth) estimated from drogued surface drifter data, Argo floats, and near‐surface winds.Ocean velocity data were obtained from the GlobCurrent Project to the wind stress (τ→) is expressed by Rio, Mulet, and Picot (2014):υ→ek(z)=β(z).τ→.eiθ(z)These products are combined with the Ekman currents estimated from Argo floats and drifter data in conjunction with wind stress estimates from the European Centre for Medium‐Range Weather Forecasts (ECMWF). At depth z (0 and 15 m), the Ekman response .Summary statistics of 271 A per locus ranged from 2 (locus G42) to 14 (locus Orn 12). The expected heterozygosity was higher than observed at Orn 4, Orn 11, Orn 12, Orn 16, G01, G21, G25, G27, G30, G32, G53, and G58. Following Bonferroni correction, Orn 5, Orn 12, Orn 16, Orn 17, Orn 32, G03, G21, G22, G27, G32, G36, G42, and G53 deviated significantly from HWE. However, out of the 12 populations, Orn 5 deviated significantly from HWE in 5 populations, Orn 12 in 6, Orn 16 in 3, Orn 17 in 5, Orn 32 in 1, G21 in 5, G22 in 2, G32 in 6, G36 in 2, G42 in 9, and G53 in 1 population. The analyses were also conducted after removing loci that deviated from HWE, which resulted in a smaller dataset with 8 loci from 257 individuals. The results from analyses of the smaller dataset did not contradict those obtained from using the full dataset, and hence, all loci were retained  and lowest in Zavora . At the subspecies level, NA and AR were highest in P. h. rubellus .Genetic variability was high at most loci, but low at Orn 21 (PIC = 0.072) and G27 (PIC = 0.185). The N3.2K = 3 was optimal for the P. homarus subspecies dataset , some evidence of admixture was observed, especially when the locprior model was not used. With locprior, all P. h. rubellus morphotypes showed some evidence of admixture with P. h. megasculptus without locprior, but all clustered with P. h. rubellus when locprior was used. Of the P. h. rubellus morphotypes in the South African populations, 12% showed evidence of admixture with other subspecies without locprior, but when the locprior model was used, one individual from Port St Johns (5%), and another from Mdumbi (5%) corresponded to the P. h. homarus cluster. Out of six individuals from Zavora that were morphologically identified as P. h. rubellus, 4 (67%) showed a high degree of admixture with P. h. homarus, even when using the locprior model—thus suggesting that interbreeding and high genetic variability occurs predominantly at this location.In Madagascar, 20% of P. h. megasculptus; Figure P. h. rubellus; Figure P. h. homarus; Figure P. h. homarus and P. h. rubellus in southern Mozambique, where they are sympatric. Genetic and geographic distance were weakly correlated  suggesting that geographic distance plays a minor role in genetic differentiation . The first axis accounted for 55% of the fitted variation and 35% of the total variation, and the second axis explained 42% of the fitted variation and 27% of the total variation , and that larval recruits of June 2009 could explain 8% of the variation, but was not significant . Geography explained 13% of the total variation  and was significant  and Kenya, the peak breeding season of e Figure  and Janue Figure  along wie Figure  and S3. Particles released in Yemen in June were retained in the Gulf of Aden, with a high rate of reaching the coast (>95% in 2009 and 33% in 2010). Those released in January were advected offshore into the NW Indian Ocean, with <2% of the particles reaching the coast in either year.Particles released in June in Kenya were retained near their release site in both years (>50% in 2010), with some dispersal northwards into Somalia in 2009. Those released in January were swept eastwards, potentially entrained in the South Equatorial Return Current. Few particles returned to the coast after 120 days (6.8% in 2009 and 9.7% in 2010), but a small proportion entered the northern Mozambique Channel in 2009. Overall, trajectories reflect dispersal within eddies and gyres, high seasonal and inter‐annual variability, and retention in eddies near release locations at several sites in June.3.4.2Particle density plots for SW Indian Ocean sites  for the peak breeding season in January are shown in Figure Particles released in southeast Madagascar in both years and seasons tracked across the Mozambique Channel toward the mainland coast of southern Mozambique and eastern South Africa, and most became entrained in eddies, remaining in the channel or south of it after 120 days. Although some particles released in January reached the mainland coast after 120 days (1.6% in 2009 and 1.7% in 2010), many were close to it, just off the shelf. Some 2% of particles released in January were returned to southern Madagascar, and of those released in June, 1.2% were returned.Particles released in January at all sites in eastern South Africa were advected southwestwards by the Agulhas Current, and either reached the coast, retroflected into the SW Indian Ocean, or leaked into the SE Atlantic after 120 days. Some 13.4% of particles released at Blood Reef reached the coast after 120 days in 2009 and 10.2% in 2010, mostly to the south of their release locations. Particles released from the southernmost sites rarely reached the coast after 120 days, suggesting that populations occurring here receive larvae from sites further to the north. Particles released in June (outside the main breeding season) were dispersed further offshore than those released in January at nearly all sites. On average, particles released in January at South African sites reached the coast in 10% (2009) and 5% (2010) of cases after 120 days, compared to <1% (2009) and 6% (2010) of particles released in June. High seasonal and inter‐annual variability in dispersal patterns were also observed in the SW Indian Ocean region, with evidence that particles can become trapped and retained in eddies near, or downstream of their release locations, despite the narrow shelf and proximity of the Agulhas Current along the shelf‐edge.44.1P. homarus in the Western Indian Ocean, based on fast‐evolving nuclear microsatellite markers. We also used a seascape genetics approach to relate the observed genetic structure to oceanographic influences. Three clear genetic clusters corresponded to samples from the Arabian Sea , SW Indian Ocean (P. h. rubellus), and the more tropical region in‐between (P. h. homarus). A contact zone between P. h. homarus and P. h. rubellus near Zavora  was inferred from the high degree of admixed individuals originating from Zavora in the STRUCTURE analysis, and from the genetic transition zone in the Geneland analysis.We examined the fine‐scale population genetic structure and phylogeography of P. h. homarus (Kenya) and P. h. megasculptus (Oman and Yemen) are evolutionarily distinct  and inhabit distinct geographic ranges, with some overlap in Oman . Nevertheless, more conserved mitochondrial and nuclear DNA markers could not differentiate the two groups  were more closely related to those in Kenya, thousands of kilometers away , than to those in Chidenguele . This provides strong evidence for the presence of a phylogeographic barrier between subspecies in the Delagoa Bight.For the SW Indian Ocean populations, spatially explicit clustering provided empirical support for a barrier to gene flow between 4.2P. h. homarus larvae originating from more tropical waters to the north of Zavora in Mozambique. Nevertheless, low densities of P. h. homarus do occur in eastern South Africa—potentially originating from Zavora or further north, and they must have survived the temperature gradient associated with southwards dispersal into cooler coastal waters. The absence of definitive evidence for hybrids between the two forms supports a hypothesis of specific mating and spawning preferences that may be spatially and/or temporally distinct, and potentially maintained through adaptation and behavioral reproductive isolation  or leaked into the SE Atlantic basin through ring shedding, eddies, and filaments  are approaching spatio‐temporal resolutions to resolve submesoscale processes, they are unable to represent the correct levels of variability, particularly in the highly dynamic Agulhas Current  and of P. h. megasculptus and P. h. homarus in the NW Indian Ocean and Kenya (June). Simulations were further restricted to 2009 and 2010 and showed considerable inter‐annual variability—a factor that has been implicated in recruitment patterns of species with drifting larvae (Botsford, Panulirus homarus females can carry up to four batches of eggs per year, releasing them during different months (Al‐Marzouqi et al., P. homarus in the Western Indian Ocean.Particle tracking simulations were constrained to January and June to provide seasonal contrast to dispersal patterns. The simulations included the peak breeding seasons of P. homarus subspecies, along with isolation by distance. Eddies in the Arabian Sea potentially retain larvae in that region, thus contributing to the differentiation between P. h. megasculptus and P. h. homarus. A steep genetic gradient between P. h. homarus and P. h. rubellus was demonstrated in the Delagoa Bight ecoregion in Mozambique. Virtual particles released south of the Bight were advected southwestwards by boundary currents, or reached the coast near or downstream of their release locations. Minimum SST was correlated with genetic variability, suggesting ambient temperature and larval tolerance as selective factors in dispersal success. Ocean currents and SST may play key roles in maintaining the cooler subtropical and warmer tropical distribution ranges of P. h. rubellus and P. h. homarus in the SW Indian Ocean.In conclusion, a seascape genetics approach illustrated that complex physical oceanography and biogeographic boundaries could explain genetic diversity among None declared.S.P.S., J.C.G., and S.W.‐M. conceived the sampling design; S.P.S. conducted laboratory work; S.P.S. and M.G.H.‐D. conducted analyses and wrote the manuscript; J.C.G., S.W.‐M., and B.C.B. contributed to versions of the manuscript.https://doi.org/10.5061/dryad.hf068m7.Data are available from the Dryad Digital Repository:  Click here for additional data file. Click here for additional data file.


Deducing the evolutionary histories of dog breeds can be challenging due to convergent traits and frequent admixture. In this report, we have explored the relationships of indigenous Finnish hunting spitz breeds among other northern Eurasian hunting breeds using commercially available SNP analysis (the MyDogDNA panel test). We find that Nordic hunting breeds Finnish Spitz, Nordic Spitz and the Karelian Bear Dog, as well as the reindeer herding Lapphund and Lapponian herder are all closely related and have common origins with the northeastern Eurasian Laika breeds, rather than with other Scandinavian Spitz breeds, such as Elkhounds and Swedish Vallhund. By tracing admixture events and direction of gene flow, we also elucidate the complex interactions between the breeds and provide new insight into the history of Swedish Elkhound and Russian-European Laika. The findings, together with an analysis of genetic differentiation between the populations, not only help to understand the origins of the breeds but also provide interesting possibilities to revive genetic diversity, lost during the breeding history, by backcrossing breeds to their hypothetical ancestry. Generat century ,4., Iden century , and theBefore genome-wide genetic analyses became available, reconstructing the evolutionary relationships of contemporary breeds was virtually impossible due to the wealth of convergent traits . AlthougNorbottenspets, a Swedish breed of Finnish origin [In the present study we have further explored the relationship of three Finnish hunting Spitz breeds: Finnish Spitz, Nordic Spitz (h origin ) and Karh origin  that orih origin , indicath origin . Using gSNP data for 1,319 SNP markers for the 13 breeds used in this study  was obtaAll dog samples included in the study had originally been submitted for commercial testing at Genoscoper Laboratories, with owners providing consent for the use of their dog’s DNA data for research purposes. All dogs were registered and their identity checked  prior the taking of the DNA sample. Only samples with genotype calls for at least 95% of markers were included in the study to ensure high quality data. The breeds to study were chosen based on their geographical affinities and FCI  grouping (Spitz and primitive types), with the exception of Finnish Hound, which was included because of its known genetic influence on the Nordic Spitz ,11. GenoSamples included in this study reached a call rate of at least 99% of the analyzed markers and the median heterozygosity for each breed was calculated based on all analyzed individuals. To illustrate genetic differences between individuals, multidimensional scaling (MDS) analysis was performed. MDS is an eigen-decomposition principal component analysis transforming distances into similarities .Incomplete lineage sorting can produce discrepancy between the phylogenetic tree for a specific gene and the overall taxa in a phylogenetic tree , for exaIn order to take into account the historical admixture between the breeds, we also reconstructed the phylogeny using TreeMix v. 1.13 . TreeMixk = 2–15 and the population assignment was tested using STRUCTURE HARVESTER [FST) was quantified using the elements in STRUCTURE v. 2.3.4[The genetic structure among the breeds was visualized using Bayesian hierarchical clustering in STRUCTURE v. 2.3.4. software ,26. ThreARVESTER . Because v. 2.3.4.http://mydogdna.com/ → breeds →search for a breed → genetic relationships).The used 1,319 performed well in separating breeds  and can Firstly, we wanted to establish the evolutionary relationships of the Finnish hunting Spitz breeds among the other contemporary breeds in Fennoscandia. The problem with most sequence-based phylogenetic analyses is that they assume that all loci share the same genealogy, which is not the case among SNP markers within the same species. Ignoring this so-called coalescent variance will result in incongruence between the gene trees and the true evolutionary history, such as seen in incomplete lineage sorting . To demoAs ancestral admixture is more than likely among breeds originating from the same geographical region, we next performed a TreeMix analysis, which estimates a maximum likelihood tree where branches represent the relationships between populations based on the majority of the alleles . InteresFST) among Finnish Spitz, Nordic Spitz and Karelian Bear Dog, using STRUCTURE and Arlequin 3.5.[FST is a measure of overall genetic divergence among subpopulations and pairwise comparisons of the closely related breeds can help to determine a theoretical minimum for crossbreeding [FST.To estimate the proportions of shared ancestry among the breeds showing admixture, we visualized the genetic substructure of these populations using STRUCTURE . Unlike quin 3.5.. FST is breeding . In natuN is the effective population size and m the migration rate per generation. The migration minimum might be useful to know when the potential of breed crosses as a tool to increase genetic diversity in the receiving breed, needs to be assessed. If the Nordic Spitz and Finnish Spitz are considered as a one combined population, Nordic Spitz had an FST of 0.018, while Finnish Spitz showed much higher degree of differentiation with an FST of 0.289. Similarly, in Karelian Bear Dog and Nordic Spitz comparison, Karelian Bear Dog has FST of 0.210 and Nordic Spitz 0.035, wheras the differentiation between Karelian Bear Dog and Russian-European Laika is more uniform, with FST‘s of 0.167 and 0.111 respectively.Where Advances in genome-wide SNP analyses have provided powerful tools to understand the patterns and processes in population genetics and evolution, and have also been applied extensively to study dog populations and breeds ,30,31. IWe have previously shown that Finnish Spitz and Nordic Spitz are closely related, likely originating from the same founder population . In contWhile all analyses agree with a rough separation of the Spitz breeds into Scandinavian, Finnish and Laika clades, they differ in placing individual breeds within these. It is also apparent that the analyses cannot satisfactorily solve deep divergences between the breeds, likely due to the high variability in the markers used in this study, as pointed out earlier. However, more comprehensive phylogenies for world dog breeds exists ,10 and aSNAPP and TreeMix results differ by some important aspects from those from MrBayes. While the latter places Karelian Bear Dog among the Laika breeds, both SNAPP and TreeMix rather support its affinity with Finnish and Nordic Spitz . TreeMixAnother surprising aspect of the phylogenetic analyses was the high genetic differentiation between the Norwegian Elkhound, Grey and the Swedish Elkhound, with MrBayes placing the Swedish Elkhound to a basal branch of Laika Breeds, although with low posterior probability . This isFinnish Hound was known to have influenced the genetic makeup of the contemporary Nordic Spitz population due to the occurrence of the same genetic disease, Finnish Hound progressive early-onset ataxia, in the two breeds ,12. All FST of 0.018, while Finnish Spitz showed much higher degree of differentiation with an FST of 0.289. To demonstrate the difference, these numbers correspond to the migration of 13.6 individuals per generation (Nm) from the Finnish Spitz to the Nordic Spitz population, but only 0.6 individuals in the reverse direction. As these figures equal the balance between migration and population differentiation, the numbers also provide a rough estimate of how many mixed-breed litters were possible per generation, without noticeable impact on the breed in question. Similarly to Finnish Spitz [Hz) rate  and 0.11  for the Russian-European Laika. Although the breed crossing preference in the case of Karelian Bear Dog would be purely a matter of opinion, crossing with Nordic Spitz might be considered as a reconstruction of the ancestral breed.When comparing genetic differentiation between Finnish Spitz and Nordic Spitz, Nordic Spitz had an Hz) rate , the useHz) rate , TreeMixHz) rate . When Noexchange , suggestAs a conclusion, the results of our study show that geography and cultural context is an important determining factor of breed relationships. While the Finnish Spitz breeds have close affinity with the Laika breeds, pointing to common origins somewhere in eastern Eurasia, the evolutionary origins of the Scandinavian hunting Spitz breeds remains a challenge for future studies.S1 File(ZIP)Click here for additional data file.S1 FigUsing randomly picked individual genotype samples does not influence the overall topology of the tree compare , but has(PDF)Click here for additional data file.


The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame. Sesamum indicum L. (2n = 26), is an ancient oilseed crop belonging to the genus Sesamum, family Pedaliaceae, in the order Tubiflorae. Sesame have been used for oil and food for more than 4000 years [Sesame, 00 years , and it dicum L. n = 26, i00 years . The oil00 years , 6. Sesa00 years . However00 years , indeter00 years , nonsync00 years , and sus00 years  Further 00 years . The undSeveral agro-morphological characterization studies have been conducted on various genetic resources of sesame –15 to idIn the last decade, different types of high-throughput and cost-effective SNP detection platforms have been developed . Of thesThe comprehensive and accurate characterization of germplasm and, therefore, the utilization of this germplasm in plant breeding research is limited by the large amount of genetic resources. An efficient selection of these genetic resources can be obtained using the core collection concept, which allows the use of a limited set of genotypes to represent the whole collection with a minimum of repetitiveness . In sesaThe Mediterranean sesame core collection consists of 103 accessions , and 95 MspI to validate the restriction enzyme digestion.Each accession was grown in pots, and the leaves were harvested from 3 week-old plants. DNA was extracted using the CTAB method  with minVspI restriction enzyme was used instead of the EcoRI restriction enzyme employed in the original ddRAD protocol. Digestion products were cleaned with Ampure XP beads (Beckman Coulter Genomics) followed by P1 and P2 adapter ligation using T4 ligase buffer. The 3’ end of theP1 adapter was also modified to complement the overhanging VspI restriction cut site. Following ligation, each reaction was subjected to PCR amplification (15 cycles) using genotype specific indexed PCR primers. The PCR products were then checked on an agarose gel and pooled in equal concentration. A final step, the pooled products were size selected (400-500bp). The ddRAD sequencing data have been deposited in the National Center for Biotechnology Information (NCBI) Sequence-Read Archive (SRA) database with the accession number of PRJNA560319.A reduced representative genomic library was prepared before subjecting each sesame accession to Illumina 150bp PE sequencing. A modified version of the ddRAD method  was follVspI and MspI sequences were trimmed. The processed sequences were then aligned to the sesame reference genome “Zhongzhi13 V2.0” [www.usegalaxy.org) software framework. Genotype specific individual BAM  files were subjected to variant calling using freebayes  [The raw reads were demultiplexed with Je (v1.2)  and orga13 V2.0”  using Bo13 V2.0”  with the.0.46–0)  for furtK) from 2 to 8 to identify the optimal number of populations present within the95 accessions. The following parameters were used: a burn-in period of 10000 and a Markov Chain Monte Carlo replication of 10000. The best K-value (the number of subpopulations) was estimated with the use of the ad-hoc statistic ΔK [http://taylor0.biology.ucla.edu/structureHarvester) [http://btismysore.in/strplot) online tool [Before conducting the genetic and population analyses, the SNP-containing file (.vcf) were converted to the related software input file formats by PGD Spider v2.1.1.5 . Geneticistic ΔK  via the rvester) . Each seine tool , with gehttp://tree.bio.ed.ac.uk/software/figtree). The software Arlequin V3.5 [ST) for the subpopulations and to calculate the genetic variation between and within geographical groups with analysis of molecular variance (AMOVA). An FST value of 0 indicated no genetic divergence within the subpopulations and a value of 1 indicated complete extreme division. Populations were considered to have little differentiation when FST ≤ 0.05, moderate differentiation when 0.05 < FST ≤ 0.15, strong differentiation when 0.15 < FST ≤ 0.25, and very strong differentiation when FST> 0.25 [A principal coordinate analysis (PCoA) was performed with the PAST software V3.23 . The phyuin V3.5  was usedST> 0.25 .Sesamum indicum L. reference genome was 81.89%. A total of 56648 unique SNPs were initially called from the accessions using a variant calling pipeline. In total, 5292 polymorphic SNP markers were selected  content per accession . The higselected  for furtselected . The proselected .Genetic diversity analysis for the collection and the continental subgroups was conducted with GenAlex program V6.5 . The meaK) from 2 to 8 and conducting twenty runs for each K-value. The results obtained from STRUCTURE were assessed via Structure Harvester [K value. The largest delta K was observed at K = 3, suggesting the presence of three main clusters  in the sesame panel  was between the American and European continental groups. The corresponding FST values between the continental groups were moderate for Asia vs. Europe  and lower for Asia vs. Africa (0.05) and Asia vs. America (0.04)  .A phylogenetic tree consisting of 95 sesame accessions was constructed based on the UPGMA clustering method with 5292 high-quality SNPs obtained from ddRAD . The sesK = 3. All groups had accessions from Asia, and Group I, Group II, and Group III consisted of 20, 24, and 15 accessions, respectively, from different geographic regions and continents. The remaining accessions were clustered as an admixture, based on structure analysis.Principal coordinate analysis (PCoA) indicated the existence of four subgroups among the95 accessions of our study . The firRevealing the population structure and diversity of a collection is the best way to achieve efficient management of crop genetic resources to improve breeding programs and to understand the phylogenetic relations of accessions. The present investigation used genome-wide SNP analysis to investigate the diversity and population structure of the Mediterranean sesame core collection consisting of 95 accessions from 21 geographically different regions. A total of about 350 M raw sequence reads were acquired from the next-generation sequencing platform, and the number of reads varied between 1.55 and 6.33 M for the accessions in the collection . This flOryza ssp. [The average value of gene diversity (0.28) was higher in the present study than in the earlier reports for the sesame collections analyzed with different marker types , 61, 66.yza ssp. . Laurentyza ssp.  also obtSesamum indicum L. seeds were dispersed to a wide geography from one center, leading to the observed genetically similar backgrounds. A majority of the accessions of Iran origin showed a tendency to cluster together with the accessions of the neighboring country, Turkey (ST) was observed in the accessions collected from Asia and America in the present investigation  in sesame crop to obtain high quality SNPs. The gene diversity values calculated based on the 5292 SNPs suggest the Mediterranean sesame core collection is highly genetically diverse. The collection therefore presents useful genetic data for future molecular based studies. This study also supports the idea; ecological and geographical factors less effective in the evolution of sesame.The present research showed the effectiveness of ddRAD in characterizing the genetic diversity and population structure of sesame collection and also demonstrated usefulness of restriction enzymes Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.


Lancea tibetica (Mazaceae), an endemic herb to QTP and adjacent highlands. We sequenced chloroplast and nuclear ribosomal DNA fragments for 429 individuals, collected from 29 localities, covering their major distribution range at the QTP. A total of 19 chloroplast haplotypes and 13 nuclear genotypes in two well-differentiated lineages, corresponding to populations into two groups isolated by Tanggula and Bayangela Mountains. Meanwhile, significant phylogeographical structure was detected among sampling range of L. tibetica, and 61.50% of genetic variations was partitioned between groups. Gene flow across the whole region appears to be restricted by high mountains, suggesting a significant role of geography in the genetic differences between the two groups. Divergence time between the two lineages dated to 8.63 million years ago, which corresponded to the uplifting of QTP during the late Miocene and Pliocene. Ecological differences were found between both the lineages represent species-specific characteristics, sufficient to keep the lineages separated to a high degree. The simulated distribution from the last interglacial period to the current period showed that the distribution of L. tibetica experienced shrinkage and expansion. Climate changes during the Pleistocene glacial-interglacial cycles had a dramatic effect on L. tibetica distribution ranges. Multiple refugia of L. tibetica might have remained during the species history, to south of the Tanggula and north of Bayangela Mountains, both appeared as topological barrier and contributed to restricting gene flow between the two lineages. Together, geographic isolation and climatic factors have played a fundamental role in promoting diversification and evolution of L. tibetica.Qinghai-Tibetan Plateau (QTP) is an important biodiversity hub, which is very sensitive to climate change. Here in this study, we investigated genetic diversity and past population dynamics of  The Qinghai-Tibetan Plateau (QTP) is one of the largest and youngest plateaus in the world, formed by several uplift events after the collision of the Indian tectonic plate with the Asian plate, about 40 Ma (million years ago) . FurtherJuniperus przewalskii , L. tibetica mainly occurs in Gansu, Qinghai, Sichuan, Xizang, and Yunnan in China. It should be noted that few CVH herbarium records of L. tibetica are mainly before the 1960s. Some locations with just one or two records are difficult to sample again in our field investigation. In this study, a total of 429 individuals were collected from 29 populations covering the major distribution range of L. tibetica . All the sampling locations were geo-referenced, and voucher specimens deposited into the Herbarium of Northwest Plateau Institute of Biology (HNWP), Chinese Academy of Sciences.According to the Flora of China  and herbtrnH-psbA, matK, trnL-F and rbcL) and two nuclear ribosomal internal transcribed spacer regions (ITS1 and ITS2) were amplified for all samples (2+), 1 μL of dNTPs (each 10 mM), 0.5 μL of each primer (50 μM), and 1 U of Taq DNA polymerase . The amplification temperature followed a profile of 95°C for 1 min; 30 cycles of 95°C for 30 s, 55°C for 30 s and 72°C for 1 min 30 s; extension at 72°C for 10 min. PCR products were sequenced with an ABI 377XL DNA sequencer (Applied Biosystems). The program CLUSTAL X  method . Four in samples . PCR ampLUSTAL X  was usedLUSTAL X . All seqHd) and nucleotide diversity (Pi) were also calculated in DnaSP. The program PERMUT (HS), total gene diversity (HT), genetic differentiation (GST) and population subdivision of phylogenetically ordered alleles (NST) /HT  and to check the geographical distribution pattern.During all analyses, insertion–deletion polymorphisms (indels) were coded as presence/absence characters. After alignment, cpDNA haplotypes and ITS genotypes were identified and distinguished using DnaSP v5.0 . The levm PERMUT  was usedes (NST) . The GST -HS)/HT . The U-sK = 2–10, starting from 1,000 random initial conditions for each run, to obtain the maximal value of FCT for the most appropriate K-value and grouping method. Genetic differentiation based on cpDNA was estimated through analysis of molecular variance (AMOVA) as implemented in the program ARLEQUIN v3.5 (Nm = ([1/FST]-1)/2. Genetic distances were estimated in ARLEQUIN with 1,000 permutation tests.Population subdivision analysis was performed in the program SAMOVA v1.0 , to defiUIN v3.5 . To calcP. rhinanthoides and P. chinensis were selected as outgroups, as Pedicularis and Lancea were formerly in the same family Scrophulariaceae , where τ is the total number of mutations and u is the mutation rate per generation for the whole analyzed sequence. The value of u is calculated as u = μkg, where μ is the substitution rate per nucleotide site in 1 year, k is mean sequence length of the analyzed DNA region and g is the generation time of the plant. We used the substitution rates (2 × 10-9 s s-1 year-1) of cpDNA  was used as the outgroup in analyzing ITS data , last glacial maximum (20 ka), and last interglacial (135 ka) periods  in all individuals was 2,179 bp, included 14 substitutions and four indels  was 0.6247 and nucleotide diversity (Pi) was 0.00108  and were highest at K = 5 when populations 6, 14, and 15 formed three groups (these populations had a high proportion of private haplotypes). The average genetic diversity (HS) was 0.311, while the total genetic diversity (HT) was 0.644. The NST (0.662) was significantly higher than GST (0.507), as shown by a U-test (P < 0.01), indicating significant phylogeographical structure in L. tibetica. AMOVA revealed that 61.50% of genetic variation was partitioned among groups, 15.50% among populations within the group, and 22.94% within populations . A background test of both lineages also showed that the ecological niches of the two lineages are well differentiated  (Camellia flavida (0.35) (L. tibetica (0.149) was lower than that among the different populations (0.249). The seeds of L. tibetica are small and wingless and disperse near the parent plants, a feature that is likely to have enhanced the degree of genetic differentiation by restricting gene flow (The average effective gene flow within the distribution range of a (0.41)  and Camea (0.35) . Higher ene flow . Howeverene flow .L. tibetica comprises two major cpDNA groups. One group has its main geographic distribution to the north of the Tanggula and Bayangela Mountains, while the other group lies mainly to the south of the QTP. Gene flow across the whole region appears to be restricted by high mountains, suggesting a significant role of geography in the genetic differences between the two groups. Similarly, the ITS sequence variation showed clearly that the divergence of L. tibetica between the major north and south lineages was around 8.63 Ma. Although the estimates of dates of origin need to be treated with caution, they correspond well with geological evidence that the QTP experienced uplift during the late Miocene and Pliocene periods  contained higher haplotype and nucleotide diversities. It is likely that populations located in the Tanggula Mountains could survive in alternative habitats within a short distance, allowing biodiversity to persist during climate modifications (According to ications . These pications .L. tibetica from our sample range, bringing together molecular phylogeography and species distribution modeling, indicate that a combination of geographic isolation and climatic factors have played a fundamental role in promoting diversification and evolution of this species. This study provides valuable evidence that advances research on genetic differentiation on the QTP.In conclusion, analyses of FZ and SC conceived and designed the experiments. MX and ZT performed the experiments. MX, ZT, FZ, and GK analyzed the data. QG, RX, YZ, and JY contributed reagents, materials, and analysis tools. MZ wrote the paper. FZ, SC, and GK reviewed and edited the paper. All authors approved the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


The profession of genetic counseling  began nearly 50 years ago in the United States, and has grown internationally in the past 30 years. While there have been many papers describing the profession of genetic counseling in individual countries or regions, data remains incomplete and has been published in diverse journals with limited access. As a result of the 2016 Transnational Alliance of Genetic Counseling (TAGC) conference in Barcelona, Spain, and the 2017 World Congress of Genetic Counselling in the UK, we endeavor to describe as fully as possible the global state of genetic counseling as a profession. We estimate that in 2018 there are nearly 7000 genetic counselors with the profession established or developing in no less than 28 countries. When you do not have it, you do not realize you are missing it, but when you have it, you cannot live without it!” While the service of genetic counseling was in existence much earlier, the profession of genetic counseling  began in the United States (US) in 1969 , 3 led tThe international expansion of genetic counseling has been a topic of interest for the past decade. The Transnational Alliance of Genetic Counseling (TAGC) was established by Janice Edwards (USC) via a Jane Engleberg Memorial Fellowship through NSGC in 2006 . TAGC fohttp://www.eurogentest.org/index.php?id=679, accessed May 5, 2018), and university level training that is available in different countries. Examples of these differences include: the length of training, specific curriculum, and amount of clinical training; the background of individuals who are recruited into the profession  , with many papers from that edition referenced for readers who desire more detailed information, and a commentary by some co-authors of this paper  was established in 2014 . There iThe first training program in Japan was started in the early 2000’s. Curriculum and clinical training requirements are based on the US training model, although all program directors are physicians, and psychologists are used to teach the psychosocial curriculum in most programs. There is a national certification process; international graduates may request an application for certification examination. GCs in Japan work in cancer genetics, prenatal, pediatric, and neurogenetics areas, as well as more general genetic counseling positions, and are mostly employed in larger cities at larger (often academic) medical centers or in private practice.Genetic counseling services began in 1994  and GCs Genetic counseling training includes clinical training and a research requirement, has a significant focus on public health, including rare disorders and newborn screening. Many of the entering students have prior background in the sciences or various healthcare professions. Education is provided in English and Filipino, taking into account the many dialects across the Philippines, and funding is available for individuals from diverse regions to attend the program and return to their province in order to provide services countrywide. GCs in the Philippines are involved in various clinical activities, research and academic endeavors.The genetic counseling profession in Singapore is still developing; the job description and scope of practice is not formalized across the country and the role is not yet recognized as an Allied Health profession. MSGCs trained in countries outside Singapore provide clinical genetic counseling in cancer genetics, general medical genetics (pediatrics/adult) and prenatal genetics, and research roles. The National Cancer Centre Singapore (NCCS) is spearheading efforts to develop GC-led clinics and paired GC-geneticist clinics, modelled on the NSGC scope of practice. This model has resulted in improved efficiencies and cost-savings .There are 2 Master’s level training programs , and certification is provided by the KSMG .A single 2-year master’s degree program  requires at least 300 internship hours  prior to certification. Trainees are recruited from baccalaureate backgrounds including life science or related field, such as medicine, nursing, or medical technology. GCs work genetic counseling centers, private prenatal service providers, laboratories or other related organizations .Currently in Africa, there are medical genetics services in many countries, but the only formal genetic counseling services and training programs are in South Africa . Genetic counseling training started in 1989 in South Africa, and there are currently two 2-year master’s degree training programs  , 47, 48.We believe that in 2018 there are nearly 7000 genetic counselors globally, in at least 28 countries. Greater than 60% are practicing in North America. As described above, most countries with training programs in genetic counseling have adopted a 2-year Master’s degree approach, although there is variation in methods and requirements for training, certification, and registration/licensure. Our data suggests that flexibility in how the profession develops and expands will remain necessary to acknowledge the international variation in laws, health systems, and cultures. Genetic counseling remains a growing profession globally, and international collaboration and growing reciprocal agreements support ongoing improvements across training, regulation, and scopes of practice.


Aedes aegypti is associated with dengue, yellow fever, chikungunya and Zika viruses. This vector is widespread in tropical and subtropical areas, and can also occur in temperate areas at higher latitudes. The geographical distribution of Ae. aegypti continues to spread due to human activities. This is the first study to examine the population genetic structure of this insect in El Salvador, Central America.Aedes aegypti larvae were collected from six geographical regions of El Salvador: Sonsonate, San Salvador, Chalatenango, Usulután, San Miguel and Morazán. Larvae were raised into adults, identified and preserved. Two molecular markers, amplified fragment length polymorphism (AFLP) genotyping and mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 (cox1) sequencing, were used to investigate population genetic structure.cox1 sequences produced a haplotype network which consisted of 3 haplogroups and 10 haplotypes. Haplogroup 1 had low haplotype and nucleotide diversity and was found in all six regions. Haplogroups 2 and 3 had higher haplotype and nucleotide diversity, and were less abundant; haplogroup 3 was found in only 3 of the six regions studied. Bottleneck tests were significant, suggesting that populations had undergone a recent bottleneck. A maximum likelihood tree, which combined samples from this study with available sequences in GenBank, suggested that two genetically divergent lineages had been introduced.Structure analysis found two genetically distinct populations; one occurs predominantly in the north and west, and a mix of two populations occurs in the southeast of the country. Genetic distances ranged from 0.028 (2.8%) to 0.091 (9%), and an AMOVA analysis found 11% variation between populations. Mitochondrial DNA Ae. aegypti in El Salvador. The mtDNA sequences clustered into two lineages, as found in previous studies. Samples in El Salvador may be introduced from regions in North and South America where past eradication was not complete. Future study of genotypes in surrounding countries would provide a more complete picture of the movement and potential source of introductions of this vector. The distribution of the lineages and haplogroups may further our understanding of the epidemiology of Ae. aegypti associated vector borne diseases.Relatively high genetic diversity was found in The online version of this article (10.1186/s13071-018-3226-5) contains supplementary material, which is available to authorized users. Aedes aegypti is associated with yellow fever, dengue, chikungunya and Zika viruses. These diseases impact the health of millions globally each year. It is estimated that at least 50 million per year are infected with dengue, with inhabitants of 100 or more countries at risk of infection [Aedes aegypti typically occurs in tropical and subtropical regions of the world, but can also occur in temperate regions at higher latitudes [The mosquito atitudes . This moAe. aegypti on a global scale [Ae. aegypti vary in their ecology and are considered subspecies. The sylvatic ancestral form of Ae. aegypti, Ae. aegypti formosus, resides primarily in forested environments and tree holes, and a second anthropophilic form, Ae. aegypti aegypti, occurs in urban areas in homes where water is stored [Studies have examined genetic diversity of al scale –7. In Afs stored , 7–9. Ths stored , 5. In as stored , 10.Ae. aegypti in numerous countries in the Western Hemisphere, Asia and Australia. A variety of molecular markers have been utilized in these studies including microsatellites and mitochondrial DNA. Studies have found evidence for one, two or three introduced clades of Ae. aegypti outside of their region of origin of Africa [Ae. aegypti from the northeast coast of Mexico suggest two divergent lineages and two introductions [Ae. aegypti; low nucleotide diversity suggested passive dispersal between Argentine populations and those from adjacent countries [Ae. aegypti in the Western Hemisphere could be populations that persisted through eradication programs, which might reinvade surrounding regions [Ae. aegypti was later reintroduced [Ae. aegypti were more closely related to those from Venezuela, where eradication did not occur. The former study along with a subsequent study in Brazil suggested that the Ae. aegypti populations currently found in Brazil are populations which were reintroduced in the country after eradication was achieved [Ae. aegypti are introduced into a region, they could undergo genetic divergence due to environmental factors and geographical barriers [Ae. aegypti in Peru were found to be divergent on different sides of the Andes, possibly due to climatic differences and geographical isolation [Regional studies have investigated the genetic diversity of introduced f Africa –13. For ductions . In Brazductions , 16. Resountries . In Boli regions . In Brazachieved . Other sbarriers , 20. Forsolation , 20.Ae. aegypti is the primary vector of dengue, chikungunya and Zika virus [Aedes aegypti was previously eradicated from El Salvador, and from much of the Western Hemisphere, in the 1950s and 1960s [Ae. aegypti by 1961. However, in El Salvador, Ae. aegypti was reintroduced in a shipment of tires from the USA to San Salvador in 1965 [Aedes aegypti is currently widespread through the country. In 2014, chikungunya cases were first reported in El Salvador, followed by the first reports of Zika in 2015 [Ae. aegypti can vary in vector competence and insecticide resistance, and thus respond differentially to control [Ae. aegypti in Central America. The objectives of this study were to examine the genetic variability of populations of Ae. aegypti in six regions of El Salvador, and to investigate the number of possible introductions and lineages of this insect in the country.In El Salvador, Central America, ka virus . El Salvnd 1960s , 22. Sim in 1965 . By 1982 in 1965 , 25. The in 2015 . Previou in 2015 . For exa control . Little Ae. aegypti were collected in six departments of the country: Sonsonate, San Salvador, Chalatenango, Usulután, San Miguel and Morazán  at the University of El Salvador, in San Salvador. In the laboratory, larvae from each collection site were placed into plastic cups with distilled water and maintained in wire mesh cages (20 × 10 × 10 cm) until adults emerged. Each day, cages were checked for newly emerged adults, which were frozen and later identified to the species level based on morphology. Only adult females were used for this study.Adult females were used for DNA extraction, with at least 30 adult females individually extracted from each of the six regions. DNA extraction was completed with the Qiagen DNEasy® Blood and Tissue Extraction Kit  following standard protocols , using aMseI-CAT/EcoRI-ACG; (ii) MseI-CAC/EcoRI-ACT; and (iii) MseI-CAC/EcoRI-ACA. Details of AFLP reactions are described in Joyce et al. [Amplified fragment length polymorphisms were produced for each mosquito using three primer combinations with procedures described by  and modie et al. . Initiale et al.  was run e et al. , and eace et al.  using the et al.  to detere et al. .A Mantel test was used to examine the relationship between genetic distance and geographical distance (isolation by distance) using GenAlex 6.5 . An analBottleneck version 1.2.02 was used to test whether there was a significant departure from an equilibrium expectation of heterozygotes in each population . We usedc oxidase subunit 1 (cox1) (known as the ‘barcode’) using the universal forward primer LCO1490 (5'-GGT CAA CAA ATC ATA AAG ATA TTG G-3') and the reverse primer HCO2198 (5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3') [via 1000 bootstrap replicates [For each insect, DNA was used to sequence a ~650 bp region of mitochondrial DNA cytochrome T CA-3') , 39. A pT CA-3') . SequencT CA-3') . Using tT CA-3') . ML analplicates .cox1 sequences were used to determine the overall number of haplotypes, haplotype diversity, nucleotide diversity and Tajima’s D using DNAsp 5.10 [The mitochondrial DNA Asp 5.10 ; Tajima’Asp 5.10 .Ae. aegypti previously sequenced which were available in the GenBank database. Samples included in the tree were selected in the following manner. First, one individual from each of the three most common mitochondrial haplogroups in El Salvador was used for a blast search. Resulting sequences which were 99–100% similar were retrieved, and those from North and South America were selected for inclusion in the tree to compare with those from El Salvador [Ae. aegypti [via 1000 bootstrap replicates.Additionally, a combined maximum likelihood phylogenetic tree was constructed using samples from El Salvador and individuals of Salvador . SeveralSalvador . In addiSalvador  were inc aegypti . In this aegypti . From El aegypti . The maxFrom collections in the six regions, 137 samples were used for DNA extraction Tables . The thrr = 0.976, P = 0.010) , and found 11% genetic variation among the six populations (Table P < 0.001), indicating each population had undergone a recent bottleneck. Results from the IAM model were significant for each of these populations at P < 0.001.Nei’s genetic distance between the populations ranged from 0.028 to 0.091 Table . Smallerns Table . BottlenThe principal components analysis found that the first axis accounted for 44.75% of the variation, while the second and third axes explained 26.20% and 13.43% of the variation, respectively ; San Salvador (n = 11); San Ignacio (n = 11); Jiquilisco (n = 14); San Miguel (n = 16); and Morazán (n = 20). The neighbor-joining consensus tree of individuals from El Salvador produced 3 groups, with 0.01 (1%) genetic distance between groups 1 and 2, and 1% between groups 2 and 3. Between groups 1 and 3, the genetic distance was ~2%. A maximum likelihood tree also indicated three groups , and the overall nucleotide diversity was 0.016  and not for the other five regions  and Morazán, also in the south and eastern region, consisted of a mix of the two groups. Genetic distances were largest between San Miguel and Chalatenango (nearly 10%) and the overall AMOVA of the six populations found 11% genetic variation. These values are similar to those found in other studies; for example, 15% in Colombia [The data from the Structure Harvester analysis of the AFLP data found there were two genetically divergent groups of Colombia , 19% in Colombia  and 20% Ae. aegypti [Ae. aegypti aegypti. Other studies have suggested that divergence may also occur between populations from the rainy season and the dry season [There are several explanations for the two genetically distinct groups found in the Structure Harvester analysis. Studies have suggested at least two subspecies of  aegypti , 7, 48 wy season . SeasonaAe. aegypti in Colombia and Venezuela [A large degree of genetic diversity was also found in the mitochondrial DNA sequences in this study. There were three haplogroups with a total of 10 haplotypes, with an overall haplotype diversity of 0.610 and a nucleotide diversity of 0.015. These values are relatively high, and are similar to those found by Bennett et al. [enezuela , 49. In The most abundant haplotype sequenced in the present study was haplotype 1, which was found in all six regions of the country. In Sonsonate, on the Pacific coast of El Salvador, over 90% of individuals sequenced were haplogroup 1, and the nucleotide diversity in Sonsonate was the lowest of all regions (0.003) Fig. . Low nucAe. aegypti have similarly found phylogentic trees with two lineages and varying levels of support [In El Salvador, the second most abundant haplotype observed  occurred more frequently in San Ignacio, Chalatenango than in the other five departments Fig. . San Ign support , 48, 49.cox1 sequences from El Salvador. These individuals formed a small subgroup of the first lineage of the combined phylogenetic tree. While several previous studies of Ae. aegypti have suggested that three lineages have been introduced in the Western Hemisphere [Ae. aegypti have been introduced into El Salvador. The third haplogroup in our study was found in the capital city San Salvador, and in the south and east portion of El Salvador, in San Miguel and Morazán. The third (red) haplogroup clustered in the first lineage with the blue haplogroup from El Salvador, yet had much higher haplotype and nucleotide diversity. This group had no match to sequences in GenBank which was 99–100% similar, suggesting it is from an area which has yet to be included in global level population analyses.A third haplogroup  (TIFF 4202 kb)Additional file 2:Figure S2. Results from a Structure Harvester analysis of all six populations of Ae. aegypti in this study. Each row shows the probability of K populations and delta K. The most likely number of populations was K = 2. (TIFF 5816 kb)Additional file 3:Figure S3. Mantel test to examine the relationship between genetic distance and geographical distance for six populations of Ae. aegypti . (TIFF 1791 kb)Additional file 4:Figure S4. Principal components analysis using genetic distance output of AMOVA of the six populations of Ae. aegypti in the study. (TIFF 1744 kb)


Eristalis tenax migrations on the East Coast of the USA and provide evidence for migration among North American hoverflies. We wish to raise awareness of this phenomenon and suggest approaches to advance the study of hoverfly migration in North America and elsewhere.The seasonal migration of huge numbers of hoverflies is frequently reported in Europe from mountain passes or spurs of land. The movement of such large numbers of beneficial insects is thought to provide significant ecosystem services in terms of pollination and pest control. Observations from the East Coast of the USA during the 1920s indicate the presence of migratory life histories among some hoverfly species there, but 90 years have now passed since the last reported observation of hoverfly migration in the USA. Here, we analyse video footage taken during a huge northward migration of hoverflies on 20 April 2017 on the West Coast of California. The quantification of migrant numbers from this footage allows us to estimate the passage of over 100 000 hoverflies in half an hour over a 200 m section of headland in Montaña de Oro State Park (San Luis Obispo County). Field collections and analysis of citizen science data indicate different species from the previously reported  Worldwide, there are many migratory insect species but only a handful of iconic migrants, mostly made up of large butterflies, dragonflies or major crop pests ,2. WhileEristalis tenax , werspecies; . Surpriso County . We anal2.2.1.https://www.ffmpeg.org) and each frame visualized with ImageJ (https://imagej.nih.gov/ij/). Hoverfly numbers were quantified as they passed a set point a third of the way through the field of view. High-resolution 20 MP still images of the hoverfly migration were analysed to quantify numbers and identify potential species.Migrant numbers were quantified from a video recording taken at 30 fps and 8 MP resolution with an Olympus E-M1 mark II camera . The video was converted to an uncompressed AVI file using FFMPEG software . We searched for verifiable records using the description ‘Syrphidae’ covering North America. Subsequently, we selected data west of −114° longitude to represent the West Coast. Raw data are available in the electronic supplementary material, file S4.Hoverflies were collected from San Luis Obispo County  over a two-week period in April 2018 using hand nets. Permission was obtained from the State of California Natural Resources Agency: Department of Parks and Recreation (Ref: 17-820-38). Distributional data for the candidate species were obtained from the citizen science website iNaturalist (3.a). We were able to estimate hoverfly numbers based on a video recording documenting the migration . We detected the transit of 660 hoverflies during the 35 s recording. When scaled to the 30 min of observed migration, this is around 34 000 hoverflies passing over this small section of trail no wider than 20 m. Analysis of higher resolution still images taken from the same position as the recording, and without quality reduction brought about by video compression, allowed us to detect four times the number of migrants in each image . These numbers indicate around 136 000 hoverflies may have passed this point; however, migration was observed at a similar density over an estimated 200 m wide section of trail, indicating that total numbers may have considerably exceeded this.Our observations of hoverfly migration took place on 20 April 2017 from 10.00 to 10.30 at an elevation of 80−100 m above the nearby sea level at Montaña de Oro State Park, California . Many thfigure 2b–d). Analysis of these images suggests a single species of relatively large, predominantly black and yellow/orange hoverfly. This coloration and appearance allow us to exclude E. tenax, which was previously observed to migrate along the East Coast of the USA by Shannon [Scaeva pyrastri , the black and yellow Syrphus opinator, and the smaller Eupodes fumipennis and Eupodes volucris.Unfortunately, no specimens were captured during this observation, but high-resolution photos taken at random were used to identify the species involved b–d. Anal Shannon . To dete Shannon ,10, and https://www.inaturalist.org). Records from Syrphus, Scaeva and Eupeodes spp. all occurred in high abundance in California in April, with observations occurring up through Oregon, Washington, British Columbia and into Alaska as spring commenced into summer, then through increasingly lower latitudes through the autumn and winter (S. pyrastri was more abundant in 2017 (n = 42 versus 23 in 2016 and 2018).To identify if these candidate species also had ranges that extended up the West Coast through spring and summer, indicative of migratory movements, we obtained records from the iNaturalist database . Hence, as in previous observations in the USA, Scandinavia and the UK, it seems that the coastal topology served to concentrate migrant numbers [Vanessa cardui [Our results indicate key conditions during which the northwards migration of hoverflies on the West Coast of the USA can become observable. Two factors appear to be particularly important in this case, the first is the presence of a headland, constrained on one side by the Pacific Ocean, and on the other by the mountains of Montaña de Oro State Park b. Hence, numbers ,7. The s numbers . Given ta cardui  and thesa cardui . By conta cardui , restrica cardui .Scavea, Syrphus and Eupeodes spp. from analysis of citizen science data (Scavea, Syrphus and Eupeodes spp. are highly indicative of migratory behaviour. In support of our results, we note that Eupeodes spp. have previously been reported to spike in numbers in March in the Los Angeles Basin, then disappear from the region over summer, which again is indicative of an influx of migrants, although no directional movements have been noted [Syrphus, although this requires confirmation through the capture of active migrants. However, our evidence does not rule out the presence of multiple species, a scenario that may be likely given the diversity of hoverflies found in North America, the prevalence of migratory life histories within the family and the mix of species often found during migrations in Europe [Migration is widespread and well documented within European hoverflies ,10, and nce data . Citizenen noted . Unfortun Europe ,10.5.Our study demonstrates the presence of migratory life histories of some hoverflies on the West Coast of North America and quantifies the scale of a huge migratory event that occurred in 2017 where hundreds of thousands of hoverflies passed over a 200 m front in only 30 min. The only previous reports of hoverfly migration within the USA occurred over 90 years ago on the East Coast , hence t


Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine‐scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine‐scale genetic patterns among localities.Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian  Overall, estimates of population connectivity can inform the design and management of conservation areas for protecting endangered or economically important species  along the coast of Chile and Perú, between 10°S and 44°S , Los Molinos (MO), and Chaihuín (CH)  were randomly collected within one meter of the measuring tape. Each percha can contain from a few to several dozens of individuals. We randomly sampled up to 16 individuals per percha that were preserved in 80% ethanol at 4°C. For each individual, we recorded its location along the corresponding transect. GPS coordinates from each transect were taken using a Garmin GPS.) Figure  that spa2.2www.australomics.cl). For more information on the PCR protocol, marker details, and thermocycler profiles, see Giles et al. , number of alleles (Na), number of private alleles (PAP), observed (Ho), and unbiased expected heterozygosity (uHe) were estimated for each site and each locus using the software GenAlEx v6.503  were determined using Genepop  within our data set. Each population is characterized by a set of allele frequencies that are used to assign individuals to populations based on their genotypes. We ran STRUCTURE varying K from K = 1 to K = 10. For each K, the model was run ten times with a burn‐in of 200,000 iterations and 500,000 subsequent iterations. The most likely K was selected visually by inspecting the relationship between the maximum likelihood of the model given the data (LnP(D))  implemented in GenAlEx v6.503. Population pairwise  Wright,  was dete2.52.5.1r) was estimated for each class distance. We performed 9,999 random permutations and 10,000 bootstraps to determine the 95% confidence intervals around the null hypothesis of no spatial autocorrelation (r = 0). Significant positive r values for a given geographic distance indicate that samples in that distance are more closely related to each other than the average of all the transect samples. On the contrary, significant negative r values indicate that samples in that distance class are less closely related to each other than the average of all the transect samples.Spatial autocorrelation was determined at the scale up to 50 m within each of the six transects sampled at the three localities with the purpose of evaluating whether genetic similarity between individuals correlates with geographic distance between them  within each percha by locality, (b) within each point by locality, and (c) within each transect by locality. We evaluated whether average pairwise relatedness between individuals within a hierarchical level was different than the average relatedness across the entire data set at that hierarchical level. In other words, if dispersal is limited at one of these hierarchical levels, then one would expect to find higher mean relatedness among individuals at that level, compared to mean relatedness at the hierarchical level above. Genetic relatedness between pairs of individuals was generated in GenAlEx v6.503 using the Lynch and Ritland  estimatop‐value associated with the likelihood ratio test was ≤0.01. Significance levels for the pairwise likelihood values were estimated using 10,000 simulations for the null hypothesis of unrelated pairs of individuals and for the primary hypothesis of full‐sibling pairs. We then compared the proportion of full‐siblings within and among each hierarchical sampling level. To test whether proportions were significantly different, we used a two‐proportions Z test implemented in R v3.4.0  to 0.35 (ME02). We could not rule out that observed deviations from HWE were due to the presence of null alleles. Therefore, we conducted the genetic structure analyses with and without correction for null alleles. Significant genotypic linkage disequilibrium was found in 11 of 270 comparisons (4%), and only three comparisons remained significant after FDR correction, but no association was found across sites or loci. Interestingly, we found two pairs of individuals with identical multilocus genotypes found in Mehuín and Chaihuín and another four pairs of individuals with genotypes differentiated by only one loci found in Chaihuín. Since the multilocus probability of identity (PI) and identity of siblings (PISibs) in our data set were low , it is very likely that these individuals are the product of self‐fertilization.A total of 917 samples were genotyped, but from these 903 samples were successfully genotyped at eight or more loci and thus conform the final data set. All ten microsatellite loci were polymorphic in all samples, and on average, 21 alleles were found for each locus  of the total genetic variation occurred among localities, 31% (p < .001) was attributed to variation among individuals, and 67% (p < .001) occurred within individuals  and within 5 of 20 perchas in Chaihuín . For Los Molinos, the average relatedness coefficients of the six perchas analyzed were not significantly different from random expectations. We also evaluated the average relatedness coefficients at higher hierarchical levels. For instance, observed average relatedness coefficients were also higher than expected by chance in some cases when all samples were grouped by points . At the higher level (transect), only one average relatedness coefficient was significantly different than expected by chance, ME01 (p ≤ .01). However, this coefficient was negative and close to zero, indicating that the average relatedness within ME01 was lower than mean relatedness across both Mehuín transects.We examined the average relatedness coefficients at different hierarchical levels. We found that mean pairwise relatedness within perchas was, in some cases, significantly higher than the mean relatedness of the transect to which perchas belonged Figure . Signifiχ2 = 11.4, df = 1, p < .1; points χ2 = 15.9, df = 1, p < .1; transects χ2 = 17.7, df = 1, p < .1). For Los Molinos, the proportions of full‐siblings were not significantly different at any hierarchical level . For Chaihuín, the proportion of full‐siblings within perchas was significantly higher than among perchas . In the other two hierarchical levels, there are no significant differences .We analyzed the proportion of full‐siblings at the different hierarchical levels. The highest proportion of full‐sibling pairs was found within perchas for all localities, ranging from 2.5% to 3.2% Figure . The proFinally, we also examined how kinship coefficients were distributed within and among localities. Overall kinship coefficients ranged from −0.19 to 0.91 within localities and from −0.20 to 0.40 among localities Figure . Interes4Corallium rubrum . Second, we found that occasionally, related individuals settle together or in very close proximity. Third and last, we confirm the presence of a genetic break between −39.42°S and −39.85°S latitude. Our data indicate there is no evidence to suggest that this break can be explained by differences in fine‐scale population structure; thus, we open the avenue for further studies that can help understand the nature of this genetic discontinuity.In the past several decades, genetic studies conducted at fine spatial scales have shown that many marine organisms are not distributed randomly at small scales despite high potential for larval dispersal , has provided evidence of spatial genetic structure between individuals that were only 0–5 m apart. Interestingly, however this fine‐scale spatial genetic structure was only found for individuals at low latitudes, while individuals at higher latitudes were randomly distributed at the scale up to 60 m. In contrast, a study of the solitary ascidian Microcosmus squamiger found a lack of genetic differentiation among localities separated by tens of kilometers. Here, the authors hypothesize that this could be due to the naturally active dispersal capabilities of this species or due to the two large commercial ports, north and south of the studied coastline, that likely have contributed to dispersal of Microcosmus squamiger  characteristic of low dispersal capacity Cea, , we expeP. chilensis has a wide geographic distribution  and two sites to the north, Talcahuano (36°S) and Antofagasta (23°S) . As such, it is unlikely that differences in sampling zones between localities explain the genetic differentiation found. Additionally, the genetic differentiation of Mehuín does not appear to be a product of limited larval dispersal at least at the scale of 40 km because genetic homogeneity was found between the localities of Pilolcura and Chaihuín  and which suggests that dispersal might be occasionally limited in this species (D'Aloia & Neubert, In summary, we confirm the presence of a genetic break of P. chilensis appears to be greater than that estimated in laboratory conditions, sampling that considers larger transects such as 100–200 m could help to better characterize dispersal of this organism. In this way, more optimal conservation management could be designed if significant intercepts are obtained from spatial autocorrelation analyses (Brauer, Unmack, Hammer, Adams, & Beheregaray, Since the larval dispersal potential of The authors declare no conflict of interest.PSA conceived the study; PSA, SMG, EG, and SQC conducted sampling; SMG performed molecular analyses; SMG and PSA analyzed and interpreted the data; SMG wrote the first draft of the manuscript and all co‐authors contributed. This study is part of the Master's thesis of SMG. Click here for additional data file.